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EBISPOT / efo

Github repo for the Experimental Factor Ontology (EFO)
https://www.ebi.ac.uk/efo/
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Improved xrefs for HER2 negative breast carcinoma (EFO:0009780) #1606

Closed dhimmel closed 2 years ago

dhimmel commented 2 years ago

Here's all the info for HER2 negative breast carcinoma from efo-edit.owl:

# Class: efo:EFO_0009780 (HER2 negative breast carcinoma)

AnnotationAssertion(obo:IAO_0000115 efo:EFO_0009780 "A biologic subset of breast carcinoma defined by absence of HER2."^^xsd:string)
AnnotationAssertion(obo:IAO_0000117 efo:EFO_0009780 "Annalisa Buniello"^^xsd:string)
AnnotationAssertion(efo:definition_citation efo:EFO_0009780 "PMID:28864454"^^xsd:string)
AnnotationAssertion(oboInOwl:hasDbXref efo:EFO_0009780 "https://www.cancer.gov/publications/dictionaries/cancer-terms/def/her2-negative"^^xsd:string)
AnnotationAssertion(rdfs:label efo:EFO_0009780 "HER2 negative breast carcinoma"^^xsd:string)
SubClassOf(efo:EFO_0009780 efo:EFO_0000305)
SubClassOf(efo:EFO_0009780 ObjectSomeValuesFrom(efo:EFO_0000784 ObjectUnionOf(obo:UBERON_0000310 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000310))))

Note that it's missing xrefs like:

Looking at EFO:1000294 for HER2 Positive Breast Carcinoma, there's many cross-references:

How do we go about adding the missing xrefs for EFO:0009780? If we just add the MONDO xref, will the remaining xrefs be imported from MONDO... such that it's best to add as many xrefs to MONDO and just allow EFO to import them all from the single MONDO xref?

zoependlington commented 2 years ago

Hi @dhimmel, I will add the mapping for the Mondo term which will then bring int he Mondo x-refs. It is best in these cases to ensure that the Mondo term has x-refs as when mapped to EFO these will be brought in.

To do (for self): Add mapping as follows:

http://purl.obolibrary.org/obo/MONDO_0000618 http://www.ebi.ac.uk/efo/EFO_0009780 Her2-receptor negative breast cancer HER2 negative breast carcinoma

dhimmel commented 2 years ago

Thanks @zoependlington! 🚀

It is best in these cases to ensure that the Mondo term has x-refs as when mapped to EFO these will be brought in.

Do the MONDO xrefs only get brought in on the initial xref addition to EFO, or do will the xrefs periodically get updated from MONDO? Am wondering since if only at the moment of import, we should make sure I add the MONDO xrefs first!

zoependlington commented 2 years ago

They will be consistently updated as our Mondo import is dynamic - this means that any changes in Mondo will also be reflected in EFO.

dhimmel commented 2 years ago

any changes in Mondo will also be reflected in EFO

Awesome. Went ahead and added more comprehensive xrefs to MONDO in https://github.com/monarch-initiative/mondo/pull/4992

zoependlington commented 2 years ago

I've added the mapping in EFO so after Mondo adds these x-refs and releases they will be available in the subsequent EFO release. Moving this ticket to Done.