POC Conf. Call 9-10-13

POC meeting, Skype Conference Call; Date: Tuesday Sept 10th, 2013 10am PST/1pm EST

In attendance:

Absent:

- please see the Items_for_future_meetings page, will be moved here before the meeting

NSF PI meeting Sept 4th-6th in DC

• PJ and DWS attended

Any news?

OBO Foundry Review of Plant Ontology

Principle 1: The Ontology is Open

Some improvement desirable

"The self-review states that the PO is released under a Creative Commons license. However, it is not specified which Creative Commons license has been chosen. The ontology file does not contain a statement about the license or the policy for reuse of the ontology. However, the information is available on the website e.g. at http://plantontology.org/docs/otherdocs/principles_rationales.html: Plant Ontology by Plantontology.org is licensed under a Creative Commons Attribution-NoDerivs 3.0 United States License."

"We recommend that the exact license chosen be included in an additional ontology annotation in the ontology file."

"According to the OBO Foundry principle 1 documentation, this should make use of two annotations using the following properties:

• dc:license
• rdfs:comment

The license type goes in the dc:license field. The mode of attribution goes in the rdfs:comment field. "

"While 'Creative Commons 3.0 CC-by license' is recommended, this is not mandatory and therefore the chosen attribution-noderivs license is also compatible with the Open principle. However, we urge you to consider weakening the license to one that encourages sharing and reuse without constraint to further the adoption by the community and the value of the resource for the community."

Principle 2: Common Format

Pass

The ontology is available in both OBO and OWL formats. It should be noted that the OBO form of the ontology contains semantics which are not yet available in the OWL form (i.e. the treat-xrefs-as-isa and treat-xrefs-as-genus-differentiae constructs). These are supported by the Oort release manager and can be instantiated in OWL versions of the ontology. See https://code.google.com/p/owltools/wiki/OortOptions

Principle 5: Clearly Delineated Content

Some improvement desirable

"There are several sub-issues that are contained in this principle.

Firstly, the ontology needs to have a clearly delineated scope as expressed in a statement of scope. PO does have a clearly delineated scope, and this scope does not substantially duplicate the scope of any other OBO Library ontology.

Secondly, the ontology needs to have a clear upper level with root terms having definitions that indicate the content of the sub-ontologies included in the ontology. Here, we have some concerns as detailed below.

Thirdly, the ontology should not contain terminology that overlaps with other OBO ontologies except where content has been imported for reuse in specific contexts appropriate to the domain of the ontology.

Finally, the ontology should provide adequate coverage with respect to its stated domain so as to justify its use in applications. Concerns about the upper levels of the plant ontology:

"The definition of the root term ‘plant anatomical entity’ appears intended to be a plant specific subclass of the CARO term ‘anatomical entity’ and is defined as “An anatomical entity that is or was part of a plant.” The CARO class states that an anatomical entity is part of or located in an organism (or virus or viroid in the upcoming release of CARO), however here you include things that were once part of a plant. In OBI or ERO, such entities would be considered specimens or samples. Can you explain why this is needed? If it is justified, there is some cross-ontology coordination that should be performed.

"There is a need to define the high-level distinction between plant structure vs. portion of plant substance better: currently ‘plant structure’ is defined as anatomical entity that is or was part of a plant; but substances are also (or were also) part of a plant. This is likely because these are intended to be subclasses of the CARO classes, that have more specific differentia, however, there is no mireot or subclass assertion to these classes other than in the comment field. Explicit use of the CARO classes will help differentiate these top-level nodes, and inclusion of their logical class definitions can help with error-checking."

" If you consider the above point on the definition of ‘anatomical entity’ referring to in vivo entities, you could consider moving ‘in vitro plant structure’ to be its own root outside anatomical entity, as it would technically be a derived structure and not part of or located within an organism (or are most of these simple plants cultured in vitro?). Efforts have been made recently in the CL and OBI to represent such things (e.g. “in environment” vs. “ex environment”, you could potentially leverage some of these design patterns and/or coordinate with them. Other concerns from somewhat random sampling:

"‘cultured plant embryo’ has two asserted superclasses. While asserted multiple inheritance is debatable in terms of ontology maintenance or ontological rigor (GO has a lot of this), in this case the example ensues because of a lack of logical class expression on this class. For example, this class could instead leverage a class restriction that states ‘plant embryo’ and is_specified_output of some in vitro plant culturing. In this way, you would infer the second parent, ‘in vitro plant structure’ (dependent on how you define things as per above). This would mean higher quality axioms, easier ontology maintenance, and interoperability with other ontologies such as OBI."

Principle 6: Textual Definitions

Some improvement desirable We applaud the fact that the ontology does contain text definitions for all terms included in the ontology (see Appendix: Metrics) and for its extensive synonyms in numerous languages. However, we note that some of the text definitions do not exactly match the formal definitions as given in equivalence class or subclass axioms (specific examples contained below) and furthermore that not all of the textual definitions are as clear as they could be e.g. by following the genus differentiae pattern (examples below). We advise continued evolution of the textual definitions contained in the ontology towards greater clarity for the benefit of all users, and gradual inclusion of a greater number of equivalent class definitions. Specific points:  Definitions such as that for ‘microgametophyte’, referencing IDs within the text, should be converted into logical definitions.  ‘pollen’ is textually defined as located_in some ‘pollen sac’ and logically it has the relationship part_of some pollen sac. This is an inconsistency with respect to the normal usage of these two relationships.

leaf development stage (PO:0001050)

• See Google Doc for revisions in progress. Need to open trackers for these.

Upcoming meetings and Presentations 2013-2014:

• The Plant Genomics Congress USA, St Louis, September 23rd & 24th, 2013

No one from PO is planning to attend

• PAG 2014 January 11-15, 2014 - San Diego, CA, USA

• • PJ has been contacted by PAG organizers; Suggest slightly new focus "Plant Ontologies and Systems Biology"
  • Ideas for speakers- someone from GO and others?>>

• • Registration is now open: PAG 2014. Early reg'n till Nov. 1st

Next meeting scheduled for Tuesday, Sept 24th, 2013 at 10am Pacific/1pm Eastern

-MAG has requested the meeting be moved to 10:30am Pacific/1:30 pm Eastern- would that works for the others in the group?