{"action":"created","issue":{"url":"https://api.github.com/repos/geneontology/go-site/issues/595","repository_url":"https://api.github.com/repos/geneontology/go-site","labels_url":"https://api.github.com/repos/geneontology/go-site/issues/595/labels{/name}","comments_url":"https://api.github.com/repos/geneontology/go-site/issues/595/comments","events_url":"https://api.github.com/repos/geneontology/go-site/issues/595/events","html_url":"https://github.com/geneontology/go-site/issues/595","id":312717899,"number":595,"title":"WormBase GPI is splitting some lines causing neo pipeline to break","user":{"login":"cmungall","id":50745,"avatar_url":"https://avatars1.githubusercontent.com/u/50745?v=4","gravatar_id":"","url":"https://api.github.com/users/cmungall","html_url":"https://github.com/cmungall","followers_url":"https://api.github.com/users/cmungall/followers","following_url":"https://api.github.com/users/cmungall/following{/other_user}","gists_url":"https://api.github.com/users/cmungall/gists{/gist_id}","starred_url":"https://api.github.com/users/cmungall/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmungall/subscriptions","organizations_url":"https://api.github.com/users/cmungall/orgs","repos_url":"https://api.github.com/users/cmungall/repos","events_url":"https://api.github.com/users/cmungall/events{/privacy}","received_events_url":"https://api.github.com/users/cmungall/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"vanaukenk","id":1730534,"avatar_url":"https://avatars2.githubusercontent.com/u/1730534?v=4","gravatar_id":"","url":"https://api.github.com/users/vanaukenk","html_url":"https://github.com/vanaukenk","followers_url":"https://api.github.com/users/vanaukenk/followers","following_url":"https://api.github.com/users/vanaukenk/following{/other_user}","gists_url":"https://api.github.com/users/vanaukenk/gists{/gist_id}","starred_url":"https://api.github.com/users/vanaukenk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vanaukenk/subscriptions","organizations_url":"https://api.github.com/users/vanaukenk/orgs","repos_url":"https://api.github.com/users/vanaukenk/repos","events_url":"https://api.github.com/users/vanaukenk/events{/privacy}","received_events_url":"https://api.github.com/users/vanaukenk/received_events","type":"User","site_admin":false},"assignees":[{"login":"vanaukenk","id":1730534,"avatar_url":"https://avatars2.githubusercontent.com/u/1730534?v=4","gravatar_id":"","url":"https://api.github.com/users/vanaukenk","html_url":"https://github.com/vanaukenk","followers_url":"https://api.github.com/users/vanaukenk/followers","following_url":"https://api.github.com/users/vanaukenk/following{/other_user}","gists_url":"https://api.github.com/users/vanaukenk/gists{/gist_id}","starred_url":"https://api.github.com/users/vanaukenk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vanaukenk/subscriptions","organizations_url":"https://api.github.com/users/vanaukenk/orgs","repos_url":"https://api.github.com/users/vanaukenk/repos","events_url":"https://api.github.com/users/vanaukenk/events{/privacy}","received_events_url":"https://api.github.com/users/vanaukenk/received_events","type":"User","site_admin":false}],"milestone":null,"comments":9,"created_at":"2018-04-09T23:03:13Z","updated_at":"2018-04-23T13:36:28Z","closed_at":null,"author_association":"OWNER","body":"File:\r\nftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/PRJNA13758/annotation/gene_product_info/c_elegans.PRJNA13758.current.gene_product_info.gpi.gz\r\n\r\nSome of the description lines include newlines, causing a single line to be split over two lines, breaking parsing. For example:\r\n\r\n```\r\n$ gzip -dc mirror/c_elegans.PRJNA13758.current.gene_product_info.gpi.gz | grep -n -B1 CELE_C33A11 \r\n24676-WB        WBGene00007877  nfki-1  Nuclear Factor of Kappa light polypeptide gene enhancer in b(B)-cells \r\n24677:Inhibitor, delta and zeta related nbid-1|CELE_C33A11.1    protein_coding_gene     taxon:6239              UniProtKB:G5EDE9\r\n--\r\n24678-WB        C33A11.1        nfki-1  Nuclear Factor of Kappa light polypeptide gene enhancer in b(B)-cells \r\n24679:Inhibitor, delta and zeta related nbid-1|CELE_C33A11.1    transcript      taxon:6239      WB:WBGene00007877       \r\n--\r\n24680-WB        WP:CE24824      NFKI-1  Nuclear Factor of Kappa light polypeptide gene enhancer in b(B)-cells \r\n24681:Inhibitor, delta and zeta related nbid-1|CELE_C33A11.1    protein taxon:6239      WB:C33A11.1     UniProtKB_GCRP:G5EDE9|UniProtKB:G5EDE9\r\n```\r\n\r\ncc @rankishore "},"comment":{"url":"https://api.github.com/repos/geneontology/go-site/issues/comments/383577568","html_url":"https://github.com/geneontology/go-site/issues/595#issuecomment-383577568","issue_url":"https://api.github.com/repos/geneontology/go-site/issues/595","id":383577568,"user":{"login":"vanaukenk","id":1730534,"avatar_url":"https://avatars2.githubusercontent.com/u/1730534?v=4","gravatar_id":"","url":"https://api.github.com/users/vanaukenk","html_url":"https://github.com/vanaukenk","followers_url":"https://api.github.com/users/vanaukenk/followers","following_url":"https://api.github.com/users/vanaukenk/following{/other_user}","gists_url":"https://api.github.com/users/vanaukenk/gists{/gist_id}","starred_url":"https://api.github.com/users/vanaukenk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vanaukenk/subscriptions","organizations_url":"https://api.github.com/users/vanaukenk/orgs","repos_url":"https://api.github.com/users/vanaukenk/repos","events_url":"https://api.github.com/users/vanaukenk/events{/privacy}","received_events_url":"https://api.github.com/users/vanaukenk/received_events","type":"User","site_admin":false},"created_at":"2018-04-23T13:36:28Z","updated_at":"2018-04-23T13:36:28Z","author_association":"CONTRIBUTOR","body":"@cmungall - the duplicate WP:CE52235 protein ids are actually cases where two genes encode the same protein sequence.  We have other cases like this, e.g. histones.  For annotation, depending on the data being annotated, the curator could either select the unique gene ID for annotation or might need to select the protein if the specific genetic locus was not known. \r\n\r\n@tonysawfordebi - yes, I had remembered these existing properties over the weekend :-).  Here are the gpi properties (and values that I'm aware of) relating to sequences, including the ones you mention above:\r\n\r\n     db_subset=TrEMBL or Swiss-Prot\r\n     uniprot_proteome=UP000001940 (C. elegans, for example)\r\n     is_isoform=?\r\n     reference_proteome=?\r\n\r\nWrt the gpi files submitted by MODs, we (WB) thought it might be useful to indicate which of the UniProtKB accessions we reference were part of the GCRP.  Looking at these property tags I'm not sure which one we should use and what makes most sense for the value.  Would something like this work for the MOD files:\r\n\r\nuniprot_gcrp=YES \r\n\r\nAlso, for properties like db_subset and reference_proteome, is it implicit that these properties refer to the source in column 1 or should we make the property names more explicit wrt the database?\r\n\r\nWill need to update:  https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-1_2.md\r\n\r\n     "}}
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