[tdwg-guid] Re: Bibliographic metadata

Roderic Page r.page at bio.gla.ac.uk
Thu Nov 29 20:12:42 CET 2007


Dear Chuck,

On 29 Nov 2007, at 18:54, Chuck Miller wrote:

> Rod,
>
> Although DOIs are really great and should be added by those who can, I
> think we have not choice but to accept the bibliographic data that
> exists and get on with collecting it, messy or not.

I'm not arguing against having bibliographic metadata -- I'm arguing  
for GUIDs, and that if they exist we should use them. There are a lot  
of DOIs out there, as well as Handles (DSpace repositories) and SICIs  
(served by JSTOR). If we link names to these we greatly increase the  
value of our resources.

>
> I don't know that I agree with your hypothesis: "...without an external
> GUID for the publication I think nomenclators will be of limited use.
> Merely reproducing bibliographic metadata is ultimately an exercise in
> pain, given that most metadata contains errors or omissions..."
>
> Is it true that *most* bibliographic metadata contains errors or
> omissions, or would it be true to say that *some* or *more than we'd
> like* metadata contain errors?  And is it true that errors or omissions
> make nomenclators "of limited use"?  I would agree that  
> errors/omissions
> would surely limit use in some way, but I don't know that the magnitude
> of it rises to the level of declaring nomenclators "of limited use".
> Maybe it's just a semantic difference.

I rather overstated things perhaps -- obviously, nomenclators are very  
useful -- but based on my experience in finding existing DOIs for  
taxonomic literature, or harvesting large databases such as the AMNH's  
DSpace collection of publications, the number of times I encounter  
errors or ambiguities is enough to drive me nuts.

So, rather than letting my frustration get the better of me, what I  
should have said is that nomenclators can be even more useful if they  
use GUIDs for literature.

What I would very much NOT to see happen is nomenclators pump out LSID  
metadata that simply recycles bibliographic metadata. If this is all we  
do then we miss the point of LSIDs and RDF, namely integration. GUIDs,  
particularly universally used GUIDs make integration possible -- lots  
of metadata tags don't get us to this goal. Shared GUIDs do.

>
> I think we have to accept that bibliographic metadata with errors or
> omissions is better than *no* bibliographic metadata and a nomenclator
> with some errors is better than *no* nomenclator. And, we need to
> continue to appeal for the *addition* of DOIs and such by those who can
> add them.

Agreed. I'm in the middle of working on several tools to help deal with  
this, such as a tool to match journal names (early version here  
http://bioguid.info/journal.php ), an OpenURL resolver to find GUIDs  
from metadata (early version here http://bioguid.info/openurl.php), and  
reference parsing tools (web version here  
http://bioguid.info/references/ , there is also a CGI interface being  
used by David Shorthouse's Ajax tools). These are all pretty crude, and  
I'm hoping to overhaul the OpenURL tool before the end of the year.

My sense is that, at least in the short term, our community needs to  
assign GUIDs for much of the existing taxonomic literature. These GUIDs  
need to be easy to assign to references, and easily discoverable. I  
don't think this is too difficult to do. We don't need to wait for DOIs  
to get this stuff off the ground.

Regards

Rod

>
> Chuck
>
> -----Original Message-----
> From: tdwg-guid-bounces at lists.tdwg.org
> [mailto:tdwg-guid-bounces at lists.tdwg.org] On Behalf Of Roderic Page
> Sent: Thursday, November 29, 2007 12:26 PM
> To: Richard Pyle
> Cc: tdwg-guid at lists.tdwg.org
> Subject: Re: [tdwg-guid] TDWG LSID Resolver broken?
>
> Dear Richard,
>
> Quick comments on the metadata the LSID serves:
>
> 1. The dates in the TaxonName:publication section are a bit of a mess
> (one date lacks a year, and "11/26/1998 12:00:00 AM" is not an ISO
> standard date, it is also open to ambiguity given that the US writes
> month/day/year whereas Europeans write day/month/year). I think
> YYYY-MM-DD is the way to go to avoid major headaches. I've blogged
> about the mess DiGIR providers have created by not using ISO standard
> dates.
>
> 2. There's no journal name or ISSN so we don't know where this was
> published. I guess one could get this via the parent citation resource,
>
> but if you have all the other metadata included in the RDF, why not the
>
> journal?
>
> 3. The article in question has a DOI, hence it would be nice to link to
>
> that (doi:10.1007/BF02725185). I know you're working towards this, but
> without an external GUID for the publication I think nomenclators will
> be of limited use. Merely reproducing bibliographic metadata is
> ultimately an exercise in pain, given that most metadata contains
> errors or omissions, and the poor user has to dela with this when they
> try and track down the reference (or, more interestingly, try and link
> the literature together).
>
> Regards
>
> Rod
>
>
>
>
> On 29 Nov 2007, at 18:04, Richard Pyle wrote:
>
>> Thanks Rod,
>>
>> The two LSIDs in your links are truncated due to line wrap in my
>> original
>> message.  They should be:
>>
>> urn:lsid:zoobank.org:act:20889795-7EC7-42F3-A4C3-D1D97704A609
>>
>> urn:lsid:bishopmuseum.org:tnu:20889795-7EC7-42F3-A4C3-D1D97704A609
>>
>> Both have essentially identical WSDL data -- though it might be cached
>
>> still
>> from yesterday.
>>
>> WSDL looks mostly the same as IPNI:
>>
>> http://zoobank.bishopmuseum.org/authority/?lsid=urn:lsid:zoobank.org:
>> act:208
>> 89795-7EC7-42F3-A4C3-D1D97704A609
>>
>> http://nsdb.bishopmuseum.org/authority/?lsid=urn:lsid:
>> bishopmuseum.org:tnu:2
>> 0889795-7EC7-42F3-A4C3-D1D97704A609
>>
>> No doubt both of these will be truncated/line-wrapped as well....
>>
>> Sally:  might be DNS, but the DNS record hasn't changed for the
> ZooBank
>> service since it was originally created, and I know it was working
>> through
>> the TDWG resolver back before/during Bratislava.
>>
>> Lee:  I've been pestering Kevin about other issues I ran into setting
>
>> up the
>> new nsdb LSID resolver, but I figured that the problem was with the
>> TDWG
>> resolver service, since Rod's tester seems to work fine on both (or am
>
>> I
>> missing something about your tester, Rod?)  But now that I see that
>> the nsdb
>> LSIDs resolve through the TDWG site fine, I'm beginning to suspect the
>> problem is with IIS on the ZooBank server.  The Code really is
>> identical (if
>> anything, it should be broken on the nsdb version, not the zoobank
>> version).
>>
>> Hmmm....
>>
>> Many thanks for all the feedback so far!
>>
>> Aloha,
>> Rich
>>
>>
>> ________________________________
>>
>> 	From: Roderic Page [mailto:r.page at bio.gla.ac.uk]
>> 	Sent: Wednesday, November 28, 2007 10:57 PM
>> 	To: Richard Pyle
>> 	Cc: tdwg-guid at lists.tdwg.org
>> 	Subject: Re: [tdwg-guid] TDWG LSID Resolver broken?
>> 	
>> 	
>> 	Rich,
>>
>> 	The authority WSDL looks to be empty. I can't get either LSIDs
> to
>> work now with my tester. If you look at
>>
>> 	
>> http://nsdb.bishopmuseum.org/authority/?lsid=urn:lsid:
>> bishopmuseum.org:tnu:2
>> 0889795-7EC7-42F3-A4C3-D
>>
>> 	or
>>
>> 	
>> http://zoobank.bishopmuseum.org/authority/?lsid=urn:lsid:zoobank.org:
>> act:208
>> 89795-7EC7-42F3-A4C3-D1D977
>>
>> 	you'll see a pretty empty WSDL file. Compare this to, say,
> IPNI's:
>>
>> 	
>> http://www.ipni.org/authority/authority?lsid=urn:lsid:ipni.org:names:
>> 2001272
>> 8-1:1.1
>>
>> 	I suspect there's a problem with Zoobank's code, and it might
> have
>> taken a while to appear as my tester caches the WSDLs for 24 hours.
>>
>> 	Regards
>>
>> 	Rod
>>
>>
>>
>>
>>
>> 	On 28 Nov 2007, at 23:27, Richard Pyle wrote:
>>
>>
>>
>> 		VERY strange!
>>
>> 		This LSID does not work:
>>
>> 	
>> http://lsid.tdwg.org/urn:lsid:zoobank.org:act:20889795-7EC7-42F3-A4C3-
>
>> D1D977
>> 		04A609
>>
>> 		But this one does:
>>
>> 	
>> http://lsid.tdwg.org/urn:lsid:bishopmuseum.org:tnu:20889795-7EC7-42F3-
>
>> A4C3-D
>> 		1D97704A609
>>
>>
>> 		Even though these are the exact same record from the
> exact
>> same database,
>> 		and the latter resolver was created from the exact same
>> source code as the
>> 		former.
>>
>> 		Both seem to work fine on Rod's tester page, except the
>> latter has one
>> 		failure (5a), while in the former it is just a warning.
>>
>> 		Go figure....
>>
>> 		Rich
>>
>> 		________________________________
>>
>> 		From: Paul Kirk [mailto:p.kirk at cabi.org]
>> 		Sent: Wednesday, November 28, 2007 11:57 AM
>> 		To: Richard Pyle
>> 		Subject: RE: [tdwg-guid] TDWG LSID Resolver broken?
>>
>> 		
>> 		
>>
>> 		
>> 		
>>
>> 		Hi Rich,
>>
>> 		
>> 		
>>
>> 		works OK for IF LSIDs
>>
>> 		
>> 		
>>
>>
> http://lsid.tdwg.org/urn:lsid:indexfungorum.org:names:296755
>> 	
>> <http://lsid.tdwg.org/urn:lsid:indexfungorum.org:names:296755>
>>
>> 		
>> 		
>>
>> 		Cheers,
>>
>> 		
>> 		
>>
>> 		Paul
>>
>> 		________________________________
>>
>> 		From: tdwg-guid-bounces at lists.tdwg.org on behalf of
> Richard
>> Pyle
>> 		Sent: Wed 28/11/2007 21:52
>> 		To: tdwg-guid at lists.tdwg.org
>> 		Subject: [tdwg-guid] TDWG LSID Resolver broken?
>>
>> 		
>> 		
>>
>> 		
>> 		
>>
>>
>> 		Hi All,
>>
>> 		
>> 		
>>
>> 		I'm testing the ZooBank LSID resolver, and I can't seem
> to
>> get any
>> 		of my
>> 		LSIDs to work with the TDWG LSID resolver
>> (http://lsid.tdwg.org/)
>> 		They used
>> 		to work a couple months ago, but now they don't.
>>
>> 		
>> 		
>>
>> 		For example:
>>
>> 		
>> 		
>>
>> 	
>> urn:lsid:zoobank.org:act:20889795-7EC7-42F3-A4C3-D1D97704A609
>>
>> 		
>> 		
>>
>> 		This works fine on Rod's Tester site:
>>
>> 		
>> 		
>>
>> 		http://linnaeus.zoology.gla.ac.uk/~rpage/lsid/tester/
>>
>> 		
>> 		
>>
>> 		Any ideas???
>>
>> 		
>> 		
>>
>> 		Thanks,
>> 		Rich
>>
>> 		
>> 		
>>
>> 		Richard L. Pyle, PhD
>> 		Database Coordinator for Natural Sciences
>> 		and Associate Zoologist in Ichthyology
>> 		Department of Natural Sciences, Bishop Museum
>> 		1525 Bernice St., Honolulu, HI 96817
>> 		Ph: (808)848-4115, Fax: (808)847-8252
>> 		email: deepreef at bishopmuseum.org
>> 		http://hbs.bishopmuseum.org/staff/pylerichard.html
>>
>> 		
>> 		
>>
>> 		
>> 		
>>
>> 		
>> 		
>>
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>>
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>>
>> 		----------------------------------------
>> 	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
>>
>>
>> 	
>>
>>
>>
>>
>>
> ----------------------------------------------------------------------- 
> -
>
> ----------------------------------------
> 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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------------------------------------------------------------------------ 
----------------------------------------
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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