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Identifiers
ktym edited this page May 16, 2014
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2 revisions
Making Identifiers.org URIs as the de facto (and primary?) IDs for RDF in life sciences would be a good idea for interoperability, although we need to design missing common IDs especially for genomes. Also, it is important to host cross references among those IDs as RDF and at SPARQL endpoint. We may achieve this with sustainable collaboration of Bio2RDF (US/Canada), EdgeStore (Japan) and Id.org (UK).
IDs represented in RDF should use Identifiers.org URIs primarily.
- Need to provide and maintain cross references among those Id.org URIs
- Bio2RDF, EdgeStore
- Need to make agreement on Sequence IDs
- http://identifiers.org/genome/taxonomy_id/biosample_id/sequence_id ???
- Ensembl, NCBI, RefSeq, UCSC, GRC, FANTOM, GMOD, TogoWS, UBSID
- How to deal with versions and liftover?
- Need to make agreement on Taxonomy IDs
- Id.org, UniProt, NCBI CGI, NCBI OBO, NCBI taxdump
- If resources already have canonical URIs, which properties to specify Id.org URIs and canonical URIs?
- rdfs:seeAlso, owl:sameAs
- How to assign URIs for objects which doesn't have IDs in original data formats? (INSDC features and exons, promoters etc.)
- HTTP URI, UUID URN, blank node
- RDF version of Identifiers.org need to be updated
- Content negotiation
- OK: curl http://identifiers.org/taxonomy/9606
- NG: curl http://identifiers.org/taxonomy/9606.rdf
- OK: curl http://info.identifiers.org/taxonomy/9606
- OK: curl http://info.identifiers.org/taxonomy/9606.rdf (*1)
- NG: curl -H "Accept: application/rdf+xml" http://identifiers.org/taxonomy/9606
- OK: curl -H "Accept: application/rdf+xml" http://info.identifiers.org/taxonomy/9606 (*2)
- results of *1 and *2 differs in order and rdf:about (what should be?)
- http://identifiers.org/db/ --> http://identifiers.org/db
- a ""; is invalid (entity or entry or just an ID for external entry?)
- Content negotiation
% wget http://info.identifiers.org/taxonomy/9606.rdf
% rapper -i guess -o turtle 9606.rdf
rapper: Parsing URI file:///Users/ktym/9606.rdf with parser guess
rapper: Serializing with serializer turtle
rapper: Error - URI file:///Users/ktym/9606.rdf:13 - RDF term about is forbidden as a property attribute.
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix vcard: <http://www.w3.org/2006/vcard/ns#> .
@prefix doap: <http://usefulinc.com/ns/doap#> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix edam: <http://identifiers.org/edam/> .
@prefix mir: <http://identifiers.org/> .
<http://identifiers.org/>
dcterms:alternative "MIRIAM Resolver"@en-gb ;
dcterms:description "General cross-referencing and annotation framework, providing unique and perennial URIs for life science data." ;
dcterms:title "Identifiers.org"@en-gb ;
rdfs:seeAlso <http://www.ebi.ac.uk/miriam/> .
<http://identifiers.org/miriam.collection/MIR:00000006>
dcterms:alternative "NCBI taxonomy", "NEWT" ;
dcterms:identifier "MIR:00000006" ;
dcterms:title "Taxonomy"@en-gb .
<http://identifiers.org/miriam.resource/MIR:00100007>
mir:primary "true" ;
mir:reliability "100" ;
mir:state "Resource working" ;
dcterms:title "Taxonomy at NCBI"@en-gb ;
doap:homepage <http://www.ncbi.nlm.nih.gov/Taxonomy/> ;
vcard:country-name "USA" ;
vcard:organisation-name "National Center for Biotechnology Information" .
<http://identifiers.org/miriam.resource/MIR:00100019>
mir:reliability "100" ;
mir:state "Resource working" ;
dcterms:title "Taxonomy at Uniprot"@en-gb ;
doap:homepage <http://www.uniprot.org/taxonomy/> ;
vcard:country-name "United Kingdom" ;
vcard:organisation-name "European Bioinformatics Institute" .
<http://identifiers.org/miriam.resource/MIR:00100299>
mir:reliability "98" ;
mir:state "Probably up (Ajax)" ;
dcterms:title "Taxonomy at European Nucleotide Archive (ENA)"@en-gb ;
doap:homepage <http://www.ebi.ac.uk/ena/> ;
vcard:country-name "UK" ;
vcard:organisation-name "European Bioinformatics Institute, Hinxton, Cambridge" .
<http://identifiers.org/miriam.resource/MIR:00100507>
mir:reliability "100" ;
mir:state "Resource working" ;
dcterms:title "Taxonomy through BioPortal"@en-gb ;
doap:homepage <http://bioportal.bioontology.org/> ;
vcard:country-name "USA" ;
vcard:organisation-name "National Center for Biomedical Ontology, Stanford" .
<http://info.identifiers.org/taxonomy/9606.rdf>
--> should be http://identifiers.org/taxonomy/9606 or http://info.identifiers.org/taxonomy/9606
dcterms:URI <http://identifiers.org/taxonomy/9606> ;
dcterms:date "2014-04-16T03:55:57.990+01:00" ;
dcterms:identifier "9606" ;
dcterms:publisher <http://identifiers.org/> ;
dcterms:source <http://identifiers.org/miriam.collection/MIR:00000006> ;
dcterms:title "Entity 9606 provided by the data collection Taxonomy (MIR:00000006)."@en-gb ;
sio:SIO_000671 [
sio:SIO_000300 "9606" ;
a edam:data_2091, <http://idtype.identifiers.org/taxonomy/>
--> remove trailing slash? http://idtype.identifiers.org/taxonomy so that it can be written as idorg:taxonomy
] ;
a "" ;
--> rdf:type "literal" is wrong.
rdfs:seeAlso <http://purl.bioontology.org/ontology/NCBITAXON/obo:NCBITaxon_9606>, <http://www.ebi.ac.uk/ena/data/view/Taxon:9606>, <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606>, <http://www.uniprot.org/taxonomy/9606> .
<http://purl.bioontology.org/ontology/NCBITAXON/obo:NCBITaxon_9606>
dcterms:format "application/xhtml+xml" ;
dcterms:publisher <http://identifiers.org/miriam.resource/MIR:00100507> .
<http://www.ebi.ac.uk/ena/data/view/Taxon:9606>
dcterms:format "application/xhtml+xml" ;
dcterms:publisher <http://identifiers.org/miriam.resource/MIR:00100299> .
<http://www.ebi.ac.uk/miriam/>
dcterms:format "text/html" ;
dcterms:title "MIRIAM Registry"@en-gb .
<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606>
dcterms:format "application/xhtml+xml" ;
dcterms:publisher <http://identifiers.org/miriam.resource/MIR:00100007> .
<http://www.uniprot.org/taxonomy/9606>
dcterms:format "application/xhtml+xml" ;
dcterms:publisher <http://identifiers.org/miriam.resource/MIR:00100019> .