OBO Foundry

Link to OBO Foundry home page

The Plant Ontology is applying for membership. This was discussed at the POC Conf calls: May 10th and 17th, 2011

Link to the list of principles:[Accepted]

ICBO Presentation- July 2011

ICBO Program

-LC will present the Plant Ontology on Thursday, July 28th, 3:40pm in the session: "Introduction to The OBO Foundry Initiative":

Goal of the session: To give the representatives of the 4 ontologies listed the opportunity to make their case, informally, for OBO Foundry membership. Each representative should prepare slides addressing the principles listed here: Accepted principles

Since most of these principles are trivially satisfied, the presentations should focus rather on those areas where there are problems.

The draft program of the OBO Foundry session:

3:30 Barry Smith: Introduction to the OBO Foundry initiative

3:40 Laurel Cooper: Plant Ontology

4:00 Bjorn Peters: Ontology for Biomedical Investigations

4:20 Albert Goldfain: Ontology for General Medical Science

4:40 Lindsay Cowell: Infectious Disease Ontology

5:00-5:30 General Discussion

May 17th, 2011

POC_Conf._Call_5-17-11#OBO_Foundry_Acceptance

Comments: Need to display a list of webpages that use the PO and encourage other groups to link to the PO and where the PO is integrated into their search engines.

Need an impressive web page, volunteer to link to them

-1000 Transcriptome project- DWS will encourage them to have a link to PO, adopt the PO rather than free text for annotations

BS: Need to demonstrate utility, will help with getting re-funded

May 10th, 2011

POC_Conf._Call_5-10-11#Review_for_OBO_Foundry_Acceptance

BS brought up the topic of review for OBO Foundry acceptance at the POC_Conf._Call_4-19-11. He suggested that the PO can be submitted for OBO Foundry membership within the next few weeks.

List of Foundry Principles:[Accepted] with a brief summary of each:

• FP 001 open:

The ontology must be open and available to be used by all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed under the original name or with the same identifiers.

• FP 002 format:

The ontology is in, or can be expressed in, a common shared syntax. This may be either the OBO syntax, extensions of this syntax, or OWL.

• FP 003 URIs:

The ontology possesses a unique identifier space within the OBO Foundry. The identifier uniquely and persistently identifies a definition, which itself unambiguous identifies some type of biological entity. The identifier is for the definition: it is NOT the name and it is NOT an identifier for the name.

• FP 004 versioning:

The ontology provider has procedures for identifying distinct successive versions.

• FP 005 delineated content:

The ontology has a clearly specified and clearly delineated content. The ontology must be orthogonal to other ontologies already lodged within OBO.

• FP 006 textual definitions:

The ontologies include textual definitions for all terms.

• FP 007 relations:

The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the OBO Relation Ontology.

• FP 008 documented:

The ontology is well documented.

• FP 009 users:

The ontology has a plurality of independent users.

• FP 010 collaboration:

The ontology will be developed collaboratively with other OBO Foundry members.

• FP 011 locus of authority:

single locus of authority, tracker (SOP), responsive help desk

• FP 012 naming conventions:

See naming conventions

• FP 016 maintenance

OBO is an open community and, by joining the initiative, the authors of an ontology commit to its maintenance in light of scientific advance and to working with other members to ensure the improvement of these principles over time

We reviewed the list and feel that we are in compliance on all of them, although the PGDSO still needs to be completely revised. LC will contact BS (since he was not present) and find out what the procedure is for applying for OBO Foundry acceptance. PJ thought we just send an email with a request to be considered.