[Taxacom] accepted names using the uBio web services?

Roderic Page r.page at bio.gla.ac.uk
Wed Jun 18 03:56:04 CDT 2008


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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---------------------------------------------------------
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
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