Investigation

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Investigation


Investigations/Studies/Assays are modeled according to ISA-TAB standards

Contents

Investigation

High level concept to link related studies. Investigations are created by submitting ISA-TAB files.

A Investigation may have versions, which are Investigations that are linked to their predecessor.

Get a list of investigations

Description Get a list of all investigations
Resource Investigation
Method GET
URI /investigation
Parameters
Header Parameters Accept:text/uri-list, application/rdf+xml subjectid:SECURITY-TOKEN
Media Type (input)
Results List of investigations
Media Type (output) text/uri-list, application/rdf+xml
Status code 200, 400


Description Get a list of user related investigations
Resource Investigation
Method GET
URI /investigation
Parameters
Header Parameters User:USER_URI subjectid:SECURITY-TOKEN
Media Type (input) Accept:application/rdf+xml, application/json, text/uri-list
Results list of investigations owned/uploaded by a specific user
Media Type (output) application/rdf+xml, application/json, text/uri-list
Status code 200, 400

Links: Page, Edit with form



Query all investigations

Description Query all investigations with SPARQL
Resource Investigation
Method GET
URI /investigation
Parameters query
Header Parameters Accept: one of text/plain (n-triples), text/turtle, application/rdf+xml (for CONSTRUCT queries), subjectid:SECURITY-TOKEN
Media Type (input)
Results Query result
Media Type (output) application/sparql-results+xml (SELECT queries), text/plain (n-triples), text/turtle, application/rdf+xml (CONSTRUCT queries)
Status code 200

Links: Page, Edit with form



Create an investigation

Description Create a new investigation from ISA-TAB files
Resource Investigation
Method POST
URI /investigation
Parameters optional params:
  • allowReadByUser: one or multiple userservice-URIs (User)
  • allowReadByGroup: one or multiple userservice-URIs (Organisations, Projects)
  • summarySearchable: true/false (default is false)

required params (when upload not in isa-tab format):

  • type: one of noData/unformattedData/ftpData
  • title: string
  • abstract: string
  • owningOrg: one userservice-URI (Organisations)
  • owningPro: one or multiple userservice-URIs (Projects)
  • authors: one or multiple userservice-URIs (User)
  • keywords: one or multiple owl-URIs
  • ftpFile: one or multiple filenames (only for type ftpData)

optional params (when upload not in isa-tab format):

  • licenses: string
Header Parameters subjectid:SECURITY-TOKEN
Media Type (input) multipart/form-data:
  • upload ISA-TAB files (isa-tab zip archive)
  • upload unformatted data (zip archive, required params)
  • upload without data (ftp filename, required params)
  • upload without data (required params)
Results Task URI
Media Type (output) text/uri-list
Status code 202, 400, 401

cURL example 

curl -Lk -X POST -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \
https://services.toxbank.net/investigation?allowReadByUser=USER_URI1,USER_URI2&allowReadByGroup=GROUP_URI1,GROUP_URI2&summarySearchable=VALUE

curl -Lk -X POST -i -H "subjectid:MYTOKEN" -d "type=noData" -d "title=STRING" -d "abstract=STRING" -d "owningOrg=GROUP_URI" \ 
-d owningPro=GROUP_URI1,GROUP_URI2" -d "authors=USER_URI1,USER_URI2" -d "keywords=OWL_URI1,OWL_URI2" -d "allowReadByUser=USER_URI1,USER_URI2" \
-d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d "summarySearchable=VALUE" https://services.toxbank.net/investigation

curl -Lk -X POST -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \
https://services.toxbank.net/investigation?type=unformattedData&title=STRING&abstract=STRING&owningOrg=GROUP_URI&owningPro=GROUP_URI1,GROUP_URI2 \
&authors=USER_URI1,USER_URI2&keywords=OWL_URI1,OWL_URI2&allowReadByUser=USER_URI1,USER_URI2&allowReadByGroup=GROUP_URI1,GROUP_URI2 \
&summarySearchable=VALUE

curl -Lk -X POST -i -H "subjectid:MYTOKEN" -d "type=ftpData" -d "title=STRING" -d "abstract=STRING" -d "owningOrg=GROUP_URI" \
-d owningPro=GROUP_URI1,GROUP_URI2" -d "authors=USER_URI1,USER_URI2" -d "keywords=OWL_URI1,OWL_URI2" -d "licenses=STRING" \
-d "ftpFile=FILENAME_A,FILENAME_B" -d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" \
-d "summarySearchable=VALUE" https://services.toxbank.net/investigation

Links: Page, Edit with form



Get an investigation

Description Get an investigation representation
Resource Investigation
Method GET
URI /investigation/{id}
Parameters
Header Parameters Accept: one of text/tab-separated-values, text/uri-list, application/zip, text/plain (n-triples), text/turtle, application/rdf+xml, subjectid:SECURITY-TOKEN
Media Type (input)
Results Investigation ISA-TAB file, list of study, assay and data URIs, zipped ISA-TAB files (including studies, assays and data files) or RDF representation
Media Type (output) text/tab-separated-values, text/uri-list, application/zip, text/plain, application/rdf+xml
Status code 200, 400, 401, 404

Links: Page, Edit with form



Create a new version of an investigation

Description Create a new version of an investigation
Resource Investigation
Method POST
URI /investigation/{id}
Parameters
Header Parameters
Media Type (input) multipart/form-data
Results URI of new investigation version
Media Type (output) text/uri-list
Status code

Will create a new investigation which is linked to the original investigation, the original investigation will remain intact Links: Page, Edit with form



Delete an investigation

Description Delete an investigation
Resource Investigation
Method DELETE
URI /investigation/{id}
Parameters
Header Parameters subjectid:SECURITY-TOKEN
Media Type (input)
Results Success message
Media Type (output) text/plain
Status code 200, 401

Links: Page, Edit with form



Study

The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied.

A Study has associated Assays, it is the result of executing a set of Protocols.

A Study has an Author (an User).


N3 representation of a study 

<http://toxbank.net/services/study/Study_3>
     a       tb:Study ;
     tb:hasAbstract "This is an abstract"^^xsd:string ;
     tb:hasAssay http://toxbank.net/services/study/Study_3/assay/Assay_7> ;
     tb:hasAuthor tb:OliviaSanger ;
     tb:hasKeyword "abc"^^xsd:string ;
     tb:hasOwner tb:ORG5 ;
     tb:isSummarySearchable
             "true"^^xsd:boolean ;
     tb:project tb:DETECTIVE ;
     tb:versionInfo "1"^^xsd:string .


Get a list of studies of an investigation

Description Get a list of studies
Resource Investigation
Method GET
URI /investigation/{id}/study
Parameters
Header Parameters
Media Type (input) none
Results List of studies
Media Type (output) text/uri-list
Status code 200,400,401,402,403

Links: Page, Edit with form



Add a new study to an investigation

Description Add/update studies, assays or data to an investigation
Resource Investigation
Method PUT
URI /investigation/{id}
Parameters optional params:
  • allowReadByUser: one or multiple userservice-URIs (User)
  • allowReadByGroup: one or multiple userservice-URIs (Organisations, Projects)
  • summarySearchable: true/false (default is false)
  • published: true/false (default is false)

required params (when upload not in isa-tab format):

  • type: one of noData/unformattedData/ftpData
  • title: string
  • abstract: string
  • owningOrg: one userservice-URI (Organisations)
  • owningPro: one or multiple userservice-URIs (Projects)
  • authors: one or multiple userservice-URIs (User)
  • keywords: one or multiple owl-URIs
  • ftpFile: one or multiple filenames (only for type ftpData)
Header Parameters subjectid:SECURITY-TOKEN
Media Type (input) multipart/form-data
Results Task URI
Media Type (output) text/uri-list
Status code 202, 400, 401, 423

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. Investigations without ISA-TAB formated data can be edited by parameters and data files posted as form data replace existing data. Links: Page, Edit with form



Get a study representation

Description Get a study, assay, data representation
Resource Investigation
Method GET
URI /investigation/{id}/isatab/{filename}
Parameters
Header Parameters subjectid:SECURITY-TOKEN
Media Type (input)
Results Study, assay, data representation in ISA-TAB format
Media Type (output) text/tab-separated-values
Status code 200, 400, 401, 404

Links: Page, Edit with form




Assay

Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements (data).

An Assay serves as a container, associating a Protocol with the generated data.

N3 representation of an Assay 

 <http://toxbank.net/services/study/Study_3/assay/Assay_7>
     a       tb:Assay ;
     tb:hasData "http://abc.de/dataset/D123"^^xsd:anyURI ;
     tb:hasData "http://abc.de/dataset/D456"^^xsd:anyURI ;
     tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;
     tb:isPartOfStudy <http://toxbank.net/services/study/Study_3>.

<http://toxbank.net/services/study/Study_4/assay/Assay_11>
     a       tb:Assay ;
     tb:hasData "http://my.com/dataset/mydataset"^^xsd:anyURI ;
     tb:hasProtocol <http://toxbank.net/services/protocol/Protocol_9> ;
     tb:isPartOfStudy
             <http://toxbank.net/services/study/Study_4>.

Get a list of assays in a study

Description Get a list of all assays in a study
Resource Investigation
Method GET
URI /investigation/{id}/study/{id}/assay
Parameters
Header Parameters
Media Type (input)
Results List of assay URIs
Media Type (output) text/uri-list
Status code 200,400,401,402,403

Links: Page, Edit with form



Get an assay representation

Description Get an assay representation
Resource Investigation
Method GET
URI /investigation/{id}/study/{id}/assay/{id}
Parameters
Header Parameters
Media Type (input)
Results Assay representation in ISA-TAB or RDF format
Media Type (output) text/tab-separated-values, application/sparql-results+json
Status code 200,400,401,402,403

Links: Page, Edit with form



Add an assay to a study

Description Add an assay to a study
Resource Investigation
Method POST
URI /investigation/{id}/study/{id}/assay
Parameters
Header Parameters
Media Type (input) multipart/form-data
Results URI of the new assay
Media Type (output) text/uri-list
Status code 200,202,400,401,402,403

Assays should be submitted as attachment in ISA-TAB format (text/tab-separated-values). Links: Page, Edit with form



Data

Get data associated with an Assay

Description Get all data associated with an assay
Resource Investigation
Method GET
URI /investigation/{id}/study/{id}/assay/{id}/data
Parameters
Header Parameters
Media Type (input)
Results Links to datasets
Media Type (output) text/uri-list
Status code 200,400,401,402,403

Links: Page, Edit with form



Add data to an assay

Description Upload assay data
Resource Investigation
Method POST
URI /investigation/{id}/study/{id}/assay/{id}/data
Parameters
Header Parameters
Media Type (input) multipart/form-data
Results URI of new dataset
Media Type (output) text/uri-list
Status code 200,202,400,401,402,403

Upload data files in their native format (e.g. CEL files, ISA-TAB data). Links: Page, Edit with form


Retrieved from "http://api.toxbank.net/index.php/Investigation"
Facts about InvestigationRDF feed
HasOperationAPI Investigation:List  +, API Investigation:Query  +, API Investigation:Create  +, API Investigation:View  +, API Investigation:Add  +, API Investigation:Delete  +, API Study:RetrieveList  +, API Study:Upload  +, API Study:Retrieve  +, API Study:RetrieveStudyAssays  +, API Study:RetrieveStudyAssay  +, API Study:UploadStudyAssay  +, API Study:RetrieveStudyData  + and API Study:UploadAssayData  +
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