Plant Ontology Response to OBO Foundry Review

The Plant Ontology underwent a rigorous review in 2013 and was accepted as a full member of the OBO Foundry

Review document: Media:PO_Review_August_2013.pdf

OBO Foundry Principles

Domain of ontology: Plant anatomy, morphology and growth and development and their association to plant genomics data for all plants.

Our specific recommendations are contained in the report below. Thank you for participating in the OBO Foundry review process.

Summary of Review Findings

In general, we found that the Plant Ontology is a good ontology, largely following the principles as laid down by the Foundry. We have some specific recommendations for improvements but found no major significant shortfalls in the offering. The following table summarises the findings of this review on a per principle basis, and detailed discussion of each point follows.

#	Principle	Comments
1.	Open	Some improvement desirable
2.	Common format	Pass
3.	Foundry URIs	Pass
4.	Versioning	Pass
5.	Clearly delineated content	Some improvement desirable
6.	Textual definitions	Some improvement desirable
7.	Relations	Some improvement desirable
8.	Documentation	Pass
9.	Plurality of users	Pass
10.	Collaboration	Pass
11.	Single locus of authority	Pass
12.	Naming conventions	Pass
16.	Maintenance	Pass

PO Responses to OBO Foundry Review of Plant Ontology

Responses to the points requiring improvement shown in italics

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." Reply: We chose the CC-BY-ND license, because in the past the derivatives (including changing the relationships and graph besides adding new terms) were created and it was difficult for us to track. Also by having ND clause, users are encouraged to go back to the source and request their suggested edits.

see link: http://www.obofoundry.org/wiki/index.php/FP_001_open

Comment From CM: “ I would put a LICENSE file in the same directory as the ontology, as is standard for software releases. You can defer responsibility on the dc:license field for now, it should be known by the reviewer that these things are difficult for obo format users.”

Done: The license info is at the bottom of every page of the browser, plus we created a License wiki page with the human-readable version of the file. The full text of the legal version of the license was also copied to a text file and saved in the Live Tag folder. * We also added a note about the license as a comment in header.

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

Reply: We can do this at the next release, as we use Oort to generate various different versions of the file anyway, or not depending on the effect. Should add a comment on the Release SOP Page if we are going to do so.

Principle 3: Foundry-style URIs

"Pass"

"The ontology uses numeric Foundry URIs."