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 ), 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 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
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/T...
In RDF we make use of CITO (http://purl.org/spar/cito/) to model this relationship
https://github.com/plazi/TreatmentOntologies and here an example
http://tb.plazi.org/GgServer/rdf/87F5BDFA6C63C7B74A85A1B39AE6CACE
Donat
From: tdwg-content [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Richard Pyle Sent: Wednesday, April 20, 2016 12:30 AM To: 'Nico Franz' nico.franz@asu.edu Cc: tdwg-content@lists.tdwg.org; vocab@noreply.github.com; 'Michael Rosenberg (Faculty)' msr@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/ 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@asu.edu] Sent: Tuesday, April 19, 2016 11:58 AM To: Richard Pyle Cc: Gaurav Vaidya; greg whitbread; tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org; vocab@noreply.github.commailto:vocab@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@bishopmuseum.orgmailto:deepreef@bishopmuseum.org> wrote:
- 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).
- 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