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[wbs] response to 'W3C PROV Vocabulary Extension Survey'

From: WBS Mailer on behalf of satya.sahoo@case.edu <webmaster@w3.org>
Date: Sun, 27 Jan 2013 00:36:02 +0000
To: satya.sahoo@case.edu,zednis@rpi.edu,public-prov-comments@w3.org
Message-Id: <wbs-dd2472d56d4d12436759c9035686f1c8@cgi.w3.org>
The following answers have been successfully submitted to 'W3C PROV
Vocabulary Extension Survey' (Provenance Working Group) for Satya Sahoo.


---------------------------------
Vocabulary  Extension Information
----
Please provide the name and url of the vocabulary, ontology or other
extension to PROV.
Name: Systems molecular biology provenance ontology (SysPro) URL:
http://physiomimi.case.edu/sempod/index.php/Main_PageDescription: The
Systems molecular biology provenance ontology (SysPro) is used in the
Semantic Proteomics Dashboard (SemPoD) to enable researchers at the Case
Center for Proteomics and Bioinformatics (CPB) to query proteomics data
across projects and allow integration with legacy data. SysPro models
provenance metadata together with domain information, also called semantic
provenance, to support multiple query functionalities in an intuitive query
interface. The SysPro ontology extends the PROV-ontology (PROV-O) and
re-uses terms from existing proteomics standards, such as the minimum
information required for reporting a molecular interaction experiment
(MIMIx), and the minimum information about a proteomics experiment
(MIAPE).

Further information at:
http://physiomimi.case.edu/sempod/index.php/Main_Page


---------------------------------
Contact Information
----

Name: Catherine Jayapandian, Satya SahooEmail: sempodcwru@googlegroups.com

---------------------------------
PROV Encodings Supported
----
Choose all that apply

 * [x] PROV-O
 * [ ] PROV-N
 * [ ] PROV-XML
Please list any additional supported encodings (e.g. PROV-JSON, PROV-CSV,
etc.) in the free-text area below: None


---------------------------------
Feature Coverage
----
Indicate covered features by selecting one of the following below:
 * 1) I Don't Know
 * 2) Used Directly
 * 3) Extended 

 * Entity: [ 3 +++ (highest) ] 
 * Activity: [ 3 +++ (highest) ] 
 * Agent: [ 3 +++ (highest) ] 
 * Generation: [ 2 ++ ] 
 * Usage: [ 2 ++ ] 
 * Communication: [ No opinion ] 
 * Derivation: [ No opinion ] 
 * Attribution: [ No opinion ] 
 * Association: [ No opinion ] 
 * Delegation: [ No opinion ] 
 * Start: [ 2 ++ ] 
 * End: [ 2 ++ ] 
 * Invalidation: [ No opinion ] 
 * Revision: [ No opinion ] 
 * Quotation: [ No opinion ] 
 * PrimarySource: [ No opinion ] 
 * Person: [ 2 ++ ] 
 * Organization: [ No opinion ] 
 * SoftwareAgent: [ 2 ++ ] 
 * Plan: [ 2 ++ ] 
 * Influence: [ No opinion ] 
 * Bundle: [ No opinion ] 
 * Specialization: [ No opinion ] 
 * Alternate: [ No opinion ] 
 * Collection: [ No opinion ] 
 * EmptyCollection: [ No opinion ] 
 * Membership: [ No opinion ] 
 * Identifier: [ No opinion ] 
 * Attributes: [ No opinion ] 
 * Label: [ No opinion ] 
 * Location

: [ 2 ++ ] 
 * Role: [ 3 +++ (highest) ] 
 * Type: [ No opinion ] 
 * Value: [ No opinion ] 
Rationale: Though many molecular system biology research centers now have
significant infrastructure in terms of instrumentation to acquire
‘omics datasets, most of these datasets end up in study-specific data
silos. SemPoD, using SysPro, enables cross-linking datasets across
‘omics and clinical studies as part of the translational research
roadmap, facilitates integration with legacy data, and allows seamless
query across different types of data. 

SysPro captures the experimental conditions or provenance, for example
sample type, instrumentation, sample preparation, and statistical measures,
to facilitate integration, filtering, and query research data in the Case
CPB.


---------------------------------
Provenance Exchange
----
Is this vocabulary extension generated or consumed by an implementation,
which one(s)?
 SemPoD application 

These answers were last modified on 27 January 2013 at 00:34:17 U.T.C.
by Satya Sahoo

Answers to this questionnaire can be set and changed at
https://www.w3.org/2002/09/wbs/46974/prov-vocabulary-survey/ until
2013-01-31.

 Regards,

 The Automatic WBS Mailer
Received on Sunday, 27 January 2013 00:36:05 GMT

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