Investigation

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Investigation


Contents

Study

A Study is the specific instance of executing a set of Protocols.

A Study may consists of several (optionally ordered) Assays. An Assay serves as a container, associating a Protocol with the generated data. A Study has an Author (an User).

A Study may have versions, a Study version is another Study.

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 .


Retrieve the List of Studies

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



Upload a new Study

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



Retrieve a single Study

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



Retrieve Metadata of a single Study

Description Retrieves study metadata
Resource Investigation
Method GET
URI /study/{id}/metadata
Parameters TBD
Header Parameters
Media Type (input) none
Results Study metadata in supported Media Type formats
Media Type (output) text/uri-list, RDF, JSON, XML
Status code 200,400,401,402,403

Links: Page, Edit with form



Study versions

N3 representation of a Study with a previous version

<http://toxbank.net/services/study/Study_4>
     a       tb:Study ;
     tb:hasAbstract "This is another abstract"^^xsd:string ;
     tb:hasAssay http://toxbank.net/services/study/Study_4/assay/Assay_11> ;
     tb:hasAuthor tb:OliviaSanger ;
     tb:hasKeyword "cell"@en , "protein"@en ;
     tb:hasOwner tb:ORG5 ;
     tb:isSummarySearchable
             "true"^^xsd:boolean ;
     tb:project tb:DETECTIVE ;
     tb:studyPriorVersion
             <http://toxbank.net/services/study/Study_3>;
     tb:versionInfo "2"^^xsd:string .

Upload a new Study version

Description Creates a new study version
Resource Investigation
Method POST
URI /study/{id}/versions
Parameters TBD, file content in multipart web form, with predefined metadata, or any supported representation
Header Parameters
Media Type (input) multipart web form - application/x-www-form-urlencoded, RDF, JSON
Results Task URI, when complete - URI of the new study , e.g. /study/S123
Media Type (output) text/uri-list
Status code 200,400,401,402,403

Links: Page, Edit with form



Retrieve Versions of a single Study

Description Retrieves the study versions
Resource Study
Method GET
URI /study/{id}/versions
Parameters TBD, search options to filter the requested versions
Header Parameters SECURITY-TOKEN
Media Type (input) none?
Results Links to studies (representation in supported format)
Media Type (output) URI,RDF,JSON,XML
Status code 200,400,401,402,403

Links: Page, Edit with form



Assays

Two proposals:

  • Rename to "Step"
  • Keep "Assay" as it is compatible with ISA-TAB, but use an appropriate title in user interface.
from ISA-TAB discussion - while developing new technology, there may be a "technology tuning step" , and then running the experiment  itself, and generate data.   
On ISA-TAB web page http://isatab.sourceforge.net/case_studies.html there are examples of organisations using it for stem cells experiments (Harward Medical School).
bii system or in-house systems
Another example of a system using ISA-TAB is The Nutritional Phenotype Database http://www.dbnp.org/

A single protocol and one or more datasets, associated with a Study.

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>.

Retrieve all Assays

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



Retrieve a single Assay

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



Upload a single Assay

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



Retrieve a Protocol, associated with an Assay

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



Retrieve Datasets, 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



Upload Assay Data

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).

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