Hi Egon, All,
If something is identifiable by a String, but there is no official RDF serialization. Then I would make the identifier property in question a subproperty of
https://www.wikidata.org/wiki/Property:P973
The value should then be the "most" official url of a webpage having the thing identified by the string as its topic.
Lets take the example of Property:P351 (Entrez Gene ID) There is no offical RDF for Entrez Gene. So I would have made it a
p:P351 instanceof p:P973 .
Then formatter URL would need a capturing group because it is the inverse of the current logic.
p:P351 p:P1630 "https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&...)"
Then the example
wd:Q14911732 p:P351 "1017"
Would instead be recorded in the backend as
wd:Q14911732 p:P351 https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=default&list_uids=1017
I do believe the current UI view is correct, I just think URLs/URIs should be the preferred solution for identifiers in WikiData.
Regards, Jerven
On 02/05/16 20:00, Egon Willighagen wrote:
Hi Jerven, all
On Fri, Apr 29, 2016 at 3:29 PM, Jerven Tjalling Bolleman jerven.bolleman@sib.swiss 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
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Jerven Bolleman Jerven.Bolleman@sib.swiss 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
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