Difference between revisions of "Plant Ontology Response to OBO Foundry Review"
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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. | 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. | ||
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''Done: The license info is at the bottom of every page of the browser, plus we created a [http://wiki.plantontology.org/index.php/Creative_Commons_License 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. '' | ''Done: The license info is at the bottom of every page of the browser, plus we created a [http://wiki.plantontology.org/index.php/Creative_Commons_License 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. '' | ||
Revision as of 23:16, 20 October 2013
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
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.
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."
