[tdwg-content] most GUIDs/URIs for names/taxon stuff not ready for prime time
steve.baskauf at vanderbilt.edu
Thu Jan 6 16:10:41 CET 2011
A quick comment about ubio.org's LSID resolution: I took a look at the
complete RDF source and noticed that the namespace declarations for
"ubi:" and "gla:" don't start with "http://". I'm pretty sure that
isn't kosher RDF, although neither of the RDF validators complained
about it (doesn't give me much confidence in RDF validators). So much
for being overly optimistic about there being one source that worked
I should say that I'm not an advocate of LSIDs. I actually don't like
them at all. I simply investigated them in this context as something
that might work in a Linked Data context. I should also say that I'm
not necessarily an advocate of Linked Data - I'm in the "wait and see"
camp. I'd like to give it a chance but I'm not betting the store on
it. I AM an advocate of having identifiers that are persistent and
globally unique and it appears that both Catalog of Life and IPNI (in my
view) flunk the persistence test if you just look at the URI (LSID with
version) as a string (which you SHOULD be able to do) that can be an
unchanging identifier. We desperately need persistent and globally
unique identifiers for a lot of things. If they resolve to RDF/XML then
that's a bonus. We need an Emperor, clothing is somewhat optional.
A few specific responses:
Roderic Page wrote:
> These issues won't go away simply by replacing LSIDs with HTTP URIs.
> Some of the linked data sources go belly up fairly regularly (notably http://bio2rdf.org
The reason I see HTTP URIs [capable of producing either HTML or RDF/XML
through content negotiation] as something of greater value than LSIDs is
that people can at a minimum get a web page out of it. That's the
cake. If some people can also use them to get RDF for the Linked Data
dream, that's the icing. The fact that HTTP URI GUIDs fail to "work" is
similar to the fact that regular web URLs fail to work. That doesn't
stop people from using the web and it shouldn't stop well designed (i.e.
http://www.w3.org/TR/cooluris/ and http://www.w3.org/Provider/Style/URI)
URIs from being used as GUIDs.
> IPNI supports versioning of LSIDs, but the LSID without the version is
> also valid (it resolves to the latest version). I think this is a
> perfectly valid thing to do. Versioning matters to some, but not
> everyone cares about it, IPNI supports both views. If you want to cite
> a specific version, do so, if not, don't.
OK, I guess as long as people can just leave the version off if they
want, they'll get unchanging strings for their identifiers and so I
guess that moves them into the "usable" column. But as far as I'm
concerned, putting the versions on adds to the confusion. If I can say
this without launching an unnecessary thread about the opacity of GUIDs,
nobody is supposed to be looking at any GUID itself to infer meaning
about the identified object. That "no-no" seems to be exactly what
Catalog of Life and IPNI seem to be suggesting that people do with the
LSID version numbers they are tacking on. Get rid of them.
> The data/metadata distinction is a complete red herring and has side-
> tracked more LSID conversations than I care to remember. The
> distinction stems from LSIDs originally being conceived as identifiers
> for large data objects (e.g., sequences, images, binary streams) that
> people want accurately versioned so that could reproduce digital
> experiments. In this scenario, metadata can change because it's not
> what mattered for this reproducibility. Some people think of data
> about taxonomic names as "metadata", and then we're off on a wild
> goose chase about should LSIDs change when metadata changes. I
> wouldn't loose any sleep over this (see discussion of IPNI above).
Agreed. The important thing is that the identifier for a certain
"thing" (however the "thing" is defined) should not change. I have
previously expressed the opinion that it won't really work to have any
URI (sensu Linked Data) point to "data" and that all URIs serving as
GUIDs should be considered to reference non-information resources (which
by definition have only "metadata"). Under that scenario, all resource
properties are "metadata" and subject to change. The data vs. metadata
argument then becomes irrelevant.
> Regarding DOIs for books, these are uncommon, although there are moves
> to express ISBNs within the DOI framework, so there may be more of
> these. But for a DOI to exist someone has to claim ownership of a
> resource and register the DOI with CrossRef. For a lot of older
> literature there won't be a publisher around to do this, but that's
> where BHL comes in.
Then PLEASE BHL, create simple, unchanging URIs [suitable for use in the
Linked Data world] to identify your resources. If you don't want to
provide RDF/XML, that's fine for now. You can wait and see if that is
necessary later. But at least create URIs that COULD be used for Linked
Data in the future and that are not long and loaded with "?" and "&"
characters. I don't know how to do that because I'm not a server dude.
But it apparently isn't that hard to do with a mod rewrite. I know
there are at least three people (probably more) on this list who do that
routinely - Rod does it with his bioguid.info site (i.e. "cool" URI
http://bioguid.info/doi:10.1093/bib/bbn022 gets written into "ugly" URL
http://bioguid.info/openurl.php?id=doi:10.1093/bib/bbn022 but nobody
cares as long as the "cool" URI doesn't change).
My two cents worth...
> In summary, we're in a mess, and I don't think this is really down to
> technology. It's a failure of our community to create the appropriate
> resources (e.g., centralised, curated resources of identifiers and
> associated metadata for names, publications, and specimens).
> On 6 Jan 2011, at 05:32, Steve Baskauf wrote:
>> Well, I have continued my quest for resolvable, RDF-producing GUIDs
>> taxon/name-related stuff. I have gotten a lot of good information
>> reading Rod Page's BMC Bioinformatics paper
>> (http://dx.doi.org/10.1186/1471-2105-10-S14-S5) and from investigating
>> his http://bioguid.info/ site.
>> >From the standpoint of the "sec./sensu" part of a TNU/taxon concept,
>> based on the recent discussion, it sounds like the DIO solution for
>> publications is a good direction to go IF resolution services
>> RDF comes into existence and IF it becomes possible to actually search
>> for the DIOs of more obscure publications. I tried using Rod's site
>> look up a journal article using the ISSN, volume, and page and the web
>> interface found the DOI and generated RDF just fine. However, an
>> attempt to use the web to find the DIO of Gleason and Cronquist's
>> of vascular plants of Northeastern United States and adjacent Canada
>> failed despite a half hour of effort (I found the UPC, the LOC call
>> number, and the ISBN, but no DOI). Maybe there just isn't a DOI for
>> but there should be a way for me to know that. So DOIs for books and
>> old journal articles are not really ready for prime time.
>> >From the standpoint of the "scientific name" part of a TNU/taxon
>> concept, I had better luck (sort of). Rod's "Status of biodiversity
>> services" page (http://www.bioguid.info/status/) was really cool. I
>> resources I hadn't known about before. I tried out several of the
>> services that claimed to issue LSIDs.
>> Catalog of Life's LSIDs didn't work with either the
>> http://www.bioguid.info/ or http://lsid.tdwg.org/ proxies with
>> either a
>> web browser or the OpenLink RDF browser. I only got an empty RDF
>> element in response.
>> Index Fungorum was down.
>> IPNI seemed to work. However, I was somewhat appalled to observe that
>> they seem to change the revision identifier any time that they change
>> any part of the metadata. That renders the LSID useless as a
>> GUID for the name and I believe is inconsistent with the design of
>> where the revision is only supposed to change if the underlying data
>> itself (NOT metadata) changes. (Catalog of Life says that they change
>> the revision identifier EACH YEAR for all of their records! That's
>> worse!) If I'm remembering the TDWG LSID recommendations, it is not
>> even recommended to use the revision part of an LSID at all in the
>> biodiversity informatics context.
>> ubio.org's LSIDs seemed to work properly.
>> [sorry - didn't try zoobank since I was looking for plants]
>> I don't know which (if any) of the Web sites listed on Rod's status
>> use generic HTTP URI guids (rather than LSIDs) to refer to taxon
>> I tried out the Global Names index that Pete was mentioning. The URI
>> version of the UUIDs (e.g.
>> do resolve under content negotiation, but the only useful information
>> that the RDF representation seems to provide is the actual name string
>> that was used to generate the UUID. Until some other useful linked
>> information is added to the RDF, there doesn't seem to be much
>> in pointing a semantic client to the URI over just using a string
>> literal for the name.
>> So the bottom line is that of the LSID services for names that I've
>> tried so far, only ubio.org seems to have LSIDs for names that are
>> unchanging, can work as a proxied URI, and that produce actual useful
>> RDF. That's pretty disappointing given the apparently huge amount of
>> work that's been put into building these various systems.
>> Steven J. Baskauf, Ph.D., Senior Lecturer
>> Vanderbilt University Dept. of Biological Sciences
>> postal mail address:
>> VU Station B 351634
>> Nashville, TN 37235-1634, U.S.A.
>> delivery address:
>> 2125 Stevenson Center
>> 1161 21st Ave., S.
>> Nashville, TN 37235
>> office: 2128 Stevenson Center
>> phone: (615) 343-4582, fax: (615) 343-6707
>> tdwg-content mailing list
>> tdwg-content at lists.tdwg.org
> Roderic Page
> Professor of Taxonomy
> Institute of Biodiversity, Animal Health and Comparative Medicine
> College of Medical, Veterinary and Life Sciences
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
> Email: r.page at bio.gla.ac.uk
> Tel: +44 141 330 4778
> Fax: +44 141 330 2792
> AIM: rodpage1962 at aim.com
> Facebook: http://www.facebook.com/profile.php?id=1112517192
> Twitter: http://twitter.com/rdmpage
> Blog: http://iphylo.blogspot.com
> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
VU Station B 351634
Nashville, TN 37235-1634, U.S.A.
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 343-6707
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