tdwg / tnc

Taxonomic Names and Concepts Interest Group

Taxon Names and Concepts Interest Group

Convenor

Niels Klazenga

Royal Botanic Gardens Victoria, Australia

[email protected]

Motivation

The aim of the Taxon Names and Concepts (TNC) group is to promote the understanding of taxonomic names and their relation to described taxa (taxon concepts). Taxonomic names and concepts are the fundamental units for communicating biological information. This group promotes the effective use of taxonomic names and concepts in biodiversity information for describing specimens and observations.

An important part of this process requires that standards for this information must be defined in order to enable the effective sharing and exchange of biodiversity information. Broad implementation of a standard framework for taxon concept use will enhance taxonomic data quality and the quality of biological analyses that incorporate taxonomic data. This framework will also expand the usefulness and reliability of both legacy taxonomic data and that yet to be compiled or produced.

Becoming Involved

The TNC group is open to all interested parties. Watch this repository to stay abreast of the issues as they arise. Core membership is available to those who actively participate in our discussions and attend our meetings. Currently, the TNC is undertaking a major revision of the Taxonomic Concept Transfer Schema (TCS). We are also still seeking use cases and case studies to do with the exchange of taxonomic data.

History and Context

The Taxon Names and Concepts subgroup was formed at TDWG 2003 from the earlier Taxon Names group with the remit of proposing a data transfer standard for taxonomic names and concepts (taxa). The group has explored many of the issues surrounding the use and representation of names and concepts and has iteratively developed an exchange schema, the Taxonomic Concept Transfer Schema (TCS) which was ratified at TDWG 2005 and released as TCS 1.01. TCS has never enjoyed high utilisation, as rapid technological changes and changes in the domain made the format less suitable for data exchange. Therefore, at a workshop at TDWG 2018, it was decided that the TNC should undertake a major revision of TCS.

Summary

The aim of the Taxon Names and Concepts group (TNC) is to:

• promote the understanding and use of taxonomic names and their relation to described taxa (taxon concepts), and
• how these are related to other biodiversity information models such as those describing specimens and observations.

The primary scope of the TNC group includes Taxonomic Names as controlled by the codes of nomenclature, Taxon Concepts, Vernacular names and their relationships. However, in order to fully understand taxon names and concepts, the TNC group is interested in other TDWG standards in which taxon names and concepts are used or with which they are defined. In particular, taxonomic publications in which the names and concepts are described or cited; biological specimens which typify the taxon names, circumscribe the concepts or that may have been identified as belonging to a particular taxon; and character descriptions that are used in describing taxonomic concepts.

The group:

• develops and promotes the use of standard data models for representing taxon names and taxon concepts (taxa),
• monitors their use and where appropriate proposes changes to the standards,
• produces reference implementations and tools and
• documentation and publications promoting the appropriate use of taxonomic names and concepts.

Resources

TNC Home page: http://www.tdwg.org/community/tnc/
TNC Wiki: https://github.com/tdwg/tnc/wiki

TCS Repository: https://github.com/tdwg/tcs, includes the current release of TCS and the TCS User Guide.

Google doc for up-to-date specification (working draft)

Diagram of up-to-date specification

tnc's Issues

Wikibase instance to manage development of specification

We have been looking for a better platform to work on the redevelopment of our specification than the Google Doc we are currently using (which was already an improvement on the Markdown document we started with) and the way that ABCD 3 makes use of Wikibase gave some of us the idea that we had found it.

Last week, I finally got around to experimenting with Wikibase. The result can be seen at https://data.rbg.vic.gov.au/tnu-wiki/. I think it works pretty well. I have set it up slightly differently from what the ABCD 3 team has done in that I have used Properties rather than Items for our properties. This way they can be used right-away, which enabled me to put the examples in as well.

While doing the rather tedious job of putting all the terms in, I made sure that they all had definitions (descriptions in Wikibase). The only terms that do not have definitions yet are the parsed authorship terms, as trying to reconcile these with botanical practice did my head in.

I am still trying to find the resources to set up a SPARQL endpoint. Once it's up I think it can be used to produce most of the documentation we need straight from the database.

This is a closed site, as I have had some issues with spam users on Mediawiki sites in the past, but I am happy to set up accounts for people who would like to contribute examples and/or comments. Core members of the TNC do not have a choice, by the way, they'll get an account inflicted on them whether they want to or not.

Handling of Vernacular Names

Placeholder

In TCS Vernacular Names are treated as relationships between Taxon Concepts, but it is not quite clear how. In the meeting of 2018-12-04 it was suggested that vernacularName could be a property on a TaxonomicName object, but after some more discussion it was agreed that they are better treated as TaxonomicNames in their own right. We need to explore what the options are with real-life examples.

Consider using SKOS-XL for labels

Issue created to discuss TNC-related aspects of tdwg/tag#22.

For my take om @baskaufs's example, see this gist.

Submit proposal for workshop(s) at biodiversity_next (TDWG 2019)

Call for proposals for break-out sessions (symposia and workshops) was sent last week. TNC will (propose to) organise a workshop. Deadline for submission is Friday, 30 Nov. 2018.

The call for Symposia and Workshops and the form can be found at https://biodiversitynext.org/call-for-symposia/. The main bit of work is the < 300 words abstract.

I propose to title the workshop 'Names for Biodiversity' again, ask for two sessions initially, put it in the Standards track and mark it as 'highly relevant' for the Infrastructure track, 'relevant' for the Science track and 'not so relevant' for the Policy and International Coordination track.

Teleconference 9/10 July 2019

Teleconference 20/21 August 2019

The next teleconference will be on Tuesday 20 August at 21:00 UTC. There will be a repeat performance Wednesday 21 August at 8:00 UTC.

We'll have realistically two more meetings before biodiversity_next and the workshop, so I would like to move on to the Taxonomic Name Usage Relationship Assertions. From the work I've done in the past week (see next issue), this seems pretty straightforward and I think we are in a good position to complete that before the workshop.

Zoom invitation

RBG Victoria is inviting you to a scheduled Zoom meeting.

Topic: TDWG/TNC teleconference
Time: Aug 21, 2019 07:00 AM Canberra, Melbourne, Sydney

Join Zoom Meeting
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Meeting times

Location	Local Time	Time Zone	UTC Offset
Melbourne (Australia - Victoria)	Wednesday, 21 August 2019 at 7:00:00 am	AEST	UTC+10 hours
Wellington (New Zealand - Wellington)	Wednesday, 21 August 2019 at 9:00:00 am	NZST	UTC+12 hours
Honolulu (USA - Hawaii)	Tuesday, 20 August 2019 at 11:00:00 am	HST	UTC-10 hours
San Francisco (USA - California)	Tuesday, 20 August 2019 at 2:00:00 pm	PDT	UTC-7 hours
St. Louis (USA - Missouri)	Tuesday, 20 August 2019 at 4:00:00 pm	CDT	UTC-5 hours
New York (USA - New York)	Tuesday, 20 August 2019 at 5:00:00 pm	EDT	UTC-4 hours
London (United Kingdom - England)	Tuesday, 20 August 2019 at 10:00:00 pm	BST	UTC+1 hour
Copenhagen (Denmark)	Tuesday, 20 August 2019 at 11:00:00 pm	CEST	UTC+2 hours
Corresponding UTC (GMT)	Tuesday, 20 August 2019 at 21:00:00

Second meeting

Location	Local Time	Time Zone	UTC Offset
Melbourne (Australia - Victoria)	Wednesday, 21 August 2019 at 6:00:00 pm	AEST	UTC+10 hours
Wellington (New Zealand - Wellington)	Wednesday, 21 August 2019 at 8:00:00 pm	NZST	UTC+12 hours
Honolulu (USA - Hawaii)	Tuesday, 20 August 2019 at 10:00:00 pm	HST	UTC-10 hours
San Francisco (USA - California)	Wednesday, 21 August 2019 at 1:00:00 am	PDT	UTC-7 hours
St. Louis (USA - Missouri)	Wednesday, 21 August 2019 at 3:00:00 am	CDT	UTC-5 hours
New York (USA - New York)	Wednesday, 21 August 2019 at 4:00:00 am	EDT	UTC-4 hours
London (United Kingdom - England)	Wednesday, 21 August 2019 at 9:00:00 am	BST	UTC+1 hour
Copenhagen (Denmark)	Wednesday, 21 August 2019 at 10:00:00 am	CEST	UTC+2 hours
Corresponding UTC (GMT)	Wednesday, 21 August 2019 at 08:00:00

Proposed: 'protonym' property on TaxonomicName

This is a proposal to include a 'protonym' property in the TaxonomicName class. This property will directly link the TaxonomicName to its primary or 'protologue' TaxonomicNameUsage, which will obviate the need to find the primary TNU among all the name's usages to do something simple like finding a name's protologue or basionym.

The label of the term might need some discussion, as I believe in zoology 'protonym' is synonymous with 'basionym', which is less inclusive than the intended usage, which includes new combinations and names with new status.

Name variants and the definition of tnu:TaxonomicName

Following on from the conference call, and @deepreef’s comment that
perhaps we still don’t have a precise definition for tnu:TaxonomicName,
and that the issue has always been “kicked down the road”, and that we
would do well to sort this out now, I’ll open this thread! Let’s also
refer to @baskaufs’s figure which is getting some editing and comments.

Take the question: are “Delphinium brownii J. Smith” and “Delphinium
browni J. Smith” one instance of tnu:TaxonomicName or two?

One opinion seemed to be that our common understanding of a name was of
an abstract entity, and that a single name (with or without a
protonym) might have a number of variants that are not of the same
nature as the base name itself. We might model this as:

:TN1   :hasOrthographicVariant      "Delphinium brownii J. Smith" ,
                                    "Delphinium browni J. Smith" .

with usages perhaps modeled:

:TNU1  tnu:taxonomicNameUsageLabel  "Delphinium brownii J. Smith" ;
       tnu:taxonomicName            :TN1 .
:TNU2  tnu:taxonomicNameUsageLabel  "Delphinium browni J. Smith"  ;
       tnu:taxonomicName            :TN1 .

Another view is that since we often do not have a protonym, and we
encounter every name via a name usage, we are better off modeling
name variants thus:

:TNU3  tnu:taxonomicNameUsageLabel  "Delphinium brownii J. Smith" ;
:TNU4  tnu:taxonomicNameUsageLabel  "Delphinium browni J. Smith" .

and (I think I heard this correctly):

:TNU3  tnu:taxonomicName            :TN3 .
:TNU4  tnu:taxonomicName            :TN4 .
:TN3   tnu:taxonomicNameStringWithAuthor "Delphinium brownii J. Smith" .
:TN4   tnu:taxonomicNameStringWithAuthor "Delphinium browni J. Smith" .
:TN3   owl:differentFrom            :TN4 .

Perhaps I misunderstood though, and perhaps there are other ways people
see this? I know this has probably been talked about, around and around
for many years.

I’m particularly interested as I’m currently in the process of
reconciling names between different DBs (IPNI, Tropicos, ThePlantList,
Flora of North America; see here and here), and I often want to
say that two variants refer to the “same” name, but don’t quite know how
to define that “one name.” Having a crystal clear definition of
tnu:TaxonomicName would be helpful.

TODO Relationships

Placeholder for work on Taxonomic Name Usage Relationships, for project board.

Planned for early 2019.

TODO Core concepts

Placeholder for work on Core concepts, for project board.

Core concepts include all concepts in the TaxonomicName class, as well as the name and publication detail properties in the TaxonomicNameUsage class.

Should we have parsed authorship properties?

In the meeting of 4 December (#20) we decided on not having parsed authorship properties. In a comment on the meeting notes @mdoering makes a case in favour of having them:

There are various levels of parsing. Parsing the entire authorship to individual authors is harder, but I believe we should at least keep basionym/bracket authorship separate from the combination authorship. And probably also have the year parsed out for each of them because these are things one often needs to compare or process. But even splitting authorteams into lists of individual authors is sth that people deal with (both GNA and GBIF name parsers do it) and I would very welcome a standard that allows to exchange such parsed data.

Warrants more discussion...

Compile document with use cases

Placeholder for project board.

Teleconference 4 December 2018

The next meeting of the TNC will be Tuesday, 4 December 2018 at 20:00 UTC. Times for other time zones are in the table below.

We will be discussing properties of the TaxonomicName and TaxonomicNameUsage classes and hopefully make some real progress towards a working document by the end of the year.

Location	Local Time	Time Zone	UTC Offset
Melbourne (Australia - Victoria)	Wednesday, 5 December 2018 at 7:00:00 am	AEDT	UTC+11 hours
Wellington (New Zealand - Wellington)	Wednesday, 5 December 2018 at 9:00:00 am	NZDT	UTC+13 hours
Honolulu (USA - Hawaii)	Tuesday, 4 December 2018 at 10:00:00 am	HST	UTC-10 hours
San Francisco (USA - California)	Tuesday, 4 December 2018 at 12:00:00 noon	PST	UTC-8 hours
St. Louis (USA - Missouri)	Tuesday, 4 December 2018 at 2:00:00 pm	CST	UTC-6 hours
New York (USA - New York)	Tuesday, 4 December 2018 at 3:00:00 pm	EST	UTC-5 hours
London (United Kingdom - England)	Tuesday, 4 December 2018 at 8:00:00 pm	GMT	UTC
Berlin (Germany - Berlin)	Tuesday, 4 December 2018 at 9:00:00 pm	CET	UTC+1 hour
Corresponding UTC (GMT)	Tuesday, 4 December 2018 at 20:00:00

Teleconference 2/3 April 2019

The next teleconference is on 2 or 3 April, depending on where people are. We will commence discussing Taxon Concept Relationships.

I thought the second meeting we (or some of us) had last time was worthwhile, so we are doing that again. Like last time, we will continue building the specification in the first meeting and mainly talk about ancillary issues in the second meeting.

Zoom link

RBG Victoria is inviting you to a scheduled Zoom meeting.

Topic: TDWG/TNC teleconference
Time: Apr 3, 2019 7:00 AM Canberra, Melbourne, Sydney

Join Zoom Meeting
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Meeting ID: 242 495 160
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First meeting times

Location	Local Time	Time Zone	UTC Offset
Melbourne (Australia - Victoria)	Wednesday, 3 April 2019 at 7:00:00 am	AEDT	UTC+11 hours
Wellington (New Zealand - Wellington)	Wednesday, 3 April 2019 at 9:00:00 am	NZDT	UTC+13 hours
Honolulu (USA - Hawaii)	Tuesday, 2 April 2019 at 10:00:00 am	HST	UTC-10 hours
San Jose (USA - California)	Tuesday, 2 April 2019 at 1:00:00 pm	PDT	UTC-7 hours
St. Louis (USA - Missouri)	Tuesday, 2 April 2019 at 3:00:00 pm	CDT	UTC-5 hours
New York (USA - New York)	Tuesday, 2 April 2019 at 4:00:00 pm	EDT	UTC-4 hours
London (United Kingdom - England)	Tuesday, 2 April 2019 at 9:00:00 pm	BST	UTC+1 hour
Copenhagen (Denmark)	Tuesday, 2 April 2019 at 10:00:00 pm	CEST	UTC+2 hours
Corresponding UTC (GMT)	Tuesday, 2 April 2019 at 20:00:00

Second meeting times

Location	Local Time	Time Zone	UTC Offset
Melbourne (Australia - Victoria)	Wednesday, 3 April 2019 at 7:00:00 pm	AEDT	UTC+11 hours
Wellington (New Zealand - Wellington)	Wednesday, 3 April 2019 at 9:00:00 pm	NZDT	UTC+13 hours
Honolulu (USA - Hawaii)	Tuesday, 2 April 2019 at 10:00:00 pm	HST	UTC-10 hours
San Jose (USA - California)	Wednesday, 3 April 2019 at 1:00:00 am	PDT	UTC-7 hours
St. Louis (USA - Missouri)	Wednesday, 3 April 2019 at 3:00:00 am	CDT	UTC-5 hours
New York (USA - New York)	Wednesday, 3 April 2019 at 4:00:00 am	EDT	UTC-4 hours
London (United Kingdom - England)	Wednesday, 3 April 2019 at 9:00:00 am	BST	UTC+1 hour
Copenhagen (Denmark)	Wednesday, 3 April 2019 at 10:00:00 am	CEST	UTC+2 hours
Corresponding UTC (GMT)	Wednesday, 3 April 2019 at 08:00:00

Other ontologies

To complement the [TCS is just fine as it is thread(https://github.com//issues/7) I think there are some other approaches/vocabularies/ontologies that are worthwhile considering. These may well already be familiar to people in this conversation, but some of them are new to me (or at least were put into a vague "must read at some point" category).

@frmichel and colleagues have a nice paper "A Model to Represent Nomenclatural and Taxonomic Information as Linked Data. Application to the French Taxonomic Register, TAXREF" https://hal.archives-ouvertes.fr/hal-01617708 which compares various ways of modelling names and taxa, and describes their solution, namely TAXREF

Laurenne et al, describe the TaxMeOn model: Laurenne, N., Tuominen, J., Saarenmaa, H., & Hyvönen, E. (2014). Making species checklists understandable to machines – a shift from relational databases to ontologies. Journal of Biomedical Semantics, 5(1), 40. doi:10.1186/2041-1480-5-40

Chawuthai et al. describe the LTK model: Chawuthai, R., Takeda, H., Wuwongse, V., & Jinbo, U. (2016). Presenting and preserving the change in taxonomic knowledge for linked data. Semantic Web, 7(6), 589–616. doi:10.3233/sw-150192

I find the LTK model especially interesting as it models change in taxonomies. Also relevant is this cool essay by Ian Robinson: Time-Based Versioned Graphs Robinson describes a simple way to use timestamps to support versioning in graphs, which strikes me as pretty much exactly the problem "taxonomic concepts" are trying to solve.

Put another way, it is straightforward to model names and trees, and demonstrably that is adequate for a lot of science to be done. NCBI, GBIF, regional GBIF nodes, pretty much any biodiversity project that includes a taxonomic classification all follow some variation of this. What these databases don't do is model change, they tend to update the names and tree as and when they chose. It seems to me that having versions of trees, and being able to compute the differences between those versions would enable us to answer what seems to the core taxonomic concept question : "this data was associated with this 'taxon' at this time, what should it be associated with now?".

Teleconference 19 November 2019 20:00 UTC

Dear all,
Sorry for the latish notice. As I haven't done too good a job of informing people about the outcome of the workshop at Biodiversity_Next – conference was rather busy and then I got ill – I thought we have a bit of a debrief, especially for people who weren't there. We'll start our real work again in the new year.

Zoom invitation

RBG Victoria is inviting you to a scheduled Zoom meeting.

Topic: TDWG Taxonomic Names and Concepts Interest Group
Time: Nov 20, 2019 07:00 AM Canberra, Melbourne, Sydney

Join Zoom Meeting
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Meeting ID: 261 057 832

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Note: this is a new meeting number, as the old meeting has disappeared from my account

Timezones

Location	Local Time	Time Zone	UTC Offset
Melbourne (Australia - Victoria)	Wednesday, 20 November 2019 at 7:00:00 am	AEDT	UTC+11 hours
Wellington (New Zealand - Wellington)	Wednesday, 20 November 2019 at 9:00:00 am	NZDT	UTC+13 hours
Honolulu (USA - Hawaii)	Tuesday, 19 November 2019 at 10:00:00 am	HST	UTC-10 hours
San Francisco (USA - California)	Tuesday, 19 November 2019 at 12:00:00 noon	PST	UTC-8 hours
St. Louis (USA - Missouri)	Tuesday, 19 November 2019 at 2:00:00 pm	CST	UTC-6 hours
New York (USA - New York)	Tuesday, 19 November 2019 at 3:00:00 pm	EST	UTC-5 hours
London (United Kingdom - England)	Tuesday, 19 November 2019 at 8:00:00 pm	GMT	UTC
Berlin (Germany - Berlin)	Tuesday, 19 November 2019 at 9:00:00 pm	CET	UTC+1 hour
Corresponding UTC (GMT)	Tuesday, 19 November 2019 at 20:00:00

Taxon, Taxon Concept and Taxon Name Usage: definitions and relationships

You write:
A taxonomic concept is a taxonomic name instance establishing or circumscribing a taxonomic entity - often linking synonymic inclusions and adding annotations, description…

I think it's cleaner to say that the taxonomic concept is a theory of a certain taxonomy identity. And then "taxonomic concept label" (name sec. source) is the "name" for that theory.

More or less like here: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0174-5
...

Best, Nico

Compile document with user profiles

Placeholder for project board

TCS2 and DwCA

In 2017, I contacted Markus (@mdoering) about a taxon concept relationship extension/module for DwCA. He noted that there wasn't one and encouraged me to draft one, which I did (dwca-tcs). He then uploaded this to the GBIF RS sandbox (tcrel).

The extension has not been used by an IPT installation for data upload yet, so remains simply a suggestion/pointer/proof-of-concept, but I thought I would draw it to the attention of this group. Now that the TCS2 group is active, I imagine/hope that one product would be an "official" TCS2 extension for DwCA.

(Excited to see what's going on in this group. Sadly can't make the teleconference next week.)

Cam

TNU Hackathon 7 April 2020

The Taxonomic Names and Concepts Interest Group is organising a hackathon to work on the new TNU Standard. This will be the first of a series of hackathons where we will all work on the same set of Google Docs – which will be the basis of the eventual standard – at (approximately) the same time. The hackathon will start on Tuesday 7 April at 12 am GMT and will in principle last 24 hours, but because of time differences will probably go on a bit longer. A Zoom meeting (https://zoom.us/j/607907193) has been set up, which will stay open for the duration of the hackathon.

The following Google Docs have been set up:

• Introduction
• Structure
• Term list
  This is the document we have been working in all the time.
• TNU definition
  This is to flesh out the definition of Taxonomic Name Usage and how it relates to Taxon, Taxon Concept, etc.
• Use cases
• Examples
• Literature
  Here we collate a list of references to relevant literature – preferrably with links – so that everybody can easily find the papers. This is not necessarily the bibliography of the standard.

I think during this first hackathon we will focus on the literature list and use cases, but people who rather work on the other documents are free to do so, during the hackathon and at any other time.

Compile list of implementations around Names and Concepts

Use of Data Packages

@mdoering mentioned the use of Data Packages in issue #1, which is now closed.

Just elevating this to a separate issue, to keep it on the radar.

@mdoering, still interested in this?

TODO Typification

Placeholder for work on Typification, for project board.

Teleconference 14 January 2020 20:00 UTC

I made a last-minute decision to go to the Netherlands at the end of January and I am trying to get a meeting in before I go. I thought we could discuss what the standard documentation should look like, what should go into BISS and what not, and how to go about it. We can then start off at the next meeting after I'm back at the end of February. I reckon, if we want it available at the TDWG meeting at the end of September, we will only have a few months to write everything.

Zoom invitation

RBG Victoria is inviting you to a scheduled Zoom meeting.

Topic: TDWG Taxonomic Names and Concepts Interest Group
Time: Jan 15, 2020 07:00 AM Canberra, Melbourne, Sydney

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Meeting ID: 472 131 712

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Meeting times

Location	Local Time	Time Zone	UTC Offset
Melbourne (Australia - Victoria)	Wednesday, 15 January 2020 at 7:00:00 am	AEDT	UTC+11 hours
Wellington (New Zealand - Wellington)	Wednesday, 15 January 2020 at 9:00:00 am	NZDT	UTC+13 hours
Honolulu (USA - Hawaii)	Tuesday, 14 January 2020 at 10:00:00 am	HST	UTC-10 hours
San Francisco (USA - California)	Tuesday, 14 January 2020 at 12:00:00 noon	PST	UTC-8 hours
St. Louis (USA - Missouri)	Tuesday, 14 January 2020 at 2:00:00 pm	CST	UTC-6 hours
New York (USA - New York)	Tuesday, 14 January 2020 at 3:00:00 pm	EST	UTC-5 hours
London (United Kingdom - England)	Tuesday, 14 January 2020 at 8:00:00 pm	GMT	UTC
Berlin (Germany - Berlin)	Tuesday, 14 January 2020 at 9:00:00 pm	CET	UTC+1 hour
Corresponding UTC (GMT)	Tuesday, 14 January 2020 at 20:00:00

Add web links to README.md standards, products, protocols)

TCS is just fine as it is

I propose a different, hopefully complementary, approach to this discussion. I am going to argue that the existing TCS (i.e., the TDWG LSID version https://github.com/tdwg/ontology/tree/master/ontology/voc) is absolutely fine and exactly what we need. If you disagree I'm going to ask you to prove me wrong. The way I think we could test whether TCS works is to explicitly test it. This will require some messing about with RDF and SPARQL (gack) but I think this way we can make some progress.

Idea

I propose the following:

1. we have a triple store that has the TCS loaded up, together with some real examples.
2. We test the assertion that TCS does everything we need by writing SPARQL queries.
3. If we can write a sensible query then TCS passes that test
4. If we can't write a query, or if we could write a better query if TCS was modified, then we have a list of things we need to change/add.

I know SPARQL is hideous at times, but it is powerful, and it enables us to have explicit tests that we can discuss. Note that the core of SPARQL is matching paths in graphs, so if we have a model of the things we care about and their relationships, and we can draw paths between them ("connect the dots"), then we can convert that into SPARQL.

SPARQL

OK, so I've set up a SPARQL interface here: https://funny-leather.glitch.me It is connected to a triple store that I will add data to (if anyone has data they want added, just let me know. If anybody wants to work on some queries, also let me know).

Examples

We have a bunch of use cases from @deepreef and @jgerbracht. So what I have in mind is taking these one by one and, if they are in scope, coming up with a query to address each use case. To start with I've loaded an example name Begonia elachista Moonlight & Tebbitt urn:lsid:ipni.org:names:77160201-1 into the triple store.

Names Test 0: Is this a name?

The first test is whether a string is a scientific name. Not on the use case list, but a starting point. So, is Begonia elachista a name? The SPARQL query is:

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX tn: <http://rs.tdwg.org/ontology/voc/TaxonName#>

SELECT * 
WHERE { 
  ?thing tn:nameComplete "Begonia elachista" .
  ?thing rdf:type ?type . 
  ?type rdfs:label ?label .
} 

You can run the query here and see that the answer is "yes":

thing	type	label
1	urn:lsid:ipni.org:names:77160201-1:1.2.1.2	http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName

"Begonia elachista" has type http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName and via the TCS vocabulary we can get an English language string saying that type is a "Taxon Name". +1 for TCS.

Names Test 1: In what publication was a scientific name first established?

This is the first question on @deepreef 's list. The query is:

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX tn: <http://rs.tdwg.org/ontology/voc/TaxonName#>
PREFIX tcom: <http://rs.tdwg.org/ontology/voc/Common#>

SELECT * 
WHERE { 
  ?thing tn:nameComplete "Begonia elachista" .
  ?thing tcom:publishedIn ?publishedIn . 
} 

Try it

And the answer is:

thing	publishedIn
urn:lsid:ipni.org:names:77160201-1:1.2.1.2	Eur. J. Taxon. 281: 5. 2017 [17 Feb 2017] [epublished]

Now ideally we'd have a DOI for this publication (it is
https://doi.org/10.5852/ejt.2017.281 ) but IPNI often doesn't know the DOI, and even if it does it doesn't include them in the RDF. But there is a term in TCS that we could use, so if we added the DOI to the triple store we would get the DOI. So +1 to TCS.

Note that if we want something more granular than a link to the level of article, and the 5 in "Eur. J. Taxon. 281: 5. 2017 [17 Feb 2017] [epublished]" is a more granular link at the level of page, then we will need additional terms (such as the W3C annotation terms).

Names Test 6: Where is the type specimen for a scientific name?

I'd argue that this query is partly outside the scope of TCS as once we link to a specimen then it's up to whatever vocabulary describes the specimen to give us that information. However, with some databases we can get close:

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX tn: <http://rs.tdwg.org/ontology/voc/TaxonName#>
PREFIX tcom: <http://rs.tdwg.org/ontology/voc/Common#>

SELECT * 
WHERE { 
  ?thing tn:nameComplete "Begonia elachista" .
  ?thing tn:typifiedBy ?typifiedBy . 
  ?typifiedBy tn:typeSpecimen ?typeSpecimen .
}

Try it

thing	typifiedBy	typeSpecimen
urn:lsid:ipni.org:names:77160201-1:1.2.1.2	b0	Moonlight & Daza 318, MOL
urn:lsid:ipni.org:names:77160201-1:1.2.1.2	b1	Moonlight & Daza 318, E
urn:lsid:ipni.org:names:77160201-1:1.2.1.2	b2	Moonlight & Daza 318, MO
urn:lsid:ipni.org:names:77160201-1:1.2.1.2	b3	Moonlight & Daza 318, USM

IPNI stores names for type specimens, not links :(. In an ideal world these types would be linked to something, such as GBIF or a URL to the natural history collection's web database. Looking at GBIF's records for this species GBIF: 9451157 we can get links for some of these types, e.g. "Moonlight & Daza 318, E" is occurrence https://www.gbif.org/occurrence/1305189344 (see also http://data.rbge.org.uk/herb/E00785221 ). So to fully answer this question we need to have the occurrence information in RDF, and create a link between IPNI and the specimen identifiers. But this is not a limitation of TCS, so +1.

Summary

These are just some preliminary notes, and the examples are pretty trivial, but I think it might provide a way forward. If we can explicitly state what it is we want to do, have some examples using "real" data (which may be from an existing provider, or we may have to create some data sets) then I think we will be able to more clearly define what it is we're after, and whether my claim that the existing TCS is all we need is, indeed, correct.

More appropriate name for TaxonRelationshipAssertion class

We have adopted the TaxonRelationshipAssertion element from TCS, but have never really discussed the name of the class.

In the discussion around vernacular names (#47), the class was frequently mentioned and @jar remarked that it is not appropriate to call it "TaxonSomething", as they are relations between Taxonomic Name Usages.

It seems logical to call the class TaxonomicNameUsageRelationshipAssertions, but we restricted the type of relationships in this class to the horizontal relationships between taxon concepts (isCongruentTo, includes, isIncludedIn, overlaps, intersects and excludes) and there are several relationships between TNUs in the standard that are not in this class.

It would be nice to come up with a name for the class that reflects the types of relationships we allow in it. Any suggestions? I would prefer to not call it RCC-5 Relationships (if only because we have a term that is not in RCC-5) or Set Relationships.

Revise TNC Charter

We need to, or think it is a good idea to, send a revised charter to the TDWG Executive. The document that is being worked on is https://github.com/tdwg/tnc/blob/master/charter.md.

To be completed by 21 Nov. 2018

Merge TaxonomicName into TaxonomicNameUsage

In the discussion around the Darwin Core RDF Guide that @baskaufs summarised, @deepreef stated that a Taxonomic Name is a special form of a Taxonomic Name Usage (using slightly different terms). At the time I read this (only a few months ago) my first thought was 'Oh, rubbish!', but with all the discussions we have had in the TNC in the last six month, I have slowly moved to @deepreef's position.

We have had difficulty deciding which property goes in which class (or I have, as we haven't had any strong disagreements) and there is the outstanding issue of defining the classes and deciding where one class ends and the other begins.

I think (at the moment...) that we can do with one class what we can do with the two classes, by adding a 'primary taxonomic name usage' property (cf. #32), which would then replace the taxonomicName property (and be equivalent with dwc:scientificNameID). I think we could even keep calling the property taxonomicName.

Teleconference 24 September 2019 21:00 UTC

The next meeting of the TNC will be on September 24 at 21:00 UTC. Times for other time zones are in the table below. Note that in Australia, New Zealand and Hawaii the meeting will fall on the 25^th. I am doing just one meeting this time, as last time it was just Greg and me in the second meeting. If anybody from Europe is desperate to join, just let me know and I will organise a second one.

I have made an executive decision to leave out all the hybrid- and fungi-related relationship types until someone makes a strong case for having them. This leaves us with only vernacular names still to discuss, so that will be the main topic of the meeting. Furthermore, we could have a good swing at trying to do the typification and circumscription before biodiversity_next, as I think this could be pretty straightforward.

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Location	Local Time	Time Zone	UTC Offset
Melbourne (Australia - Victoria)	Wednesday, 25 September 2019 at 7:00:00 am	AEST	UTC+10 hours
Wellington (New Zealand - Wellington)	Wednesday, 25 September 2019 at 9:00:00 am	NZST	UTC+12 hours
Honolulu (USA - Hawaii)	Tuesday, 24 September 2019 at 11:00:00 am	HST	UTC-10 hours
San Francisco (USA - California)	Tuesday, 24 September 2019 at 2:00:00 pm	PDT	UTC-7 hours
St. Louis (USA - Missouri)	Tuesday, 24 September 2019 at 4:00:00 pm	CDT	UTC-5 hours
New York (USA - New York)	Tuesday, 24 September 2019 at 5:00:00 pm	EDT	UTC-4 hours
London (United Kingdom - England)	Tuesday, 24 September 2019 at 10:00:00 pm	BST	UTC+1 hour
Berlin (Germany - Berlin)	Tuesday, 24 September 2019 at 11:00:00 pm	CEST	UTC+2 hours
Corresponding UTC (GMT)	Tuesday, 24 September 2019 at 21:00:00

Assign properties to TaxonomicName and TaxonomicNameUsage classes

TaxonomicName and TaxonomicNameUsage are the class names we have decided to use for now. Next step is to assign properties from TCS or TDWG Ontology to these classes.

To be completed early December 2019.

Names for Biodiversity Workshop notes

Teleconference 24 March 2020 20:00 UTC

Dear all,
We've had quite a bit of activity in the GitHub Issues in the last week or so. I would like to make use of the momentum and get us all together (virtually) for a meeting on 24 March 2020 at 20:00 UTC (see table with other time zones below).

I will be setting up some hackathons in the next months. In the meeting I would like to discuss how to best go about it.

Also, @deepreef suggested that we should also work on a way to exchange literature references and agents, which was enthusiastically seconded by two other core members, so we'll talk about that as well, and whether we should do it now or after we finished the draft standard.

I have set up one meeting for 20:00 GMT, which is quite early in the morning for those of us who are in Australia, If that time is not suitable for our European members and they would like to come to the meeting as well, I will be happy to arrange another meeting 11 or 12 hours later. The Australians will join you in both meetings.

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Time zones

Location	Local Time	Time Zone	UTC Offset
Melbourne (Australia - Victoria)	Wednesday, 25 March 2020 at 7:00:00 am	AEDT	UTC+11 hours
Wellington (New Zealand - Wellington)	Wednesday, 25 March 2020 at 9:00:00 am	NZDT	UTC+13 hours
Honolulu (USA - Hawaii)	Tuesday, 24 March 2020 at 10:00:00 am	HST	UTC-10 hours
San Francisco (USA - California)	Tuesday, 24 March 2020 at 1:00:00 pm	PDT	UTC-7 hours
St. Louis (USA - Missouri)	Tuesday, 24 March 2020 at 3:00:00 pm	CDT	UTC-5 hours
New York (USA - New York)	Tuesday, 24 March 2020 at 4:00:00 pm	EDT	UTC-4 hours
London (United Kingdom - England)	Tuesday, 24 March 2020 at 8:00:00 pm	GMT	UTC
Berlin (Germany - Berlin)	Tuesday, 24 March 2020 at 9:00:00 pm	CET	UTC+1 hour
Corresponding UTC (GMT)	Tuesday, 24 March 2020 at 20:00:00

Convert TNU document to Google Doc

Document is currently in AsciiDoc. It was decided in the meeting this morning that a Google Doc will be easier to work with.

Teleconference 6/7 November 2018

Time for our second meeting.

Looking at the World Clock, now that we in the Southern Hemisphere are on Daylight Saving Time and the Northern Hemisphere is back on Standard Time, I think we might be able to get away with a single meeting. I found it quite hard the last time having to inform the second meeting about what had been discussed at the first one. Also, I think it would be good to have us all in the same meeting. If 8 or 9 pm turns out too late for our European (and African) colleagues, we can organise a second meeting.

Proposed times are the following:

Melbourne: Wednesday, 7 November 2018 at 7:00 am
Wellington: Wednesday, 7 November 2018 at 9:00 am
Honolulu: Tuesday, 6 November 2018 at 10:00 am
San Francisco: Tuesday, 6 November 2018 at 12:00 noon
Nashville: Tuesday, 6 November 2018 at 2:00 pm
New York: Tuesday, 6 November 2018 at 3:00 pm
London: Tuesday, 6 November 2018 at 8:00 pm
Berlin: Tuesday, 6 November 2018 at 9:00 pm

List generated using timeanddate.com’s Meeting Planner
http://www.timeanddate.com/worldclock/meetingdetails.html?iso=20181106T2000&p1=152&p2=264&p3=103&p4=224&p5=171&p6=179&p7=136&p8=37

In this meeting we will follow up on the actions from the previous meeting, i.e deconstructing TCS and "convert" it to Markdown and completing the new charter for the Interest Group, as well as discuss how we will proceed.

A Zoom invitation and a link to a Google Doc with a more worked out agenda will follow.

Teleconference 6 March 2019

The next meeting of the TNC will be on Tuesday, 5 March at 8 pm GMT and Wednesday, 6 March at 8 am GMT.

I thought we try two meetings within the 24-hour period, which we'll have to do anyway when daylight-saving ends (or starts), but make them slightly different meetings. In the first meeting we will mainly focus on the specification document we are developing, like we have done in previous meetings, while the second meeting will mostly be about things we'll have to do around the new standard, i.e. use cases, serializations, reference implementations etc. This way I hope nothing will be left behind – we can work at multiple fronts, but it is probably not such a good idea to do it all in the same meeting – but I also hope it will keep people engaged who might not be interested in discussing every single property in great detail.

So, in the first meeting we will be talking about the upcoming workshops at biodiversity_next (briefly) and then commence with going over the properties of the TaxonomicNameUsage class. We completed the TaxonomicName class at the last meeting, but nothing is written in stone, of course, so if someone comes up with a reason to revisit that, we'll do that (also briefly).

In the second meeting we will quickly go over what we have discussed in the first meeting and than move on to other topics of concern (/interest).

The document we are working on – and will be discussing at least in the first meeting – is https://docs.google.com/document/d/1bcfjhh0ztmXKz7P9G0ni7vYZc3MtH4LLxlCZjswF2k4. Please also have a look at issue #32.

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• The second meeting will use the same Zoom link as the first meeting. I will just have to change the times after the first meeting.

First meeting: 5 Mar., 8 pm GMT

Location	Local Time	Time Zone	UTC Offset
Melbourne (Australia - Victoria)	Wednesday, 6 March 2019 at 7:00:00 am	AEDT	UTC+11 hours
Wellington (New Zealand - Wellington)	Wednesday, 6 March 2019 at 9:00:00 am	NZDT	UTC+13 hours
Honolulu (USA - Hawaii)	Tuesday, 5 March 2019 at 10:00:00 am	HST	UTC-10 hours
San Francisco (USA - California)	Tuesday, 5 March 2019 at 12:00:00 noon	PST	UTC-8 hours
St. Louis (USA - Missouri)	Tuesday, 5 March 2019 at 2:00:00 pm	CST	UTC-6 hours
New York (USA - New York)	Tuesday, 5 March 2019 at 3:00:00 pm	EST	UTC-5 hours
London (United Kingdom - England)	Tuesday, 5 March 2019 at 8:00:00 pm	GMT	UTC
Berlin (Germany - Berlin)	Tuesday, 5 March 2019 at 9:00:00 pm	CET	UTC+1 hour
Corresponding UTC (GMT)	Tuesday, 5 March 2019 at 20:00:00

Second meeting: 6 Mar., 8 am GMT

Location	Local Time	Time Zone	UTC Offset
Melbourne (Australia - Victoria)	Wednesday, 6 March 2019 at 7:00:00 pm	AEDT	UTC+11 hours
Wellington (New Zealand - Wellington)	Wednesday, 6 March 2019 at 9:00:00 pm	NZDT	UTC+13 hours
Honolulu (USA - Hawaii)	Tuesday, 5 March 2019 at 10:00:00 pm	HST	UTC-10 hours
San Francisco (USA - California)	Wednesday, 6 March 2019 at 12:00:00 midnight	PST	UTC-8 hours
St. Louis (USA - Missouri)	Wednesday, 6 March 2019 at 2:00:00 am	CST	UTC-6 hours
New York (USA - New York)	Wednesday, 6 March 2019 at 3:00:00 am	EST	UTC-5 hours
London (United Kingdom - England)	Wednesday, 6 March 2019 at 8:00:00 am	GMT	UTC
Berlin (Germany - Berlin)	Wednesday, 6 March 2019 at 9:00:00 am	CET	UTC+1 hour
Corresponding UTC (GMT)	Wednesday, 6 March 2019 at 08:00:00

TCS fragment as starting place

Email from @baskaufs:

Hi Greg,

Here is a link to the page/diagram that I was talking about yesterday:

https://github.com/tdwg/rdf/blob/master/TCSBasedTaxon.md

When we were working on the DwC RDF Guide, we were considering including this bit of TCS as part of the recommendations. However, as you know, TCS itself was an XML schema and the RDF representation was just one of the vocabularies included in the TDWG ontologies, which had no official standards status in TDWG. So since the RDF model wasn’t part of a standard, we didn’t feel comfortable including it. Plus, at that time I was assuming that there would soon be a TCS 2.0 and we would leave the job to that. However, after years, that hasn’t happened yet, so the issue of how to robustly represent taxon/taxon concept/TNU is still open.

As I said, I trotted this diagram around to some people like Nico Franz, Rich Pyle, and others who generally have strong opinions and although they like to have different names for the TaxonConcept bubble, they did not object to the fundamental idea of the taxon/taxon concept/TNU having four basic properties: nameString, hasName (linking to a URI), accordingToString, and accordingTo (linking to a URI). I feel like pretty much everything that people have been wanting to build can be built on top of this basic structure (which is embodied in an adopted standard, TCS).

If you want to talk more about this, just grab me sometime before we leave.

Steve

Teleconference 8 October 2019 20:00 UTC

We decided to have one last meeting before Biodiversity_next to discuss Circumscription, so that we'll have covered everything that is in TCS. This meeting will be held on 8 October at 20:00 UTC.

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Location	Local Time	Time Zone	UTC Offset
Melbourne (Australia - Victoria)	Wednesday, 9 October 2019 at 7:00:00 am	AEDT	UTC+11 hours
Honolulu (USA - Hawaii)	Tuesday, 8 October 2019 at 10:00:00 am	HST	UTC-10 hours
San Francisco (USA - California)	Tuesday, 8 October 2019 at 1:00:00 pm	PDT	UTC-7 hours
St. Louis (USA - Missouri)	Tuesday, 8 October 2019 at 3:00:00 pm	CDT	UTC-5 hours
New York (USA - New York)	Tuesday, 8 October 2019 at 4:00:00 pm	EDT	UTC-4 hours
London (United Kingdom - England)	Tuesday, 8 October 2019 at 9:00:00 pm	BST	UTC+1 hour
Berlin (Germany - Berlin)	Tuesday, 8 October 2019 at 10:00:00 pm	CEST	UTC+2 hours
Corresponding UTC (GMT)	Tuesday, 8 October 2019 at 20:00:00

Document use of NomenclaturalNoteType properties

Properties in TCS that have the NomenclaturalNoteType as their range include spellingCorrectionOf, basionym, basedOn, conservedAgainst, laterHomonymOf, sanctioned, replacementNameFor and publicationStatus. Most of these look like relationships between primary name usages, but, since they do not require taxonomic opinion, they might, if only for practical purposes, be treated as properties on a TaxonomicName object. In today's meeting it was agreed to document how these elements are used in some current implementation – and what an ideal implementation would look like – on the Wiki.

The need for "intersects" as a TNU relationship type in addition to the five RCC-5 types

TaxonNameUsages (cf. TaxonConcepts) are classes or sets, and can be related to each other in the standard set relationship ways: 1. congruent with, 2. superset of, 3. subset of, 4. overlaps, and 5. does not overlap (Franz and Peet 2009). In the context of Taxon Concepts, these have been referred to as RCC-5 articulations (Franz et al. 2015). Note that the term 'overlaps' implies that there exist both members of set A that are not in set B and vice versa.

When encoding real world cases of the relationship between TNUs, I have often found that there is insufficient information in a taxonomic publication to determine the exact RCC-5 term to use. For example, an author may simply say that a specimen that is now named as TNU2 was previously named as TNU1, without explicitly stating that, e.g., all members of TNU1 are now called TNU2, with other additional members (which would be TNU2 > TNU1). All we know for certain in these cases is that there is at least one member in common between TNU1 and TNU2, i.e., not(TNU1 | TNU2). But we do not yet have a term for not(TNU1 | TNU2).

I propose that we need a new term intersects to meet the practical goal of recording information about TNU relationships. The property intersects is a superproperty of congruent with, superset of, subset of, and overlaps.

(PS: @nielsklazenga asked me to open this issue to generate some discussion; we tentatively already added intersects to the GDoc.)

Teleconference 7/8 May 2019

The next set of meetings is on Tuesday, 7 May at 21:00 UTC and Wednesday, 8 May at 08:00 UTC.

Like last time, we'll make an attempt to start with the TNU relationships, but there are a few things that came out of the previous meetings that need to be revisited first. More information to follow...

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First meeting times:

Location	Local Time	Time Zone	UTC Offset
Melbourne (Australia - Victoria)	Wednesday, 8 May 2019 at 7:00:00 am	AEST	UTC+10 hours
Wellington (New Zealand - Wellington)	Wednesday, 8 May 2019 at 9:00:00 am	NZST	UTC+12 hours
Honolulu (USA - Hawaii)	Tuesday, 7 May 2019 at 11:00:00 am	HST	UTC-10 hours
San Francisco (USA - California)	Tuesday, 7 May 2019 at 2:00:00 pm	PDT	UTC-7 hours
St. Louis (USA - Missouri)	Tuesday, 7 May 2019 at 4:00:00 pm	CDT	UTC-5 hours
New York (USA - New York)	Tuesday, 7 May 2019 at 5:00:00 pm	EDT	UTC-4 hours
London (United Kingdom - England)	Tuesday, 7 May 2019 at 10:00:00 pm	BST	UTC+1 hour
Berlin (Germany - Berlin)	Tuesday, 7 May 2019 at 11:00:00 pm	CEST	UTC+2 hours
Corresponding UTC (GMT)	Tuesday, 7 May 2019 at 21:00:00

Second meeting times:

Location	Local Time	Time Zone	UTC Offset
Melbourne (Australia - Victoria)	Wednesday, 8 May 2019 at 6:00:00 pm	AEST	UTC+10 hours
Wellington (New Zealand - Wellington)	Wednesday, 8 May 2019 at 8:00:00 pm	NZST	UTC+12 hours
Honolulu (USA - Hawaii)	Tuesday, 7 May 2019 at 10:00:00 pm	HST	UTC-10 hours
San Francisco (USA - California)	Wednesday, 8 May 2019 at 1:00:00 am	PDT	UTC-7 hours
St. Louis (USA - Missouri)	Wednesday, 8 May 2019 at 3:00:00 am	CDT	UTC-5 hours
New York (USA - New York)	Wednesday, 8 May 2019 at 4:00:00 am	EDT	UTC-4 hours
London (United Kingdom - England)	Wednesday, 8 May 2019 at 9:00:00 am	BST	UTC+1 hour
Berlin (Germany - Berlin)	Wednesday, 8 May 2019 at 10:00:00 am	CEST	UTC+2 hours
Corresponding UTC (GMT)	Wednesday, 8 May 2019 at 08:00:00

Fix broken links and outdated information in TDWG website

There are some broken links and outdated information relating to TNC on the TDWG website. We need to fix that, or where we can't fix it ourselves, report it.

Agents and References

Side note: Emerging from the CoL meeting was a renewed interest on creating a workflow to generate "clean" data buckets for literature and for agents (specifically agents as authors of literature). We may want to farm that out to an entirely separate group, but every time we've done that in the past it gets neglected and/or abandoned. Because Literature/Agents are of such fundamental importance to TNU-space, I think an argument could be made to include it within the scope of this effort. But another argument could be made to spin it off as a separate discussion group. I favor the former, but in any case, this will require minimally a set of separate issues. (i.e., we don't want to dwell on it here). I'll leave it to someone else to create the appropriate issue, as I'm still a GitHub noob.

Originally posted by @deepreef in #47 (comment)

TCS Markdown documents

As agreed at the meeting of 17/18 September, I have created Markdown documents of the TCS Schema. They can be found at https://github.com/tdwg/tnc/tree/master/tcs-deconstructed. These documents, or bits thereof, can be used as anchor point for further discussion of or comments about TCS.

This would have been better is a pull request, but I didn't think of that in time.

Define scope of TCS2

The scope of TCS2 and the covered information entities is unclear to me. So far the discussion in #1 has nearly exclusively dealt with Taxonomic Concepts and their relations. When I look at the ratified TCS schema and the aim of this group it should be much broader:

The aim of the Taxon Names and Concepts (TNC) group is to promote the understanding of taxonomic names and their relation to described taxa (taxon concepts). Taxonomic names and concepts are the fundamental units for communicating biological information. This group promotes the effective use of taxonomic names and concepts in biodiversity information for describing specimens and observations.

What about:

• structured name objects, nomenclatural relations and their status according to the codes?
• core vocabularies such as ranks?
• identifying and representing author objects?
• type specimens, species and subsequent designations?
• how does TCS2 deal with literature citations?

Proposed: 'protonym' property on TaxonomicNameUsage

I was just going to reopen issue #32, as the concept of protonym came up again in the discussion around issue #45, but the proposal has significantly changed, so I thought it best to open a new issue.

The protonym property was not included in the draft specification that was presented at the workshop at Biidiversity_Next, but I think we should include it. Earlier discussions were influenced by discussion around issue #34 to merge TaxonomicName into TaxonomicNameUsage and the idea that the protonym property could replace the basionym (and replaced synonym) property. I think we should completely separate these things. basionym and replaced synonyms are properties for names and have to be in accordance with the relevant nomenclatural code, while protonym is used to link Taxonomic Name Usages to an "original" Name Usage in a data graph. While in many cases the protonym can be inferred from the basionym or replaced synonym (I find myself doing coalesce(basionym_id, replaced_synonym_id, id) a lot), in non-trivial name histories – where either the protonym name or the taxonomic name are illegitimate or invalid, or where a name is accepted in a genus where the combination is not available – it cannot (or rather, the inference would be incorrect). In any case, protonym and basionym are different concepts. Having the protonym property allows us to use the basionym property exactly in accordance with the nomenclatural codes, without having to stretch the definitions to accommodate e.g. invalid names.

While the original proposal had protonym as a property of a TaxonomicName, @deepreef always intended it to be a property of a TaxonomicNameUsage and this proposal follows him. With this we will have separated concerns and made the TaxonomicNameUsage class independent of the TaxonomicName class: we could use e.g. a SKOS Extended Label (#25) instead of a TaxonomicName and everything would still work.

Vernacular names

We discussed vernacular names in our teleconference of 24 September 2019. At the time we introduced a vernacularName property on the TaxonomicNameUsage object and a VernacularName class that would be its object. The VernacularName class would contain taxonomicNameUsage, language and preferredName properties. However, somehow, in the diagram I presented at Biodiversity_Next, the VernacularName object had a taxonomicName instead of a taxonomicNameUsage property.

I can't remember whether I made a mistake in the minutes of the meeting or in the diagram, but I now think it would be best to not have a VernacularName class at all and have a TaxonomicNameUsage as the object for the vernacularName property. We can add the preferredName flag to the TaxonomicNameUsage class (maybe rename it to isPreferredVernacularName); I had already put dcterms:language in the TaxonomicName class.

I think other people at the meeting might have been here already at the meeting, but what are people's thoughts?

I think this keeps us very close to TCS, where Vernacular Name was a Taxon Relationship Type. In fact, one can deal with what users of "scientific names" would call "vernacular names" by way of Taxon Relationship Assertions, which might be more appropriate in, for example, ethnobiological studies, or for people who don't want to use scientific names themselves, but still want to refer to vernacular name usages by others.

We could also include a scientificName property in the TaxonomicNameUsage class for usages where the taxonomicName is a vernacular name (like in field guides).

Teleconference 29 January 2019

The next meeting of the TNC will be Tuesday, 29 January 2019 at 20:00 UTC. Times for other time zones are in the table below. Zoom conference details will follow later.

The following will be on the agenda:

TNC charter

I don't want to spend too much meeting time on this, so I propose a little hackathon in February.

Workshop before TDWG 2019

This is not the workshop at biodiversity_next for which we submitted the proposal in November, but a longer workshop for TNC core members and some other invitees before the conference (i.e. a names_first workshop). I think our meetings so far have been very useful, but they are always over very quickly, and I think it would be valuable to have a longer meeting where we are all in the same room (also, when daylight-saving ends, or starts, it will be harder to have teleconferences where everybody can be). So I would like to discuss a two-day workshop before the conference. The timing will be good, as by then we have lots of things to cut short and.or complete.

New standard document

https://docs.google.com/document/d/1bcfjhh0ztmXKz7P9G0ni7vYZc3MtH4LLxlCZjswF2k4

This will hopefully be the main course. In order for people to get a better sense of how we are tracking I have divided the things we need to discuss into five broad categories, here given in the order I think we should discuss them:

• Core terms (#26)
  This includes everything in TaxonomicName and the name and publication details in TaxonomicNameUsage.

• Relationships (#16)
  This is really core in TCS, but has taken a bit of a back seat in the TDWG Taxon Concept LSID Ontology and certainly in implementations. We need to get them back up there, which is why I've put them right after the Core terms.

• Typification (#28)
  Needs no explanation.

• Circumscription (#27)
  This is ostensibly very important in TCS, but unclear (to me at least) how to properly implement, especially the character circumscription. I am not sure if there are any implementations that have implemented circumscription and think it has become less important (I mean strictly for what we are talking about in the TNC) now that we are talking about taxonomic name usages rather than taxon concepts.

• Facts
  I don't think this is in TCS, but is mentioned in the TDWG Taxon Concept LSID Ontology and is important in the Berlin Model. I think facts are better dealt with by another interest group.

At this time we are still very much in the 'Core terms' category. At the meeting we will revisit the authorship, as it has been the subject of a fair amount of discussion after our previous meeting and then move on to core concepts in the TaxonomicNameUsage class.

Location	Local Time	Time Zone	UTC Offset
Melbourne (Australia - Victoria)	Wednesday, 30 January 2019 at 7:00:00 am	AEDT	UTC+11 hours
Wellington (New Zealand - Wellington)	Wednesday, 30 January 2019 at 9:00:00 am	NZDT	UTC+13 hours
Honolulu (USA - Hawaii)	Tuesday, 29 January 2019 at 10:00:00 am	HST	UTC-10 hours
San Francisco (USA - California)	Tuesday, 29 January 2019 at 12:00:00 noon	PST	UTC-8 hours
St. Louis (USA - Missouri)	Tuesday, 29 January 2019 at 2:00:00 pm	CST	UTC-6 hours
New York (USA - New York)	Tuesday, 29 January 2019 at 3:00:00 pm	EST	UTC-5 hours
London (United Kingdom - England)	Tuesday, 29 January 2019 at 8:00:00 pm	GMT	UTC
Berlin (Germany - Berlin)	Tuesday, 29 January 2019 at 9:00:00 pm	CET	UTC+1 hour
Corresponding UTC (GMT)	Tuesday, 29 January 2019 at 20:00:00

TODO Circumscription

Placeholder for work on Circumscription, for project board.

Teleconference 17/18 September 2018

The first teleconference (since TDWG 2018) of the Taxonomic Names and Concepts Interest Group will be held on 17 or 18 September 2018, depending on your location. I've picked two times, Monday, 17 September at 21:00 UTC and Tuesday, 18 September at 08:00 UTC, which should give everyone a chance to attend at least one meeting at a reasonable hour. People who are keen should feel free to attend both meetings.

I will add the Zoom link in this spot later. We are having video conferencing equipment, which comes with a Zoom account, installed here at the Royal Botanic Gardens Victoria this Friday, so I don't have the account details yet.

This first meeting will be about what we intend to do until TDWG 2019 and how we will go about our business. Later meetings will be more fun.

Agenda

1. Charter
   • Goals
   • Core members
2. Where do we start and how do we proceed?
3. Use of GitHub repositories, issues and wikis.

(I might change that later when I have a better idea on how to fit it all together)