[tdwg-tag] [tdwg-content] Canonical name parsing
Steve Baskauf
steve.baskauf at vanderbilt.edu
Wed Mar 14 22:06:08 CET 2012
I do not have an opinion on this issue but wanted to note that the
TaxonName part of the TDWG Ontology appears to be fully functional.
Given that the TaxonName and TaxonConcept ontologies are based on TCS,
there may be existing terms (based on TCS) with stable URIs to represent
exactly what people want to say. They wouldn't be Darwin Core terms,
but they would be defined and have stable URIs nonetheless. For example,
http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete
which can be abbreviated tn:nameComplete
where tn:=http://rs.tdwg.org/ontology/voc/TaxonName#
is defined as "The complete uninomial, binomial or trinomial name
without any authority or year components."
Thus one could mark up data as
<tn:nameComplete>Homo sapiens</tn:nameComplete>
and theoretically this would have meaning to the extent to which people
take the TDWG Ontology seriously. But that is a different item for
discussion...
Steve
To view the rdf, see:
http://code.google.com/p/tdwg-ontology/source/browse/trunk/ontology/voc/TaxonName.owl
and
http://code.google.com/p/tdwg-ontology/source/browse/trunk/ontology/voc/TaxonConcept.owl
On 3/14/2012 3:15 PM, Kennedy, Jessie wrote:
>
> Peter –you just described what TCS offered….this was all covered in
> the discussion on TCS… (and many more things that have been discussed
> recently)
>
> The guide to using it covers some of the thoughts behind these issues
> I think…
>
> http://www.tdwg.org/fileadmin/subgroups/tnc/User_Guide.pdf
>
> *From:*tdwg-tag-bounces at lists.tdwg.org
> [mailto:tdwg-tag-bounces at lists.tdwg.org] *On Behalf Of *Peter Desmet
> *Sent:* 14 March 2012 20:11
> *To:* Paul Kirk
> *Cc:* TDWG content mailing list; Donald Hobern (GBIF); TDWG TAG
> mailing list; Christian Gendreau; dev Developers
> *Subject:* Re: [tdwg-tag] [tdwg-content] Canonical name parsing
>
> Hi Paul,
>
> Higher taxon: "Magnoliidae Novák ex Takhtajan" (a subclass).
>
> - scientificName: Magnoliidae Novák ex Takhtajan
>
> - taxonRank: subclass
>
> But there are no terms to share the canonical name "Magnoliidae". The
> only available options are kingdom, phylum, class, order, family,
> genus, subgenus, specificEpithet, infraspecificEpithet, none of which
> are appropriate.
>
> Solution:
>
> - canonicalScientificName: Magnoliidae
>
> Infrageneric taxon: "Abies sect. Amabilis (Matzenko) Farjon &
> Rushforth" (a section)
>
> - scientificName: Abies sect. Amabilis (Matzenko) Farjon & Rushforth
>
> - taxonRank: section
>
> - genus: Abies
>
> But there are no terms to share "Abies Amabilis", "Abies sect.
> Amabilis", "Abies section Amabilis" or even "Amabilis". The only
> available options are kingdom, phylum, class, order, family, genus,
> subgenus, specificEpithet, infraspecificEpithet, none of which are
> appropriate. Why we have subgenus, but not *infragenericEpithet* is
> another issue. I would at least be able to share "Amabilis".
>
> Solution:
>
> - canonicalScientificName: Abies Amabilis
>
> - taxonRank: section
>
> Peter
>
> There is no place to share the canonical name "Magnoliidae" for this
> taxon.
>
> On Wed, Mar 14, 2012 at 14:37, Paul Kirk <p.kirk at cabi.org
> <mailto:p.kirk at cabi.org>> wrote:
>
> 'For higher taxa or infrageneric taxa, these terms are not sufficient'
> ... why?
>
> Paul
>
> ------------------------------------------------------------------------
>
> *From:*tdwg-tag-bounces at lists.tdwg.org
> <mailto:tdwg-tag-bounces at lists.tdwg.org>
> [tdwg-tag-bounces at lists.tdwg.org
> <mailto:tdwg-tag-bounces at lists.tdwg.org>] on behalf of Peter Desmet
> [peter.desmet at umontreal.ca <mailto:peter.desmet at umontreal.ca>]
> *Sent:* 14 March 2012 18:26
> *To:* Richard Pyle
> *Cc:* TDWG content mailing list; Donald Hobern (GBIF); dev Developers;
> Christian Gendreau; TDWG TAG mailing list
>
>
> *Subject:* Re: [tdwg-tag] [tdwg-content] Canonical name parsing
>
> Rich,
>
> I wished those terms were sufficient, but as mentioned in the
> justification for
> http://code.google.com/p/darwincore/issues/detail?id=150:
>
> genus, specificEpithet, infraspecificEpithet: concatenated, this terms are identical to the canonicalScientificName for genera, species and infraspecific taxa. For higher taxa or infrageneric taxa, these terms are not sufficient. In addition, there is some ambiguity regarding the genus definition: for synonyms, is it the accepted genus or the genus that is part of the synonym name? See:http://lists.tdwg.org/pipermail/tdwg-content/2010-November/002052.html. In the former case, the genus cannot be used to concatenate a canonicalScientificName.
>
> To give an example for a higher taxon:
>
> scientificName: Magnoliidae Novák ex Takhtajan
>
> taxonRank: subclass
>
> There is no place to share the canonical name "Magnoliidae" for this
> taxon.
>
> Peter
>
> On Wed, Mar 14, 2012 at 14:13, Richard Pyle <deepreef at bishopmuseum.org
> <mailto:deepreef at bishopmuseum.org>> wrote:
>
>
> I guess the parts that confuse me are:
>
> 1) What providers are able to produce a canonicalScientificName as per
> Peter’s definition, but are unable to provide the pre-parsed elements
> of genus | subgenus | specificEpithet | infraspecificEpithet?
>
> 2) What consumers could make use of a canonicalScientificName as per
> Peter’s definition, but are unable to make (even better) use of the
> pre-parsed elements of genus | subgenus | specificEpithet |
> infraspecificEpithet?
>
> Aloha,
> Rich
>
>
>
>
> From: tdwg-content-bounces at lists.tdwg.org
> <mailto:tdwg-content-bounces at lists.tdwg.org>
> [mailto:tdwg-content-bounces at lists.tdwg.org
> <mailto:tdwg-content-bounces at lists.tdwg.org>] On Behalf Of Peter Desmet
> Sent: Wednesday, March 14, 2012 7:03 AM
> To: Donald Hobern (GBIF)
> Cc: TDWG content mailing list; Christian Gendreau; Tim Robertson
> [GBIF]; TDWG TAG mailing list; dev Developers
> Subject: Re: [tdwg-content] Canonical name parsing
>
>
> Hi Donald,
>
> scientificName, with its current definition [1] is a great term and
> should be continued to used as such. As with most Darwin Core terms,
> it offers flexibility, so its not an impediment for publishing data.
> In the GBIF context, this term is considered mandatory: records
> without it are ignored during indexing (I believe). All of this can stay.
>
> canonicalScientificName would be an additional term with a clear rule
> (see my proposed definition [2]). This is the case for other Darwin
> Core terms as well, such as
> decimalLatitude [3], minimalElevationInMeters [4] or countryCode [5].
> They serve as an ready-to-use addition/alternative to verbatimLatitude
> [6], verbatimElevation [7] and country [8] respectively. These terms
> don't stop anyone from publishing data, but data publishers who can
> provide this kind of information have the choice to do so. It would be
> the same for canonicalScientificName.
>
> And yes, an aggregator like GBIF can play an important role in
> providing consistent data to its users and figuring out what they
> really need, but not all data is consumed that way. In addition, I
> hope a user would be able to download cleaned data from the GBIF
> portal as Darwin Core. Wouldn't it be nice that the parsed
> canonicalScientificName created by GBIF can be provided in its proper
> term? There are users out there who want this!
>
> Regards,
>
> Peter
>
> [1] http://rs.tdwg.org/dwc/terms/index.htm#scientificName
> [2] http://code.google.com/p/darwincore/issues/detail?id=150
> [3] http://rs.tdwg.org/dwc/terms/index.htm#decimalLatitude
> [4] http://rs.tdwg.org/dwc/terms/index.htm#minimumElevationInMeters
> [5] http://rs.tdwg.org/dwc/terms/index.htm#countryCode
> [6] http://rs.tdwg.org/dwc/terms/index.htm#verbatimLatitude
> [7] http://rs.tdwg.org/dwc/terms/index.htm#verbatimElevation
> [8] http://rs.tdwg.org/dwc/terms/index.htm#country
>
> On Wed, Mar 14, 2012 at 11:19, Donald Hobern (GBIF) <dhobern at gbif.org
> <mailto:dhobern at gbif.org>> wrote:
> >
> > Hi Peter.
> >
> > I certainly agree that aggregators only represent one use case here
> but, having seen a lot of the mess of real-world data, I don't believe
> that simply adding a new term will fix this problem for the users you
> describe. To get the results you want, we would need a sufficiently
> large majority of data sets to follow the rules perfectly that we
> could ignore those that were non-conformant. This would mean we
> should mandate that every data set must use the new element (with or
> without the existing scientificName element) and that they must
> present scientific names in the expected way (or else have their data
> considered non-compliant). Until now, the philosophy on publishing
> Darwin Core data has been to make it as easy as possible for data
> providers to expose their data, even at the expense of greater
> complexity for consumers. I suspect that we would have a lot less
> data available for use now if we had taken a more stringent approach.
> >
> > In some ways, this proposal reminds me of the structures in ABCD
> which seek to offer users verbatim and more normalised ways to
> represent several types of information. This actually makes consuming
> all the possible forms of such data very complex, since a record may
> contain all variant forms or just any one of them. If multiple forms
> are available, which one should be considered the primary version?
> >
> > I suspect that things may also get complicated as soon as you
> discuss botanical subspecies, varieties, subvarieties, forms and
> subforms. There are recommended ways to abbreviate the rank markers
> in these cases but some variation can be expected.
> >
> > Of course aggregators should be providing more robust services for
> accessing exactly what you want in a consistent, predictable way and I
> would suggest that the best place to attack the problem is to define
> exactly what a typical user needs to see and then for GBIF and similar
> projects to work on delivering predictable data downloads and web
> services that clean out all of these nomenclatural inconsistencies -
> and perhaps also add value in other ways such as augmenting the data
> with associated environmental values (as the Atlas of Living Australia
> does). This would allow us all to work together on developing a
> consistent and predictable algorithm for handling interpretation of
> name strings, including synonymy, misspellings, virus names and
> everything else that makes this such a difficult problem.
> >
> > Best wishes,
> >
> > Donald
> >
> > ----------------------------------------------------------------------
> > Donald Hobern - GBIF Director - dhobern at gbif.org
> <mailto:dhobern at gbif.org>
> > Global Biodiversity Information Facility http://www.gbif.org/
> > GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
> > Tel: +45 3532 1471 <tel:%2B45%203532%201471> Mob: +45 2875 1471
> <tel:%2B45%202875%201471> Fax: +45 2875 1480 <tel:%2B45%202875%201480>
> > ----------------------------------------------------------------------
> >
> >
> > -----Original Message-----
> > From: peter.desmet.cubc at gmail.com
> <mailto:peter.desmet.cubc at gmail.com>
> [mailto:peter.desmet.cubc at gmail.com
> <mailto:peter.desmet.cubc at gmail.com>] On Behalf Of Peter Desmet
> > Sent: Wednesday, March 14, 2012 3:41 PM
> > To: Tim Robertson [GBIF]
> > Cc: Donald Hobern (GBIF); dev Developers; TDWG content mailing list;
> TDWG TAG mailing list; Christian Gendreau
> > Subject: Re: Canonical name parsing
> >
> > Hi Tim,
> >
> > I agree, aggregators like GBIF and Canadensys will have to deal with
> clean and dirty data in each field anyway: they need code libraries to
> deal with this and it is good that these are being developed. But,
> that doesn't help someone who wants to use data from a Darwin Core
> Archive with his data in Excel or a Roderic Page who wants to get
> things done for a prototype.
> > Having to use Java libraries or even the Name Parser [1] (though both
> > great) is a barrier to data use. Darwin Core (Archives) is not only
> used for machine to machine interaction, humans use it too, and I
> think we should allow easy hacking (I mean this in the good sense),
> especially for something as important as the scientific name.
> > In addition, as a data publisher (e.g. for our VASCAN checklist) I
> > *do* have the information to provide a clean and simple to use
> canonicalScientificName, but I just can't share it via the otherwise
> excellent biodiversity sharing standard Darwin Core. I think that's a
> pity.
> >
> > Peter
> >
> > [1] http://tools.gbif.org/nameparser/
> > [2] http://data.canadensys.net/vascan
> >
> > PS: Yes, Canadensys will use the GBIF interpretation libraries.
> Since we develop in Java as well, using those libraries is as easy as
> the proverbial "one line of code". We're looking forward in testing
> them and providing patches to enhance them. Open source FTW! :-)
> >
> >
> > On Wed, Mar 14, 2012 at 07:32, Tim Robertson [GBIF]
> <trobertson at gbif.org <mailto:trobertson at gbif.org>> wrote:
> > > Hi Peter,
> > >
> > > I'm replying off the TDWG list, since it is a bit of a tangent to
> your discussion. If you feel it is relevant, please CC the list again.
> > >
> > > At GBIF as you know, we have to interpret all kinds of quality of
> content. I tend to agree with Donald that this would not really help
> in consumption, as in my experience we will have to deal with both
> clean and dirty data in each field *anyway* when this is used at
> network scale. I would rather see us evolve the interpretation
> libraries to handle all the corner cases, which we need to develop
> anyway. We already do a pretty decent job at extracting canonicals.
> This is further enhanced when you couple the extracted canonical with
> a fuzzy match against the "authoritative names" we can now index
> thanks to the availability of checklists in DwC-A format.
> > >
> > > I know you are a Java shop. Are you using the GBIF interpretation
> libraries [1] at the moment? If not, is there a reason why you don't?
> > > They are used in all GBIF projects (portal, checklistbank etc),
> and the more we enhance them, the better it is for everyone. We have
> a significant test coverage [2,3] and there have been quite some man
> months (years?) spent already in their development and with some real
> regular expression experts (most notably Markus D. and Dave M.). All
> our work is Maven-ized, versioned and available in our Maven
> repository [4].
> > >
> > > I hope these are interesting to you. We would welcome any patches
> to enhance them, or assistance in identifying the corner cases and
> capturing those as unit tests.
> > >
> > > Hope this helps,
> > > Tim
> > >
> > > [1]
> > > http://code.google.com/p/gbif-ecat/source/browse/trunk/ecat-common/src
> > > /main/java/org/gbif/ecat/parser/NameParser.java
> > > [2]
> > > http://code.google.com/p/gbif-ecat/source/browse/trunk/ecat-common/src
> > > /test/java/org/gbif/ecat/parser/NameParserTest.java
> > > [3]
> > > http://code.google.com/p/gbif-ecat/source/browse/trunk/ecat-common/src
> > > /#src%2Ftest%2Fresources [4]
> > >
> http://repository.gbif.org/index.html#nexus-search;quick~ecat-common
> <http://repository.gbif.org/index.html#nexus-search;quick%7Eecat-common>
> > >
> >
> >
> >
> > --
> > Peter Desmet
> > Biodiversity Informatics Manager
> > Canadensys - www.canadensys.net <http://www.canadensys.net>
> >
> > Université de Montréal Biodiversity Centre
> > 4101 rue Sherbrooke est
> > Montreal, QC, H1X2B2
> > Canada
> >
> > Phone: 514-343-6111 #82354 <tel:514-343-6111%20%2382354>
> > Fax: 514-343-2288 <tel:514-343-2288>
> > Email: peter.desmet at umontreal.ca <mailto:peter.desmet at umontreal.ca>
> / peter.desmet.cubc at gmail.com <mailto:peter.desmet.cubc at gmail.com>
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> >
> >
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>
>
>
> --
> Peter Desmet
> Biodiversity Informatics Manager
> Canadensys - www.canadensys.net <http://www.canadensys.net>
>
> Université de Montréal Biodiversity Centre
> 4101 rue Sherbrooke est
> Montreal, QC, H1X2B2
> Canada
>
> Phone: 514-343-6111 #82354 <tel:514-343-6111%20%2382354>
> Fax: 514-343-2288 <tel:514-343-2288>
> Email: peter.desmet at umontreal.ca <mailto:peter.desmet at umontreal.ca> /
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> Peter Desmet
> Biodiversity Informatics Manager
> Canadensys - www.canadensys.net <http://www.canadensys.net>
>
> Université de Montréal Biodiversity Centre
> 4101 rue Sherbrooke est
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> --
> Peter Desmet
> Biodiversity Informatics Manager
> Canadensys - www.canadensys.net <http://www.canadensys.net>
>
> Université de Montréal Biodiversity Centre
> 4101 rue Sherbrooke est
> Montreal, QC, H1X2B2
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