[Taxacom] accepted names using the uBio web services?

Roderic Page r.page at bio.gla.ac.uk
Thu Jun 19 03:55:21 CDT 2008


Dear Ken-ichi,

On 18 Jun 2008, at 17:01, Ken-ichi Ueda wrote:

> 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.

The gla and ubio predicates date from early efforts to assign LSIDs to  
taxonomic names. My now defunct Taxonomic Search Engine (see http://dx.doi.org/10.1186/1471-2105-6-48 
  ) assigned LSIDs to names served by several name servers. I order to  
do this I developed a simple vocabulary ("gla"). You can get some  
basic information about each gla predicate by resolving the  
corresponding LSID. For example, gla:rank is urn:lsid:lsid.zoology.gla.ac.uk:predicates:rank 
. Put this into your resolver of choice and you will get a RDF  
document describing the term. There's also some background in my 2006  
paper http://jbi.nhm.ku.edu/index.php/jbi/article/viewArticle/25 .

When uBio started serving LSIDs they used my vocabulary for some  
terms, and added their own. Simililary, you can get RDF for any uBio  
predicate by resolving the corresponding LSID "urn:lsid:ubio.org:predicates 
:" + the predicate, e.g. urn:lsid:ubio.org:predicates:hasSYNConcept .

My vocabulary, and that of uBio were develpped before TDWG developed  
their own (http://wiki.tdwg.org/twiki/bin/view/TAG/LsidVocs ), which  
IMHO are rather more verbose than they need to be.


>
>
> 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.

I'm sure lots of us would kill for such a service, although as Geoff  
Read pointed out, there are complications. Making a service that  
summarised uBio's information would get us part of the way there.

Regards

Rod





>
>
> -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
>>>>
>>>> _______________________________________________
>>>> Taxacom mailing list
>>>> Taxacom at mailman.nhm.ku.edu
>>>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>>>> ************************************************************************
>>>> The information contained in this e-mail and any files  
>>>> transmitted with
>>>> it is confidential and is for the exclusive use of the intended  
>>>> recipient.
>>>> If you are not the intended recipient please note that any  
>>>> distribution,
>>>> copying or use of this communication or the information in it is  
>>>> prohibited.
>>>>
>>>> Whilst CAB International trading as CABI takes steps to prevent the
>>>> transmission of viruses via e-mail, we cannot guarantee that any  
>>>> e-mail or
>>>> attachment is free from computer viruses and you are strongly  
>>>> advised to
>>>> undertake your own anti-virus precautions.
>>>>
>>>> If you have received this communication in error, please notify  
>>>> us by
>>>> e-mail at cabi at cabi.org or by telephone on +44 (0)1491 829199 and  
>>>> then
>>>> delete the e-mail and any copies of it.
>>>>
>>>> CABI is an International Organization recognised by the UK  
>>>> Government
>>>> under Statutory Instrument 1982 No. 1071.
>>>>
>>>>
>>>> **************************************************************************
>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Taxacom mailing list
>>> Taxacom at mailman.nhm.ku.edu
>>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>>>
>>
>> ---------------------------------------------------------
>> 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
>> http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>>
>>
>>
>>
>>
>>
>

---------------------------------------------------------
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
http://taxonomy.zoology.gla.ac.uk/rod/rod.html







---------------------------------------------------------
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
http://taxonomy.zoology.gla.ac.uk/rod/rod.html








More information about the Taxacom mailing list