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@lists.tdwg.org [mailto:tdwg-guid-bounces@lists.tdwg.org] On Behalf Of Roderic Page Sent: Thursday, November 29, 2007 12:26 PM To: Richard Pyle Cc: tdwg-guid@lists.tdwg.org Subject: Re: [tdwg-guid] TDWG LSID Resolver broken?
Dear Richard,
Quick comments on the metadata the LSID serves:
- 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.
- 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?
- 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@bio.gla.ac.uk] Sent: Wednesday, November 28, 2007 10:57 PM To: Richard Pyle Cc: tdwg-guid@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 theexact
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 thelatter has one failure (5a), while in the former it is just a warning.
Go figure.... Rich ________________________________ From: Paul Kirk [mailto:p.kirk@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 LSIDshttp://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@lists.tdwg.org on behalf ofRichard
Pyle Sent: Wed 28/11/2007 21:52 To: tdwg-guid@lists.tdwg.org Subject: [tdwg-guid] TDWG LSID Resolver broken?
Hi All,I'm testing the ZooBank LSID resolver, and I can't seemto
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, RichRichard 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@bishopmuseum.org http://hbs.bishopmuseum.org/staff/pylerichard.html_______________________________________________ tdwg-guid mailing list tdwg-guid@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-guidP Think Green - don't print this email unless you reallyneed to
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_______________________________________________ tdwg-guid mailing list tdwg-guid@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@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@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@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