UniProt uses FALDO

[Jerven Bolleman]

Hi guys,

Just wanted to let you know that UniProt since release2014_01 uses FALDO for position information.

see http://www.uniprot.org/uniprot/P77967.ttl for examples

Regards,
Jerven

[Hilmar Lapp]

Nice work! Wouldn't it be appropriate to move the namespace to something more canonical, such as a OBO Library PURL?

BTW unrelated to FALDO, Jerven I notice that you're giving DOIs in the doi: prefix notation. The recommended representation for DOIs has been changed to the HTTP-proxied form (http:/dx.doi.org/... or http://doi.org/...) about 2 years ago.

-hilmar

> --
> You received this message because you are subscribed to the Google Groups "FALDO" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to faldo+un...@googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.

--
Hilmar Lapp -:- lappland.io

[Jerven Bolleman]

The biohackathon URI was picked to show that faldo was supported by
the biohackathon. This is as stable an URI as any, and comparable to
OBO foundry that is.
Of course you can also use a raw github URI or mint one of your own.
Stable dereferenceable uri's are important but at some point the
social/engineering challenges are limited (often a the very same
point).

DOI's in uniprot are still dcterms:identifiers, which use matches
http://data.nature.com/query?query=SELECT%20?p%20?o%20where%20{%3Chttp://dx.doi.org/10.1038/nature10624%3E%20?p%20?o%20}

The thing about actually using a more interesting relation for a DOI
and uniprot/pubmed
is to distinguish what a DOI actually represents. Is a DOI format
specific or not?
Its been bugging us and is one of the reasons we have not refactored
the citation code recently (in UniProt).

Regards,
Jerven

Jerven Bolleman
m...@jerven.eu

[Michel Dumontier]

You should look at DOIs as pointers to document metadata. publishers often give you an abstract, etc, and give links to hmtl, pdf, etc. i don't know enough about DOIs regarding whether you can add an extra bit to request a specific format.

m.

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

[Hilmar Lapp]

On Jan 28, 2014, at 12:01 PM, Michel Dumontier wrote:

i don't know enough about DOIs regarding whether you can add an extra bit to request a specific format.

You can; it's through content negotiation: http://www.crosscite.org/cn/

-hilmar

[Jerven Bolleman]

Thanks HIlmar,

The http://dx.doi.org/10.1126/doi:10.1093/dnares/3.3.109 uri is a
representation of the article. And we can say

<http://dx.doi.org/10.1126/doi:10.1093/dnares/3.3.109> owl:sameAs
<http://purl.uniprot.org/citation/8905231>

Although I saw that the bug of owl:sameAs NCBI webpage is still in.
Need to write some more c++ code to fix that :(

Regards,
Jerven

--
Jerven Bolleman
m...@jerven.eu

[Hilmar Lapp]

On Jan 28, 2014, at 12:31 PM, Jerven Bolleman wrote:

> The http://dx.doi.org/10.1126/doi:10.1093/dnares/3.3.109 uri is a

That DOI doesn't resolve. Perhaps you mean http://dx.doi.org/10.1093/dnares/3.3.109 instead? What's the 10.1126 prefix stand for?

[Michel Dumontier]

Here's what i get when i dereference

  <rdf:Description rdf:about="http://dx.doi.org/10.1093/dnares/3.3.109">

    <ns0:identifier xmlns:ns0="http://purl.org/dc/terms/">10.1093/dnares/3.3.109</ns0:identifier>

  </rdf:Description>

  <rdf:Description rdf:about="http://dx.doi.org/10.1093/dnares/3.3.109">

    <ns0:sameAs xmlns:ns0="http://www.w3.org/2002/07/owl#" rdf:resource="info:doi/10.1093/dnares/3.3.109"/>

  </rdf:Description>

  <rdf:Description rdf:about="http://dx.doi.org/10.1093/dnares/3.3.109">

    <ns0:sameAs xmlns:ns0="http://www.w3.org/2002/07/owl#" rdf:resource="doi:10.1093/dnares/3.3.109"/>

  </rdf:Description>

  <rdf:Description rdf:about="http://dx.doi.org/10.1093/dnares/3.3.109">

    <ns0:doi xmlns:ns0="http://prismstandard.org/namespaces/basic/2.1/">10.1093/dnares/3.3.109</ns0:doi>

  </rdf:Description>

  <rdf:Description rdf:about="http://dx.doi.org/10.1093/dnares/3.3.109">

    <ns0:doi xmlns:ns0="http://purl.org/ontology/bibo/">10.1093/dnares/3.3.109</ns0:doi>

m.

 

[Peter Ansell]

Hi all,

I didn't realise that DataCite also supported content negotiation
along with CrossRef!

http://www.crosscite.org/cn/

Back on topic though, all of it seems to go through the standard
http://dx.doi.org/ URIs, which seems to make them more authoritative
for semantic web purposes than the formal "info:doi/" standard.

http://info-uri.info/registry/OAIHandler?verb=GetRecord&metadataPrefix=reg&identifier=info:doi/

Cheers,

Peter

[Hilmar Lapp]

On Jan 28, 2014, at 5:21 PM, Peter Ansell wrote:

> Back on topic though, all of it seems to go through the standard
> http://dx.doi.org/ URIs, which seems to make them more authoritative
> for semantic web purposes than the formal "info:doi/" standard.

It's not only that. info:doi URIs aren't HTTP URIs, one of the cornerstones of LD.

[Peter Ansell]

On 29 January 2014 09:30, Hilmar Lapp <hl...@drycafe.net> wrote:
>
> On Jan 28, 2014, at 5:21 PM, Peter Ansell wrote:
>
>> Back on topic though, all of it seems to go through the standard
>> http://dx.doi.org/ URIs, which seems to make them more authoritative
>> for semantic web purposes than the formal "info:doi/" standard.
>
> It's not only that. info:doi URIs aren't HTTP URIs, one of the cornerstones of LD.
>

I forgot to mention that they have formally closed the info registry
to new entries, for that reason.

http://info-uri.info/

Cheers,

Peter