Stream: genomics
Topic: Phenopackets
Kevin Power (Oct 11 2018 at 13:58):
I noticed this comment from @Alejandro Metke in a separate stream:
I am part of the GA4GH Clinical & Phenotypic Data Capture Work Stream and I've been pushing the use of FHIR as a potential replacement of other standards such as Phenopackets (http://phenopackets.org/).
Wanted to add this comment to our #genomics stream for possible comments from the community? This seems like a great idea for a profile (or two)?
Jamie Jones (Oct 11 2018 at 20:30):
Definitely an interesting read at https://github.com/phenopackets/phenopacket-format/wiki/Overview-of-Phenotype-Exchange-Format
Kevin Power (Oct 11 2018 at 21:07):
Just to be clear, is this the right schema as of today?
https://github.com/phenopackets/phenopacket-schema
Alejandro Metke (Oct 11 2018 at 22:27):
Just to be clear, is this the right schema as of today?
https://github.com/phenopackets/phenopacket-schema
Yes, that is the current version and it has been aligned with FHIR to some extent. We also wrote a prototype of a FHIR to Phenopackets transformation service.
Kevin Power (Oct 12 2018 at 11:52):
Do you have some examples of what is produced?
Alejandro Metke (Oct 15 2018 at 22:48):
This is a sample input:
{ "resourceType": "Bundle", "type": "collection", "entry": [ { "resource": { "resourceType": "Patient", "id": "p-mild", "meta": { "versionId": "2", "lastUpdated": "2018-09-25T21:08:23.928+00:00" }, "text": { "status": "generated", "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><table class=\"hapiPropertyTable\"><tbody><tr><td>Date of birth</td><td><span>01 January 2016</span></td></tr></tbody></table></div>" }, "name": [ { "use": "official", "family": "Girl", "given": [ "Demo" ], "prefix": [ "Miss" ] } ], "gender": "female", "birthDate": "2016-01-01" } }, { "resource": { "resourceType": "Condition", "id": "c-6", "meta": { "versionId": "1", "lastUpdated": "2018-09-25T20:02:15.342+00:00", "tag": [ { "system": "http://hl7.org/fhir/v3/ObservationValue", "code": "SUBSETTED", "display": "Resource encoded in summary mode" } ] }, "clinicalStatus": "active", "verificationStatus": "confirmed", "code": { "coding": [ { "system": "http://purl.obolibrary.org/obo/hp.owl", "code": "HP:0000316", "display": "Hypertelorism" } ] }, "subject": { "reference": "Patient/p-mild" }, "context": { "reference": "Encounter/enc-mild" } } }, { "resource": { "resourceType": "Condition", "id": "c-5", "meta": { "versionId": "1", "lastUpdated": "2018-09-25T20:02:15.342+00:00", "tag": [ { "system": "http://hl7.org/fhir/v3/ObservationValue", "code": "SUBSETTED", "display": "Resource encoded in summary mode" } ] }, "clinicalStatus": "active", "verificationStatus": "confirmed", "code": { "coding": [ { "system": "http://purl.obolibrary.org/obo/hp.owl", "code": "HP:0001363", "display": "Craniosynostosis" } ] }, "subject": { "reference": "Patient/p-mild" }, "context": { "reference": "Encounter/enc-mild" } } }, { "resource": { "resourceType": "Condition", "id": "c-4", "meta": { "versionId": "1", "lastUpdated": "2018-09-25T20:02:15.342+00:00", "tag": [ { "system": "http://hl7.org/fhir/v3/ObservationValue", "code": "SUBSETTED", "display": "Resource encoded in summary mode" } ] }, "clinicalStatus": "active", "verificationStatus": "confirmed", "code": { "coding": [ { "system": "http://purl.obolibrary.org/obo/hp.owl", "code": "HP:0000248", "display": "Brachycephaly" } ] }, "subject": { "reference": "Patient/p-mild" }, "context": { "reference": "Encounter/enc-mild" } } } ] }
Alejandro Metke (Oct 15 2018 at 22:49):
And this is a sample output:
{ "patient": { "id": "p-mild", "dateOfBirth": "2016-01-01T00:00:00Z", "sex": { "id": "PATO:0000383", "label": "female" }, "phenotypes": [ { "type": { "id": "HP:0000316", "label": "Hypertelorism" } }, { "type": { "id": "HP:0001363", "label": "Craniosynostosis" } }, { "type": { "id": "HP:0000248", "label": "Brachycephaly" } } ] }, "metaData": { "created": "2018-10-15T22:42:59Z", "createdBy": "FHIR converter", "resources": [ { "id": "pato", "name": "Phenotype And Trait Ontology", "namespacePrefix": "PATO", "url": "http://purl.obolibrary.org/obo/pato.owl", "version": "2018-08-14" }, { "id": "hp", "namespacePrefix": "HP", "url": "http://purl.obolibrary.org/obo/hp.owl" } ] }, "vcf": { "path": "/data/Pfeiffer.vcf" }, "genomeAssembly": "GRCH_37" }
Alejandro Metke (Oct 15 2018 at 22:50):
Note that this was just a demo, so the VCF location and the genome assembly are added externally.
Last updated: Apr 12 2022 at 19:14 UTC
