http://api.toxbank.net/index.php?title=Special:Contributions&feed=atom&deletedOnly=&limit=250&target=Mrautenberg&topOnly=&year=&month=
ToxBank API Wiki - User contributions [en]
2024-03-28T20:02:17Z
From ToxBank API Wiki
MediaWiki 1.17.0
http://api.toxbank.net/index.php/API_Investigation:Dashboard
API Investigation:Dashboard
2014-08-13T16:00:06Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get investigation data for GUI dashboard<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation/{id}/dashboard<br />
|REST_header_param=Accept: application/json, subjectid:SECURITY-TOKEN<br />
|REST_op_result=TaskURI as text/uri-list or Investigation data as json<br />
|REST_op_mime_output=text/uri-list, application/json<br />
|REST_op_status=202, 200<br />
}}</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Dashboard
API Investigation:Dashboard
2014-08-13T15:59:01Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get investigation data for GUI dashboard<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation/{id}/dashboard<br />
|REST_header_param=Accept: application/json, subjectid:SECURITY-TOKEN<br />
|REST_op_result=TaskURI or Investigation data as json<br />
|REST_op_mime_output=application/json, text/uri-list<br />
|REST_op_status=202, 200<br />
}}</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Dashboard
API Investigation:Dashboard
2014-08-13T15:56:03Z
<p>Mrautenberg: Created page with "{{REST Operations |REST_op_description=Get investigation data for GUI dashboard |REST_resource=Investigation |REST_op_method=GET |REST_op_uri=/investigation/{id}/dashboard |REST_..."</p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get investigation data for GUI dashboard<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation/{id}/dashboard<br />
|REST_header_param=Accept: application/json, subjectid:SECURITY-TOKEN<br />
}}</div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2014-08-13T11:27:56Z
<p>Mrautenberg: /* Get investigation dashboard contents */</p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
get a URI list of all investigation:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get a RDF representation of a users investigations:<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get JSON URI/modified date list:<br />
curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get URI list of the users investigations URIs:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
<br />
== Get a list of uploaded FTP files ==<br />
{{HasOperation |id=API_Investigation:FTPfiles}}<br />
<br />
== Get informations from published investigations ==<br />
{{HasOperation |id=API_Investigation:Sparql}}<br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
== Get investigation data creation subtaskuri ==<br />
{{HasOperation |id=API_Investigation:SubtaskURI}}<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata<br />
<br />
== Get investigation data ==<br />
{{HasOperation |id=API_Investigation:SparqlInvestigaton}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsBySample/{biosample}<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorvaluesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesAndAssaysByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesWithDatanodesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationDetails<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationEndpointTechnology<br />
<br />
== Get investigation data for dashboard contents ==<br />
{{HasOperation |id=API_Investigation:Dashboard}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/dashboard<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Add/update studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add/update studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Get a protocol uri associated with a Study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyProtocol}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol<br />
<br />
<!--<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
--><br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix dc: <http://purl.org/dc/terms/> .<br />
@prefix ot: <http://www.opentox.org/api/1.2#> .<br />
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> .<br />
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .<br />
<br />
<investigation_uri> a <http://onto.toxbank.net/isa/Investigation>,<br />
ot:Investigation;<br />
dc:title "TG Gate: The Toxicogenomics Project";<br />
<http://onto.toxbank.net/api/hasKeyword> "http://www.owl-ontologies.com/toxbank.owl/K169",<br />
"http://www.owl-ontologies.com/toxbank.owl/K223",<br />
"http://www.owl-ontologies.com/toxbank.owl/K9",<br />
"http://www.owl-ontologies.com/toxbank.owl/K348";<br />
<http://onto.toxbank.net/api/hasOrganisation> <service_uri/organisation/G33>,<br />
<service_uri/organisation/G20>;<br />
<http://onto.toxbank.net/api/hasOwner> <service_uri/user/U271>;<br />
<http://onto.toxbank.net/api/hasProject> <service_uri/project/G17>;<br />
<http://onto.toxbank.net/api/isPublished> false;<br />
<http://onto.toxbank.net/api/isSummarySearchable> false;<br />
<http://onto.toxbank.net/isa/hasStudy> <investigation_uri/S1>;<br />
dc:abstract "TGGATE dataset is a toxicogenomics dataset generated through the Toxicogenomics Project. The Toxicogenomics Project ... ";<br />
dc:modified "19 May 2014 12:24:58 IST" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2014-08-13T11:27:25Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
get a URI list of all investigation:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get a RDF representation of a users investigations:<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get JSON URI/modified date list:<br />
curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get URI list of the users investigations URIs:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
<br />
== Get a list of uploaded FTP files ==<br />
{{HasOperation |id=API_Investigation:FTPfiles}}<br />
<br />
== Get informations from published investigations ==<br />
{{HasOperation |id=API_Investigation:Sparql}}<br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
== Get investigation data creation subtaskuri ==<br />
{{HasOperation |id=API_Investigation:SubtaskURI}}<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata<br />
<br />
== Get investigation data ==<br />
{{HasOperation |id=API_Investigation:SparqlInvestigaton}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsBySample/{biosample}<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorvaluesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesAndAssaysByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesWithDatanodesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationDetails<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationEndpointTechnology<br />
<br />
== Get investigation dashboard contents ==<br />
{{HasOperation |id=API_Investigation:Dashboard}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/dashboard<br />
<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Add/update studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add/update studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Get a protocol uri associated with a Study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyProtocol}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol<br />
<br />
<!--<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
--><br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix dc: <http://purl.org/dc/terms/> .<br />
@prefix ot: <http://www.opentox.org/api/1.2#> .<br />
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> .<br />
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .<br />
<br />
<investigation_uri> a <http://onto.toxbank.net/isa/Investigation>,<br />
ot:Investigation;<br />
dc:title "TG Gate: The Toxicogenomics Project";<br />
<http://onto.toxbank.net/api/hasKeyword> "http://www.owl-ontologies.com/toxbank.owl/K169",<br />
"http://www.owl-ontologies.com/toxbank.owl/K223",<br />
"http://www.owl-ontologies.com/toxbank.owl/K9",<br />
"http://www.owl-ontologies.com/toxbank.owl/K348";<br />
<http://onto.toxbank.net/api/hasOrganisation> <service_uri/organisation/G33>,<br />
<service_uri/organisation/G20>;<br />
<http://onto.toxbank.net/api/hasOwner> <service_uri/user/U271>;<br />
<http://onto.toxbank.net/api/hasProject> <service_uri/project/G17>;<br />
<http://onto.toxbank.net/api/isPublished> false;<br />
<http://onto.toxbank.net/api/isSummarySearchable> false;<br />
<http://onto.toxbank.net/isa/hasStudy> <investigation_uri/S1>;<br />
dc:abstract "TGGATE dataset is a toxicogenomics dataset generated through the Toxicogenomics Project. The Toxicogenomics Project ... ";<br />
dc:modified "19 May 2014 12:24:58 IST" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:FTPfiles
API Investigation:FTPfiles
2014-05-22T08:47:09Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get a list of uploaded FTP files of a user<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation/ftpfiles<br />
|REST_header_param=Accept: one of < text/uri-list, application/json > , subjectid:SECURITY-TOKEN<br />
|REST_op_result=list of files<br />
|REST_op_mime_output=application/json text/uri-list<br />
|REST_op_status=200<br />
}}<br />
==== cURL example ====<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" https://services.toxbank.net/investigation/ftpfiles</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:FTPfiles
API Investigation:FTPfiles
2014-05-22T08:44:01Z
<p>Mrautenberg: Created page with "{{REST Operations |REST_op_description=Get a list of uploaded FTP files of a user |REST_resource=Investigation |REST_op_method=GET |REST_op_uri=/investigation/ftpfiles |REST_head..."</p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get a list of uploaded FTP files of a user<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation/ftpfiles<br />
|REST_header_param=Accept: one of < text/uri-list, application/json > , subjectid:SECURITY-TOKEN <br />
|REST_op_result=list of files<br />
|REST_op_mime_output= application/json text/uri-list <br />
|REST_op_status=200<br />
}}</div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2014-05-22T08:40:36Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
get a URI list of all investigation:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get a RDF representation of a users investigations:<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get JSON URI/modified date list:<br />
curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get URI list of the users investigations URIs:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
<br />
== Get a list of uploaded FTP files ==<br />
{{HasOperation |id=API_Investigation:FTPfiles}}<br />
<br />
== Get informations from published investigations ==<br />
{{HasOperation |id=API_Investigation:Sparql}}<br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
== Get investigation data creation subtaskuri ==<br />
{{HasOperation |id=API_Investigation:SubtaskURI}}<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata<br />
<br />
== Get investigation data ==<br />
{{HasOperation |id=API_Investigation:SparqlInvestigaton}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsBySample/{biosample}<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorvaluesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesAndAssaysByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesWithDatanodesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationDetails<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationEndpointTechnology<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Add/update studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add/update studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Get a protocol uri associated with a Study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyProtocol}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol<br />
<br />
<!--<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
--><br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix dc: <http://purl.org/dc/terms/> .<br />
@prefix ot: <http://www.opentox.org/api/1.2#> .<br />
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> .<br />
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .<br />
<br />
<investigation_uri> a <http://onto.toxbank.net/isa/Investigation>,<br />
ot:Investigation;<br />
dc:title "TG Gate: The Toxicogenomics Project";<br />
<http://onto.toxbank.net/api/hasKeyword> "http://www.owl-ontologies.com/toxbank.owl/K169",<br />
"http://www.owl-ontologies.com/toxbank.owl/K223",<br />
"http://www.owl-ontologies.com/toxbank.owl/K9",<br />
"http://www.owl-ontologies.com/toxbank.owl/K348";<br />
<http://onto.toxbank.net/api/hasOrganisation> <service_uri/organisation/G33>,<br />
<service_uri/organisation/G20>;<br />
<http://onto.toxbank.net/api/hasOwner> <service_uri/user/U271>;<br />
<http://onto.toxbank.net/api/hasProject> <service_uri/project/G17>;<br />
<http://onto.toxbank.net/api/isPublished> false;<br />
<http://onto.toxbank.net/api/isSummarySearchable> false;<br />
<http://onto.toxbank.net/isa/hasStudy> <investigation_uri/S1>;<br />
dc:abstract "TGGATE dataset is a toxicogenomics dataset generated through the Toxicogenomics Project. The Toxicogenomics Project ... ";<br />
dc:modified "19 May 2014 12:24:58 IST" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2014-05-08T07:42:34Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
get a URI list of all investigation:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get a RDF representation of a users investigations:<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get JSON URI/modified date list:<br />
curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get URI list of the users investigations URIs:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
<br />
== Get informations from published investigations ==<br />
{{HasOperation |id=API_Investigation:Sparql}}<br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
== Get investigation data creation subtaskuri ==<br />
{{HasOperation |id=API_Investigation:SubtaskURI}}<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata<br />
<br />
== Get investigation data ==<br />
{{HasOperation |id=API_Investigation:SparqlInvestigaton}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsBySample/{biosample}<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorvaluesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesAndAssaysByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesWithDatanodesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationDetails<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationEndpointTechnology<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Add/update studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add/update studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Get a protocol uri associated with a Study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyProtocol}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol<br />
<br />
<!--<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
--><br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix foaf: <http://xmlns.com/foaf/0.1/> .<br />
@prefix tbisa: <http://onto.toxbank.net/isa/> .<br />
@prefix dcterms: <http://purl.org/dc/terms/> .<br />
<http://onto.toxbank.net/isa/BIII1/I2215><br />
a tbisa:Investigation ;<br />
tbisa:hasAccessionID<br />
"BII-I-1" ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_3977> , <http://onto.toxbank.net/isa/BIII1/ISA_3975> , <http://onto.toxbank.net/isa/BIII1/ISA_3976> ;<br />
tbisa:hasStudy <http://onto.toxbank.net/isa/BIII1/S212> , <http://onto.toxbank.net/isa/BIII1/S213> ;<br />
dcterms:abstract """Background<br />
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell- (skipped) ...engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:issued "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:SubtaskURI
API Investigation:SubtaskURI
2014-05-08T07:41:46Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get investigation data subtask<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation/{id}/subtaskuri<br />
|REST_header_param=Accept: text/uri-list or application/json, subjectid:SECURITY-TOKEN<br />
|REST_op_result=SubTaskURI URI to task<br />
|REST_op_mime_output=text/uri-list, application/json<br />
|REST_op_status=200<br />
}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/subtaskuri</div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2014-05-08T07:41:22Z
<p>Mrautenberg: /* cURL example */</p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
get a URI list of all investigation:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get a RDF representation of a users investigations:<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get JSON URI/modified date list:<br />
curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get URI list of the users investigations URIs:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
<br />
== Get informations from published investigations ==<br />
{{HasOperation |id=API_Investigation:Sparql}}<br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
== Get investigation data creation subtaskuri ==<br />
{{HasOperation |id=API_Investigation:SubtaskURI}}<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata<br />
<br />
== Get investigation data ==<br />
{{HasOperation |id=API_Investigation:SparqlInvestigaton}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsBySample/{biosample}<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorvaluesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesAndAssaysByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesWithDatanodesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationDetails<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationEndpointTechnology<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Add/update studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add/update studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Get a protocol uri associated with a Study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyProtocol}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol<br />
<br />
<!--<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
--><br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix foaf: <http://xmlns.com/foaf/0.1/> .<br />
@prefix tbisa: <http://onto.toxbank.net/isa/> .<br />
@prefix dcterms: <http://purl.org/dc/terms/> .<br />
<http://onto.toxbank.net/isa/BIII1/I2215><br />
a tbisa:Investigation ;<br />
tbisa:hasAccessionID<br />
"BII-I-1" ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_3977> , <http://onto.toxbank.net/isa/BIII1/ISA_3975> , <http://onto.toxbank.net/isa/BIII1/ISA_3976> ;<br />
tbisa:hasStudy <http://onto.toxbank.net/isa/BIII1/S212> , <http://onto.toxbank.net/isa/BIII1/S213> ;<br />
dcterms:abstract """Background<br />
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell- (skipped) ...engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:issued "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2014-05-08T07:41:01Z
<p>Mrautenberg: Undo revision 1116 by Mrautenberg (talk)</p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
get a URI list of all investigation:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get a RDF representation of a users investigations:<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get JSON URI/modified date list:<br />
curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get URI list of the users investigations URIs:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
<br />
== Get informations from published investigations ==<br />
{{HasOperation |id=API_Investigation:Sparql}}<br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
== Get investigation data creation subtaskuri ==<br />
{{HasOperation |id=API_Investigation:SubtaskURI}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/subtaskuri<br />
<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata<br />
<br />
== Get investigation data ==<br />
{{HasOperation |id=API_Investigation:SparqlInvestigaton}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsBySample/{biosample}<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorvaluesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesAndAssaysByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesWithDatanodesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationDetails<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationEndpointTechnology<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Add/update studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add/update studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Get a protocol uri associated with a Study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyProtocol}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol<br />
<br />
<!--<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
--><br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix foaf: <http://xmlns.com/foaf/0.1/> .<br />
@prefix tbisa: <http://onto.toxbank.net/isa/> .<br />
@prefix dcterms: <http://purl.org/dc/terms/> .<br />
<http://onto.toxbank.net/isa/BIII1/I2215><br />
a tbisa:Investigation ;<br />
tbisa:hasAccessionID<br />
"BII-I-1" ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_3977> , <http://onto.toxbank.net/isa/BIII1/ISA_3975> , <http://onto.toxbank.net/isa/BIII1/ISA_3976> ;<br />
tbisa:hasStudy <http://onto.toxbank.net/isa/BIII1/S212> , <http://onto.toxbank.net/isa/BIII1/S213> ;<br />
dcterms:abstract """Background<br />
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell- (skipped) ...engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:issued "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2014-05-08T07:38:47Z
<p>Mrautenberg: Reverted edits by Mrautenberg (talk) to last revision by Dgebele</p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
get a URI list of all investigation:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get a RDF representation of a users investigations:<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get JSON URI/modified date list:<br />
curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get URI list of the users investigations URIs:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
<br />
== Get informations from published investigations ==<br />
{{HasOperation |id=API_Investigation:Sparql}}<br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata<br />
<br />
== Get investigation data ==<br />
{{HasOperation |id=API_Investigation:SparqlInvestigaton}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsBySample/{biosample}<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorvaluesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesAndAssaysByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesWithDatanodesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationDetails<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationEndpointTechnology<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Add/update studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add/update studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Get a protocol uri associated with a Study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyProtocol}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol<br />
<br />
<!--<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
--><br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix foaf: <http://xmlns.com/foaf/0.1/> .<br />
@prefix tbisa: <http://onto.toxbank.net/isa/> .<br />
@prefix dcterms: <http://purl.org/dc/terms/> .<br />
<http://onto.toxbank.net/isa/BIII1/I2215><br />
a tbisa:Investigation ;<br />
tbisa:hasAccessionID<br />
"BII-I-1" ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_3977> , <http://onto.toxbank.net/isa/BIII1/ISA_3975> , <http://onto.toxbank.net/isa/BIII1/ISA_3976> ;<br />
tbisa:hasStudy <http://onto.toxbank.net/isa/BIII1/S212> , <http://onto.toxbank.net/isa/BIII1/S213> ;<br />
dcterms:abstract """Background<br />
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell- (skipped) ...engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:issued "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2014-05-08T07:37:42Z
<p>Mrautenberg: /* cURL example */</p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
get a URI list of all investigation:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get a RDF representation of a users investigations:<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get JSON URI/modified date list:<br />
curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get URI list of the users investigations URIs:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
<br />
== Get informations from published investigations ==<br />
{{HasOperation |id=API_Investigation:Sparql}}<br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
== Get investigation data creation subtaskuri ==<br />
{{HasOperation |id=API_Investigation:SubtaskURI}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/subtaskuri<br />
<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata<br />
<br />
== Get investigation data ==<br />
{{HasOperation |id=API_Investigation:SparqlInvestigaton}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsBySample/{biosample}<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorvaluesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesAndAssaysByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesWithDatanodesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationDetails<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationEndpointTechnology<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Add/update studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add/update studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Get a protocol uri associated with a Study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyProtocol}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol<br />
<br />
<!--<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
--><br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix foaf: <http://xmlns.com/foaf/0.1/> .<br />
@prefix tbisa: <http://onto.toxbank.net/isa/> .<br />
@prefix dcterms: <http://purl.org/dc/terms/> .<br />
<http://onto.toxbank.net/isa/BIII1/I2215><br />
a tbisa:Investigation ;<br />
tbisa:hasAccessionID<br />
"BII-I-1" ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_3977> , <http://onto.toxbank.net/isa/BIII1/ISA_3975> , <http://onto.toxbank.net/isa/BIII1/ISA_3976> ;<br />
tbisa:hasStudy <http://onto.toxbank.net/isa/BIII1/S212> , <http://onto.toxbank.net/isa/BIII1/S213> ;<br />
dcterms:abstract """Background<br />
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell- (skipped) ...engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:issued "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:SubtaskURI
API Investigation:SubtaskURI
2014-05-08T07:36:29Z
<p>Mrautenberg: Created page with "{{REST Operations |REST_op_description=Get investigation data subtask |REST_resource=Investigation |REST_op_method=GET |REST_op_uri=/investigation/{id}/subtaskuri |REST_header_pa..."</p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get investigation data subtask<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation/{id}/subtaskuri<br />
|REST_header_param=Accept: text/uri-list or application/json, subjectid:SECURITY-TOKEN<br />
|REST_op_result=SubTaskURI URI to task<br />
|REST_op_mime_output=text/uri-list, application/json<br />
|REST_op_status=200<br />
}}</div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2014-05-08T07:33:18Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
get a URI list of all investigation:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get a RDF representation of a users investigations:<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get JSON URI/modified date list:<br />
curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get URI list of the users investigations URIs:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
<br />
== Get informations from published investigations ==<br />
{{HasOperation |id=API_Investigation:Sparql}}<br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Get investigation data creation subtaskuri ==<br />
{{HasOperation |id=API_Investigation:SubtaskURI}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/subtaskuri<br />
<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata<br />
<br />
== Get investigation data ==<br />
{{HasOperation |id=API_Investigation:SparqlInvestigaton}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsBySample/{biosample}<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorsByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorvaluesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesAndAssaysByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesWithDatanodesByInvestigation<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationDetails<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationEndpointTechnology<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Add/update studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add/update studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Get a protocol uri associated with a Study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyProtocol}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol<br />
<br />
<!--<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
--><br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix foaf: <http://xmlns.com/foaf/0.1/> .<br />
@prefix tbisa: <http://onto.toxbank.net/isa/> .<br />
@prefix dcterms: <http://purl.org/dc/terms/> .<br />
<http://onto.toxbank.net/isa/BIII1/I2215><br />
a tbisa:Investigation ;<br />
tbisa:hasAccessionID<br />
"BII-I-1" ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_3977> , <http://onto.toxbank.net/isa/BIII1/ISA_3975> , <http://onto.toxbank.net/isa/BIII1/ISA_3976> ;<br />
tbisa:hasStudy <http://onto.toxbank.net/isa/BIII1/S212> , <http://onto.toxbank.net/isa/BIII1/S213> ;<br />
dcterms:abstract """Background<br />
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell- (skipped) ...engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:issued "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Sparql
API Investigation:Sparql
2014-01-17T09:46:43Z
<p>Mrautenberg: /* cURL example */</p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get information from investigations<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=investigation/sparql/{template_name}<br />
|REST_op_params=params per template(template_name):<br />
* no params needed for investigation_and_characteristics, investigations_and_factors and investigations_and_protocols<br />
* factorValues: URI array for investigation_by_factors and protocols_by_factors template <br />
* geneIdentifiers: Array of Strings for investigation_by_genes (e.G.: uniprot:P10809,genesymbol:HSPD1,unigene:Hs.595053,refseq:NM_002156,entrez:3329)<br />
* value: String for investigation_by_characteristic_name, investigation_by_characteristic_value, investigation_by_characteristic and investigation_by_factor<br />
|REST_header_param=Accept: one of < application/sparql-results+xml, application/json, text/uri-list, text/html > , subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation data as sparql-results+xml json uri-list html<br />
|REST_op_mime_output=application/sparql-results+xml application/json text/uri-list text/html<br />
|REST_op_status=200<br />
}}<br />
Get information from published investigations via predefined SPARQL queries. (e.G.: https://services.toxbank.net/investigation/sparql/investigations_and_protocols ) . You may also use camelcase notation for templatenames (e.G.: InvestigationsAndProtocols, InvestigationByFactors). <br />
<br />
==== cURL example ====<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" https://services.toxbank.net/investigation/sparql/investigation_and_characteristics<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "value=http://purl.obolibrary.org/obo/NEWT_4932" https://services.toxbank.net/investigation/sparql/investigation_by_characteristic<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "value=organism" https://services.toxbank.net/investigation/sparql/investigation_by_characteristic_name<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "value=Saccharomyces cerevisiae (Baker's yeast)" https://services.toxbank.net/investigation/sparql/investigation_by_characteristic_value<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "values=http://purl.obolibrary.org/chebi/CHEBI:39867" https://services.toxbank.net/investigation/sparql/investigation_by_factor<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "factorValues=['http://purl.obolibrary.org/chebi/CHEBI:39867']" https://services.toxbank.net/investigation/sparql/investigation_by_factors<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "value=0.035" https://services.toxbank.net/investigation/sparql/investigation_by_foldchange<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "geneIdentifiers=['uniprot:P10809','genesymbol:HSPD1','unigene:Hs.595053']" https://services.toxbank.net/investigation/sparql/investigation_by_genes<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "value=0.65614" https://services.toxbank.net/investigation/sparql/investigation_by_pvalue<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "value=0.805517" https://services.toxbank.net/investigation/sparql/investigation_by_qvalue<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/sparql/investigations_and_factors<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/sparql/investigations_and_protocols<br />
<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' -d "factorValues=['http://purl.obolibrary.org/chebi/CHEBI:39867']" https://services.toxbank.net/investigation/sparql/protocols_by_factors</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Create
API Investigation:Create
2013-12-12T10:35:39Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Create a new investigation from ISA-TAB files<br />
|REST_resource=Investigation<br />
|REST_op_method=POST<br />
|REST_op_uri=/investigation<br />
|REST_op_params=optional params:<br />
* allowReadByUser: one or multiple userservice-URIs (User)<br />
* allowReadByGroup: one or multiple userservice-URIs (Organisations, Projects)<br />
* summarySearchable: true/false (default is false)<br />
|REST_header_param=subjectid:SECURITY-TOKEN<br />
|REST_op_mime_input=multipart/form-data, upload ISA-TAB files (isa-tab zip archive)<br />
|REST_op_result=Task URI<br />
|REST_op_mime_output=text/uri-list<br />
|REST_op_status=202<br />
}}<br />
==== cURL example ====<br />
curl -Lk -X POST -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation</div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2013-12-12T10:35:02Z
<p>Mrautenberg: /* cURL example */</p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
get a URI list of all investigation:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get a RDF representation of a users investigations:<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get JSON URI/modified date list:<br />
curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get URI list of the users investigations URIs:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
<br />
== Get informations from published investigations ==<br />
{{HasOperation |id=API_Investigation:Sparql}}<br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata<br />
<br />
== Get investigation data ==<br />
{{HasOperation |id=API_Investigation:SparqlInvestigaton}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorsByInvestigation<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Add/update studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add/update studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Get a protocol uri associated with a Study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyProtocol}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol<br />
<br />
<!--<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
--><br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix foaf: <http://xmlns.com/foaf/0.1/> .<br />
@prefix tbisa: <http://onto.toxbank.net/isa/> .<br />
@prefix dcterms: <http://purl.org/dc/terms/> .<br />
<http://onto.toxbank.net/isa/BIII1/I2215><br />
a tbisa:Investigation ;<br />
tbisa:hasAccessionID<br />
"BII-I-1" ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_3977> , <http://onto.toxbank.net/isa/BIII1/ISA_3975> , <http://onto.toxbank.net/isa/BIII1/ISA_3976> ;<br />
tbisa:hasStudy <http://onto.toxbank.net/isa/BIII1/S212> , <http://onto.toxbank.net/isa/BIII1/S213> ;<br />
dcterms:abstract """Background<br />
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell- (skipped) ...engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:issued "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Create
API Investigation:Create
2013-12-12T10:33:06Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Create a new investigation from ISA-TAB files<br />
|REST_resource=Investigation<br />
|REST_op_method=POST<br />
|REST_op_uri=/investigation<br />
|REST_op_params=optional params:<br />
* allowReadByUser: one or multiple userservice-URIs (User)<br />
* allowReadByGroup: one or multiple userservice-URIs (Organisations, Projects)<br />
* summarySearchable: true/false (default is false)<br />
|REST_header_param=subjectid:SECURITY-TOKEN<br />
|REST_op_mime_input=multipart/form-data, upload ISA-TAB files (isa-tab zip archive)<br />
|REST_op_result=Task URI<br />
|REST_op_mime_output=text/uri-list<br />
|REST_op_status=202<br />
}}</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Create
API Investigation:Create
2013-12-12T10:30:29Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Create a new investigation from ISA-TAB files<br />
|REST_resource=Investigation<br />
|REST_op_method=POST<br />
|REST_op_uri=/investigation<br />
|REST_op_params=optional params:<br />
* allowReadByUser: one or multiple userservice-URIs (User)<br />
* allowReadByGroup: one or multiple userservice-URIs (Organisations, Projects)<br />
* summarySearchable: true/false (default is false)<br />
|REST_header_param=subjectid:SECURITY-TOKEN<br />
|REST_op_mime_input=multipart/form-data, uploaded file can contain (i) a zip archive with ISA-TAB files <br />
|REST_op_result=Task URI<br />
|REST_op_mime_output=text/uri-list<br />
|REST_op_status=202<br />
}}</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Sparql
API Investigation:Sparql
2013-12-12T09:47:49Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get information from investigations<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=investigation/sparql/{template_name}<br />
|REST_op_params=params per template(template_name):<br />
* no params needed for investigation_and_characteristics, investigations_and_factors and investigation_and_protocols<br />
* factorValues: URI array for investigation_by_factors and protocols_by_factors template <br />
* geneIdentifiers: Array of Strings for investigation_by_genes (e.G.: uniprot:P10809,genesymbol:HSPD1,unigene:Hs.595053,refseq:NM_002156,entrez:3329)<br />
* value: String for investigation_by_characteristic_name, investigation_by_characteristic_value, investigation_by_characteristic and investigation_by_factor<br />
|REST_header_param=Accept: one of < application/sparql-results+xml, application/json, text/uri-list, text/html > , subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation data as sparql-results+xml json uri-list html<br />
|REST_op_mime_output=application/sparql-results+xml application/json text/uri-list text/html<br />
|REST_op_status=200<br />
}}<br />
Get information from published investigations via predefined SPARQL queries. (e.G.: https://services.toxbank.net/investigation/sparql/investigation_and_protocols ) . You may also use camelcase notation for templatenames (e.G.: InvestigationAndProtocols, InvestigationByFactors). <br />
<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/sparql/investigation_and_protocols<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "factorValues=['http://purl.obolibrary.org/chebi/CHEBI:39867']" https://services.toxbank.net/investigation/sparql/investigation_by_factors<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "geneIdentifiers=['uniprot:P10809','genesymbol:HSPD1','unigene:Hs.595053']" https://services.toxbank.net/investigation/sparql/investigation_by_genes<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "value=HepaRG" https://services.toxbank.net/investigation/sparql/investigation_by_characteristic_name</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Sparql
API Investigation:Sparql
2013-12-04T17:31:28Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get information from investigations<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=investigation/sparql/{template_name}<br />
|REST_op_params=params per template:<br />
* no params needed for investigation_and_characteristics, investigations_and_factors and investigation_and_protocols<br />
* factorValues: URI array for investigation_by_factors and protocols_by_factors template <br />
* value: String for investigation_by_characteristic_name, investigation_by_characteristic_value, investigation_by_characteristic and investigation_by_factor<br />
|REST_header_param=Accept: one of < application/sparql-results+xml, application/json, text/uri-list, text/html > , subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation data as sparql-results+xml json uri-list html<br />
|REST_op_mime_output=application/sparql-results+xml application/json text/uri-list text/html<br />
|REST_op_status=200<br />
}}<br />
Get information from published investigations via predefined SPARQL queries. (e.G.: https://services.toxbank.net/investigation/sparql/investigation_and_protocols ) . You may also use camelcase notation for templatenames (e.G.: InvestigationAndProtocols, InvestigationByFactors).<br />
<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/sparql/investigation_and_protocols<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "factorValues=['http://purl.obolibrary.org/chebi/CHEBI:39867']" https://services.toxbank.net/investigation/sparql/investigation_by_factors<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "value=HepaRG" https://services.toxbank.net/investigation/sparql/investigation_by_characteristic_name</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Sparql
API Investigation:Sparql
2013-12-04T17:26:13Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get information from investigations<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=investigation/sparql/{template_name}<br />
|REST_op_params=params per template:<br />
* no params needed for investigation_and_characteristics, investigations_and_factors and investigation_and_protocols<br />
* factorValues: URI array for investigation_by_factors and protocols_by_factors template <br />
* value: String for investigation_by_characteristic_name, investigation_by_characteristic_value, investigation_by_factors, investigation_by_characteristic and investigation_by_factor<br />
|REST_header_param=Accept: one of < application/sparql-results+xml, application/json, text/uri-list, text/html > , subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation data as sparql-results+xml json uri-list html<br />
|REST_op_mime_output=application/sparql-results+xml application/json text/uri-list text/html<br />
|REST_op_status=200<br />
}}<br />
Get information from published investigations via predefined SPARQL queries. (e.G.: https://services.toxbank.net/investigation/sparql/investigation_and_protocols ) . You may also use camelcase notation for templatenames (e.G.: InvestigationAndProtocols, InvestigationByFactors).<br />
<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/sparql/investigation_and_protocols<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "factorValues=['http://purl.obolibrary.org/chebi/CHEBI:39867']" https://services.toxbank.net/investigation/sparql/investigation_by_factors<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "value=HepaRG" https://services.toxbank.net/investigation/sparql/investigation_by_characteristic_name</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Sparql
API Investigation:Sparql
2013-12-04T17:15:53Z
<p>Mrautenberg: /* cURL example */</p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get information from investigations<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=investigation/sparql/{template_name}<br />
|REST_op_params=params per template:<br />
* no params needed for investigation_and_characteristics, investigations_and_factors and investigation_and_protocols<br />
* factorValues: URI array for investigation_by_factors and protocols_by_factors template <br />
* value: String for investigation_by_characteristic_name, investigation_by_characteristic_value, investigation_by_factors, investigation_by_characteristic and investigation_by_factor<br />
|REST_header_param=Accept: one of < application/sparql-results+xml, application/json, text/uri-list, text/html > , subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation data as sparql-results+xml json uri-list html<br />
|REST_op_mime_output=application/sparql-results+xml application/json text/uri-list text/html<br />
|REST_op_status=200<br />
}}<br />
Get information from published investigations via predifed SPARQL queries. (e.G.: https://services.toxbank.net/investigation/sparql/investigation_and_protocols ) . You may also use camelcase notation for templatenames (e.G.: InvestigationAndProtocols).<br />
<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/sparql/investigation_and_protocols<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "factorValues=['http://purl.obolibrary.org/chebi/CHEBI:39867']" https://services.toxbank.net/investigation/sparql/investigation_by_factors<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "value=HepaRG" https://services.toxbank.net/investigation/sparql/investigation_by_characteristic_name</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Sparql
API Investigation:Sparql
2013-12-04T17:14:21Z
<p>Mrautenberg: /* cURL example */</p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get information from investigations<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=investigation/sparql/{template_name}<br />
|REST_op_params=params per template:<br />
* no params needed for investigation_and_characteristics, investigations_and_factors and investigation_and_protocols<br />
* factorValues: URI array for investigation_by_factors and protocols_by_factors template <br />
* value: String for investigation_by_characteristic_name, investigation_by_characteristic_value, investigation_by_factors, investigation_by_characteristic and investigation_by_factor<br />
|REST_header_param=Accept: one of < application/sparql-results+xml, application/json, text/uri-list, text/html > , subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation data as sparql-results+xml json uri-list html<br />
|REST_op_mime_output=application/sparql-results+xml application/json text/uri-list text/html<br />
|REST_op_status=200<br />
}}<br />
Get information from published investigations via predifed SPARQL queries. (e.G.: https://services.toxbank.net/investigation/sparql/investigation_and_protocols ) . You may also use camelcase notation for templatenames (e.G.: InvestigationAndProtocols).<br />
<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/sparql/investigation_and_protocols<br />
<br />
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "factorValues=['http://purl.obolibrary.org/chebi/CHEBI:39867']" https://services.toxbank.net/investigation/sparql/investigation_by_factors</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Sparql
API Investigation:Sparql
2013-12-04T17:06:02Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get information from investigations<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=investigation/sparql/{template_name}<br />
|REST_op_params=params per template:<br />
* no params needed for investigation_and_characteristics, investigations_and_factors and investigation_and_protocols<br />
* factorValues: URI array for investigation_by_factors and protocols_by_factors template <br />
* value: String for investigation_by_characteristic_name, investigation_by_characteristic_value, investigation_by_factors, investigation_by_characteristic and investigation_by_factor<br />
|REST_header_param=Accept: one of < application/sparql-results+xml, application/json, text/uri-list, text/html > , subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation data as sparql-results+xml json uri-list html<br />
|REST_op_mime_output=application/sparql-results+xml application/json text/uri-list text/html<br />
|REST_op_status=200<br />
}}<br />
Get information from published investigations via predifed SPARQL queries. (e.G.: https://services.toxbank.net/investigation/sparql/investigation_and_protocols ) . You may also use camelcase notation for templatenames (e.G.: InvestigationAndProtocols).<br />
<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/sparql/investigation_and_protocols</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Sparql
API Investigation:Sparql
2013-12-04T17:00:24Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get information from investigations<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=investigation/sparql/{template_name}<br />
|REST_op_params=params per template:<br />
* no params needed for investigation_and_characteristics, investigations_and_factors and investigation_and_protocols<br />
* factorValues: URI array for investigation_by_factors and protocols_by_factors template <br />
* value: String for investigation_by_characteristic_name, investigation_by_characteristic_value, investigation_by_factors, investigation_by_characteristic and investigation_by_factor<br />
|REST_header_param=Accept: one of < application/sparql-results+xml, application/json, text/uri-list, text/html > , subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation data as sparql-results+xml json uri-list html<br />
|REST_op_mime_output=application/sparql-results+xml application/json text/uri-list text/html<br />
|REST_op_status=200<br />
}}<br />
Get information from published investigations via predifed SPARQL queries.</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Sparql
API Investigation:Sparql
2013-12-04T16:56:43Z
<p>Mrautenberg: fix typo</p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get information from investigations<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=investigation/sparql/{template_name}<br />
|REST_op_params=params for template:<br />
* no params needed for investigation_and_characteristics, investigations_and_factors and investigation_and_protocols<br />
* factorValues: URI array for investigation_by_factors and protocols_by_factors template <br />
* value: String for investigation_by_characteristic_name, investigation_by_characteristic_value, investigation_by_factors, investigation_by_characteristic and investigation_by_factor<br />
|REST_header_param=Accept: one of < application/sparql-results+xml, application/json, text/uri-list, text/html > , subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation data as sparql-results+xml json uri-list html<br />
|REST_op_mime_output=application/sparql-results+xml application/json text/uri-list text/html<br />
|REST_op_status=200<br />
}}<br />
Get information from published investigations via predifed SPARQL queries.</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Sparql
API Investigation:Sparql
2013-12-04T16:52:57Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get information from investigations<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=investigation/sparql/{template_name}<br />
|REST_op_params=params for template:<br />
* no params needed for investigation_and_characteristics, investigation_and_characteristics and investigation_and_characteristics<br />
* factorValues: URI array for investigation_by_factors and protocols_by_factors template <br />
* value: String for investigation_by_characteristic_name, investigation_by_characteristic_value, investigation_by_factors, investigation_by_characteristic and investigation_by_factor<br />
|REST_header_param=Accept: one of < application/sparql-results+xml, application/json, text/uri-list, text/html > , subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation data as sparql-results+xml json uri-list html<br />
|REST_op_mime_output=application/sparql-results+xml application/json text/uri-list text/html<br />
|REST_op_status=200<br />
}}<br />
Get information from published investigations via predifed SPARQL queries.</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Sparql
API Investigation:Sparql
2013-12-04T16:51:43Z
<p>Mrautenberg: Created page with "{{REST Operations |REST_op_description=Get information from investigations |REST_resource=Investigation |REST_op_method=GET |REST_op_uri=investigation/sparql/{template_name} |RES..."</p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get information from investigations<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=investigation/sparql/{template_name}<br />
|REST_op_params=params for template:* none for investigation_and_characteristics, investigation_and_characteristics and investigation_and_characteristics* factorValues: URI array for investigation_by_factors and protocols_by_factors template *value: String for investigation_by_characteristic_name, investigation_by_characteristic_value, investigation_by_factors, investigation_by_characteristic and investigation_by_factor<br />
|REST_header_param=Accept: one of < application/sparql-results+xml, application/json, text/uri-list, text/html > , subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation data as sparql-results+xml json uri-list html<br />
|REST_op_mime_output=application/sparql-results+xml application/json text/uri-list text/html<br />
|REST_op_status=200<br />
}}<br />
Get information from published investigations via predifed SPARQL queries.</div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2013-12-04T16:36:03Z
<p>Mrautenberg: /* Investigation */</p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
get a URI list of all investigation:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get a RDF representation of a users investigations:<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get JSON URI/modified date list:<br />
curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get URI list of the users investigations URIs:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
<br />
== Get informations from published investigations ==<br />
{{HasOperation |id=API_Investigation:Sparql}}<br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
==== cURL example ====<br />
curl -Lk -X POST -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata<br />
<br />
== Get investigation data ==<br />
{{HasOperation |id=API_Investigation:SparqlInvestigaton}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorsByInvestigation<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Add/update studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add/update studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Get a protocol uri associated with a Study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyProtocol}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol<br />
<br />
<!--<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
--><br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix foaf: <http://xmlns.com/foaf/0.1/> .<br />
@prefix tbisa: <http://onto.toxbank.net/isa/> .<br />
@prefix dcterms: <http://purl.org/dc/terms/> .<br />
<http://onto.toxbank.net/isa/BIII1/I2215><br />
a tbisa:Investigation ;<br />
tbisa:hasAccessionID<br />
"BII-I-1" ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_3977> , <http://onto.toxbank.net/isa/BIII1/ISA_3975> , <http://onto.toxbank.net/isa/BIII1/ISA_3976> ;<br />
tbisa:hasStudy <http://onto.toxbank.net/isa/BIII1/S212> , <http://onto.toxbank.net/isa/BIII1/S213> ;<br />
dcterms:abstract """Background<br />
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell- (skipped) ...engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:issued "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:SparqlInvestigaton
API Investigation:SparqlInvestigaton
2013-12-03T11:24:55Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get investigation data via predefined SPARQL templates<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation/{id}/sparql/{template_name}<br />
|REST_header_param=Accept: one of < application/sparql-results+xml, application/json, text/uri-list, text/html > , subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation data as sparql-results+xml json uri-list html<br />
|REST_op_mime_output=application/sparql-results+xml application/json text/uri-list text/html<br />
|REST_op_status=200<br />
}}<br />
Get investigation data via predefined SPARQL templates. Add one of investigation_endpoint_technology, investigation_details, factors_by_investigation or characteristics_by_investigation to an investigation plus /sparql/ URI (e.G.: https://services.toxbank.net/investigation/{id}/sparql/investigation_endpoint_technology ) . You may also use camelcase notation for templatenames (e.G.: FactorsByInvestigation).</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:SparqlInvestigaton
API Investigation:SparqlInvestigaton
2013-12-03T11:20:37Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get investigation data via predefined SPARQL templates<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation/{id}/sparql/{template_name}<br />
|REST_header_param=Accept: one of application/sparql-results+xml, application/json, text/uri-list, text/html> , subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation data as sparql-results+xml json uri-list html<br />
|REST_op_mime_output=application/sparql-results+xml application/json text/uri-list text/html<br />
|REST_op_status=200<br />
}}<br />
Get investigation data via predefined SPARQL templates. Add one of investigation_endpoint_technology, investigation_details, factors_by_investigation or characteristics_by_investigation to an investigation plus /sparql/ URI (e.G.: https://services.toxbank.net/investigation/{id}/sparql/investigation_endpoint_technology ) . You may also use camelcase notation for templatenames (e.G.: FactorsByInvestigation).</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:SparqlInvestigaton
API Investigation:SparqlInvestigaton
2013-11-29T15:40:52Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get investigation data via predefined SPARQL templates<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation/{id}/sparql/{template_name}<br />
|REST_header_param=Accept: one of text/plain (n-triples), text/turtle, application/rdf+xml, subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation metadata in n-triples, turtle or RDF format<br />
|REST_op_mime_output=text/plain (n-triples), text/turtle, application/rdf+xml<br />
|REST_op_status=200<br />
}}<br />
Get investigation data via predefined SPARQL templates. Add one of investigation_endpoint_technology, investigation_details, factors_by_investigation or characteristics_by_investigation to an investigation plus /sparql/ URI (e.G.: https://services.toxbank.net/investigation/{id}/sparql/investigation_endpoint_technology ) . You may also use camelcase notation for templatenames (e.G.: FactorsByInvestigation).</div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2013-11-29T15:36:06Z
<p>Mrautenberg: /* cURL example */</p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
get a URI list of all investigation:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get a RDF representation of a users investigations:<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get JSON URI/modified date list:<br />
curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get URI list of the users investigations URIs:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
==== cURL example ====<br />
curl -Lk -X POST -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata<br />
<br />
== Get investigation data ==<br />
{{HasOperation |id=API_Investigation:SparqlInvestigaton}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorsByInvestigation<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Add/update studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add/update studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Get a protocol uri associated with a Study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyProtocol}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol<br />
<br />
<!--<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
--><br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix foaf: <http://xmlns.com/foaf/0.1/> .<br />
@prefix tbisa: <http://onto.toxbank.net/isa/> .<br />
@prefix dcterms: <http://purl.org/dc/terms/> .<br />
<http://onto.toxbank.net/isa/BIII1/I2215><br />
a tbisa:Investigation ;<br />
tbisa:hasAccessionID<br />
"BII-I-1" ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_3977> , <http://onto.toxbank.net/isa/BIII1/ISA_3975> , <http://onto.toxbank.net/isa/BIII1/ISA_3976> ;<br />
tbisa:hasStudy <http://onto.toxbank.net/isa/BIII1/S212> , <http://onto.toxbank.net/isa/BIII1/S213> ;<br />
dcterms:abstract """Background<br />
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell- (skipped) ...engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:issued "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:SparqlInvestigaton
API Investigation:SparqlInvestigaton
2013-11-29T15:34:56Z
<p>Mrautenberg: Created page with "{{REST Operations |REST_op_description=Get investigation data via predefined SPARQL templates |REST_resource=Investigation |REST_op_method=GET |REST_op_uri=/investigation/{id}/sp..."</p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get investigation data via predefined SPARQL templates<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation/{id}/sparql/{template_name}<br />
|REST_header_param=Accept: one of text/plain (n-triples), text/turtle, application/rdf+xml, subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation metadata in n-triples, turtle or RDF format<br />
|REST_op_mime_output=text/plain (n-triples), text/turtle, application/rdf+xml<br />
|REST_op_status=200<br />
}}<br />
Get investigation data via predefined SPARQL templates. Add one of investigation_endpoint_technology, investigation_details, factors_by_investigation or character_by_investigation to an investigation plus /sparql/ URI (e.G.: https://services.toxbank.net/investigation/{id}/sparql/investigation_endpoint_technology ) . You may also use camelcase notation for templatenames (e.G.: FactorsByInvestigation).</div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2013-11-29T15:21:12Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
get a URI list of all investigation:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get a RDF representation of a users investigations:<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get JSON URI/modified date list:<br />
curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get URI list of the users investigations URIs:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
==== cURL example ====<br />
curl -Lk -X POST -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata<br />
<br />
== Get investigation data ==<br />
{{HasOperation |id=API_Investigation:SparqlInvestigaton}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/{templatename}<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Add/update studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add/update studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Get a protocol uri associated with a Study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyProtocol}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol<br />
<br />
<!--<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
--><br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix foaf: <http://xmlns.com/foaf/0.1/> .<br />
@prefix tbisa: <http://onto.toxbank.net/isa/> .<br />
@prefix dcterms: <http://purl.org/dc/terms/> .<br />
<http://onto.toxbank.net/isa/BIII1/I2215><br />
a tbisa:Investigation ;<br />
tbisa:hasAccessionID<br />
"BII-I-1" ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_3977> , <http://onto.toxbank.net/isa/BIII1/ISA_3975> , <http://onto.toxbank.net/isa/BIII1/ISA_3976> ;<br />
tbisa:hasStudy <http://onto.toxbank.net/isa/BIII1/S212> , <http://onto.toxbank.net/isa/BIII1/S213> ;<br />
dcterms:abstract """Background<br />
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell- (skipped) ...engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:issued "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset
OpenTox API 1.2 Dataset
2013-10-28T12:15:03Z
<p>Mrautenberg: </p>
<hr />
<div><h2>REST operations</h2><br />
{| <tbody> <br />
! Description<br />
! Method<br />
| <br><br />
! URI<br />
| <br><br />
! Parameters<br />
! Result<br />
! Status codes<br />
|- <br />
| Get a list of available datasets<br />
| GET<br />
| <br><br />
| /dataset<br />
| <br><br />
| <br><strong>[subjectid]</strong><br>Query parameters (optional, to be defined by service providers)<br />
| List of URIs <br>or RDF for the metadata only<br><br />
| 200,404,503<br />
|- <br />
| Get a dataset<br />
| GET<br />
| <br><br />
| /dataset/{id}<br />
| <br><br />
| <strong>[subjectid]</strong><br />
| Representation of the dataset in a supported MIME type<br />
| 200,404,503<br />
|- <br />
| Query a dataset<br />
| GET<br />
| <br><br />
| /dataset/{id}<br />
| <br><br />
| <strong>[subjectid]</strong><br><strong>compound_uris[]</strong> and/or <strong>feature_uris[]</strong> to select compounds and features; further query parameters may be defined by service providers<br><br />
| Representation of the query result in a supported MIME type<br />
| 200,404,503<br />
|- <br />
| Get metadata for a dataset<br />
| GET<br />
| <br><br />
| /dataset/{id}/metadata<br />
| <br><br />
| <strong>[subjectid]</strong><br />
| Representation of the dataset metadata in a supported MIME type<br />
| 200,404,503<br />
|- <br />
| Update metadata for a dataset<br />
| <br>PUT<br><br />
| <br><br />
| <br>/dataset/{id}/metadata<br />
| <br><br />
| <strong><br>[subjectid]</strong><br><br />
| <br>RDF or application/www-form-urlencoded<br />
| <br><br />
|- <br />
| Get a list of all compounds in a dataset<br />
| GET<br />
| <br><br />
| /dataset/{id}/compounds<br />
| <br><br />
| <strong>[subjectid]</strong><br />
| List of compound URIs<br />
| 200,404,503<br />
|- <br />
| Get a list of all features in a dataset<br />
| GET<br />
| <br><br />
| /dataset/{id}/features<br />
| <br><br />
| <strong>[subjectid]</strong><br />
| RDF or List of feature URIs (pointing to feature definitions/ontologies)<br />
| 200,404,503<br />
|- <br />
| Create a new dataset<br />
| POST<br />
| <br><br />
| /dataset<br />
| <br><br />
| Dataset representation in a supported MIME type. MIME type to be specified via <strong>Content-type</strong> header.<br><br><ul><li><em>Content-type:application/www-form-urlencoded</em><strong> dataset_uri</strong> , <strong>feature_uris[]</strong> and <strong>compound_uris[]</strong> parameters are used to specify subset of a dataset, as in GET operation;</li><li>File upload via <em>Content-type:multipart/form-data</em>: <strong>file</strong> parameter </li><li>File upload metadata: parameters as in opentox.owl</li><li><strong>[subjectid]</strong></li></ul><br><strong>[subjectid]</strong><br />
| <a title="Task" class="internal-link" href="AsyncTask#creating-a-task-post">New URI /dataset/{id} or redirect to task URI (for large uploads)</a><br><br />
| 200,202,400,503<br />
|- <br />
| <br />
{| <tbody> <br />
|- <br />
| <br><br />
| Create a new dataset using a reference featureURI list<br></tbody><br />
|}<br />
| <br>POST<br><br />
| <br><br />
| <br>/dataset<br><br />
| <br><br />
| File upload via <em>Content-type:multipart/form-data</em>: <strong>file</strong> parameter<br>Reference featureURI list (http://server/path/dataset/{dataset_id}/feature)<br>Matcher (e.g. name of feature)<br><br />
| <a title="Task" class="internal-link" href="AsyncTask#creating-a-task-post">New URI /dataset/{id} or redirect to task URI (for large uploads)</a><br />
| <br>200,202,400,503<br />
|- <br />
| Update a dataset<br />
| PUT<br />
| <br><br />
| <ul><li>/dataset/{id}</li></ul><br />
| <br><br />
| <ul><li>Data representation in a supported MIME type; </li><li><em>entries for existing compound/feature pairs will be overwritten, entries for new compound/features will be added</em></li><li>File upload metadata: Dublin core annotation parameters, as in opentox,owl#Dataset</li></ul><br><ul><li><em>Content-type:application/www-form-urlencoded</em><strong> dataset_uri</strong> , <strong>feature_uris[]</strong> and <strong>compound_uris[]</strong> parameters are used to specify subset of a dataset, as in GET operation;</li><li>File upload via <em>Content-type:multipart/form-data</em>: <strong>file</strong> parameter </li><li>File upload metadata: Dublin core annotation parameters, as in opentox,owl#Dataset</li><li><strong>[subjectid]</strong></li></ul><br />
| <a title="Task" class="internal-link" href="AsyncTask#creating-a-task-post">Dataset URI or task URI</a><br><br />
| 200,202,400,404,503<br />
|- <br />
| Remove a dataset<br />
| DELETE<br />
| <br><br />
| /dataset/{id}<br />
| <br><br />
| <strong>[subjectid]</strong><br />
| -<br />
| 200,404,503<br />
|- <br />
| Remove a part of the dataset<br />
| DELETE<br />
| <br><br />
| /dataset/{id}<br />
| <br><br />
| <strong>compound_uris[] </strong>and/or <strong>feature_uris[]</strong>; further query parameters may be defined to select the data to be deleted<br><br><strong>[subjectid]</strong><br><br />
| -<br />
| 200,404,503</tbody><br />
|}<ul><li><strong>subjectid</strong> (optional) parameter that contains the OpenSSO A&amp;A token needed to access protected services.</li></ul><h2>Queries</h2><br />
Subsets of a dataset (e.g. all data for a certain feature, all data for a set of compounds)) are accessed through query parameters. This allows us to pass full URIs as parameters and circumvents the problem of no-unique IDs (e.g. for /dataset/{id}/compound/{compound_id} URIs). The query parameters<br />
<strong>compound_uris[]</strong><br />
and<br />
<strong>feature_uris[]</strong><br />
are mandatory, more advanced queries (e.g. similarity searches) may be implemented by individual services.<br />
<h3>Examples</h3><dl><dt>Get all features of two compounds</dt><dd><code>curl -X GET http://my_dataset_service/dataset_id?</code><code>compound_uris</code><code>[]=compound1_uri&amp;</code><code>compound_uris</code><code>[]=compound2_uri</code></dd><dt>Get a single feature of a single compound</dt><dd><code>curl -X GET http://my_dataset_service/dataset_id?</code><code>compound_uris</code><code>[]=compound_uri&amp;feature_uris[]=feature_uri</code></dd><dt>Remove a compound from a dataset</dt><dd><code>curl -X DELETE http://my_dataset_service/{dataset_id}?</code><code>compound_uris[]=&lt;compound_uris&gt;</code></dd><dt>Upload an sdf to ambit server </dt><dd><code>curl -X POST -H 'Content-Type:chemical/x-mdl-sdfile' --data-binary @filename.sdf http://ambit.uni-plovdiv.bg:8080/ambit2/dataset</code></dd><dt>Get compound URIs of a dataset </dt><dd><code>curl -X GET -H 'Accept:text/uri-list' http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/{dataset_id}</code></dd><dt>Upload an sdf that contains features of an already existing dataset (if a feature name in filename.sdf matches a feature name from associated_features the corresponding URI is assigned)</dt><dd><code>curl -X POST -H 'Content-Type:chemical/x-mdl-sdfile' --data-binary @filename.sdf -d 'associated_features=http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/{datsaet_id}/feature' -d 'matcher=Name' http://ambit.uni-plovdiv.bg:8080/ambit2/dataset</code></dd></dl><br />
Together with a little bit of RDF processing you can use queries also for set operations (e.g. subsets, split, merge, intersection).<br />
<p><em>PS Take care to URI encode parameters that are sent via GET.</em></p><h2>Dataset representation</h2><h3>RDF specification</h3><h4>Metadata</h4><ul><li>[http://opentox.org/data/documents/development/RDF%20files/Dataset RDF dataset representation] (Dublin core properties +&nbsp; [http://purl.org/dc/terms/license purl.org/dc/terms/license] and [http://purl.org/dc/terms/rightsHolder purl.org/dc/terms/rightsHolder] from Dublin Core terms ontology)</li><li>Web form (application/www-form-urlencoded) - parameter names is the name of the DC/DCterms property - e.g. <strong>title</strong> for <strong>dc:title</strong> , <strong>license</strong> for <strong>dcterms:license</strong> [http://www.w3.org/TR/2011/NOTE-void-20110303/" http://www.w3.org/TR/2011/NOTE-void-20110303/]. (<span class="visualHighlight">fully qualified names are rather inconvenient - is it sufficient to use just names?</span>)<br></li><li><em>Content-type:multipart/form-data </em><em>F</em>ile upload metadata: parameters as in opentox.owl&nbsp; - verify if fully qualified dc: properties can be used as parameter names (same as for Web form)<br></li></ul><h4>Features</h4><p> [http://opentox.org/data/documents/development/RDF%20files/Dataset RDF dataset representation]</p><p>The feature URI points to a [http://opentox.org/dev/apis/api-1.2/Feature Feature] object, which allows retrieval of the Feature object as RDF and provides information about the name, units, source and the type of the feature. The feature type is denoted by a mandatory link to an ontology via owl:sameAs or directly subclassing a class from an ontology.</p><p>This allows Feature URI to point directly to an existing (fixed) ontology, or to a web service, providing access to dynamically created Feature objects.</p><h4>Conformers</h4><br />
Conformer URIs (see Compound API) can be used instead of compound URIs. The Resolving the parent structure should be done via the compound webservice.<br />
<h3>Examples</h3><br />
Multi Cell Call prediction from J48 (N3 notation):<br />
<pre>example:DatasetPredicted<br />
a ot:Dataset ;<br />
dc:identifier "http://myservice/dataset/{datasetid}"^^xsd:string ;<br />
dc:title "Multi Cell Call prediction from J48"^^xsd:string ;<br />
ot:dataEntry<br />
[ a ot:DataEntry ;<br />
ot:compound example:benzene ;<br />
ot:values<br />
[ a ot:FeatureValue ;<br />
ot:feature example:MultiCellCallPredicted ;<br />
ot:value "true"^^xsd:boolean<br />
];<br />
ot:values<br />
[ a ot:FeatureValue ;<br />
ot:feature example:MultiCellCall ;<br />
ot:value "true"^^xsd:boolean<br />
] ;<br />
] .<br />
example:benzene<br />
a ot:Compound ;<br />
dc:identifier "http://myservice/compound/{compoundid1}"^^xsd:string .<br />
example:MultiCellCallPredicted<br />
a ot:Feature ;<br />
dc:identifier "http://myservice/feature/{featureid3}"^^xsd:string ;<br />
dc:title "MultiCellCall"^^xsd:string ;<br />
ot:hasSource example:WekaJ48 .<br />
</pre><br />
Single compound with a single substructure:<br />
<pre>&lt;https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/2407&gt;<br />
a ot:Dataset ;<br />
ot:dataEntry<br />
[ a ot:DataEntry ;<br />
ot:compound &lt;https://ambit.uni-plovdiv.bg:8443/ambit2/compound/17285&gt; ;<br />
ot:values<br />
[ a ot:FeatureValue ;<br />
ot:feature &lt;https://ambit.uni-plovdiv.bg:8443/ambit2/feature/171898&gt; ;<br />
ot:value "true"^^xsd:boolean<br />
]<br />
] .<br />
&lt;https://ambit.uni-plovdiv.bg:8443/ambit2/compound/17285&gt;<br />
a ot:Compound .<br />
&lt;https://ambit.uni-plovdiv.bg:8443/ambit2/feature/171898&gt;<br />
a ot:Substructure ;<br />
dc:title "FCF" ;<br />
ot:smarts "FCF" ;<br />
ot:hasSource &lt;https://ambit.uni-plovdiv.bg:8443/ambit2/model/26469&gt; ;<br />
ot:Substructure<br />
a owl:Class ;<br />
rdfs:subClassOf ot:Feature .</pre><p>Retrieving metadata:</p><pre>curl -H "Accept:text/n3" <a href="http://apps.ideaconsult.net:8080/ambit2/dataset/1/metadata" target="_blank">http://apps.ideaconsult.net:8080/ambit2/dataset/112/metadata</a><br />
&lt;<a href="http://apps.ideaconsult.net:8080/ambit2/dataset/112" target="_blank">http://apps.ideaconsult.net:8080/ambit2/dataset/112</a>&gt;<br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; a&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ot:Dataset ;<br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; dc:title "ToxCast_ToxRefDB_20091214.txt" ;<br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; dcterms:license &lt;<a href="http://www.opendatacommons.org/licenses/pddl" target="_blank">http://www.opendatacommons.org/licenses/pddl&gt;</a> .</pre><div>&nbsp;</div><p>Adding metadata to an existing dataset (using RDF)</p><pre>curl -X PUT -H "Content-type:application/rdf+xml" -d @mymetadata.rdf http://host/dataset/{id}/metadata <br />
</pre><p>Adding metadata to an existing dataset (using web form)</p><pre>curl -X PUT -d "license=<a href="http://www.opendatacommons.org/licenses/pddl" target="_blank">http://www.opendatacommons.org/licenses/pddl</a>" -d "title=blabla" <a href="http://host/dataset/%7Bid%7D/metadata" target="_blank">http://host/dataset/{id}/metadata</a></pre><p>Specifying the metadata on upload (mimics sending a multipart web form)</p><pre>curl -X POST -F "file=@alkanes.csv" <br />
-F "license=<a href="http://www.opendatacommons.org/licenses/pddl/" target="_blank">http://www.opendatacommons.org/licenses/pddl/</a>" <br />
-F "title=Alkanes" <a href="http://host/dataset/" target="_blank">http://host/dataset/</a></pre><h2>Supported MIME types</h2><h3>Mandatory</h3><ul><li>application/rdf+xml (default)</li><li>application/www-form-urlencoded</li><li>multipart/form-data<br></li><li><span title="multipart/form-data" class="index-inst"></span><a name="idx-multipartform-data-1"></a></li></ul><h3>Optional</h3><ul><li>other RDF serialization formats<br></li><li>application/xml</li><li>text/xml</li><li>text/x-yaml</li><li>text/x-json</li><li>application/json</li><li>text/csv</li><li>text/arff</li><li>text/html</li><li>chemical/x-mdl-sdfile</li><li>...</li><li>multipart/form-data for file uploads <br></li></ul><h2>HTTP status codes</h2><br />
{| <tbody> <br />
! Interpretation<br />
! Nr<br />
! Name<br />
|- <br />
| Success<br />
| 200<br />
| OK<br />
|- <br />
| Asynchronous task started<br><br />
| 202<br />
| Accepted<br><br />
|- <br />
| Dataset not found<br />
| 404<br />
| Not Found<br />
|- <br />
| Incorrect MIME type<br />
| 400<br />
| Bad request<br />
|- <br />
| Service not available<br />
| 503<br />
| Service unavailable</tbody><br />
|}</div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2013-03-22T09:07:33Z
<p>Mrautenberg: /* Retrieve a protocol uri associated with a Study */</p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
get a URI list of all investigation:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get a RDF representation of a users investigations:<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get JSON URI/modified date list:<br />
curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get URI list of the users investigations URIs:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
==== cURL example ====<br />
curl -Lk -X POST -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Add/update studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add/update studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Get a protocol uri associated with a Study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyProtocol}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol<br />
<br />
<!--<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
--><br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix foaf: <http://xmlns.com/foaf/0.1/> .<br />
@prefix tbisa: <http://onto.toxbank.net/isa/> .<br />
@prefix dcterms: <http://purl.org/dc/terms/> .<br />
<http://onto.toxbank.net/isa/BIII1/I2215><br />
a tbisa:Investigation ;<br />
tbisa:hasAccessionID<br />
"BII-I-1" ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_3977> , <http://onto.toxbank.net/isa/BIII1/ISA_3975> , <http://onto.toxbank.net/isa/BIII1/ISA_3976> ;<br />
tbisa:hasStudy <http://onto.toxbank.net/isa/BIII1/S212> , <http://onto.toxbank.net/isa/BIII1/S213> ;<br />
dcterms:abstract """Background<br />
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell- (skipped) ...engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:issued "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Study:RetrieveStudyProtocol
API Study:RetrieveStudyProtocol
2013-03-22T09:06:54Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get a study related protocol uri<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation/{id}/protocol<br />
|REST_header_param=Subjectid:SECURITY-TOKEN<br />
|REST_op_mime_input=Accept:application/rdf+xml<br />
|REST_op_result=Protocol uris<br />
|REST_op_mime_output=application/rdf+xml<br />
}}</div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2013-03-14T07:54:08Z
<p>Mrautenberg: /* Delete individual studies, assays or data from an investigation */</p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
get a URI list of all investigation:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get a RDF representation of a users investigations:<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get JSON URI/modified date list:<br />
curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get URI list of the users investigations URIs:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
==== cURL example ====<br />
curl -Lk -X POST -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Add/update studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add/update studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Retrieve a protocol uri associated with a Study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyProtocol}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol<br />
<br />
<!--<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
--><br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix foaf: <http://xmlns.com/foaf/0.1/> .<br />
@prefix tbisa: <http://onto.toxbank.net/isa/> .<br />
@prefix dcterms: <http://purl.org/dc/terms/> .<br />
<http://onto.toxbank.net/isa/BIII1/I2215><br />
a tbisa:Investigation ;<br />
tbisa:hasAccessionID<br />
"BII-I-1" ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_3977> , <http://onto.toxbank.net/isa/BIII1/ISA_3975> , <http://onto.toxbank.net/isa/BIII1/ISA_3976> ;<br />
tbisa:hasStudy <http://onto.toxbank.net/isa/BIII1/S212> , <http://onto.toxbank.net/isa/BIII1/S213> ;<br />
dcterms:abstract """Background<br />
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell- (skipped) ...engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:issued "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Study:Delete
API Study:Delete
2013-03-14T07:53:17Z
<p>Mrautenberg: </p>
<hr />
<div><!--<br />
{{REST Operations<br />
|REST_op_description=Delete individual studies, assays, data from an investigation<br />
|REST_resource=Investigation<br />
|REST_op_method=DELETE<br />
|REST_op_uri=/investigation/{id}/{filename}<br />
|REST_header_param=subjectid:SECURITY-TOKEN<br />
|REST_op_result=Task URI<br />
|REST_op_mime_output=text/uri-list<br />
|REST_op_status=202<br />
}}<br />
--></div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2013-03-01T10:24:39Z
<p>Mrautenberg: /* cURL example */</p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
get a URI list of all investigation:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get a RDF representation of a users investigations:<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get JSON URI/modified date list:<br />
curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
get URI list of the users investigations URIs:<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation<br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
==== cURL example ====<br />
curl -Lk -X POST -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}<br />
<br />
== Add/update studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add/update studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Retrieve a protocol uri associated with a Study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyProtocol}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol<br />
<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix foaf: <http://xmlns.com/foaf/0.1/> .<br />
@prefix tbisa: <http://onto.toxbank.net/isa/> .<br />
@prefix dcterms: <http://purl.org/dc/terms/> .<br />
<http://onto.toxbank.net/isa/BIII1/I2215><br />
a tbisa:Investigation ;<br />
tbisa:hasAccessionID<br />
"BII-I-1" ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_3977> , <http://onto.toxbank.net/isa/BIII1/ISA_3975> , <http://onto.toxbank.net/isa/BIII1/ISA_3976> ;<br />
tbisa:hasStudy <http://onto.toxbank.net/isa/BIII1/S212> , <http://onto.toxbank.net/isa/BIII1/S213> ;<br />
dcterms:abstract """Background<br />
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell- (skipped) ...engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:issued "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:List
API Investigation:List
2013-03-01T10:20:26Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get a list of all investigations<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation<br />
|REST_header_param=Accept:text/uri-list, application/rdf+xml subjectid:SECURITY-TOKEN<br />
|REST_op_result=List of investigations<br />
|REST_op_mime_output=text/uri-list, application/rdf+xml<br />
|REST_op_status=200<br />
}}<br />
{{REST Operations<br />
|REST_op_description=Get a list of user related investigations<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation<br />
|REST_header_param=User:USER_URI subjectid:SECURITY-TOKEN<br />
|REST_op_mime_input=Accept:application/rdf+xml, application/json, text/uri-list<br />
|REST_op_result=list of investigations owned/uploaded by a specific user<br />
|REST_op_mime_output=application/rdf+xml, application/json, text/uri-list<br />
|REST_op_status=200<br />
}}</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Study:Upload
API Study:Upload
2012-11-02T14:09:01Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Add/update studies, assays or data to an investigation<br />
|REST_resource=Investigation<br />
|REST_op_method=PUT<br />
|REST_op_uri=/investigation/{id}<br />
|REST_op_params=optional params:<br />
* allowReadByUser: one or multiple userservice-URIs (User)<br />
* allowReadByGroup: one or multiple userservice-URIs (Organisations, Projects)<br />
* summarySearchable: true/false (default is false)<br />
* published: true/false (default is false)<br />
|REST_header_param=subjectid:SECURITY-TOKEN<br />
|REST_op_mime_input=multipart/form-data<br />
|REST_op_result=Task URI<br />
|REST_op_mime_output=text/uri-list<br />
|REST_op_status=202<br />
}}<br />
Individual ISA-TAB files (text/tab-separated-values) or zip archives of study, assay and data files can be posted as form data to add files to an existing investigation.</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Study:Upload
API Study:Upload
2012-09-14T12:24:08Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Add studies, assays or data to an investigation<br />
|REST_resource=Investigation<br />
|REST_op_method=PUT<br />
|REST_op_uri=/investigation/{id}<br />
|REST_op_params=optional params:<br />
* allowReadByUser: one or multiple userservice-URIs (User)<br />
* allowReadByGroup: one or multiple userservice-URIs (Organisations, Projects)<br />
* summarySearchable: true/false (default is false)<br />
* published: true/false (default is false)<br />
|REST_header_param=subjectid:SECURITY-TOKEN<br />
|REST_op_mime_input=multipart/form-data<br />
|REST_op_result=Task URI<br />
|REST_op_mime_output=text/uri-list<br />
|REST_op_status=202<br />
}}<br />
Individual ISA-TAB files (text/tab-separated-values) or zip archives of study, assay and data files can be posted as form data to add files to an existing investigation.</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Resource
API Investigation:Resource
2012-09-14T10:38:19Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get an ISA-TAB entry<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation/{id}/{resource}<br />
|REST_header_param=Accept: one of text/plain (n-triples), text/turtle, application/rdf+xml, subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation ISA-TAB entry in n-triples, turtle or RDF format<br />
|REST_op_mime_output=text/plain (n-triples), text/turtle, application/rdf+xml<br />
|REST_op_status=200<br />
}}</div>
Mrautenberg
http://api.toxbank.net/index.php/Investigation
Investigation
2012-09-14T10:36:22Z
<p>Mrautenberg: /* Get an ISA-TAB entry */</p>
<hr />
<div>{{REST_resource<br />
}}<br />
<br />
Investigations/Studies/Assays/Data are modeled according to [http://isatab.sourceforge.net/format.html ISA-TAB] standards.<br />
<br />
'''Investigation:''' High level concept to link related [[Investigation#Study|studies]]. <br />
<br />
'''Study:''' The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied. <br />
<br />
'''Assay:''' Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements ([[API_Data|data]]).<br />
<br />
'''Data:''' OpenTox Datasets or external files in native or other formats.<br />
<br />
Investigations can be [[Investigation#Query|queried]] with [http://en.wikipedia.org/wiki/SPARQL SPARQL]. REST operations are avialble for accessing individual investigations, studies, assays and data.<br />
<br />
Investigations are created by submitting a zip archive with [http://isatab.sourceforge.net/format.html ISA-TAB] files. Individual studies, assays and datafiles can be submitted as [http://isatab.sourceforge.net/format.html ISA-TAB] files (studies, assays) or as native data files (e.g. Affymetrix CEL files).<br />
<br />
'''Uploading ISA-TAB archives:''' Investigations can be uploaded in a zip archive with all [http://isatab.sourceforge.net/format.html ISA-TAB] files in a single folder.<br />
<br />
'''Uploading individual ISA-TAB files''': It is possible to upload individual data and study/assay [http://isatab.sourceforge.net/format.html ISA-TAB] files. In this case the client has to ensure that [http://isatab.sourceforge.net/format.html ISA-TAB] references are valid URIs or relative paths.<br />
<br />
'''Filenames:''' [http://isatab.sourceforge.net/format.html ISA-TAB] filenames (in zip archives and individual files) have to follow the conventions:<br />
<br />
i_*.txt: Investigation<br />
s_*.txt: Study<br />
a_*.txt: Assay<br />
all other filenames will be interpreted as data files<br />
<br />
Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.<br />
<br />
= Investigation =<br />
<br />
An [[Investigation|Investigation]] is a collection of related [[Investigation#Study|studies]].<br />
<br />
A [[API_Study|Study]] has associated [[API_Study#Assays|Assays]], it is the result of executing a set of [[API_Protocol|Protocols]]. A [[API_Study|Study]] has an Author (an [[API_User|User]]).<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
[[API_Study#Data|Data]] can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<!--<br />
Investigations are created by submitting [http://isatab.sourceforge.net/format.html ISA-TAB] files.<br />
<br />
<br />
A [[Investigation|Investigation]] may have [[Investigation#Add|versions]], which are [[Investigation|Investigations]] that are linked to their predecessor. <br />
--><br />
<br />
== Get a list of investigations ==<br />
{{HasOperation |id=API_Investigation:List}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://toxbanktest1.opentox.org/investigation<br />
<br />
<!-- <br />
== Query all investigations ==<br />
{{HasOperation |id=API_Investigation:Query}}<br />
--><br />
<br />
== Create an investigation ==<br />
{{HasOperation |id=API_Investigation:Create}}<br />
==== cURL example ====<br />
curl -Lk -X POST -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://toxbanktest1.opentox.org/investigation<br />
<br />
== Get an investigation representation ==<br />
{{HasOperation |id=API_Investigation:View}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://toxbanktest1.opentox.org/investigation/6f042393-8d6e-4df1-81a9-21a6f761c938<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://toxbanktest1.opentox.org/investigation/6f042393-8d6e-4df1-81a9-21a6f761c938<br />
<br />
== Get investigation metadata ==<br />
{{HasOperation |id=API_Investigation:Metadata}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://toxbanktest1.opentox.org/investigation/545407d1-8bf1-479a-b92e-5b142ee99ee1/metadata<br />
<br />
== Get an ISA-TAB entry ==<br />
{{HasOperation |id=API_Investigation:Resource}}<br />
==== cURL example ====<br />
curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://toxbanktest1.opentox.org/investigation/545407d1-8bf1-479a-b92e-5b142ee99ee1/MN20977<br />
<br />
== Delete an investigation ==<br />
{{HasOperation |id=API_Investigation:Delete}}<br />
==== cURL example ====<br />
curl -X DELETE -k -H 'subjectid:MYTOKEN' https://toxbanktest1.opentox.org/investigation/ID<br />
<br />
== Add studies, assays or data to an investigation ==<br />
{{HasOperation |id=API_Study:Upload}}<br />
<br />
==== cURL example ==== <br />
Add studies, assays or data to an investigation or update data<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \<br />
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://toxbanktest1.opentox.org/investigation/UUID<br />
Update isPublished flag in metadata<br />
curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://toxbanktest1.opentox.org/investigation/UUID<br />
<br />
<br />
<br />
<!--<br />
= Study, Assay, Data =<br />
--><br />
<br />
<!--<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a study ===<br />
<http://toxbank.net/services/study/Study_3><br />
a tb:Study ;<br />
tb:hasAbstract "This is an abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "abc"^^xsd:string ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:versionInfo "1"^^xsd:string .<br />
--><br />
<!--<br />
== Get a list of studies in an investigation ==<br />
{{HasOperation |id=API_Study:RetrieveList}}<br />
--><br />
<br />
== Get a study, assay or data representation ==<br />
{{HasOperation |id=API_Study:Retrieve}}<br />
<br />
== Delete individual studies, assays or data from an investigation ==<br />
{{HasOperation |id=API_Study:Delete}}<br />
<!--<br />
== Retrieve Metadata of a single Study ==<br />
{{HasOperation |id=API_Study:RetrieveMetadata}}<br />
--><br />
<!--<br />
= Study versions =<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Study with a previous version ===<br />
<http://toxbank.net/services/study/Study_4><br />
a tb:Study ;<br />
tb:hasAbstract "This is another abstract"^^xsd:string ;<br />
tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;<br />
tb:hasAuthor tb:OliviaSanger ;<br />
tb:hasKeyword "cell"@en , "protein"@en ;<br />
tb:hasOwner tb:ORG5 ;<br />
tb:isSummarySearchable<br />
"true"^^xsd:boolean ;<br />
tb:project tb:DETECTIVE ;<br />
tb:studyPriorVersion<br />
<http://toxbank.net/services/study/Study_3>;<br />
tb:versionInfo "2"^^xsd:string .<br />
<br />
== Upload a new Study version ==<br />
{{HasOperation |id=API_Study:UploadVersion}}<br />
<br />
== Retrieve Versions of a single Study==<br />
{{HasOperation |id=API_Study:RetrieveVersions}}<br />
--><br />
<!--<br />
= Assay =<br />
<br />
An [[API_Study#Assays|Assay]] serves as a container, associating a [[API_Protocol|Protocol]] with the generated [[API_Data|data]]. <br />
<br />
<br />
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of an Assay ===<br />
<http://toxbank.net/services/study/Study_3/assay/Assay_7><br />
a tb:Assay ;<br />
tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;<br />
tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.<br />
<br />
<http://toxbank.net/services/study/Study_4/assay/Assay_11><br />
a tb:Assay ;<br />
tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;<br />
tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;<br />
tb:isPartOfStudy<br />
<http://toxbank.net/services/study/Study_4>.<br />
<br />
<br />
== Get a list of assays in a study ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssays}}<br />
<br />
== Get an assay representation ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
<br />
== Add an assay to a study ==<br />
{{HasOperation |id=API_Study:UploadStudyAssay}}<br />
--><br />
<!--<br />
== Retrieve a Protocol, associated with an Assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyAssay}}<br />
--><br />
<!--<br />
= Data =<br />
<br />
Data can be either an [http://api.toxbank.net/index.php/OpenTox_API_1.2_Dataset OpenTox dataset] or a native data file (e.g. Affymetrix CEL file).<br />
<br />
== Get a list of data URIs for an assay ==<br />
{{HasOperation |id=API_Study:RetrieveStudyData}}<br />
<br />
== Add datafile to an assay ==<br />
{{HasOperation |id=API_Study:UploadAssayData}}<br />
<br />
== Get datafile in native format ==<br />
{{HasOperation |id=API_Study:GetAssayData}}<br />
--><br />
<br />
== Security ==<br />
see [[Protocol#Security | Protocol]]<br />
<br /><br />
<br /><br />
<br />
== Investigation metadata in RDF ==<br />
<br />
=== Investigation ===<br />
<br />
Namespace: tbisa: http://onto.toxbank.net/isa<br />
<br />
Class <br />
<investigation_uri> a tbisa:Investigation.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:abstract "String".<br />
dcterms:created "Date". <br />
dcterms:issued "Date".<br />
<br />
Object properties:<br />
<br />
tbisa:hasStudy rdfs:domain tbisa:Investigation . <br />
tbisa:hasStudy rdfs:range tbisa:Study . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
@prefix foaf: <http://xmlns.com/foaf/0.1/> .<br />
@prefix tbisa: <http://onto.toxbank.net/isa/> .<br />
@prefix dcterms: <http://purl.org/dc/terms/> .<br />
<http://onto.toxbank.net/isa/BIII1/I2215><br />
a tbisa:Investigation ;<br />
tbisa:hasAccessionID<br />
"BII-I-1" ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_3977> , <http://onto.toxbank.net/isa/BIII1/ISA_3975> , <http://onto.toxbank.net/isa/BIII1/ISA_3976> ;<br />
tbisa:hasStudy <http://onto.toxbank.net/isa/BIII1/S212> , <http://onto.toxbank.net/isa/BIII1/S213> ;<br />
dcterms:abstract """Background<br />
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell- (skipped) ...engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:issued "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" .<br />
<br />
=== Study ===<br />
<br />
Class <br />
<study_uri> a tbisa:Study.<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".<br />
dcterms:description "String".<br />
dcterms:created "Date". <br />
<br />
Object properties:<br />
<br />
tbisa:hasAssay rdfs:domain tbisa:Study . <br />
tbisa:hasAssay rdfs:range tbisa:Assay . <br />
tbisa:hasProtocol rdfs:domain tbisa:Study . <br />
tbisa:hasProtocol rdfs:range tbisa:Protocol . <br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/S1138><br />
a tbisa:Study ;<br />
tbisa:hasAccessionID<br />
"BII-S-2" ;<br />
tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055> ;<br />
tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;<br />
tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18> ;<br />
dcterms:created "29 Apr 2007 21:00:00 GMT" ;<br />
dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;<br />
dcterms:title "A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .<br />
<http://onto.toxbank.net/isa/BIII1/PA2538><br />
a tbisa:ProtocolApplication ;<br />
tbisa:appliesProtocol<br />
<http://onto.toxbank.net/isa/BIII1/P_10> .<br />
<br />
=== Protocol ===<br />
<br />
Class <br />
<protocol_uri> a tbisa:Protocol , tb:Protocol;<br />
<br />
Data properties<br />
<br />
tbisa:hasAccessionID "String" .<br />
dcterms:title "String".. <br />
<br />
Object properties:<br />
<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasProtocol<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Study ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:appliesProtocol<br />
a owl:FunctionalProperty , owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:Protocol .<br />
tbisa:hasParameterValue<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:ProtocolApplication ;<br />
rdfs:range tbisa:ParameterValue .<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
<br />
==== Example N3 ====<br />
<br />
<br />
<http://onto.toxbank.net/isa/BIII1/P_17><br />
a tbisa:Protocol ;<br />
rdfs:label "mRNA extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
tbisa:hasAccessionID<br />
"BII-S-2\\mRNA extraction" .<br />
<br />
=== Contact (Person, User ) ===<br />
<br />
Classes <br />
<person_uri> a foaf:Person , tbisa:Contact , tb:User ;<br />
<br />
Data properties<br />
<br />
(as for tb:User - foaf:family_name, foaf:givenname , etc.)<br />
<br />
Object properties:<br />
<br />
tbisa:hasOwner rdfs:range tbisa:Contact .<br />
<br />
==== Example N3 ====<br />
<br />
<http://onto.toxbank.net/isa/BIII1/ISA_3980><br />
a foaf:Person , tbisa:Contact , tb:User ;<br />
foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;<br />
foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .<br />
<br />
<br />
=== Processing node ===<br />
<br />
Classes <br />
<processingnode> a tbisa: Processing;<br />
<br />
Subclasses<br />
<br />
tbisa:DataProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:MaterialProcessing<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
tbisa:DataAcquisition<br />
rdfs:subClassOf tbisa:Processing .<br />
<br />
Object properties:<br />
<br />
tbisa:hasProtocolApplication<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:ProtocolApplication .<br />
tbisa:hasInputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .<br />
tbisa:hasOutputNode<br />
a owl:ObjectProperty ;<br />
rdfs:domain tbisa:Processing ;<br />
rdfs:range tbisa:Node .</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:Metadata
API Investigation:Metadata
2012-09-14T10:25:46Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get investigation metadata<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation/{id}/metadata<br />
|REST_header_param=Accept: one of text/plain (n-triples), text/turtle, application/rdf+xml, subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation metadata in n-triples, turtle or RDF format<br />
|REST_op_mime_output=text/plain (n-triples), text/turtle, application/rdf+xml<br />
|REST_op_status=200<br />
}}</div>
Mrautenberg
http://api.toxbank.net/index.php/API_Investigation:View
API Investigation:View
2012-09-14T10:22:41Z
<p>Mrautenberg: </p>
<hr />
<div>{{REST Operations<br />
|REST_op_description=Get an investigation representation<br />
|REST_resource=Investigation<br />
|REST_op_method=GET<br />
|REST_op_uri=/investigation/{id}<br />
|REST_header_param=Accept: one of text/tab-separated-values, text/uri-list, application/zip, text/plain (n-triples), text/turtle, application/rdf+xml, subjectid:SECURITY-TOKEN<br />
|REST_op_result=Investigation ISA-TAB file, list of study, assay and data URIs, zipped ISA-TAB files (including studies, assays and data files) or RDF representation<br />
|REST_op_mime_output=text/tab-separated-values, text/uri-list, application/zip, text/plain, application/rdf+xml<br />
|REST_op_status=200<br />
}}</div>
Mrautenberg