identifiers.org and bio2rdf.org identifiers

[Kingsley Idehen]

All,

Are there unpublished scripts that address the issue above?

For example, we have the following URIs:

[1] http://bio2rdf.org/hgnc:27538 -- Bio2RDF

[2] http://info.identifiers.org/hgnc/27538 -- Identifiers.org

In both cases, we are dealing with industry identifier "hgnc:27538" .
Thus, one would expect accurate cross references in Bio2RDF which I
suspect must have either been achieved or in the pipelines, right?

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[Jerven Bolleman]

Hi Kingsley,

Short as I need  to run

[1] http://bio2rdf.org/hgnc:27538  -- Bio2RDF

"same as"

[3] http://identifiers.org/hgnc/27538 -- Identifiers.org <!-- concept of Human Gene Nomenclature

not
[2] http://info.identifiers.org/hgnc/27538 -- Identifiers.org <!-- concept of description of URIs leading to information about Human Gene Nomenclature

Regards,

Jerven

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[Michel Dumontier]

Hi, this is a problem with identifiers.org in their formulation of the
generated link for bio2rdf - it currently points to
http://bio2rdf.org/27538, when it should point to
http://bio2rdf.org/hgnc:27538
Michel Dumontier
Associate Professor of Medicine (Biomedical Informatics), Stanford University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com

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[Kingsley Idehen]

On 10/5/16 11:12 AM, Jerven Bolleman wrote:

Hi Kingsley,

Short as I need  to run

[1] http://bio2rdf.org/hgnc:27538  -- Bio2RDF

"same as"

[3] http://identifiers.org/hgnc/27538 -- Identifiers.org <!-- concept of Human Gene Nomenclature

not
[2] http://info.identifiers.org/hgnc/27538 -- Identifiers.org <!-- concept of description of URIs leading to information about Human Gene Nomenclature

Regards,

Jerven

Hi Jerven,

That part's clear. I should have used <http://identifiers.org/hgnc/27538> , but as per usual, the browser's presentation threw me off while typing in haste. Anyway, the issue for me boils down to missing owl:sameAs relations in Bio2RDF which I assume must be something long considered by project members.

[1] http://lod.openlinksw.com/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fhgnc%3A27538&distinct=1

Kingsley

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[Kingsley Idehen]

On 10/5/16 11:17 AM, Michel Dumontier wrote:
> Hi, this is a problem with identifiers.org in their formulation of the
> generated link for bio2rdf - it currently points to
> http://bio2rdf.org/27538, when it should point to
> http://bio2rdf.org/hgnc:27538

Yes, but what about a reciprocal relation in the Bio2RDF data space?
Ideally, an owl:sameAs relation with an identifier.org URI identifying
said relation's object?

I don't want to fix this problem in some of our instances as the best
place would be in your RDFizer scripts that are used to generate Bio2RDF
data.

Kingsley

[Nick Juty]

I can't actually reply to the google group directly, but Jerven is right
on the info. domain's intent.

For the sameAs, we don't have any scripts, but we do record alternatives
(manually curated) which you can access using Web Services, or through
the SPARQL endpoint:
http://identifiers.org/services/sparql

For this query:
PREFIX owl: <http://www.w3.org/2002/07/owl#>

SELECT ?uris WHERE {
<http://bio2rdf.org/hgnc:27538> owl:sameAs ?uris
}

the results are:
<http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=27538>
<http://hgnc.bio2rdf.org/describe/?url=http://bio2rdf.org/hgnc:27538>
<http://identifiers.org/hgnc/HGNC:27538>
<http://bio2rdf.org/hgnc:27538>
urn:miriam:hgnc:HGNC%3A27538

But I'm not sure it helps you long term ..

cheers

Nick

[Kingsley Idehen]

On 10/5/16 1:08 PM, Nick Juty wrote:

I can't actually reply to the google group directly, but Jerven is right on the info. domain's intent.

For the sameAs, we don't have any scripts, but we do record alternatives (manually curated) which you can access using Web Services, or through the SPARQL endpoint:
http://identifiers.org/services/sparql

For this query:
PREFIX owl: <http://www.w3.org/2002/07/owl#>

SELECT ?uris WHERE {
 <http://bio2rdf.org/hgnc:27538> owl:sameAs  ?uris
}

the results are:
<http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=27538>
<http://hgnc.bio2rdf.org/describe/?url=http://bio2rdf.org/hgnc:27538>
<http://identifiers.org/hgnc/HGNC:27538>
<http://bio2rdf.org/hgnc:27538>
urn:miriam:hgnc:HGNC%3A27538

But I'm not sure it helps you long term ..

That is certainly useful as it provides a fallback should Bio2RDF not include the cross-reference relation that I am inquiring about.

BTW -- why does the following query produce an empty solution?

PREFIX owl: <http://www.w3.org/2002/07/owl#>

SELECT ?uris WHERE {

 ?s owl:sameAs  ?o
}

LIMIT 5

[Jerven Bolleman]

Because the identifiers.org is a rather interesting SPARQL endpoint. Instead of having about 10 TB of owl:sameAs relations it computes them on the fly from a few 1000 regex combinations. But the endpoint is fully sparql1.1. compliant per spec.

Basically, it pretends that someone emptied the DB if the query is not of form bound variable owl:sameAs unbound variable.

It's is explained in more depth in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443684/

Regards,

Jerven

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[Kingsley Idehen]

On 10/6/16 8:31 AM, Jerven Bolleman wrote:

Because the identifiers.org is a rather interesting SPARQL endpoint. Instead of having about 10 TB of owl:sameAs relations it computes them on the fly from a few 1000 regex combinations. But the endpoint is fully sparql1.1. compliant per spec.

Basically, it pretends that someone emptied the DB if the query is not of form bound variable owl:sameAs unbound variable.

It's is explained in more depth in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443684/

Regards,

Jerven

Okay.


Kingsley 

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Regards,

Kingsley Idehen	      
Founder & CEO 
OpenLink Software   (Home Page: http://www.openlinksw.com)

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