[tdwg-content] synonyms in DwC Archives

Wed Mar 19 12:39:22 CET 2014

Historical Darwin Core interjection. The term taxonID was not changed
because it is the ID referring to the class of information, which
remained "Taxon". For both consistency (a rule that every class should
have an associated identifier term with the lower camel case name of
the class followed by 'ID') and for the sake of inertia (not creating
undue burden for backward compatibility), the term name taxonID was
retained.

On Wed, Mar 19, 2014 at 2:40 AM, Markus Döring <m.doering at mac.com> wrote:
> Rod,
>
> Darwin Core deliberately uses the terminology NameUsage to refer to flat
> name OR taxon records.
> I was in favor of also replace dwc:taxonID with dwc:nameUsageID to achieve
> some consistency and be clear about what we are talking about, but we
> sticked to taxonID for reasons I cannot remember.
>
> Markus
>
>
> On 19 Mar 2014, at 06:37, Roderic Page <Roderic.Page at glasgow.ac.uk> wrote:
>
> Hi Hilmar,
>
> I think the phrase "simply names" summarises part ot the problem here. Many
> taxon databases seem determined to conflate names and taxa, and treat names
> as dumb strings rather than entities of interest (or worse, as taxa, rather
> than names of taxa). Many synonyms are relationships between names (e.g.,
> names that change because we move species to different genera are the "same"
> name), others are relationships between taxa (e.g., this set of things and
> that set of things are the members of the same set of things).
>
> We could model things much more cleanly if we distinguished between taxa and
> names for taxa, and made use of the fact that we have databases of names
> (the nomenclators) that have been serving name data and stable identifiers
> for almost a decade. It is a pity that most taxonomic databases make little
> or no use of this. Map names to those ids, have ids for taxa, and link all
> the names to the taxa to which they've been applied. Instead we have a flat
> Darwin Core with row upon row of things that we call "taxa" but which, in
> many cases, aren't.
>
> I get why we like flat Darwin Core, but sometimes the world isn't flat.
>
> Regards
>
> Rod
>
> On 19 Mar 2014, at 02:44, Hilmar Lapp <hlapp at nescent.org> wrote:
>
> Tony - your example matches pretty much what GBIF does.
>
> John - yes indeed, if using ResourceRelationship terms, it would have to be
> in an extension and not the core taxon file.
>
> Markus and all - yes, I realized after I emailed how GBIF does this. I agree
> that this has advantages. However, this way of doing synonyms requires that
> there is an identifier for the synonym. For the core use-case I'm interested
> in synonyms are metadata of taxon records and do not have their own
> identifier. For example, synonyms in NCBI don't have identifiers, and they
> don't in Catalog of Fishes. (I'm not sure they do in PaleoDB.)
>
> One could of course invent identifiers on behalf of the taxonomy providers
> in these cases, but that's a hack. I think if there is an extension for
> vernacularNames, there ought to be one as well for synonyms that are simply
> names.
>
>    -hilmar
>
>
> On Tue, Mar 18, 2014 at 6:35 PM, Markus Döring <m.doering at mac.com> wrote:
>>
>> Hi Hilmar,
>>
>> GBIF, Catalog of life and others have produced guidelines for how to
>> express taxonomies with synonyms and these are in widespread use already
>> since over a year. I will forward links tomorrow when Im back at my desk.
>>
>> The common idea is to include synonyms together with accepted taxa in the
>> core file. This allows one to also add extension data to synonyms, for
>> example bibliographic references, types data, etc. The term
>> acceptedNameUsageID is used to link to the accepted record in the core file
>> (targeting taxonID), originalNameUsageiD for the basionym and
>> taxonomicStatus to declare a specific type of synonym such as
>> homo/heterotypic or later/junior synonym. The scientificName is used both
>> for accepted and synonym records.
>>
>> You should be able to find many dwca examples in the gbif dataset search
>> when filtered for checklists:
>> http://www.gbif.org/dataset/search?type=CHECKLIST
>>
>> For example try these:
>> http://data.canadensys.net/ipt/archive.do?r=vascan
>> http://ipt.speciesfile.org:8080/archive.do?r=orthoptera
>>
>>
>> Cheers,
>> Markus
>>
>> Am 18.03.2014 um 22:44 schrieb Chuck Miller <Chuck.Miller at mobot.org>:
>>
>> Hilmar,
>>
>> Sticking strictly to Darwin Core and not adding RDF, I think there are a
>> couple of DwC terms that are attributes that can be used to identify a
>> synonym:
>>
>>
>>
>> taxonomicStatus - The status of the use of the scientificName as a label
>> for a taxon. Requires taxonomic opinion to define the scope of a taxon.
>> Rules of priority then are used to define the taxonomic status of the
>> nomenclature contained in that scope, combined with the experts opinion. It
>> must be linked to a specific taxonomic reference that defines the concept.
>> Recommended best practice is to use a controlled vocabulary. Examples:
>> "invalid", "misapplied", "homotypic synonym", "accepted".
>>
>>
>>
>> relationshipofResource - The relationship of the resource identified by
>> relatedResourceID to the subject (optionally identified by the resourceID).
>> Recommended best practice is to use a controlled vocabulary. Examples:
>> "duplicate of", "mother of", "endoparasite of", "host to", "sibling of",
>> "valid synonym of", "located within".
>>
>>
>>
>> There's also acceptedNameUsage and acceptedNameUsageID, which if used
>> infer that the name the terms are associated with is a synonym of the
>> AcceptedName.
>>
>>
>>
>> But, so far there is no guideline for how to organize synonyms in a Darwin
>> Core Archive.  They can be embedded in the core file using
>> relationshiopofResource from a synonym name to an accepted name in the same
>> file.  Or they can be in an extension file, where the extension file may be
>> called Synonyms and thus define a one-to-many "synonym relationship" from
>> the taxonID in the core file to synonym names in the extension file.  There
>> are probably other ways.  RDF adds the ability to be more explicit about the
>> relationships.
>>
>>
>>
>> Rich Pyle has lectured prolifically on this so I'm sure he has good advice
>> to offer.
>>
>>
>>
>> Chuck
>>
>>
>>
>> From: tdwg-content-bounces at lists.tdwg.org
>> [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Hilmar Lapp
>> Sent: Tuesday, March 18, 2014 2:55 PM
>> To: TDWG Content Mailing List
>> Cc: Dan Leehr
>> Subject: [tdwg-content] synonyms in DwC Archives
>>
>>
>>
>> I'm looking for recommendations on how best to put synonyms for taxon
>> records into DwC Archive format.
>>
>>
>>
>> I'm assuming that these would go into an extension file. Do I have this
>> right? What I'm having more trouble with is determining the right column
>> term. there's dwc:vernacularName, which is also in the examples, but what
>> about synonyms of different types that come with taxonomies (such as NCBI's)
>> or that result from merging taxonomies. There isn't an obvious candidate in
>> DwC, and the list at http://rs.gbif.org/core/dwc_taxon.xml doesn't have a
>> suggestion either that would seem pertinent.
>>
>>
>>
>> Any suggestions, pointers to documentation or examples?
>>
>>
>>
>>   -hilmar
>>
>>
>>
>> --
>>
>> Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io
>>
>>
>>
>> _______________________________________________
>>
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>
>
>
>
> --
> Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io
>
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>
> ---------------------------------------------------------
> 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
> Skype:  rdmpage
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> Home page:  http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> Wikipedia:  http://en.wikipedia.org/wiki/Roderic_D._M._Page
> Citations:  http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> ORCID:  http://orcid.org/0000-0002-7101-9767
>
>
>
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