Protocol

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(Design)
(N3 representation of a Protocol)
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=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Protocol ===
 
=== [http://www.w3.org/DesignIssues/Notation3 N3] representation of a Protocol ===
  @prefix tb:  <http://www.owl-ontologies.com/toxbank.owl#> .
+
  @prefix tb:  <http://onto.toxbank.net/api/> .
 
  @prefix dcterms:  <http://dublincore.org/documents/dcmi-terms/> .
 
  @prefix dcterms:  <http://dublincore.org/documents/dcmi-terms/> .
 
  <http://toxbank.net/services/protocol/Protocol_9>
 
  <http://toxbank.net/services/protocol/Protocol_9>

Revision as of 13:13, 24 November 2011

Protocol
Protocols contain document(s) and metadata, describing how to perform certain experiment (lab or in-silico).

The results of performing the experiment are recorder in a (set of) Study.

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

A Protocol includes links to a Data template URI and its Author (an User). The rest of the fields may be defined as below.

TBD: Parameter names to be added to the protocol representation, as in ISA-TAB

Contents

Security

Only a Principal Investigator (PI) is allowed to upload protocols

Design
  • Be able to specify if the user is a PI - upon registration, or later.
  • Create OpenSSO group for PI, and a policy, allowing member of the PI group to POST to /protocols
  • On protocol upload, create write/update policy, allowing only the submitter to modify /protocol/id

Protocol read rights are specified on upload, and can be modified later by the PI

Design
  • Access levels, entered via GUI have to be translated into an OpenSSO policy.
            -Only authors  - create specific policy for set of user names
            -Consortium - create policy for the group, corresponding to the selected project(s)
            -SEURAT -  create policy for the group, corresponding to the entire SEURAT cluster
            -Public -   create policy for the a group, corresponding to all registered users
            -Custom access - create specific policy for a set of user names

N3 representation of a Protocol

@prefix tb:  <http://onto.toxbank.net/api/> .
@prefix dcterms:  <http://dublincore.org/documents/dcmi-terms/> .
<http://toxbank.net/services/protocol/Protocol_9>
     a       tb:Protocol ;
     dcterms:title "Protocol title";
     dcterms:identifier "SEURAT-P1234567890";
     tb:hasAbstract "This is the abstract"^^xsd:string ;
     tb:hasAuthor tb:OliviaSanger ;
     tb:hasKeyword ""^^xsd:string ;
     tb:hasOwner tb:ORG5 ;
     tb:hasTemplate tb:Template_12 ;
     tb:isSummarySearchable "true"^^xsd:boolean ;
     tb:project tb:DETECTIVE ;
     tb:hasDocument <http://toxbank.net/services/protocol/Protocol_9/ABC.pdf> ;
     tb:versionInfo "123"^^xsd:string.
tb:ORG5
     a       tb:Organization .
tb:DETECTIVE
     a       tb:Project .
tb:OliviaSanger
     a       tb:User .

Retrieve the List of Protocols

Description Retrieves list of protocols
Resource Protocol
Method GET
URI /protocol
Parameters none, or ?search=name or paging parameters: page, pagesize or modefiedSince=UNIX-TIME-STAMP-in-ms
Header Parameters subjectid:SECURITY-TOKEN
Media Type (input) none
Results The protocol representation in supported media type
Media Type (output) text/uri-list;application/rdf+xml;text/n3
Status code 200, 400, 401, 402, 403

Links: Page, Edit with form



Upload a new Protocol

Description Uploads a protocol
Resource Protocol
Method POST
URI /protocol
Parameters (see cURL example)
Header Parameters subjectid:SECURITY-TOKEN
Media Type (input) multipart/form-data
Results Task representation in supported MIME formats
Media Type (output) text/uri-list;application/rdf+xml;text/n3
Status code 200,202,400,401,402,403,500

Links: Page, Edit with form



Retrieve Metadata of a single Protocol

Description Retrieves the protocol metadata
Resource Protocol
Method GET
URI /protocol/{id}
Parameters none
Header Parameters subjectid:SECURITY-TOKEN
Media Type (input) none
Results The metadata representation in supported media type
Media Type (output) text/uri-list;application/rdf+xml;text/n3
Status code 200,400,401,402,403

Links: Page, Edit with form



Retrieve Protocol files

Description Retrieves the document, describing the protocol
Resource Protocol
Method GET
URI /protocol/{id}/document
Parameters none
Header Parameters subjectid:SECURITY-TOKEN
Media Type (input) none
Results Protocol content in one of supported MIME format
Media Type (output) application/pdf;application/msword
Status code 200,400,401,402,403

Links: Page, Edit with form



cURL example - retrieve the protocol in PDF and Word formats

curl -X GET -H "application/pdf"  /protocol/id/file -H "subjectid:TOKEN"
curl -X GET -H "application/msword"  /protocol/id/file -H "subjectid:TOKEN"

Protocol versions

N3 representation of a Protocol with a previous version

<http://toxbank.net/services/protocol/Protocol_10>    a       tb:Protocol ;
     tb:hasAbstract "New abstract"^^xsd:string ;
     tb:isSummarySearchable
             "false"^^xsd:boolean ;
     tb:protocolPriorVersion
             <http://toxbank.net/services/protocol/Protocol_9> ;
     tb:submissionDate
             "2011-09-15T00:00:00"^^xsd:dateTime ;
     tb:versionInfo "2011-09-15"^^xsd:string .

Retrieve versions of a single Protocol

Description Retrieves the protocol versions
Resource Protocol
Method GET
URI /protocol/{id}/versions
Parameters none, or ?search=name or paging parameters: page, pagesize
Header Parameters subjectid:SECURITY-TOKEN
Media Type (input) none
Results The protocol URI or other supported representation
Media Type (output) text/uri-list;application/rdf+xml;text/n3
Status code 200,400,401,402,403

Links: Page, Edit with form



Upload a new Protocol version

Description Uploads a newprotocol version
Resource Protocol
Method POST
URI /protocol/{id}/versions
Parameters (see cURL example)
Header Parameters subjectid:SECURITY-TOKEN
Media Type (input) multipart/form-data
Results Task representation in supported MIME formats
Media Type (output) text/uri-list;application/rdf+xml;text/n3
Status code 200,202,400,401,402,403

Links: Page, Edit with form


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