[tdwg-content] synonyms in DwC Archives

Wed Mar 19 15:26:04 CET 2014

On Wed, Mar 19, 2014 at 5:35 AM, Markus Döring <m.doering at mac.com> wrote:

> Hilmar,
>
> to include synonyms in the core file they technically do not have to have
> ids on their own.

How would you recommend I do this then, i.e., which column header should be
used for that? (I'm assuming you are not requiring that I make up IDs,
which to me seems a non-starter, see below.)

Said that there is the desire in dwc archives though to require an
> identifier for a record, see last years occurrenceID discussion. The best
> would be if you could make up some identifier, for example by adding a
> -synX suffix to the accepted taxonID or even just using the name alone if
> its known to be unique within your dataset.

It is not necessarily unique. And making up identifiers can lead to all
kinds of awkward problems downstream (how do consuming applications
distinguish real identifiers that can be linked to and/resolved from those
that are simply hacks and otherwise bogus), so I agree it's possibility but
it strikes me as a last resort; we ought to be able to do better than that.

> Using an extension for synonyms would probably be useful and feel natural
> for many datasets, but I am concerned we introduce more and more
> alternative ways of expressing the same kind of data and that becomes a
> huge burden on the consumer side.
>

I share that concern in principle. However, DwCA made a deliberate choice
to flatten out its core taxon table and force a 1:1 relationship between
row and <taxon or whatever other designated type> record. Since there may
be multiple synonyms for a taxon, of different types, I'm not sure how you
would do this in the core table unless you mint an identifier for each one
that doesn't have one from the nomenclator, and cast all records into type
Taxon, whether that's what they are or not.

All - to come back to my original question, I fully agree with the concerns
re: proper treatment of synonyms for nomenclatural applications. But we
also shouldn't forget that there's a wide area of application for
taxonomies as an informatics tool, to discover and connect data linked to
taxon. One of the key requirements for such applications when finding data
by taxon is to find it by all names that were or are being potentially used
to label the taxon, including basionyms, invalid names, misspellings,
vernacular names. This may turn up false positives, and I agree the more
provenance one has for the synonyms the better the ability to weed those
out subsequently. But having an extensive list of synonyms is still
critical, even if all one can say is that it's "related". Having a rich set
of synonyms was one of the driving use-cases for synthesizing the
Vertebrate Taxonomy Ontology [1] (and it's predecessor, the Teleost
Taxonomy Ontology); it was enough of a pain that we would have gladly used
an existing nomenclator's taxonomy.

What has brought me to this in the first place is the use-case of taxonomy
synthesis, and the recognition that not only have we not managed in 300
years to converge on a universal taxonomy, also there is no generally
accepted format for exchanging taxonomies. There are several dozens of
taxonomies each of which comes in its own idiosyncratic format, often
enough a straight database dump. Perhaps there's an opportunity here for
the community as a whole to converge on DwCA as a universal taxonomy
exchange format. I was going to write up some thoughts on that as a blog
post; hopefully I get to that over the next few days, as I think we're
really not far away in terms of what's missing.

   -hilmar

[1] Midford, Peter, Thomas Dececchi, James Balhoff, Wasila Dahdul, Nizar
Ibrahim, Hilmar Lapp, John Lundberg, et al. 2013. "The Vertebrate Taxonomy
Ontology: A Framework for Reasoning across Model Organism and Species
Phenotypes." *Journal of Biomedical Semantics* 4 (1): 34.
http://dx.doi.org/10.1186/2041-1480-4-34

>
>
> Here are links to the documents I mentioned before:
>
>   Publishing Species Checklists, Best Practices
>   http://www.gbif.org/resources/2548
>
>   GBIF GNA Profile Reference Guide for Darwin Core Archive, Core Terms and
> Extensions:
>   http://www.gbif.org/resources/2562
>
>
> The GBIF documents are from 2011 and likely in need for some update in
> specific areas, but they still provide a good overview and lots of details.
>
> In addition there is a Catalog of Life document that I cannot find online
> anymore so I have uploaded the last version I have here:
>   i4Life Darwin Core Archive Profile
>
> https://dl.dropboxusercontent.com/u/457027/ChecklistExchangeFormat-v1.6.pdf
>
>
> Markus
>
>
>
> > 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.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
> >>
> >>
> >>
> >> _______________________________________________
> >>
> >> tdwg-content mailing list
> >> tdwg-content at lists.tdwg.org
> >> http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >
> >
> >
> > --
> > Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io
> >
>
>

-- 
Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io
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