{"action":"created","issue":{"url":"https://api.github.com/repos/monarch-initiative/phenoCompare/issues/22","repository_url":"https://api.github.com/repos/monarch-initiative/phenoCompare","labels_url":"https://api.github.com/repos/monarch-initiative/phenoCompare/issues/22/labels{/name}","comments_url":"https://api.github.com/repos/monarch-initiative/phenoCompare/issues/22/comments","events_url":"https://api.github.com/repos/monarch-initiative/phenoCompare/issues/22/events","html_url":"https://github.com/monarch-initiative/phenoCompare/issues/22","id":371736537,"node_id":"MDU6SXNzdWUzNzE3MzY1Mzc=","number":22,"title":"similarity calculation for sets of phenotypes","user":{"login":"hannahblau","id":8484992,"node_id":"MDQ6VXNlcjg0ODQ5OTI=","avatar_url":"https://avatars1.githubusercontent.com/u/8484992?v=4","gravatar_id":"","url":"https://api.github.com/users/hannahblau","html_url":"https://github.com/hannahblau","followers_url":"https://api.github.com/users/hannahblau/followers","following_url":"https://api.github.com/users/hannahblau/following{/other_user}","gists_url":"https://api.github.com/users/hannahblau/gists{/gist_id}","starred_url":"https://api.github.com/users/hannahblau/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hannahblau/subscriptions","organizations_url":"https://api.github.com/users/hannahblau/orgs","repos_url":"https://api.github.com/users/hannahblau/repos","events_url":"https://api.github.com/users/hannahblau/events{/privacy}","received_events_url":"https://api.github.com/users/hannahblau/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2018-10-18T22:21:55Z","updated_at":"2018-12-18T01:23:04Z","closed_at":null,"author_association":"MEMBER","body":"What similarity function to implement for comparing sets of HPO terms in the gsppc (gene set phenotypic profile comparison) R notebook? The first version used Jaccard similarity. Could re-implement one of the similarity functions from\r\nHPOSim: An R Package for Phenotypic Similarity Measure and Enrichment Analysis Based on the Human Phenotype Ontology\r\nYue Deng, Lin Gao, Bingbo Wang, Xingli Guo\r\nPLOS ONE, 9 February 2015\r\n\r\nHowever, I don't think this paper has a good metric for comparing sets qua sets. They propose computing the pairwise similarity of every pair of elements (one from the first set, one from the second set) and then choosing the max similarity or the mean or..."},"comment":{"url":"https://api.github.com/repos/monarch-initiative/phenoCompare/issues/comments/448061207","html_url":"https://github.com/monarch-initiative/phenoCompare/issues/22#issuecomment-448061207","issue_url":"https://api.github.com/repos/monarch-initiative/phenoCompare/issues/22","id":448061207,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0ODA2MTIwNw==","user":{"login":"hannahblau","id":8484992,"node_id":"MDQ6VXNlcjg0ODQ5OTI=","avatar_url":"https://avatars1.githubusercontent.com/u/8484992?v=4","gravatar_id":"","url":"https://api.github.com/users/hannahblau","html_url":"https://github.com/hannahblau","followers_url":"https://api.github.com/users/hannahblau/followers","following_url":"https://api.github.com/users/hannahblau/following{/other_user}","gists_url":"https://api.github.com/users/hannahblau/gists{/gist_id}","starred_url":"https://api.github.com/users/hannahblau/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hannahblau/subscriptions","organizations_url":"https://api.github.com/users/hannahblau/orgs","repos_url":"https://api.github.com/users/hannahblau/repos","events_url":"https://api.github.com/users/hannahblau/events{/privacy}","received_events_url":"https://api.github.com/users/hannahblau/received_events","type":"User","site_admin":false},"created_at":"2018-12-18T01:23:04Z","updated_at":"2018-12-18T01:23:04Z","author_association":"MEMBER","body":"@pnrobinson @LCCarmody \r\nThree genes from the GPI pathway/anchored groups have associated OMIM entries listed in the _mim2gene_medgen_ file, but the OMIM ids do not appear in _phenotype.hpoa_. They are:\r\n\r\nGene                | Group |Disease\r\n-------------- | ------ | ---------\r\nPIGS (ENTREZ:94005) | Pathway | OMIM:618143\r\nART4 (ENTREZ:420) | Anchored | OMIM:616060\r\nSEMA7A (ENTREZ:8482) | Anchored | OMIM:614745\r\n\r\nHere are the corresponding lines in the _mim2gene_medgen_ file:\r\n```\r\n618143            94005  phenotype       GeneMap       NULL    -\r\n616060            420      phenotype       GeneMap       C1292294        nondisease\r\n614745            8482    phenotype       GeneMap       C3553633        nondisease\r\n``` \r\nDecided to ignore any line of _mim2gene_medgen_ that contains \"nondisease\" in sixth column. If we ever expand our interest in _mim2gene_medgen_ beyond the GPI genes, might have to worry about other values one can find in the sixth column:\r\n```\r\n$cut -f6 mim2gene_medgen | sort | uniq\r\n-\r\nComment\r\nnondisease\r\nnondisease; QTL 2\r\nnondisease; QTL 2; susceptibility\r\nnondisease; nondisease; QTL 2\r\nnondisease; question\r\nnondisease; susceptibility\r\nquestion\r\nsusceptibility\r\nsusceptibility; QTL 1\r\nsusceptibility; modifier\r\nsusceptibility; modifier; question\r\nsusceptibility; question\r\nsusceptibility; somatic\r\n```\r\n"}}
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