[Taxacom] Wikidata and Wikispecies

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Sun Oct 25 15:58:12 CDT 2015


The problem with this schema is that names are taxon identifiers! How do you give a taxon an identifier without effectively creating a new name, based on a whole new system of nomenclature? For a species, the original combination (corrected for any homonymy) should be the taxon identifier. If it isn't "machine friendly enough" then a human  INVISIBLE "machine friendly" equivalent should be used, but people see only the original combination.

Stephen

--------------------------------------------
On Mon, 26/10/15, Roderic Page <Roderic.Page at glasgow.ac.uk> wrote:

 Subject: Re: [Taxacom] Wikidata and Wikispecies
 To: "Paul Kirk" <P.Kirk at kew.org>, "TaxaCom" <taxacom at mailman.nhm.ku.edu>
 Received: Monday, 26 October, 2015, 2:08 AM
 
 Hi Paul,
 
 Sorry for the confusion. Yes,
 I mean something like this:
 
 taxon A - taxon identifier
 |
 \ - has names - + name identifier 1
                           |
                           + name
 identifier 2
                    
       |
                      
     + name identifier 3 * accepted name
 
 So, a fungus may have a GBIF
 and/or NCBI taxon id, and a list of Index Fungorum LSIDs for
 all the names that have been applied to that concept, one of
 which is flagged as “accepted” [in an ideal world we
 could just compute which name was “accepted” based on
 the set of types (specimens or taxa) in that taxon].
 
 LSIDs are fine in and of
 themselves, we just messed up the crucial step of building
 essential services on top of them (e.g., what CrossRef did
 with DOIs we should have done with LSIDs).
 
 Regards
 
 Rod
 
 ---------------------------------------------------------
 Roderic Page
 Professor of
 Taxonomy
 Institute of Biodiversity, Animal
 Health and Comparative Medicine
 College of
 Medical, Veterinary and Life Sciences
 Graham
 Kerr Building
 University of Glasgow
 Glasgow G12 8QQ, UK
 
 Email:  Roderic.Page at glasgow.ac.uk<mailto:Roderic.Page at glasgow.ac.uk>
 Tel:  +44 141 330 4778
 Skype:  rdmpage
 Facebook:  http://www.facebook.com/rdmpage
 LinkedIn:  http://uk.linkedin.com/in/rdmpage
 Twitter:  http://twitter.com/rdmpage
 Blog:  http://iphylo.blogspot.com
 ORCID:  http://orcid.org/0000-0002-7101-9767
 Citations:  http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
 ResearchGate https://www.researchgate.net/profile/Roderic_Page
 
 
 On 25 Oct
 2015, at 12:49, Paul Kirk <P.Kirk at kew.org<mailto:P.Kirk at kew.org>>
 wrote:
 
 Just a quick comment
 here Rod because when I read your post there were too many
 singulars and plurals mixed together that I was not sure
 what you were saying.
 
 So, a
 name (singular) has an identifier, a taxon (singular) could
 have a single identifier but ... a taxon could also be made
 up of more than one name identifiers for which one is
 'tagged' as the correct name for the taxon concept
 (the other name(s) [the synonyms] could be just a bunch of
 homotypic/objective synonyms of two or more of these bunches
 - i.e. heterotypic/subjective synonyms). Of course, this is
 a simplification because these taxon concepts are just based
 around the specimens which are the name bearing types - a
 more comprehensive taxon concept would include other
 specimens (museum, herbarium, fungarium accession
 'numbers'), published descriptions and illustrations
 (via DOIs) and perhaps sequence data (GenBank accession
 'numbers').
 
 Just a
 few random thoughts ...
 
 Paul
 
 p.s.
 still not sure about LSIDs :-)
 ________________________________________
 From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu<mailto:taxacom-bounces at mailman.nhm.ku.edu>>
 on behalf of Roderic Page <Roderic.Page at glasgow.ac.uk<mailto:Roderic.Page at glasgow.ac.uk>>
 Sent: 25 October 2015 12:08
 To:
 TaxaCom
 Subject: Re: [Taxacom] Wikidata and
 Wikispecies
 
 Hi Andy,
 
 Much as I like Wikidata, I’m
 a bit sceptical.
 
 From my
 perspective, leaving aside any sociology, Wikispecies’
 biggest limitation was that it didn’t cleanly separate
 taxonomic names (factual statements about who published a
 name and where and when they did that) and taxonomic
 concepts (“taxa”, the things that most biologists talk
 about, such as a particular species). For some background on
 the distinction se http://dx.doi.org/10.2307/1223932, PDF
 here http://www.hyam.net/publications/prometheus_1.pdf
 
 Not clearly separating these
 effectively doomed Wikispecies because why would you have
 two wikis for taxa? And, if you did, clearly Wikipedia was
 going to win.
 
 In my opinion
 the niche for Wikispecies was nomenclature, a wiki of
 taxonomic names where we could have all the names, their
 variants, the objective links between them, the
 publications, their dates, and their authors. Not
 necessarily exciting stuff, but vital, and also factual.
 
 Nomenclature would seem
 ideally suited to Wikidata, in that its a set of facts,
 increasingly linked to stable identifiers (DOIs for papers,
 ORCID, ISNI, etc. for people, LSIDs for names). However,
 Wikidata seems to conflate taxa and taxonomic names (to be
 fair, many taxonomic databases do this), and so you have
 things such as IPNI identifiers being associated with taxa,
 when these are identifiers for names, not taxa. There
 doesn’t seem to be a Wikidata item for taxonomic names.
 
 So, my concern is that
 Wikidata is setting itself up for problems down the line,
 problems it could avoid by rethinking how it handles
 nomenclature and taxonomy.  The analogy isn’t exact, but
 it’s a bit like the difference between a person’s name
 and the actual person. For example,today’s featured page
 on “Juliet” https://www.wikidata.org/wiki/Q15639217
 is closer to what I think Wikidata should be doing for
 taxonomic names. For example, for the actress Juliet
 Stevenson https://www.wikidata.org/wiki/Q272518
 Wikidata gives her first name not as a string
 “Juliet” but as an instance of the female given name
 “Juliet” https://www.wikidata.org/wiki/Q20000410
 . Equivalently for taxa,  it’s “accepted name” be
 an instance of taxonomic name, and all publication and
 nomenclatural stuff for the name should be associated with
 that instance.That way you could also separate identifiers
 for names (e.g., IPNI, Zoobank, ION, etc.) from identifiers
 for taxa (GBIF, EOL, NCBI, etc.).
 
 Regards
 
 Rod
 
 ---------------------------------------------------------
 Roderic Page
 Professor of
 Taxonomy
 Institute of Biodiversity, Animal
 Health and Comparative Medicine
 College of
 Medical, Veterinary and Life Sciences
 Graham
 Kerr Building
 University of Glasgow
 Glasgow G12 8QQ, UK
 
 Email:  Roderic.Page at glasgow.ac.uk<mailto:Roderic.Page at glasgow.ac.uk><mailto:Roderic.Page at glasgow.ac.uk>
 Tel:  +44 141 330 4778
 Skype:  rdmpage
 Facebook:  http://www.facebook.com/rdmpage
 LinkedIn:  http://uk.linkedin.com/in/rdmpage
 Twitter:  http://twitter.com/rdmpage
 Blog:  http://iphylo.blogspot.com
 ORCID:  http://orcid.org/0000-0002-7101-9767
 Citations:  http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
 ResearchGate https://www.researchgate.net/profile/Roderic_Page
 
 
 On 23 Oct
 2015, at 15:45, Andy Mabbett <andy at pigsonthewing.org.uk<mailto:andy at pigsonthewing.org.uk><mailto:andy at pigsonthewing.org.uk>>
 wrote:
 
 Those of you who have an
 interest in Wikispecies, or Wikidata (two
 projects hosted by the Wikimedia Foundation,
 who also host Wikipedia)
 might like to know
 that the two projects are now linked. For an
 overview, see;
 
 https://www.wikidata.org/wiki/Wikidata:Wikispecies
 
 This is the first stage of
 their integration; the second will allow
 Wikispecies to pull data from Wikidata onto its
 pages.
 
 What happens after
 that is still being discussed, but technically
 there is potential for all the data to be
 migrated to Wikidata (where
 a lot of it is
 currently duplicated), and for Wikidata to be a front
 end to view or edit that data.
 
 --
 Andy
 Mabbett
 @pigsonthewing
 http://pigsonthewing.org.uk
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