[Taxacom] accepted names using the uBio web services?

Ken-ichi Ueda kueda at ischool.berkeley.edu
Wed Jun 18 11:01:02 CDT 2008


Wow, that's awesome Rod, probably exactly what I want.  Does the
<ubio:hasSYNConcept> entity always reference an accepted name, or can
it reference any synonymous concept, accepted or otherwise?  I'm
having trouble finding the docs for the ubio and gla predicates used
in those RDFs.

It would be a little more convenient if there was  a service like the
one you described, in which you send a namebank ID and a
classification ID and it returns an accepted name, as it would save us
a call (right now it's three: namebank search for the ID, namebank
LSID for the available synonyms and classification IDs, and then
classification LSID for the accepted name).  The ultimate service for
our needs would probably be a name search with the option of including
the all the accepted synonyms in all the classifications, or perhaps
in a subset of classifications specified in the request, so we could
just make one call.

-Ken-ichi


On Wed, Jun 18, 2008 at 1:56 AM, Roderic Page <r.page at bio.gla.ac.uk> wrote:
> Dear Ken,
>
> I encountered a similar issue when doing some work on ants a while back (see
> http://semant.blogspot.com/2006_06_01_archive.html ).
>
> If you look at the metadata associated with a uBio name (accessible using
> their LSIDs, for example by sticking
> http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org: in front
> of, say, namebank:655121, or using a LSID resolver such as
> http://linnaeus.zoology.gla.ac.uk/~rpage/lsid/ or http://lsid.tdwg.org/ )
> you can make the links you need.
>
> For example, http://www.ubio.org/browser/details.php?namebankID=655121 gives
> you
> ============================
> <?xml version="1.0" encoding="utf-8"?>
>        <rdf:RDF
>            xmlns:dc="http://purl.org/dc/elements/1.1/"
>            xmlns:dcterms="http://purl.org/dc/terms/"
>            xmlns:ubio="urn:lsid:ubio.org:predicates:"
>            xmlns:gla="urn:lsid:lsid.zoology.gla.ac.uk:predicates:"
>            xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
>
>                <rdf:Description
> rdf:about="urn:lsid:ubio.org:namebank:655121">
>
>  <dc:identifier>urn:lsid:ubio.org:namebank:655121</dc:identifier>
>                        <dc:creator rdf:resource="http://www.ubio.org"/>
>                        <dc:subject>Hyla crucifer (Wied-Neuwied,
> 1838)</dc:subject>
>                        <ubio:taxonomicGroup>Amphibia</ubio:taxonomicGroup>
>                        <ubio:recordVersion>7</ubio:recordVersion>
>                        <ubio:canonicalName>Hyla
> crucifer</ubio:canonicalName>
>                        <dc:title>Hyla crucifer</dc:title>
>                        <dc:type>Scientific Name</dc:type>
>                        <ubio:lexicalStatus>Unknown
> (Default)</ubio:lexicalStatus>
>                        <gla:rank>Species</gla:rank>
>                        <gla:mapping
> rdf:resource="http://www.cbif.gc.ca/pls/itisca/next?v_tsn=173500&taxa=&p_format=&p_ifx=cbif&p_lang="/>
>                        <ubio:lexicalVariant
> rdf:resource="urn:lsid:ubio.org:namebank:2812644"/>
>                        <gla:objectiveSynonym
> rdf:resource="urn:lsid:ubio.org:namebank:2812644"/>
>                        <ubio:hasSYNConcept
> rdf:resource="urn:lsid:ubio.org:classificationbank:1390223"/>
>                        <ubio:hasSYNConcept
> rdf:resource="urn:lsid:ubio.org:classificationbank:1646257"/>
>                        <ubio:hasSYNConcept
> rdf:resource="urn:lsid:ubio.org:classificationbank:1871546"/>
>                        <ubio:hasSYNConcept
> rdf:resource="urn:lsid:ubio.org:classificationbank:2207108"/>
>                </rdf:Description>
>        </rdf:RDF>
> ============================
> If you then resolve any of the ubio:hasSYNConcept relationships, you will
> get this how that classification handles this name. For example,
>  http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:classificationbank:1390223 gives
> you
> ============================
> <?xml version="1.0" encoding="utf-8"?>
> <rdf:RDF
>            xmlns:dc="http://purl.org/dc/elements/1.1/"
>            xmlns:dcterms="http://purl.org/dc/terms/"
>            xmlns:ubio="urn:lsid:ubio.org:predicates:"
>            xmlns:gla="urn:lsid:lsid.zoology.gla.ac.uk:predicates:"
>            xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
>
>                <rdf:Description
> rdf:about="urn:lsid:ubio.org:classificationbank:1390223">
>
>  <dc:identifier>urn:lsid:ubio.org:classificationbank:1390223</dc:identifier>
>                        <ubio:namebankIdentifier
> rdf:resource="urn:lsid:ubio.org:namebank:26067"/>
>                        <dc:creator rdf:resource="http://www.ubio.org"/>
>                        <dc:title>Pseudacris crucifer (Wied-Neuwied,
> 1839)</dc:title>
>        <ubio:classificationName>Integrated Taxonomic Information System ITIS
> (Aug. 10 2003)</ubio:classificationName>
> <ubio:classificationDescription><![CDATA[This compilation was transcribed
> from the monthly  (Aug, 10, 2003)<A
> href=http://www.itis.usda.gov/ftp_download.html>ITIS export file</A>.
>  Automated and manual parsing tools map ITIS data elements to uBio
> identifiers.   Refer to <A href=http://www.itis.usda.gov/>ITIS</A> for an
> authoritative version of these data.]]></ubio:classificationDescription>
> <gla:rank>Species</gla:rank>
> <ubio:canonicalName>Pseudacris crucifer</ubio:canonicalName>
> <gla:synonym rdf:resource="urn:lsid:ubio.org:namebank:655121"/><gla:synonym
> rdf:resource="urn:lsid:ubio.org:namebank:655245"/><gla:synonym
> rdf:resource="urn:lsid:ubio.org:namebank:655122"/><ubio:hasChild
> rdf:resource="urn:lsid:ubio.org:classificationbank:1390224"/>
> <ubio:hasChild rdf:resource="urn:lsid:ubio.org:classificationbank:1390225"/>
> <gla:parent rdf:resource="urn:lsid:ubio.org:classificationbank:1363678"/>
> <gla:lineage>
> <rdf:Seq>
> <rdf:li rdf:resource="urn:lsid:ubio.org:classificationbank:1363678"/>
> <rdf:li rdf:resource="urn:lsid:ubio.org:classificationbank:1363660"/>
> <rdf:li rdf:resource="urn:lsid:ubio.org:classificationbank:1363592"/>
> <rdf:li rdf:resource="urn:lsid:ubio.org:classificationbank:1363591"/>
> <rdf:li rdf:resource="urn:lsid:ubio.org:classificationbank:1446436"/>
> <rdf:li rdf:resource="urn:lsid:ubio.org:classificationbank:1363590"/>
> <rdf:li rdf:resource="urn:lsid:ubio.org:classificationbank:1391664"/>
> <rdf:li rdf:resource="urn:lsid:ubio.org:classificationbank:1351740"/>
> <rdf:li rdf:resource="urn:lsid:ubio.org:classificationbank:1477061"/>
> <rdf:li rdf:resource="urn:lsid:ubio.org:classificationbank:2344772"/>
> </rdf:Seq>
> </gla:lineage>          </rdf:Description>
>        </rdf:RDF>
> ============================
> This is Pseudacris crucifer in the ITIS classification for August 10, 2003.
> The other classifications are different versions of ITIS, and one for
> Sp2000.
> If the name doesn't have a link to a classification, you may need to resolve
> the links, such as gla:objectiveSynonym. For example,
> http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:2812644 resolves
> to:
> ============================
> <?xml version="1.0" encoding="utf-8"?>
>        <rdf:RDF
>            xmlns:dc="http://purl.org/dc/elements/1.1/"
>            xmlns:dcterms="http://purl.org/dc/terms/"
>            xmlns:ubio="urn:lsid:ubio.org:predicates:"
>            xmlns:gla="urn:lsid:lsid.zoology.gla.ac.uk:predicates:"
>            xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
>
>                <rdf:Description
> rdf:about="urn:lsid:ubio.org:namebank:2812644">
>
>  <dc:identifier>urn:lsid:ubio.org:namebank:2812644</dc:identifier>
>                        <dc:creator rdf:resource="http://www.ubio.org"/>
>                        <dc:subject>Hyla crucifer</dc:subject>
>                        <ubio:taxonomicGroup>Amphibia</ubio:taxonomicGroup>
>                        <ubio:recordVersion>0</ubio:recordVersion>
>                        <ubio:canonicalName>Hyla
> crucifer</ubio:canonicalName>
>                        <dc:title>Hyla crucifer</dc:title>
>                        <dc:type>Scientific Name</dc:type>
>                        <ubio:lexicalStatus>Canonical
> form</ubio:lexicalStatus>
>                        <gla:rank>Species</gla:rank>
>                        <ubio:lexicalVariant
> rdf:resource="urn:lsid:ubio.org:namebank:655121"/>
>                        <gla:objectiveSynonym
> rdf:resource="urn:lsid:ubio.org:namebank:655121"/>
>                </rdf:Description>
>        </rdf:RDF>
>
> ============================
> Note the <gla:objectiveSynonym
> rdf:resource="urn:lsid:ubio.org:namebank:655121"/>. This is the name we've
> already looked at, so you'd go from 2812644 to 655121, and then to the
> classification of your choice.
> Hope this helps.
> I guess what would be useful is to have a web service that, for a given
> classification in uBio, returns the accepted name. Is this what you want? If
> so, I could look at writing one.
> Regards
>
> Rod
>
> On 18 Jun 2008, at 09:02, Ken-ichi Ueda wrote:
>
>> Thanks, Paul.  I've actually been using Catalogue of Life and it's
>> wonderful for this very reason ... but uBio has way, way more names,
>> especially common names, which are especially important for my
>> project, which is targeted at amateur naturalists (check out
>> www.inaturalist.org if you're curious).
>>
>> Are there other name services (with web services) that have have
>> accepted status AND have coverage anywhere close to uBio?
>>
>> -Ken-ichi
>>
>>
>> On Wed, Jun 18, 2008 at 12:50 AM, Paul Kirk <p.kirk at cabi.org> wrote:
>>>
>>> your best bet would be the Catalogue of Life ... but not all AVC
>>> (Accepted, Valid, Correct) names have all the nomenclatural (homotypic,
>>> 'whatever then word is in ICZN speak') names included. I did not check
>>> this name.
>>>
>>> Cheers,
>>>
>>> Paul
>>>
>>> -----Original Message-----
>>> From: taxacom-bounces at mailman.nhm.ku.edu
>>> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Ken-ichi Ueda
>>> Sent: 18 June 2008 08:29
>>> To: taxacom
>>> Subject: [Taxacom] accepted names using the uBio web services?
>>>
>>> Hi all,
>>>
>>> Is there a way to get the currently accepted name of an outdated taxon
>>> name using the uBio web services?
>>>
>>> For example, if I call namebank_search for "Hyla crucifer," an outdated
>>> scientific name of Pseudacris crucifer (Spring Peeper, a frog from the
>>> eastern US), I get several namebank objects back at the species level:
>>> 2812644, 6805040, 655121, and 4827754. Calling namebank_object on each
>>> of these returns lots of data about the names, but nothing I can see
>>> that indicates a link to the accepted name, Pseudacris crucifer. Looking
>>> at these IDs on the website (say,
>>> http://www.ubio.org/browser/details.php?namebankID=655121), it seems
>>> that uBio can make that link, at least in the classification. The
>>> results from classificationbank_search and classificationbank_object
>>> didn't seem to provide any connections to an accepted name either.
>>>
>>> So, can anyone recommend a way to get at name status using the uBio web
>>> services?  Am I missing something, or is this just not possible?
>>>
>>> My apologies if this is too technical (or perhaps too simple!) for this
>>> list.  If there's a more code-oriented biodiversity informatics list
>>> somewhere, please let me know.
>>>
>>> -Ken-ichi
>>>
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>>
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>
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> DEEB, FBLS
> 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
>
> http://iphylo.blogspot.com
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>
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