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monarch-initiative / monarch-legacy

Monarch web application and API
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OMIM_608372 is missing gene #346

Open nlwashington opened 10 years ago

nlwashington commented 10 years ago

this disease: http://monarchinitiative.org/disease/OMIM_608372 http://www.omim.org/entry/608372 this is located to 1q21-q23, and has a "gene" associated with is, that has been given an HGNC identifier, and the underlying OMIM db has the entrezgene id too. but it seems to be missing from the interface.

nlwashington commented 10 years ago

So, the gene shows up on the "gene" version of this page: http://monarchinitiative.org/gene/OMIM_608372 This is one of those annoying multiple-personality omim identifiers, being both a gene and a disease. What do we expect to happen here?

pnrobinson commented 10 years ago

Actually, this is not a gene, it is a disease that has been mapped to a certain cytogenic location, but the exact gene remains unknown.

http://omim.org/entry/608372

Therefore, the assertion Gene: DFNA49 on our website is wrong, it should be listed as a disease. Make sure that the ingest pipelines knows the meaning of the "%" in the MIM entry name!

-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: Montag, 9. Juni 2014 18:37 An: monarch-initiative/monarch-app Betreff: Re: [monarch-app] OMIM_608372 is missing gene (#346)

So, the gene shows up on the "gene" version of this page: http://monarchinitiative.org/gene/OMIM_608372 This is one of those annoying multiple-personality omim identifiers, being both a gene and a disease. What do we expect to happen here?

— Reply to this email directly or view it on GitHubhttps://github.com/monarch-initiative/monarch-app/issues/346#issuecomment-45512407.

nlwashington commented 10 years ago

totally agree. but it's also odd for a disease to have a cytogenic location. anyway, as a disease, it's still missing a link in the locus/gene tab, so this ticket is still open.

nlwashington commented 10 years ago

hm, now 32 genes are showing up, suggested from http://monarchinitiative.org/disease/ORPHANET_90635, but when i go to that page, it only shows a single gene. this warrants further investigation.

pnrobinson commented 10 years ago

Following the link of that gene leads to this error:

TypeError: Cannot read property "1.0" from null

lib/monarch/api.js, line 4480 Script Stack

at lib/monarch/api.js:4480 (anonymous)
at lib/monarch/api.js:964 (anonymous)
at lib/monarch/web/webapp.js:964 (anonymous)
at stick/lib/middleware/route.js:215 (route)
at stick/lib/middleware/params.js:102 (anonymous)
at stick/lib/middleware/static.js:62 (static)
at /var/home/bamboo/start-monarch-server/lib/monarch/web/sanitize.js:7 (anonymous)
at /var/home/bamboo/start-monarch-server/lib/monarch/web/cors-middleware.js:22 (accessControl)
at stick/lib/stick.js:37 (app)
at ringo/jsgi/connector.js:42 (handleRequest)
nlwashington commented 10 years ago

hm, i do not get an api error with http://monarchinitiative.org/gene/OMIM_608372. in fact, it redirects to http://monarchinitiative.org/gene/NCBIGene:317664

pnrobinson commented 10 years ago

Hi, there was a broken link, but this seems to be a different page. Another issue is that on this webpage: http://monarchinitiative.org/gene/NCBIGene:317664 There is a link to neurolex http://neurolex.org/wiki/Nif-0000-02683 but this does not seem to have anything to do withthe gene -Peter

jmcmurry commented 8 years ago

http://monarchinitiative.org/gene/OMIM_608372 no longer redirects, but at least http://neurolex.org/wiki/Nif-0000-02683 is no longer

So many disease-is-a-gene tickets...