[tdwg-content] synonyms in DwC Archives

[Hilmar Lapp]

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<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.xmldoesn'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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