[tdwg-content] Taxonomic name usage files

Wed Apr 20 20:33:03 CEST 2016

Thanks, Terry; and agreed!

I’ll claim full-credit for the over-verbosity.  But when it comes to taxon names, and how to structure the information appropriately, I’ve tried every strategy for communicating from super-thin to super-verbose (the recent thread epitomizing the latter); and on balance, none of them are effective because there is SO MUCH noise out there in terminology, and concepts of concepts, and such.  It’s a perpetual uphill battle. My hope is that, in this case, the information was decipherable to primary audience (Nico).

Now… on the topic of uphill battles… we had some great conversations in Florence and Jönköping on how to improve TaxPub to capture the core elements of TNUs (both Protonyms and subsequent usages); but I’m not sure we ever got anywhere.  However, given the recent (excellent) progress with the PLAZI workflow, and some other things that are happening later this year in GNUB-space; perhaps it’s time to revisit those conversations, in the context of Nico’s original question, and hammer-out a functional solution (or, if not a “solution”, at least a quantum step forward).  

Aloha,

Rich

From: Terry Catapano [mailto:catapanoth at gmail.com] 
Sent: Wednesday, April 20, 2016 1:30 AM
To: Donat Agosti
Cc: tdwg-content at lists.tdwg.org; vocab at noreply.github.com; Michael Rosenberg (Faculty); Chuck Miller (Chuck.Miller at mobot.org); Robert Guralnick; Nico Franz; deepreef at bishopmuseum.org
Subject: Re: [tdwg-content] Taxonomic name usage files

Donat,

Where did Chuck ask about TaxonX? I'd like to see what the specific question is.

In general, it's more effective to clearly and briefly describe *what* we do and *why* and to not discuss what we *dont* currently do, or plan on doing. There is danger to credibility in sustained over-promising.

As is evidenced by the verbosity of this thread, there is an even greater danger to communication in over-writing.

On Wed, Apr 20, 2016 at 6:13 AM, Donat Agosti <agosti at amnh.org> wrote:

I am trying to answer two questions in this tread.

Taxonx.

Chuck asked about TaxonX. We are moving away from TaxonX to use an archival version of TaxPuB, TaxPub-green ( <https://github.com/plazi/TaxPubJATS-green> https://github.com/plazi/TaxPubJATS-green ), which is related to TaxPub that Pensoft already uses for the publishing, and which is based on NLM JATS, that is a widely used “standard” albeit in different flavors. But to have all based on JATS-TaxPub makes it easier to make use of legacy (articles converted into TaxPub) and prospective (born digital based on TaxPub) articles. Once we have this move finished we will release and note and explain in detail. But in brief, let’s focus on TaxPub.

Taxonomic names

For our work with taxonomic publications we tag all scientific taxonomic names we discover in the articles. Our main focus are names for which a taxonomic treatment is provided in the respective article, or which are cited as a reference to an earlier usage and with that a taxonomic treatment.

As an example:   <http://treatment.plazi.org/id/87F5BDFA-6C63-C7B7-4A85-A1B39AE6CACE> http://treatment.plazi.org/id/87F5BDFA-6C63-C7B7-4A85-A1B39AE6CACE 

Agosti (1990) provides a treatment of Catagylphis turcomanicus (Emery). He cites all the earlier usages of this name, beginning from the protonym to all the latter changes in combination.

With that he says, that under this understanding of this taxon, he subsumes all the earlier name usages. He does this by citing them. A visualization is provided on the right hand und “taxonomy”

A more recent example is this crab:  <http://treatment.plazi.org/id/F017F605-AC1E-BB43-FF2A-90F9555CF9CD> http://treatment.plazi.org/id/F017F605-AC1E-BB43-FF2A-90F9555CF9CD

This treatmentCitation allows us to build a citation graph which is specific in a sense that this type of taxonomic names have a relationship to an earlier specified usage. Whilst names that are found in the next have this relationship implicit, known probably to the author in most cases, and few exceptional cases to a community that maintains a name server including the currently accepted name (and then there the history that eventually leads to the protonym, such as is the case for ants (and mony more hymenoptera) on the Hymenopter Name Server). But this is a discussion in itself.

In Taxpub this is dealt with (somewhat cryptic) 

<nomenclature-citation-list>

       <nomenclature-citation>

       </nomenclature-citation>

       <nomenclature-citation>

       </nomenclature-citation>

    </nomenclature-citation-list>

See  <https://htmlpreview.github.io/?https://raw.githubusercontent.com/tcatapano/TaxPub/master/documentation/tp-nomenclature-citation-list.html> https://htmlpreview.github.io/?https://raw.githubusercontent.com/tcatapano/TaxPub/master/documentation/tp-nomenclature-citation-list.html 

In RDF we make use of CITO ( <http://purl.org/spar/cito/> http://purl.org/spar/cito/) to model this relationship

 <https://github.com/plazi/TreatmentOntologies> https://github.com/plazi/TreatmentOntologies

and here an example

 <http://tb.plazi.org/GgServer/rdf/87F5BDFA6C63C7B74A85A1B39AE6CACE> http://tb.plazi.org/GgServer/rdf/87F5BDFA6C63C7B74A85A1B39AE6CACE

Donat

From: tdwg-content [mailto: <mailto:tdwg-content-bounces at lists.tdwg.org> tdwg-content-bounces at lists.tdwg.org] On Behalf Of Richard Pyle
Sent: Wednesday, April 20, 2016 12:30 AM
To: 'Nico Franz' < <mailto:nico.franz at asu.edu> nico.franz at asu.edu>
Cc:  <mailto:tdwg-content at lists.tdwg.org> tdwg-content at lists.tdwg.org;  <mailto:vocab at noreply.github.com> vocab at noreply.github.com; 'Michael Rosenberg (Faculty)' < <mailto:msr at asu.edu> msr at asu.edu>

Subject: Re: [tdwg-content] Taxonomic name usage files

Good questions!  Note that the stuff I was describing isn’t just GNUB; it’s embedded in the DwC terms as well.  And the few elements that are missing from DwC are embedded in TCS.  The main other aspects are the Reference metadata (the ill-fated TDWG Reference standard; now looking towards NLMS), and Agents (most people I know follow FOAF). Other than those, the main missing holes (in both GNUB and DwC) are the Appearance stuff, and perhaps a more robust approach to the relationshipAssertion stuff.

Maybe a task for TCS 2.0?

Once the standards fleshed out, I imagine the way to implement this stuff in new literature is via something along the lines of Pensoft’s PWT (now arpha):  <http://arpha.pensoft.net/> http://arpha.pensoft.net/  The natural group to focus on this would be PLAZI, which has been going gangbusters in recent months on capturing structured treatments from existing literature. [Pssst… Donat…. That’s your cue….]

Rich

From: Nico Franz [ <mailto:nico.franz at asu.edu> mailto:nico.franz at asu.edu] 
Sent: Tuesday, April 19, 2016 11:58 AM
To: Richard Pyle
Cc: Gaurav Vaidya; greg whitbread;  <mailto:tdwg-content at lists.tdwg.org> tdwg-content at lists.tdwg.org;  <mailto:vocab at noreply.github.com> vocab at noreply.github.com; Michael Rosenberg (Faculty)
Subject: Re: [tdwg-content] Taxonomic name usage files

Thanks, Rich, for catching me up.

   So then if we can apparently cover a good bit of ground (with what I assume you'd call a "smart [or the only] way of implementing GNUB"), this does raise the question of how to bring this as close as possible to the peer-review/publication process where an author team may be motivated to express their intentions related to name usages in various explicit, structurally recorded ways.

Best, Nico

On Tue, Apr 19, 2016 at 2:09 PM, Richard Pyle <deepreef at bishopmuseum.org> wrote:

> 1. Given a multitude of well established and precise historical name usages, I explicitly don't want to commit to one in particular
> that my present usage is congruent with, or not. (Indeed, I kind of think this is what the name withOUT a sec. does, "explicitly").

Yes! Exactly!

> I choose to be vague - any past usage is ok with me, here.

During the TCS days, this is what we referred to as a "Nomenclatural Concept", which is roughly the sum/average of all historical treatments, more or less (ambiguity and vagueness deliberate/intentional).

> I think we can presently model the vagueness (by integrating on the strings alone), but not the deliberateness thereof (in contrast to other situations where vagueness is not intended)?

Yes - a TNU without any relationshipAssertions.  Basically, the only implied associations with other TNUs is via the Protonym link (i.e., a Nomenclatural Assertion).

> 2. Franz. 2010. Revision of Apotomoderes (Insecta: Coleoptera). => Actually, "Insecta" here is more of a social concession to an outdated data filing paradigm than
> a claim to an active speaker role (related to name usages that I actually care about). I am not intending to apply my taxonomic expertise to "Insecta";
> that is *out of scope* (though the string is being written).

So... in that case, the question is whether to represent "Insecta" as used in Franz 2010 as a scientific name, or  vernacular name (two different ways of modelling names, as the latter do not have structured Codes).  Even if you fall on the side of using it as a scientific (taxon) name, you can still create a TNU for it.  In the spirit of Walter's pioneering work on this stuff, TNUs only represent "potential" taxa.

Aloha,
Rich

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