Hi Jerven, all On Fri, Apr 29, 2016 at 3:29 PM, Jerven Tjalling Bolleman <[email protected]> wrote: > Could I be so bold to suggest that in Wikidata we should strive > to use external URI's for identifiers not Strings. > > For example in Wikidata, there are a lot of UniProt accessions. > e.g. behind the property https://www.wikidata.org/wiki/P352 > and there is a formatter for a URL. > > I think this is the wrong way round, there should be an URL/URI there > and a formatter to generate a local string for display purposes. > > And of course for chembl the URL/URI to use would be > > <http://rdf.ebi.ac.uk/resource/chembl/molecule/CHEMBL101690? > > There a 2 advantages to this. It allows easier federates queries from > the source databases into wikidata (no URI conversions etc..) > The second is that these URIs are clearly not ambiguous.
What would you suggest for identifiers that do not have an official RDF serialization? Egon > Regards, > Jerven > > > On 28/04/16 23:49, Julie McMurry wrote: >>> >>> "One should also point out to the authorities maintaining these IDs >> >> that they should spend some effort on producing a workable solution for >> this. It seems they should be the first to provide a resolver service >> (or maybe it would be an "ID search engine" if it is so complicated). >> >> With the qualifiers in place, Wikidata can also be used to achieve this, >> of course, but it seems we are just manually reverse engineering >> something that should be done at the site of whoever is controlling the >> ID registration." >> >> Well said, Markus. A most hearty agreement here on my side and one >> colleagues and I have been trying to raise awareness of for a long time >> now (http://bit.ly/id-guidance). One of the challenges is that databases >> are already being asked to do more with less. They can see the utility >> of such a service to others, but when I've asked DBs before (not naming >> names), traction has been limp (I've yet to ask Chembl). Sometimes it >> works out though. For instance, KEGG used to have 12 different >> type-specific URLs, corresponding to: >> >> kegg.compound >> kegg.disease >> kegg.drug >> kegg.environ >> kegg.genes >> kegg.genome >> kegg.glycan >> kegg.metagenome >> kegg.module >> kegg.orthology >> kegg.pathway >> kegg.reaction >> >> Thankfully, they've collapsed those to a single URL pattern. >> >> The databases that find it the toughest are not those who simply don't >> embed typing, but rather those that don't embed typing AND ALSO have >> local identifiers that would otherwise collide. For instance, a >> prominent bio database is in this boat (not naming names) and would like >> to make things better but it is hard and messy due to the collisions. >> >> FYI 345 of the 560+ records in the identifiers.org >> <http://identifiers.org> corpus are type-specific at the level of >> identifiers.org <http://identifiers.org>'s namespace; these roll up to >> ~300 providers. >> >> The question though is what WikiData is trying to accomplish. Say you >> encounter the chembl ID CHEMBL308052 >> <http://linkedchemistry.info/chembl/chemblid/CHEMBL308052> do you need >> to retrieve the type of the entity for reasons other than determining >> what URL to use? >> >> How are you representing entity labels / IDs to users? >> >> Best, >> Julie >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> Wikidata mailing list >> [email protected] >> https://lists.wikimedia.org/mailman/listinfo/wikidata >> > > -- > ------------------------------------------------------------------- > Jerven Bolleman [email protected] > SIB Swiss Institute of Bioinformatics Tel: +41 (0)22 379 58 85 > CMU, rue Michel Servet 1 Fax: +41 (0)22 379 58 58 > 1211 Geneve 4, > Switzerland www.sib.swiss - www.uniprot.org > Follow us at https://twitter.com/#!/uniprot > ------------------------------------------------------------------- > > > _______________________________________________ > Wikidata mailing list > [email protected] > https://lists.wikimedia.org/mailman/listinfo/wikidata -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ImpactStory: https://impactstory.org/EgonWillighagen _______________________________________________ Wikidata mailing list [email protected] https://lists.wikimedia.org/mailman/listinfo/wikidata
