EFO: add xref details to node data #21
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bfoltyn
changed the title
|
@dhimmel I don't know why, but I can't add add you as a reviewer. 
Could you please review this PR? |
dhimmel
reviewed
Nov 9, 2023
| return { | ||
| k: v[["xref_id", "sources", "relation"]].to_dict(orient="records") | ||
| for k, v in xref_details.groupby("efo_id") | ||
| } |
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Can you paste a couple examples of xref_details values here?
There was a problem hiding this comment.
EFO:0000479
"xref_details": [
{
"xref_id": "cohd:438383",
"sources": [
"MONDO:equivalentTo"
],
"relation": null
},
{
"xref_id": "DOID:2224",
"sources": [
"EFO:0000479",
"MONDO:equivalentTo"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "gard:0006594",
"sources": [
"MONDO:equivalentTo"
],
"relation": null
},
{
"xref_id": "icd10:D47.3",
"sources": [
"DOID:2224",
"ORDO:3318/e",
"Orphanet:3318"
],
"relation": null
},
{
"xref_id": "icd9:238.71",
"sources": [
"DOID:2224",
"EFO:0000479",
"MONDO:equivalentTo",
"MONDO:i2s",
"i2s"
],
"relation": null
},
{
"xref_id": "icdo:9962/3",
"sources": [
"NCIT:C3407"
],
"relation": null
},
{
"xref_id": "mesh:D013920",
"sources": [
"DOID:2224",
"EFO:0000479",
"MONDO:equivalentTo",
"ORDO:3318/e",
"Orphanet:3318",
"Orphanet:3318/e"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "MONDO:0005029",
"sources": null,
"relation": null
},
{
"xref_id": "meddra:10015493",
"sources": [
"ORDO:3318/e",
"Orphanet:3318",
"Orphanet:3318/e"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "NCIT:C3407",
"sources": [
"DOID:2224",
"EFO:0000479",
"MONDO:equivalentTo",
"MONDO:exact-label-match",
"exact-label-match"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "omim:187950",
"sources": null,
"relation": null
},
{
"xref_id": "omim:601977",
"sources": null,
"relation": null
},
{
"xref_id": "omim:614521",
"sources": null,
"relation": null
},
{
"xref_id": "oncotree:ET",
"sources": [
"MONDO:equivalentTo"
],
"relation": null
},
{
"xref_id": "orphanet:3318",
"sources": [
"DOID:2224",
"MONDO:equivalentTo"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "orphanet:71493",
"sources": [
"DOID:2224",
"MONDO:relatedTo"
],
"relation": null
},
{
"xref_id": "snomedct:109994006",
"sources": [
"DOID:2224",
"EFO:0000479",
"MONDO:equivalentTo"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "umls:C0040028",
"sources": [
"DOID:2224",
"MONDO:equivalentTo",
"NCIT:C3407",
"ORDO:3318/e",
"Orphanet:3318",
"Orphanet:3318/e"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "snomedct:128844009",
"sources": null,
"relation": "skos:closeMatch"
},
{
"xref_id": "snomedct:189508006",
"sources": null,
"relation": "skos:closeMatch"
},
{
"xref_id": "snomedct:189513005",
"sources": null,
"relation": "skos:closeMatch"
},
{
"xref_id": "snomedct:189514004",
"sources": null,
"relation": "skos:closeMatch"
},
{
"xref_id": "snomedct:191333009",
"sources": null,
"relation": "skos:closeMatch"
},
{
"xref_id": "snomedct:234499005",
"sources": null,
"relation": "skos:closeMatch"
},
{
"xref_id": "snomedct:307652003",
"sources": null,
"relation": "skos:closeMatch"
},
{
"xref_id": "snomedct:65471002",
"sources": null,
"relation": "skos:closeMatch"
}
],EFO:0000489
"xref_details": [
{
"xref_id": "DOID:0050936",
"sources": [
"MONDO:equivalentTo"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "MONDO:0000550",
"sources": null,
"relation": null
},
{
"xref_id": "NCIT:C48576",
"sources": [
"MONDO:equivalentTo"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "NCIT:C48576",
"sources": [
"MONDO:equivalentTo"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "umls:C1257877",
"sources": [
"MONDO:equivalentTo",
"NCIT:C48576"
],
"relation": "skos:exactMatch"
}
],EFO:0000640
"xref_details": [
{
"xref_id": "DOID:4465",
"sources": [
"EFO:0000640",
"MONDO:equivalentTo"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "gard:0009572",
"sources": [
"MONDO:equivalentTo"
],
"relation": null
},
{
"xref_id": "gard:0009575",
"sources": [
"MONDO:equivalentTo",
"shared-umls-xref"
],
"relation": null
},
{
"xref_id": "icd10:C64",
"sources": [
"ORDO:319298/ntbt",
"ORDO:47044/attributed",
"ORDO:47044/ntbt",
"Orphanet:319298",
"Orphanet:47044"
],
"relation": null
},
{
"xref_id": "MONDO:0017884",
"sources": null,
"relation": null
},
{
"xref_id": "mesh:C538614",
"sources": null,
"relation": "skos:exactMatch"
},
{
"xref_id": "NCIT:C6975",
"sources": [
"DOID:4465",
"EFO:0000640",
"MONDO:equivalentTo"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "omim:605074",
"sources": [
"DOID:4465",
"EFO:0000640",
"MONDO:equivalentTo",
"ORDO:47044/e",
"Orphanet:47044"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "oncotree:PRCC",
"sources": [
"MONDO:equivalentTo"
],
"relation": null
},
{
"xref_id": "orphanet:319298",
"sources": [
"MONDO:equivalentTo"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "orphanet:47044",
"sources": [
"MONDO:equivalentTo",
"OMIM:605074"
],
"relation": null
},
{
"xref_id": "snomedct:733608000",
"sources": [
"MONDO:equivalentTo"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "umls:C1306837",
"sources": [
"DOID:4465",
"MONDO:equivalentTo",
"NCIT:C6975",
"ORDO:319298/e",
"Orphanet:319298",
"Orphanet:319298/e"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "umls:C1336078",
"sources": [
"DOID:4465",
"MONDO:equivalentTo"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "umls:C2931899",
"sources": null,
"relation": "skos:exactMatch"
},
{
"xref_id": "umls:CN205129",
"sources": [
"MONDO:equivalentTo"
],
"relation": "skos:exactMatch"
},
{
"xref_id": "NCIT:C27890",
"sources": null,
"relation": "skos:closeMatch"
},
{
"xref_id": "Orphanet:47044",
"sources": null,
"relation": "skos:exactMatch"
},
{
"xref_id": "snomedct:4797003",
"sources": null,
"relation": "skos:closeMatch"
},
{
"xref_id": "umls:C1336839",
"sources": null,
"relation": "skos:closeMatch"
}
],There was a problem hiding this comment.
Looks great.
One note for future investigation is that it'd be nice to understand what the MONDO:equivalentTo source refers to (i.e. where it originates and how) and whether it implies (or should imply) a skos:exactMatch relation.
nxontology_data/efo/efo.py
Outdated
| ) | ||
|
|
||
| return { | ||
| k: v[["xref_id", "sources", "relation"]].to_dict(orient="records") |
There was a problem hiding this comment.
Would it be nicest to have relation come before sources, since relation is generally of greater interest and information content per character? Not a strong preference.
dhimmel
approved these changes
Nov 9, 2023
@dhimmel Ok, I removed it |
Output in 7201f20 |
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#18