{"action":"opened","issue":{"url":"https://api.github.com/repos/geneontology/go-site/issues/45","labels_url":"https://api.github.com/repos/geneontology/go-site/issues/45/labels{/name}","comments_url":"https://api.github.com/repos/geneontology/go-site/issues/45/comments","events_url":"https://api.github.com/repos/geneontology/go-site/issues/45/events","html_url":"https://github.com/geneontology/go-site/issues/45","id":57271456,"number":45,"title":"BET:0000000 as an entity_type in db-xrefs.yaml","user":{"login":"cmungall","id":50745,"avatar_url":"https://avatars.githubusercontent.com/u/50745?v=3","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":null,"milestone":null,"comments":0,"created_at":"2015-02-11T03:12:48Z","updated_at":"2015-02-11T03:12:48Z","closed_at":null,"body":"From tony:\r\n\r\nNow that db-xrefs.yaml/json is in production, there is a small issue\r\nthat I think needs to be taken care of, concerning the use of\r\nBET:0000000 as an entity_type.\r\n\r\nBET:0000000 is used as the root of the entity_type hierarchy in\r\ngo-upper.obo, which means that, given that all of the other entity_types\r\ndefined in go-upper are, by definition, descendants of BET:0000000,\r\n*any* entity type can be identified by the id_syntax regexps from the\r\nfollowing databases:\r\n\r\n<snip>\r\n- database: CAZY\r\n  name: Carbohydrate Active EnZYmes\r\n  description: The CAZy database describes the families of\r\nstructurally-related catalytic and carbohydrate-binding modules (or\r\nfunctional domains) of enzymes that degrade, modify, or create\r\nglycosidic bonds.\r\n  generic_urls:\r\n    - http://www.cazy.org/\r\n  entity_types:\r\n    - type_name: entity\r\n      type_id: BET:0000000\r\n      id_syntax: (CE|GH|GT|PL)\\d+\r\n      url_syntax: http://www.cazy.org/[example_id].html\r\n      example_id: CAZY:PL11\r\n      example_url: http://www.cazy.org/PL11.html\r\n\r\n- database: dbSNP\r\n  name: NCBI dbSNP\r\n  generic_urls:\r\n    - http://www.ncbi.nlm.nih.gov/projects/SNP\r\n  entity_types:\r\n    - type_name: entity\r\n      type_id: BET:0000000\r\n      id_syntax: \\d+\r\n      url_syntax:\r\nhttp://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=[example_id]\r\n      example_id: dbSNP:rs3131969\r\n      example_url:\r\nhttp://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs3131969\r\n\r\n- database: DOI\r\n  name: Digital Object Identifier\r\n  generic_urls:\r\n    - http://dx.doi.org/\r\n  entity_types:\r\n    - type_name: entity\r\n      type_id: BET:0000000\r\n      id_syntax: 10\\.[0-9]+\\/.*\r\n      url_syntax: http://dx.doi.org/DOI:[example_id]\r\n      example_id: DOI:10.1016/S0963-9969(99)00021-6\r\n      example_url: http://dx.doi.org/DOI:10.1016/S0963-9969(99)00021-6\r\n\r\n- database: ECO\r\n  name: Evidence Code ontology\r\n  generic_urls:\r\n    - http://www.geneontology.org/\r\n  entity_types:\r\n    - type_name: entity\r\n      type_id: BET:0000000\r\n      id_syntax: \\d{7}\r\n      example_id: ECO:0000002\r\n\r\n- database: ENA\r\n  name: European Nucleotide Archive\r\n  description: ENA is made up of a number of distinct databases that\r\nincludes EMBL-Bank, the newly established Sequence Read Archive (SRA)\r\nand the Trace Archive. International nucleotide sequence database\r\ncollaboration, comprising ENA-EBI nucleotide sequence data library\r\n(EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank\r\n  generic_urls:\r\n    - http://www.ebi.ac.uk/ena/\r\n  entity_types:\r\n    - type_name: entity\r\n      type_id: BET:0000000\r\n      id_syntax: ([A-Z]{1}[0-9]{5})|([A-Z]{2}[0-9]{6})|([A-Z]{4}[0-9]{8,9})\r\n      url_syntax: http://www.ebi.ac.uk/ena/data/view/[example_id]\r\n      example_id: ENA:AA816246\r\n      example_url: http://www.ebi.ac.uk/ena/data/view/AA816246\r\n\r\n- database: FYPO\r\n  name: Fission Yeast Phenotype Ontology\r\n  generic_urls:\r\n    - http://www.pombase.org/\r\n  entity_types:\r\n    - type_name: entity\r\n      type_id: BET:0000000\r\n      id_syntax: \\d{7}\r\n      example_id: FYPO:0000001\r\n\r\n- database: GO_REF\r\n  name: Gene Ontology Database references\r\n  generic_urls:\r\n    - http://www.geneontology.org/\r\n  entity_types:\r\n    - type_name: entity\r\n      type_id: BET:0000000\r\n      id_syntax: \\d{7}\r\n      url_syntax:\r\nhttp://www.geneontology.org/cgi-bin/references.cgi#GO_REF:[example_id]\r\n      example_id: GO_REF:0000001\r\n      example_url:\r\nhttp://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000001\r\n\r\n- database: KEGG_ENZYME\r\n  name: KEGG Enzyme Database\r\n  generic_urls:\r\n    - http://www.genome.jp/dbget-bin/www_bfind?enzyme\r\n  entity_types:\r\n    - type_name: entity\r\n      type_id: BET:0000000\r\n      id_syntax: \\d(\\.\\d{1,2}){2}\\.\\d{1,3}\r\n      url_syntax: http://www.genome.jp/dbget-bin/www_bget?ec:[example_id]\r\n      example_id: KEGG_ENZYME:2.1.1.4\r\n      example_url: http://www.genome.jp/dbget-bin/www_bget?ec:2.1.1.4\r\n\r\n- database: KEGG_REACTION\r\n  name: KEGG Reaction Database\r\n  generic_urls:\r\n    - http://www.genome.jp/kegg/reaction/\r\n  entity_types:\r\n    - type_name: entity\r\n      type_id: BET:0000000\r\n      id_syntax: R\\d+\r\n      url_syntax: http://www.genome.jp/dbget-bin/www_bget?rn:[example_id]\r\n      example_id: KEGG:R02328\r\n      example_url: http://www.genome.jp/dbget-bin/www_bget?rn:R02328\r\n\r\n- database: OBI\r\n  name: Ontology for Biomedical Investigations\r\n  generic_urls:\r\n    - http://obi-ontology.org/page/Main_Page\r\n  entity_types:\r\n    - type_name: entity\r\n      type_id: BET:0000000\r\n      id_syntax: \\d{7}\r\n      example_id: OBI:0000038\r\n\r\n- database: PMID\r\n  name: PubMed\r\n  synonyms:\r\n    - PUBMED\r\n    - PubMed\r\n  generic_urls:\r\n    - http://www.ncbi.nlm.nih.gov/PubMed/\r\n  entity_types:\r\n    - type_name: entity\r\n      type_id: BET:0000000\r\n      id_syntax: \"[0-9]+\"\r\n      url_syntax: http://www.ncbi.nlm.nih.gov/pubmed/[example_id]\r\n      example_id: PMID:4208797\r\n      example_url: http://www.ncbi.nlm.nih.gov/pubmed/4208797\r\n\r\n- database: Reactome\r\n  name: Reactome - a curated knowledgebase of biological pathways\r\n  synonyms:\r\n    - REAC\r\n  generic_urls:\r\n    - http://www.reactome.org/\r\n  entity_types:\r\n    - type_name: entity\r\n      type_id: BET:0000000\r\n      id_syntax: REACT_[0-9]+\r\n      url_syntax:\r\nhttp://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=[example_id]\r\n      example_id: Reactome:REACT_604\r\n      example_url:\r\nhttp://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_604\r\n\r\n- database: SPD\r\n  name: Schizosaccharomyces pombe Postgenome Database at RIKEN; includes\r\nOrfeome Localisation data\r\n  generic_urls:\r\n    - http://www.riken.jp/SPD/\r\n  entity_types:\r\n    - type_name: entity\r\n      type_id: BET:0000000\r\n      id_syntax: \"[0-9]{2}/[0-9]{2}[A-Z][0-9]{2}\"\r\n      url_syntax: http://www.riken.jp/SPD/[example_id].html\r\n      example_id: SPD:05/05F01\r\n      example_url: http://www.riken.jp/SPD/05/05F01.html\r\n</snip>\r\n\r\nI don't know whether suitable entity type identifiers already exist for\r\nany of these databases in go-upper, or whether some need to be found /\r\ninvented, but I don't think that leaving them as BET:0000000 is an\r\noption. Note that there are other databases in db-xrefs.yaml that are\r\ndefined as supplying entities of type BET:0000000, but they don't have\r\nid_syntax defined (yet), so aren't causing any problems,\r\n\r\nCheers,\r\nTony"}}