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phenotips / open-pedigree

A free and open-source pedigree tool by PhenoTips®
GNU Lesser General Public License v2.1
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Term suggestion shows error popup #2

Open buske opened 4 years ago

buske commented 4 years ago

The term suggestion is broken because of the lack of a configurable terminology server.

When a terminology server is not present, terms should just be added as plaintext, rather than throwing an error.

dconlan commented 4 years ago

alternative sources of terminology https://clinicaltables.nlm.nih.gov/ https://bioportal.bioontology.org/ FHIR based server like https://ontoserver.csiro.au/

AlgyTaylor commented 3 years ago

I may have capacity to look at this bug in the near future - please let me know if this has any particular requirements from your part :)

shermanlo77 commented 2 years ago

Does the fork https://github.com/aehrc/open-pedigree address this? New disorders can be added with their changes, awesome stuff! Perhaps we could ask @dconlan for a pull request or incorporate the changes here

dconlan commented 2 years ago

I am working on a a pull request with my changes for terminology fetching. I'm not happy with the forced inclusion of the FHIR specific 'system' which goes along with the code. In the FHIR world, a codeable concept needs a system and a code, where the system tells you the code system the code is from. My GA4GH FHIR format pull included an object specifically for letting the converter know what systems to use, which seemed like a better solution then forcing the code that does the webservice call to fetch the codes to know about a system when its only relevant if they are doing a query on a fhir terminology server.