Request review for the Disease Ontology for inclusion as an OBO Foundry Ontology

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Good Afternoon,
   I would like to submit the Disease Ontology for review.

 To date, DO has been developed in OBO. 
 DO development, in coordination with Chris Mungall, is moving to OWL in October, 2014.
 DO will continue to provide our HumanDO.obo file. 
 This move will involve an expansion of relations utilized in DO. The set of relations is 
 currently under discussion with Chris Mungall, Elvira Mitraka (DO postdoc) and Lynn Schriml.
 The set of relations will also be discussed with the greater OBO foundry community, specifically
 with Barry Smith prior to implementation later this year. 

Reviewing the OBO Foundry policies: 
http://www.obofoundry.org/wiki/index.php/Category:Accepted

open:
   DO is licensed under: Creative Commons Attribution 3.0 Unported License
       This is specified in the top of the doid.owl file:
                 http://www.berkeleybop.org/ontologies/doid.owl
   The owl version of DO contains the refs:comment property
   The dc:license property can be added. 

format: DO is available in a common shared syntax: both OBO and OWL

URIs: Each class and relation in DO has a unique URI identifier.
     http://purl.obolibrary.org/obo/DOID_0050132
   Disease Ontology identifiers are build from a unique prefix: DOID
   The DO's are in the format: <IDSPACE> : <NUMBER>

versioning: DO defines distinct successive versions by the HumanDO.obo SVN 
revision number. 

delineated content: the Disease Ontology specifically includes human diseases. 
                               DO is interoperable with the other OBO Foundry ontologies. 
                               For example, disease terms in the HPO are DO terms. 
                            The tope level terms are defined in coherent natural languor definitions. 
                            The definition of top most term, disease, was defined in coordination with Barry Smith, 
                            Alan Ruttenburg, Warren Kibbe and Lynn Schriml in January of 2011

textual definitions : DO currently has 33% of our terms defined with textual 
definitions. 

relations: DO only uses relations as defined by RO.  The primary relation 
currently used in DO
               to related parent and child disease terms is: is_a
                  A set of RO relations have been incorporated, to date, in DO textual definitions. 
                 These relations will be utilized to create cross-product links to a subset of OBO foundry
                 ontologies. 

documented: DO has been published in the NAR database issue in 2012, and has 
been accepted for publication 
                  in the 2015 NAR database issue. The DO website and wiki include additional documentation. 

users: DO is highly utilized by researchers and the biomedical community. We 
have documented over 50 
          biomedical projects utilizing DO. Many of these groups, listed below, work collaboratively with DO to 
           have their disease terms mapped to DO terms and to have DO terms integrated into their resources. 
            The About page on the DO website: (http://www.disease-ontology.org/about/) lists DO's extensive
            list of active users and collaborators. Among these are Reactome, PRO, HPO, EFO, MGI (Janan Eppig) 
            and the Jackson Laboratory, Genomic Medicine, IEDB, NeuroDevNet, OMIM, FlyBase, PomBase, 
           WormBase and dictyBase. 

collaboration: DO is highly committed to collaboration. We work with 
neighboring OBO Foundry ontologies. 

locus of authority: I am the principal contact and OBO Foundry editor (Lynn 
Schriml, 
                             lschriml@som.umaryland.edu OR 
                             lynn.schriml@gmail.com) for the Disease Ontology. 
                             My contact information is provided on the DO website and the OBO Foundry website. 

naming conventions : the naming conventions were extensively reviewed by Barry 
Smith during our previous 
                  review. DO updated terms across the ontology to comply with all of Barry's recommendations. 
                  New terms are created which conform to these conventions. 

maintenance: DO is continually maintained to meet the ongoing advances in 
biomedical sciences and ongoing
                    biomedical resource needs. DO receives update, addition and review requests weekly. We version 
                     the DO file with each update to the repository to enable us to continually keep up to date with 
                     the user community requests. 

Before requesting a review, please consider current OBO Foundry policies
and principles and how your ontology conforms to the principles. Priority
will be given to resources conforming to current best practices.

Please enter description of the resource to review, including:

-ontology name: The Human Disease Ontology

-contact person name:   Lynn Schriml

-contact person email:  lschriml@som.umaryland.edu OR lynn.schriml@gmail.com

-scope of ontology:  Human Diseases

-link to stable version of the ontology:
            http://sourceforge.net/p/diseaseontology/code/HEAD/tree/trunk/HumanDO.obo

-link to ontology documentation (e.g., web or wiki page):
   http://www.disease-ontology.org
  I have attached the DO NAR 2015 paper. 

-other important links (describe):

-date of previous review request (if applicable):  submitted in October, 2008 

 I thank you for your consideration of DO as an OBO Foundry ontology and look forward to your review.
 Regards,
 Lynn Schriml, Ph.D.

PI-Human Disease Ontology
Assistant Professor
University of Maryland School of Medicine
Institute for Genome Sciences
Baltimore, Maryland 21201

Original issue reported on code.google.com by lynn.sch...@gmail.com on 15 Oct 2014 at 5:59

Attachments:

• DO_NAR_paper_accepted_2015.docx

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Hi all,

Any news on the review status? Lynn was wondering if this was in the queue.

Cheers,
Melanie

Original comment by mcour...@gmail.com on 12 May 2015 at 7:31

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Original comment by mcour...@gmail.com on 12 May 2015 at 7:31

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We discussed this today. It is in progress (and has been for some time), and at 
least partially done. Colin could give more specific details.

Original comment by rlwalls2...@gmail.com on 12 May 2015 at 8:05