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monarch-initiative / monarch-disease-ontology-RETIRED

THIS IS THE OLD REPO: Use this one instead: https://github.com/monarch-initiative/mondo-build
https://github.com/monarch-initiative/mondo-build
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ORDO: Text definitions sometimes truncated #412

Closed cmungall closed 6 years ago

cmungall commented 6 years ago

E.g. https://www.ebi.ac.uk/ols/ontologies/ordo/terms?iri=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_199 has a text definition ).

image

The def on the orpha site is fine: http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Expert=199

so looks like introduced when going from xml2owl?

siiraa commented 6 years ago

OLS ticket filed at https://github.com/EBISPOT/OLS/issues/175 to investigate where the truncation occurs.

siiraa commented 6 years ago

ORDO source file at http://www.orphadata.org/data/ORDO/ordo_orphanet.owl has truncated definition. We should file this at ORDO tracker if they have one?

paolaroncaglia commented 6 years ago

@cmungall Orphanet doesn’t seem to have a tracker, but after a bit of digging in their “Contact us” web page (http://www.orpha.net/consor/cgi-bin/Directory_Contact.php?lng=EN), I’d suggest posting a message here http://www.orpha.net/consor/cgi-bin/Directory_Contact.php?lng=EN&type_list=CONTACT_FORM&StaticId=29, or a tweet (https://twitter.com/orphanet). Hope this helps.

paolaroncaglia commented 6 years ago

@cmungall Actually, there is an @Orphanet ORDO tracker, but it seems to be empty: https://github.com/Orphanet/ORDO/issues

pnrobinson commented 6 years ago

I think that it is best to go to the specific disease page on the orphoanet tracker, which can be reached by searching the disease name here: http://www.orpha.net/consor/cgi-bin/Disease.php?lng=EN

Orphanet commented 6 years ago

Dear all, It was an issue in the owl generating process for some definitions with specific typo. It has been solved in the current ORDO version. Should be automatically updated both in bioportal and OLS.

"Cornelia de Lange syndrome (CdLS) is a multisystem disorder with variable expression marked by a characteristic facial dysmorphism, variable degrees of intellectual deficit, severe growth retardation beginning before birth (2nd trimester), abnormal hands and feet (oligodactyly, or sometimes an even more severe amputation, and constant brachymetacarpia of the first metacarpus), and various other malformations (heart, kidney etc.).</efo:definition>"

cmungall commented 6 years ago

I can conform this fixes it thanks Marc @Orphanet

I will close this when we have propagated changes

nicolevasilevsky commented 6 years ago

This issue was moved to monarch-initiative/mondo#155