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phenopackets / phenopacket-schema

Repository for the GA4GH phenopacket schema
https://phenopacket-schema.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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Compatibility with ISO-IDMP Standards #237

Open lindsmith opened 3 years ago

lindsmith commented 3 years ago

Comment:

Please ensure compatibility and interoperability with ISO-IDMP standards as well as with other already existing terminologies for coding some of the aspects mentioned in the "common schema" to define the ‘Phenopacket’ on page 6 of the paper.

Page 6 is the Table of Comments in the draft, but I think this commenter is referring to this section. As an ISO Project Lead, I should be able to access the IDMP standards free of charge, if used for the development of the ISO Phenopackets Draft. I will check/confirm.

pnrobinson commented 3 years ago

@lindsmith any progress getting this documentation?

lindsmith commented 3 years ago

@pnrobinson Yes! I have the information to request watermarked versions, though there are ~6 different standards to choose from and 4 of them have associated implementation guides. As a starting point, I'll request #2 and #3 because they seem to have the highest relevance to the v2 proposed fields, but let me know if others are of interest as well.

  1. Health informatics — Identification of medicinal products — Data elements and structures for the unique identification and exchange of regulated information on substances
  2. Health informatics — Identification of medicinal products — Data elements and structures for the unique identification and exchange of regulated information on pharmaceutical dose forms, units of presentation, routes of administration and packaging
  3. Health informatics — Identification of medicinal products — Data elements and structures for the unique identification and exchange of units of measurement
  4. Health informatics — Identification of medicinal products — Data elements and structures for the unique identification and exchange of regulated medicinal product information
  5. Health informatics — Identification of medicinal products — Data elements and structures for unique identification and exchange of regulated pharmaceutical product information
  6. Health informatics — Identification of medicinal products — Core principles for maintenance of identifiers and terms
julesjacobsen commented 3 years ago

@lindsmith Did you manage to get hold of 2 and 3?

lindsmith commented 3 years ago

@julesjacobsen Yes! Sent via email a while ago, but will resend now. I unfortunately can't post them here (too "public")

julesjacobsen commented 3 years ago

The ISO 11239:2012(E) codeTermPair code and term fields are directly comparable to the Phenopacket OntologyClass id and label, but other fields are not present in the OntologyClass although these are likely present in the ontology itself.