Phenopacket export

[Daniel Danis]

When we export Phenopacket from the internal format, we have:

"diseases": [{
    "term": {
      "id": "OMIM:306400",
      "label": "GRANULOMATOUS DISEASE, CHRONIC, X-LINKED; CGD"
    }
  }]

for the disease, and

"genes": [{
    "id": "ENTREZ:1536",
    "symbol": "CYBB"
  }]

However, I do not know how to create appropriate Resource for these namespaces (OMIM, ENTREZ).

@pnrobinson do you please have any suggestions how to fix it? Otherwise the Phenopacket will not be valid, at least by the code I wrote this morning..

[Jules Jacobsen]

Like this?

- id: "omim"
    name: "Online Mendelian Inheritance in Man"
    namespacePrefix: "OMIM"
    url: "https://omim.org"
    iriPrefix: "https://omim.org/entry/"

in the Monarch curie map OMIM is defined as

'OMIM' : 'http://purl.obolibrary.org/obo/OMIM_'  # OMIM: Online Mendelian Inheritance in Man (human disease and variants)

Which doesn't resolve to anything, so I'd like to know what they are doing.

[Daniel Danis]

This looks sane enough. Maybe we could also add a list of commonly used Resources as examples to the documentation.
For me, the list of resources could look like:

• HPO
• MP
• PATO
• GENO
• ECO
• NCBITaxon
• OMIM
• MONDO
• ORPHA
• NCIT
• UBERON