[tdwg-guid] TDWG LSID Resolver broken?

Fri Nov 30 11:07:22 CET 2007

Dear Roger,

On 30 Nov 2007, at 09:48, Roger Hyam wrote:

>
> Sorry I have come into this thread late. It looks really exciting  
> stuff.
>
> The one thing I pick up on at the end was Rod offering to come up  
> with a policy for handling Handles in the RDF returned by LSIDs ;)

:-O

>
> I had previously presumed DOI and Handles could be treated as URIs  
> and therefore just used as rdf resources like this:
>
> <dc:identifier rdf:resource="doi:10.1007/BF02725185" />
>
> or in our current example
>
> <tdwg:parentPublication rdf:resource="doi:10.1007/BF02725185" />

My off-the-cuff comment was inspired by seeing a tag <doi> in the  
ontology. If you have DOIs, why not Handles, or any other GUID?  
Personally I would just use <dc:identifier>

>
> Now if we can't treat DOI/Handle as URIs I guess we could treat  
> them as strings and just use the dc identifier (possibly the worst  
> case scenario - this could be an ISBN, local catalogue code or  
> anything).
>
> <dc:identifier>doi:10.1007/BF02725185</dc:identifier>

I'm leaning towards this (or a standard representation, see below)  
because if there are multiple DOI resolvers (and there are a couple  
out there) and people use different ones, we need to decide whether  
the identifier is the same. My feeling is that RDF populated by links  
to URIs, while being Semantic Web savvy, will actually break because  
many of these URIs will be fragile, or there may be multiple URIs  
that point to the same thing. I think we may be heading for an unholy  
mess of URIs, especially as we have lots of distributed databases  
serving related information.

Put another way, if I aggregate a bunch of RDF from multiple sources  
and want to find anything related to a paper, it would be much easier  
to find things that refer to the same DOI in the same way.

>
> I presume support for DOI/Handle would have to be added to any  
> semantic web clients to understand any of these.
>
> Would it be better to take the approach we have with LSIDs where we  
> always cite a proxied version?

What if the proxy goes away?

Is there an expectation that the proxied version will serve RDF?

>
> What do other people do?

Connotea uses the INFO URI scheme, which is also used by OpenURL.  
It's a bit ugly, but at least is standardised. In this example the  
DOI would be

info:doi/10.1007/BF02725185

This scheme also supports Handles and SICIs, as well and GenBank  
sequences, and a few other identifiers (see http://info-uri.info/ 
registry/OAIHandler?verb=ListRecords&metadataPrefix=oai_dc).

>
> We could add a global property so that any object could have one or  
> hasHandle value.
>
> Any solution other than making Handles behave like regular URIs  
> means non-compliance with W3C recommendations and the need for  
> specialist client software I think.
>
> What do you think? Any ideas?

There seem to be at least two ways to approach this problem:

1. Write identifiers as strings in a canonical form likely to be  
shared by other databases, and leave it to client software to know  
how to handle them

2. Have a global proxy server for all classes of identifiers that we  
might have, and have this return RDF (and do 303 redirects, or  
whatever the Semantic Web community settle on). This was the  
motivation behind my experiments with http://bioguid.info .

Hope this makes sense...

Regards

Rod

>
> Roger
>
>
>
> On 30 Nov 2007, at 08:10, Roderic Page wrote:
>
>> Dear Rich,
>>
>>> Pyle, R.L. 2002. Pomacanthidae. pp. 3266-3286. In: Carpenter,  
>>> K.E. and V.E.
>>> Niem (Eds.) Living marine resources of the western central  
>>> Pacific.  Volume
>>> 5.  Bony fishes part 3 (Menidae to Pomacentridae). Food and  
>>> Agriculture
>>> Organization of the United Nations (FAO), Rome. i-iv+2791-3379.
>>>
>>> ...there are at least three "levels" of publication:
>>>
>>> 1) Pyle, R.L. 2002. Pomacanthidae. pp. 3266-3286.
>>>
>>> 2) Carpenter, K.E. and V.E. Niem (Eds.) Living marine resources  
>>> of the
>>> western central Pacific.  Volume 5.  Bony fishes part 3 (Menidae to
>>> Pomacentridae). Food and Agriculture Organization of the United  
>>> Nations
>>> (FAO), Rome. i-iv+2791-3379.
>>>
>>> 3) Carpenter, K.E. and V.E. Niem (Eds.) FAO species  
>>> identification guide for
>>> fishery purposes: Living marine resources of the western central  
>>> Pacific.
>>> Vols. 1-6. Food and Agriculture Organization of the United  
>>> Nations (FAO),
>>> Rome. xl+4218 pp.
>>>
>>> Granted, some might argue that number 3 is not really a separate  
>>> citable
>>> "unit", but given that it is a single page number series, I would  
>>> argue that
>>> it is.
>>>
>>> So...if we wanted to cite specifically Pyle 2002, the  
>>> parentCitationString
>>> might simply be the contents of of #2 above; or it might have two  
>>> nested
>>> parents (a parent, and agrand parent).
>>>
>>> As I said before, I'm leaning towards the simpler solution.
>>
>> Isn't this over engineering things a little? Don't you just need a  
>> GUID for the chapter (1), and a GUID for the book (2)? For the  
>> latter we have an ISBN (9251043879), so there's already a GUID for  
>> that.  I don't think we gain much from (3). Furthermore, if we use  
>> the ISBN as the GUID we know the items are linked because they  
>> share the same publisher code.
>>
>>>
>>> As for the ZooBank LSID resolver -- at this point in time  
>>> conformance trumps
>>> optimization (so we can all get off our collective arses and  
>>> serve content)
>>> -- so I'm just woking with what's up there now.  If I'm resolving  
>>> LSIDs, and
>>> I'm doing so because of TDWG standards, then I ought to conform  
>>> to existing
>>> TDWG standards on vocabularies -- right or wrong.  What we need  
>>> to do is
>>> update the TDWG standards on this (which the St. Lousi meeting was
>>> attempting to accomplish), so we can conform *and* optimize!
>>>
>>
>> The TDWG standard should need to be expanded to handle other kinds  
>> of GUIDs, notably Handles, which are being widely used in Digital  
>> Repositories.
>>
>> Regards
>>
>> Rod
>>
>>
>>
>>> Aloha,
>>> Rich
>>>
>>>
>>>
>>
>> ----------------------------------------
>> Professor Roderic D. M. Page
>> Editor, Systematic Biology
>> DEEB, IBLS
>> Graham Kerr Building
>> University of Glasgow
>> Glasgow G12 8QP
>> United Kingdom
>>
>> Phone: +44 141 330 4778
>> Fax: +44 141 330 2792
>> email: r.page at bio.gla.ac.uk
>> web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>> iChat: aim://rodpage1962
>> reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html
>>
>> Subscribe to Systematic Biology through the Society of Systematic
>> Biologists Website: http://systematicbiology.org
>> Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/ 
>> portal/
>> Find out what we know about a species: http://ispecies.org
>> Rod's rants on phyloinformatics: http://iphylo.blogspot.com
>> Rod's rants on ants: http://semant.blogspot.com
>>
>>
>>
>> _______________________________________________
>> tdwg-guid mailing list
>> tdwg-guid at lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-guid
>
>

----------------------------------------
Professor Roderic D. M. Page
Editor, Systematic Biology
DEEB, IBLS
Graham Kerr Building
University of Glasgow
Glasgow G12 8QP
United Kingdom

Phone: +44 141 330 4778
Fax: +44 141 330 2792
email: r.page at bio.gla.ac.uk
web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
iChat: aim://rodpage1962
reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html

Subscribe to Systematic Biology through the Society of Systematic
Biologists Website: http://systematicbiology.org
Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/
Find out what we know about a species: http://ispecies.org
Rod's rants on phyloinformatics: http://iphylo.blogspot.com
Rod's rants on ants: http://semant.blogspot.com

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