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obophenotype / human-phenotype-ontology

Ontology for the description of human clinical features
http://obophenotype.github.io/human-phenotype-ontology/
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phenotypes_to_genes.txt contains hpo with 0/ frequencies (absent) #9898

Closed jvreeuwijk closed 1 year ago

jvreeuwijk commented 1 year ago

Hello,

I use the phenotype_to_genes.txt file to annotate and extract (variants in) genes with a certain phenotype (and including the more specific related phenotypes).

I noticed that the latest (June 2023) phenotypes_to_genes.txt file contains HPO which have a frequency of 0/ (absent) in the genes_to_phenotype.txt file. I assume the phenotypes_to_genes.txt should not include phenotypes with a 0/ frequency or include frequency data?

Example for ANTXR2: phenotype_to_genes.txt: HP:0001249 Intellectual disability 118429 ANTXR2 OMIM:228600 genes_to_phenotype.txt: 118429 ANTXR2 HP:0001249 Intellectual disability 0/30 OMIM:228600

Thank you for this great resource.

Best regards, Jeroen Radboudumc, Nijmegen, The Netherlands

pnrobinson commented 1 year ago

For differential diagnosis, it can be important to know that affected individuals do not have the phenotypic feature in question (or that there is a low frequency). This is a relatively new resource on the HPO website and we need to better document this file -- I will try to do so before the next release.