{"action":"created","issue":{"url":"https://api.github.com/repos/airr-community/airr-standards/issues/153","repository_url":"https://api.github.com/repos/airr-community/airr-standards","labels_url":"https://api.github.com/repos/airr-community/airr-standards/issues/153/labels{/name}","comments_url":"https://api.github.com/repos/airr-community/airr-standards/issues/153/comments","events_url":"https://api.github.com/repos/airr-community/airr-standards/issues/153/events","html_url":"https://github.com/airr-community/airr-standards/pull/153","id":355717256,"node_id":"MDExOlB1bGxSZXF1ZXN0MjEyMTgxODYx","number":153,"title":"Schema gene vs segment terminology corrections","user":{"login":"javh","id":4105629,"node_id":"MDQ6VXNlcjQxMDU2Mjk=","avatar_url":"https://avatars3.githubusercontent.com/u/4105629?v=4","gravatar_id":"","url":"https://api.github.com/users/javh","html_url":"https://github.com/javh","followers_url":"https://api.github.com/users/javh/followers","following_url":"https://api.github.com/users/javh/following{/other_user}","gists_url":"https://api.github.com/users/javh/gists{/gist_id}","starred_url":"https://api.github.com/users/javh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/javh/subscriptions","organizations_url":"https://api.github.com/users/javh/orgs","repos_url":"https://api.github.com/users/javh/repos","events_url":"https://api.github.com/users/javh/events{/privacy}","received_events_url":"https://api.github.com/users/javh/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-08-30T19:11:38Z","updated_at":"2018-09-01T16:26:02Z","closed_at":null,"author_association":"COLLABORATOR","pull_request":{"url":"https://api.github.com/repos/airr-community/airr-standards/pulls/153","html_url":"https://github.com/airr-community/airr-standards/pull/153","diff_url":"https://github.com/airr-community/airr-standards/pull/153.diff","patch_url":"https://github.com/airr-community/airr-standards/pull/153.patch"},"body":"This is a collection of small terminology changes in response to a reviewer comment on the DRWG manuscript. Specifically, the issue of whether V, D, J, C should be referred to as \"genes\", \"gene segments\", or \"segments\".  With the argument that the correct terminology is \"V gene\", rather than \"V gene segment\" or \"V segment\".\r\n\r\n### From http://www.imgt.org/FAQ/#question1\r\n\r\n**Why are immunoglobulin and T cell receptor genes described as \"genes\", instead of \"gene segments\" or \"segments\"?**\r\n\r\n> Immunoglobulin and T cell receptor genes were accepted as \"genes\" by the Human Organisation (HUGO) Nomenclature Committee (HGNC) in 1999. It was the only way to have the IG and TR genes entered into the general genome databases (LocusLink, GDB, GeneCards, Entrez Gene) and to define and characterize alleles in a standardized way. This has been accepted as different definitions of a gene coexist in biology. Moreover, each IG or TR gene has its own promotor and can be transcribed as an independent transcript.\r\n\r\n### From http://www.imgt.org/ligmdb/label#\r\n\r\n**V-GENE**\r\n\r\n> gDNA of an IG or TR variable (V) gene, in germline configuration, that comprises L-PART1, V-INTRON and V-EXON, with 5'UTR and 3'UTR (including V-RS)\r\n\r\n**V-GENE-UNIT**\r\n\r\n> gDNA of an IG or TR V-GENE unit, in germline configuration, that comprises V-EXON and V-RS\r\n\r\n**V-REGION**\r\n\r\n> coding region of an IG or TR V-GENE-UNIT (includes 1 or 2 nucleotide(s) before the V-HEPTAMER, if present) in germline gDNA or cDNA (defined as CORE V-REGION), or variable (V) region usually trimmed in 3' by the V-(D)-J rearrangement in rearranged gDNA or cDNA\r\n\r\n### From http://www.insdc.org/files/feature_table.html\r\n\r\n```\r\nFeature Key           V_segment\r\n\r\nDefinition            variable segment of immunoglobulin light and heavy\r\n                      chains, and T-cell receptor alpha, beta, and gamma\r\n                      chains; codes for most of the variable region (V_region)\r\n                      and the last few amino acids of the leader peptide;\r\n\r\nOptional qualifiers   /allele=\"text\"\r\n                      /citation=[number]\r\n                      /db_xref=\"<database>:<identifier>\"\r\n                      /experiment=\"[CATEGORY:]text\"\r\n                      /gene=\"text\"\r\n                      /gene_synonym=\"text\"\r\n                      /inference=\"[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]\"\r\n                      /locus_tag=\"text\" (single token)\r\n                      /map=\"text\"\r\n                      /note=\"text\"\r\n                      /old_locus_tag=\"text\" (single token)\r\n                      /product=\"text\"\r\n                      /pseudo\r\n                      /pseudogene=\"TYPE\"\r\n                      /standard_name=\"text\"\r\n```\r\n\r\n### Interpretation\r\n\r\nAs I read all of this, and please correct me if I'm wrong, there is a difference between the INSDC and IMGT terminology regarding regions of the rearranged sequence wherein IMGT uses `V-REGION` and `V-DOMAIN` and INSDC uses `V_segment` and `V_region`, respectively. Aside from that, I think the different between \"segment\" and \"gene\" is whether you're talking about a subregion of the rearranged sequence independent of gene annotation (\"segment\") or a genomic gene (\"gene\").  Which seems consistent with the INSDC scheme, which defines `V_segment` as a coordinate span within a sequence that is has an associated `gene` and `allele` annotation.\r\n\r\n### Changes\r\n\r\nIt sounds like \"gene segment\" is the wrong term in any context, so I removed all instances of \"gene segment\" or \"segment gene\" from the schema in favor of either \"gene\" or \"segment\".  I reworded what I could to stick to \"gene\" wherever possible, using \"gene\" to mean either the gene/allele annotation or the genomic reference sequence. I used \"segment\" exclusively for fields that refer to a region or coordinate and are independent of annotation.\r\n\r\nFor example:\r\n\r\n+ **v_call:**  V gene with allele. For example, IGHV4-59*01.\r\n+ **v_sequence_start:**  Start position of the V segment in the query sequence.\r\n+ **v_germline_start:**  Alignment start position in the V gene reference sequence.\r\n+ **n1_length:** Number of untemplated nucleotides 5' of the D segment.\r\n\r\nThoughts?"},"comment":{"url":"https://api.github.com/repos/airr-community/airr-standards/issues/comments/417870600","html_url":"https://github.com/airr-community/airr-standards/pull/153#issuecomment-417870600","issue_url":"https://api.github.com/repos/airr-community/airr-standards/issues/153","id":417870600,"node_id":"MDEyOklzc3VlQ29tbWVudDQxNzg3MDYwMA==","user":{"login":"javh","id":4105629,"node_id":"MDQ6VXNlcjQxMDU2Mjk=","avatar_url":"https://avatars3.githubusercontent.com/u/4105629?v=4","gravatar_id":"","url":"https://api.github.com/users/javh","html_url":"https://github.com/javh","followers_url":"https://api.github.com/users/javh/followers","following_url":"https://api.github.com/users/javh/following{/other_user}","gists_url":"https://api.github.com/users/javh/gists{/gist_id}","starred_url":"https://api.github.com/users/javh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/javh/subscriptions","organizations_url":"https://api.github.com/users/javh/orgs","repos_url":"https://api.github.com/users/javh/repos","events_url":"https://api.github.com/users/javh/events{/privacy}","received_events_url":"https://api.github.com/users/javh/received_events","type":"User","site_admin":false},"created_at":"2018-09-01T16:26:02Z","updated_at":"2018-09-01T16:26:02Z","author_association":"COLLABORATOR","body":"> Happy with most of your changes, but is there any reason to keep the few remaining \"segments\", i.e. would it screw anything up to call these things \"genes\"?\r\n\r\nMy reasoning was that definitions like this sounded wrong to me:\r\n\r\n+ **n1_length:** Number of untemplated nucleotides 5' of the D gene.\r\n\r\nAs opposed to the following:\r\n\r\n+ **n1_length:** Number of untemplated nucleotides 5' of the D segment.\r\n\r\nBecause the former implies a dependency on the specific gene annotation or, even more confusingly, a property of the unrearranged gDNA. Whereas the latter refers only to a subregion (coordinate span) of the query sequence.  Basically, if I could substitute any subregion, like `JUNCTION` or `FWR2`, and the sentence still  made sense (even if not correct), then I used \"segment\". Anytime the description refers to a germline reference sequence or a gene annotation I used \"gene\".\r\n\r\nThere were several definitions that I thought could have used either term, so I use something like \"V gene alignment\" to try to clarify that it was an annotated sequence region. I don't really like this wording though. It let me favor the use of \"gene\" over \"segment\", but I find it clunky.\r\n\r\nI'm not sure if this adds precision or confusion, but that's why I kept some definitions as \"segment\"."}}
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