BIBO use for UniProt
Jerven Bolleman
I would like to use BIBO to describe citations in the UniProt dataset.
UniProt has long published a list of journals as flat file text document
joulist.txt[1].
I am currently translating this to RDF and am looking at bibo which
meets most of our needs. However, there is one field I am having
problems with the abbreviated title of the Journal. Bibo contains a
perfect term for it "shortTitle". Unfortunately, only bibo:Documents are
allowed to have a bibo:shortTitle.
Can this be changed or does anyone have a better idea?
We also have a property called Short. This is one of the old CODENs when
they where still 4 characters long. I think I should not encode this as
a CODEN but as a different property. What do you guys think?
Thanks and regards,
Jerven
[1]
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/jourlist.txt
Frederick Giasson
> I would like to use BIBO to describe citations in the UniProt dataset.
> UniProt has long published a list of journals as flat file text
> document joulist.txt[1].
>
Nice!
> I am currently translating this to RDF and am looking at bibo which
> meets most of our needs. However, there is one field I am having
> problems with the abbreviated title of the Journal. Bibo contains a
> perfect term for it "shortTitle". Unfortunately, only bibo:Documents
> are allowed to have a bibo:shortTitle.
>
> Can this be changed or does anyone have a better idea?
For what kind of individuals would you like to use it? (lets try to
understand your context, and then we will check if it makes sense or not
to change it).
Thanks!
Fred
Bruce D'Arcus
It sounds like he wants to use bibo:shortTitle with bibo:Journal, but
that we've defined it in such a way he can't. If that's true, then
that's a bug.
Bruce
Jerven Bolleman
On 01/14/2011 03:43 PM, Frederick Giasson wrote:
> Hi Jerven!
>> I am currently translating this to RDF and am looking at bibo which
>> meets most of our needs. However, there is one field I am having
>> problems with the abbreviated title of the Journal. Bibo contains a
>> perfect term for it "shortTitle". Unfortunately, only bibo:Documents
>> are allowed to have a bibo:shortTitle.
>>
>> Can this be changed or does anyone have a better idea?
>
> For what kind of individuals would you like to use it? (lets try to
> understand your context, and then we will check if it makes sense or not
> to change it).
>
Cerebral Blood Flow and Metabolism" which has a title. (Which I put as
bibo:title but maybe I should use dcterms:title instead). And also an
abbreviated form "J. Cereb. Blood Flow Metab.". Most likely an ISO
standard abbreviation.
The same approach is taken at periodicals.dataincubator.org but I am not
sure it is currently valid.
Regards,
Jerven
@prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl:<http://www.w3.org/2002/07/owl#> .
@base <http://purl.uniprot.org/core/> .
<http://purl.uniprot.org/journals/1000> rdf:type :Journal ,
<http://purl.org/ontology/bibo/Journal> ;
<http://purl.org/ontology/bibo/shortTitle> "J. Cereb. Blood Flow
Metab." ;
<http://purl.org/ontology/bibo/title> "Journal of Cerebral Blood Flow
and Metabolism" ;
<http://purl.org/ontology/bibo/issn> "0271-678X" ;
owl:sameAs <http://periodicals.dataincubator.org/issn/0271-678X> ;
<http://purl.org/ontology/bibo/eissn> "1559-7016" ;
<http://purl.org/ontology/bibo/coden> "JCBMDN" ;
:shortCoden "JCBFM" ;
<http://purl.org/dc/terms/publisher> "Nature Publishing Group" ;
rdfs:seeAlso "http://www.nature.com/jcbfm/"
Frederick Giasson
> It sounds like he wants to use bibo:shortTitle with bibo:Journal, but
> that we've defined it in such a way he can't. If that's true, then
> that's a bug.
Yes, seems to be an oversight.
I added this change in the "next things todo" changelog here:
Jerven: you can use it right now to describe your bibo:Journal, but it
will only make it into the ontology when we will next release a new
version (but don't worry, this change will appear :) )
Does that work?
Thanks,
Fred
Jerven Bolleman
As I doubt that this will go live on our side before march I think this
is absolutely fine.
Regards,
Jerven
PS. nicer turtle example
@base <http://purl.uniprot.org/core/> .
@prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl:<http://www.w3.org/2002/07/owl#> .
@prefix skos:<http://www.w3.org/2004/02/skos/core#> .
@prefix bibo:<http://purl.org/ontology/bibo/> .
@prefix dcterms:<http://purl.org/dc/terms/> .
<http://purl.uniprot.org/journals/1> rdf:type bibo:Journal ;
bibo:shortTitle "AAPS PharmSci" ;
bibo:title "AAPS PharmSci" ;
bibo:eissn "1522-1059" ;
bibo:coden "PHARFY" ;
dcterms:publisher "Not published" ;
rdfs:comment "Replaced by AAPS J., ends with vol. 6 in 2004."
Frederick Giasson
> As I doubt that this will go live on our side before march I think
> this is absolutely fine.
Perfect, so problem resolved :)
Thanks,
Fred
Christopher Gutteridge
remove all "-" from ISSN & ISBN so that they are easier to link?
--
Christopher Gutteridge -- http://id.ecs.soton.ac.uk/person/1248
You should read the ECS Web Team blog: http://blogs.ecs.soton.ac.uk/webteam/
Bruce D'Arcus
<c...@ecs.soton.ac.uk> wrote:
> Would it make sense to require (or strongly suggest that) people to remove
> all "-" from ISSN & ISBN so that they are easier to link?
And therefore, would it valuable to define (or reuse from somewhere)
formal data-types for these identifiers?
Bruce
Christopher Gutteridge
Jerven Bolleman
And in case of ISBN aren't the dashes significant?
Regards,
Jerven
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Christopher Gutteridge
should be written consistently so you can compare apples and apples.
Could we add a *recommendation* that the "-" are removed, but not a
requirement?
On 14/01/11 16:18, Jerven Bolleman wrote:
> I would disagree. In normal use outside of URI's these dashes are present. I would recommend to keep them for ease of conversion (no string mangling). And don't see how removing these make things easier or more difficult to link.
>
> And in case of ISBN aren't the dashes significant?
>
> Regards,
> Jerven
>
>
> On Jan 14, 2011, at 4:50 PM, Christopher Gutteridge wrote:
>
>> Isn't there urn:issn:12345678 and urn:isbn:123456789X?
>>
>> Bruce D'Arcus wrote:
>>> On Fri, Jan 14, 2011 at 10:43 AM, Christopher Gutteridge
>>>
>>> <c...@ecs.soton.ac.uk>
>>> wrote:
>>>
>>>
>>>
>>>> Would it make sense to require (or strongly suggest that) people to remove
>>>> all "-" from ISSN& ISBN so that they are easier to link?
>>>>
>>>>
>>> And therefore, would it valuable to define (or reuse from somewhere)
>>> formal data-types for these identifiers?
>>>
>>> Bruce
>>>
>>>
>>>
>> --
>> Christopher Gutteridge --
>> http://id.ecs.soton.ac.uk/person/1248
>>
>>
>> You should read the ECS Web Team blog:
>> http://blogs.ecs.soton.ac.uk/webteam/
>>
>> --
>> You received this message because you are subscribed to the Google Groups "Bibliographic Ontology Specification Group" group.
>> To post to this group, send email to bibliographic-ontolog...@googlegroups.com.
>> To unsubscribe from this group, send email to bibliographic-ontology-spec...@googlegroups.com.
>> For more options, visit this group at http://groups.google.com/group/bibliographic-ontology-specification-group?hl=en.
--
Christopher Gutteridge -- http://id.ecs.soton.ac.uk/person/1248
/ Lead Developer, EPrints Project, http://eprints.org/
/ Web Projects Manager, ECS, University of Southampton, http://www.ecs.soton.ac.uk/
/ Webmaster, Web Science Trust, http://www.webscience.org/