BET:0000000 as an entity_type in db-xrefs.yaml

[cmungall]

From tony:

Now that db-xrefs.yaml/json is in production, there is a small issue that I think needs to be taken care of, concerning the use of BET:0000000 as an entity_type.

BET:0000000 is used as the root of the entity_type hierarchy in go-upper.obo, which means that, given that all of the other entity_types defined in go-upper are, by definition, descendants of BET:0000000, any entity type can be identified by the id_syntax regexps from the following databases:

``` yaml - database: CAZY name: Carbohydrate Active EnZYmes description: The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. generic_urls: - http://www.cazy.org/ entity_types: - type_name: entity type_id: BET:0000000 id_syntax: (CE|GH|GT|PL)\d+ url_syntax: http://www.cazy.org/[example_id].html example_id: CAZY:PL11 example_url: http://www.cazy.org/PL11.html - database: dbSNP name: NCBI dbSNP generic_urls: - http://www.ncbi.nlm.nih.gov/projects/SNP entity_types: - type_name: entity type_id: BET:0000000 id_syntax: \d+ url_syntax: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=[example_id] example_id: dbSNP:rs3131969 example_url: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs3131969 - database: DOI name: Digital Object Identifier generic_urls: - http://dx.doi.org/ entity_types: - type_name: entity type_id: BET:0000000 id_syntax: 10\.[0-9]+\/.* url_syntax: http://dx.doi.org/DOI:[example_id] example_id: DOI:10.1016/S0963-9969(99)00021-6 example_url: http://dx.doi.org/DOI:10.1016/S0963-9969(99)00021-6 - database: ECO name: Evidence Code ontology generic_urls: - http://www.geneontology.org/ entity_types: - type_name: entity type_id: BET:0000000 id_syntax: \d{7} example_id: ECO:0000002 - database: ENA name: European Nucleotide Archive description: ENA is made up of a number of distinct databases that includes EMBL-Bank, the newly established Sequence Read Archive (SRA) and the Trace Archive. International nucleotide sequence database collaboration, comprising ENA-EBI nucleotide sequence data library (EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank generic_urls: - http://www.ebi.ac.uk/ena/ entity_types: - type_name: entity type_id: BET:0000000 id_syntax: ([A-Z]{1}[0-9]{5})|([A-Z]{2}[0-9]{6})|([A-Z]{4}[0-9]{8,9}) url_syntax: http://www.ebi.ac.uk/ena/data/view/[example_id] example_id: ENA:AA816246 example_url: http://www.ebi.ac.uk/ena/data/view/AA816246 - database: FYPO name: Fission Yeast Phenotype Ontology generic_urls: - http://www.pombase.org/ entity_types: - type_name: entity type_id: BET:0000000 id_syntax: \d{7} example_id: FYPO:0000001 - database: GO_REF name: Gene Ontology Database references generic_urls: - http://www.geneontology.org/ entity_types: - type_name: entity type_id: BET:0000000 id_syntax: \d{7} url_syntax: http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:[example_id] example_id: GO_REF:0000001 example_url: http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000001 - database: KEGG_ENZYME name: KEGG Enzyme Database generic_urls: - http://www.genome.jp/dbget-bin/www_bfind?enzyme entity_types: - type_name: entity type_id: BET:0000000 id_syntax: \d(\.\d{1,2}){2}\.\d{1,3} url_syntax: http://www.genome.jp/dbget-bin/www_bget?ec:[example_id] example_id: KEGG_ENZYME:2.1.1.4 example_url: http://www.genome.jp/dbget-bin/www_bget?ec:2.1.1.4 - database: KEGG_REACTION name: KEGG Reaction Database generic_urls: - http://www.genome.jp/kegg/reaction/ entity_types: - type_name: entity type_id: BET:0000000 id_syntax: R\d+ url_syntax: http://www.genome.jp/dbget-bin/www_bget?rn:[example_id] example_id: KEGG:R02328 example_url: http://www.genome.jp/dbget-bin/www_bget?rn:R02328 - database: OBI name: Ontology for Biomedical Investigations generic_urls: - http://obi-ontology.org/page/Main_Page entity_types: - type_name: entity type_id: BET:0000000 id_syntax: \d{7} example_id: OBI:0000038 - database: PMID name: PubMed synonyms: - PUBMED - PubMed generic_urls: - http://www.ncbi.nlm.nih.gov/PubMed/ entity_types: - type_name: entity type_id: BET:0000000 id_syntax: "[0-9]+" url_syntax: http://www.ncbi.nlm.nih.gov/pubmed/[example_id] example_id: PMID:4208797 example_url: http://www.ncbi.nlm.nih.gov/pubmed/4208797 - database: Reactome name: Reactome - a curated knowledgebase of biological pathways synonyms: - REAC generic_urls: - http://www.reactome.org/ entity_types: - type_name: entity type_id: BET:0000000 id_syntax: REACT_[0-9]+ url_syntax: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=[example_id] example_id: Reactome:REACT_604 example_url: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_604 - database: SPD name: Schizosaccharomyces pombe Postgenome Database at RIKEN; includes Orfeome Localisation data generic_urls: - http://www.riken.jp/SPD/ entity_types: - type_name: entity type_id: BET:0000000 id_syntax: "[0-9]{2}/[0-9]{2}[A-Z][0-9]{2}" url_syntax: http://www.riken.jp/SPD/[example_id].html example_id: SPD:05/05F01 example_url: http://www.riken.jp/SPD/05/05F01.html ```

I don't know whether suitable entity type identifiers already exist for any of these databases in go-upper, or whether some need to be found / invented, but I don't think that leaving them as BET:0000000 is an option. Note that there are other databases in db-xrefs.yaml that are defined as supplying entities of type BET:0000000, but they don't have id_syntax defined (yet), so aren't causing any problems,

Cheers, Tony

[cmungall]

• NCIT:C20130 ! protein family
• SO:0000694 ! SNP
• IAO:0000311 ! publication
• SO:0000150 ! read
• IAO:0000030 ! information content entity
• IAO:0000442 ! author role

[cmungall]

http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/experimental/upper/go-upper.obo?r1=23491&r2=23509

[cmungall]

TODO:

• decide what to do for IDs that denote classes.
  • Do we represent them using the CURIE owl:Class? (assuming a standard yaml-ld to expand to correct URI). Kind of makes the ontology owl-full-like
  • Or do we have the semantics of the type field be the union of rdf:type and rdfs:subClassOf? In which case we type_id will be the root class (but root may be meaningless for ontologies like OBI)
• can we use owl:Thing for BET:0000000

cc @davidos

[cmungall]

Note that the above commit is in my branch. If given +1 I will merge into geneontology master

[kltm]

(@cmungall changed to yaml format over "snip"--see source)

[pgaudet]

@cmungall This is not yet changed. Does it need to be addressed ?