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monarch-initiative / monarch-legacy

Monarch web application and API
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some phenotypes not properly xrefed to diseases #295

Open nlwashington opened 10 years ago

nlwashington commented 10 years ago

This phenotype http://monarchinitiative.org/phenotype/HP_0000388

Should be linked to this disease with an identical name http://monarchinitiative.org/disease/DOID_10754

cmungall commented 10 years ago

What should we do here? Auto-add a hallmark annotation?

On 23 Apr 2014, at 11:27, Nicole Washington wrote:

This phenotype http://monarchinitiative.org/phenotype/HP_0000388

Should be linked to this disease with an identical name http://monarchinitiative.org/disease/DOID_10754

Reply to this email directly or view it on GitHub: https://github.com/monarch-initiative/monarch-app/issues/295

pnrobinson commented 10 years ago

The disease otitis media ideally would have the HPO term of the same name but also pain, fever etc. We are hoping to have something like this later in the year for most of DO. It would not be a mistkae to autopopulate for the moment though. -Peter

Dr. med. Peter N. Robinson, MSc. Professor of Medical Genomics Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651 I have learned from my mistakes, and I am sure I can repeat them exactly ORCID ID:http://orcid.org/0000-0002-0736-9199 Scopus Author ID 7403719646 Appointment request: http://doodle.com/pnrobinson

Von: Chris Mungall [notifications@github.com] Gesendet: Mittwoch, 23. April 2014 21:40 An: monarch-initiative/monarch-app Betreff: Re: [monarch-app] some phenotypes not properly xrefed to diseases (#295)

What should we do here? Auto-add a hallmark annotation?

On 23 Apr 2014, at 11:27, Nicole Washington wrote:

This phenotype http://monarchinitiative.org/phenotype/HP_0000388

Should be linked to this disease with an identical name http://monarchinitiative.org/disease/DOID_10754

Reply to this email directly or view it on GitHub: https://github.com/monarch-initiative/monarch-app/issues/295

— Reply to this email directly or view it on GitHubhttps://github.com/monarch-initiative/monarch-app/issues/295#issuecomment-41205151.

nlwashington commented 10 years ago

where exactly should this be done for now? @cmungall should we have a monarch process that will generate these mappings for DOIDs, and load it as annotations for a monarch source, both into NIF and into owlsim? or should it be added to @pnrobinson repository, into individual annotation files just like is done for all the other HPO annotations now? seems like a relatively simple script to write to just get the identical label matches?

cmungall commented 10 years ago

I think the latter (i.e. into the phenotype-commons SVN repo), if @pnrobinson is OK with that. This provides an easy path for being able to override or extend.

pnrobinson commented 10 years ago

Note that some HPO terms have been added for various local databases and do not currenlty have any OMIM or Orphanet disease to which they are annotated. This is OK. Is this what you meant? -Peter

Dr. med. Peter N. Robinson, MSc. Professor of Medical Genomics Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651 I have learned from my mistakes, and I am sure I can repeat them exactly ORCID ID:http://orcid.org/0000-0002-0736-9199 Scopus Author ID 7403719646 Appointment request: http://doodle.com/pnrobinson

Von: Nicole Washington [notifications@github.com] Gesendet: Samstag, 17. Mai 2014 01:42 An: monarch-initiative/monarch-app Cc: Robinson, Peter Betreff: Re: [monarch-app] some phenotypes not properly xrefed to diseases (#295)

where exactly should this be done for now? @cmungallhttps://github.com/cmungall should we have a monarch process that will generate these mappings for DOIDs, and load it as annotations for a monarch source, both into NIF and into owlsim? or should it be added to @pnrobinsonhttps://github.com/pnrobinson repository, into individual annotation files just like is done for all the other HPO annotations now? seems like a relatively simple script to write to just get the identical label matches?

— Reply to this email directly or view it on GitHubhttps://github.com/monarch-initiative/monarch-app/issues/295#issuecomment-43390349.

mellybelly commented 9 years ago

@cmungall let us know if we can help