[Obo-format] reviewed_by tag
David Osumi-Sutherland
We're exploring ways to give credit to those who've provided expert feedback to us on the accuracy of definitions and relationships for specific sets of terms in our ontology. One way to do this would be to flag reviewed terms using a new tag-value pair in OBO. For this purpose, I'd like to request a reviewed_by tag in OBO (1.4?). We will, of course, need a corresponding OWL annotation property.
It would be useful to record two values - in addition to a name, a date or ontology version number for the review would make it clear what version of a term a reviewer has signed off on. In OWL the version info could be an annotation of an annotation. In OBO this could be in a trailing modifier (http://www.geneontology.org/GO.format.obo-1_4.shtml#S.1.4).
Does this seem reasonable?
Cheers,
David
David Osumi-Sutherland, PhD
Ontologist
FlyBase / Virtual Fly Brain
Department of Genetics,
University of Cambridge,
Downing Street,
Cambridge, CB2 3EH, UK
Tel: +44 (0)1223 333 963
Fax: +44 (0)1223 766 732
http://www.virtualflybrain.org
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Erick Antezana
I fully support your request of having a means to credit ontology
contributors. Do you have an example of the usage of such a tag?
reviewed_by: john_doe 2009-04-28T10:22:40Z
or
reviewed_by: "John Doe" [2009-04-28T10:22:40Z]
or
reviewed_by: john_doe
revision_date: 2009-04-28T10:22:40Z
or
reviwed_by: john_doe {2009-04-28T10:22:40Z} ! DNA binding RNA
polymerase II transcription factor activity corrected
What about the possible duplication of data while also using the extant tags:
created_by: jdoe
creation_date: 2009-04-28T10:22:40Z
What if there are several "reviewers"?
Does "any type" of contribution would make somebody a 'reviewer'?
(e.g. refining a definition, providing a synonym, suggesting to fix a
typo, fixing a relationship linking a given term, ...)
cheers,
Erick
Chris Mungall
I would suggest first of all getting the property into IAO ontology-metadata and then we can decide whether to add a new tag or use a generic property_value tag.
For a generic property_value tag and for the OWL translation the second is easier as it's doesn't involve multiple values for the same tag, but is obviously more limited as you can't have >1 review.
The requirements for reviews are likely to be quite varied.
Melanie Courtot
I am wondering if by review you mean some sort of endorsement, or if you just mean somebody who contributed to the term?
In the first case, you would want something like "term validated by" (but maybe it will be too granular to manage those at the term level? When does a review becomes invalid/superseded?) and in the latter we could maybe just add a curator note "synonym added on 2009-04-28T10:22:40Z by John Doe"?
Cheers,
Melanie
---
Mélanie Courtot
MSFHR/PCIRN trainee, TFL- BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada
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