[Taxacom] Wikidata and Wikispecies

JF Mate aphodiinaemate at gmail.com
Thu Oct 29 04:45:38 CDT 2015


In regards to UNITE (and as a fungal ignoramus), the number of
hypotheses seems to be <100K not 500K, and it depends on threshold
value (53K by the 1,5% default). I am quite familiar with the issues
with arthropod universal "thresholds" (or lack-of) but what is the
experience for fungal workers out there?

Best

Jason

On 29 October 2015 at 09:38, Urmas Kõljalg <urmas.koljalg at ut.ee> wrote:
>
>
> Hi all,
>
> In addition to Paul: INSDC and other publicly available DNA sequences of
> fungi are already duplicated, annotated and split into species
> hypotheses by the UNITE community (http://unite.ut.ee). The version 7
> include nearly 500 000 species hypotheses and they all are published
> with unique DOIs. All species hypotheses and their DOIs are connected to
> the taxonomic backbone. Provided by the Index Fungorum by the way.
>
> Just to add that this resource is utilised by almost all major NGS
> pipelines (QIIME, mothur, etc.) for the sequences based identification
> of fungi.
>
> You may also say that this is largest DNA barcoding project of fungi
> since 2001.
>
> Best,
>
> Urmas
>
> 29-10-2015 10:22 kirjutas Paul Kirk:
>
>> Rod,
>>
>> Your last paragraph might be interpreted by some to mean that you consider the existing resources in the domain of nomenclature and taxonomy are not useful. Since molecular data are now very important in defining taxa in the fungi perhaps Wikidata should be encouraged to duplicate the resources available from the INSDC ;-)
>>
>> Paul
>> ________________________________________
>> From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of Roderic Page <Roderic.Page at glasgow.ac.uk>
>> Sent: 27 October 2015 07:52
>> To: Andy Mabbett
>> Cc: Taxa com
>> Subject: Re: [Taxacom] Wikidata and Wikispecies
>>
>> Hi Andy,
>>
>> Not quite. In the example you give the taxon name is a simple string, whereas I'd ague it should be an item with its own properties. In the same way that for people Wikidata can first and last names as items, e..g. https://m.wikidata.org/wiki/Q272518 [1] rather than strings.
>>
>> Doing this will (a) avoid conflating names and taxa, and (b) make Wikidata a lot more attractive as a repository of nomenclatural facts, many of which are a good fit for Wikidata (dates, people, publications, specimens). It also means you could align Wikidata with the main repositories of nomenclature, such as ZooBank, ION, IPNI, etc.
>>
>> I guess I think Wikidata has an opportunity to be genuinely useful to biologists if it spends a little time to sort out how it models taxa and names, otherwise it's an opportunity missed.
>>
>> Regards
>>
>> Rod
>>
>> Sent from Outlook<http://aka.ms/Ox5hz3 [2]>
>>
>> _____________________________
>> From: Andy Mabbett <andy at pigsonthewing.org.uk<mailto:andy at pigsonthewing.org.uk>>
>> Sent: Monday, October 26, 2015 8:53 p.m.
>> Subject: Re: [Taxacom] Wikidata and Wikispecies
>> To: Roderic Page <roderic.page at glasgow.ac.uk<mailto:roderic.page at glasgow.ac.uk>>
>>
>> On 25 October 2015 at 12:08, Roderic Page <Roderic.Page at glasgow.ac.uk<mailto:Roderic.Page at glasgow.ac.uk>> wrote:
>>
>>> 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).
>>
>> On the contrary, I think it does.
>>
>> https://www.wikidata.org/wiki/Q25404 [3] is a Wikidata item representing a
>> species (taxon). One property of that item is that it is known by the
>> taxon name (P225) "Cyanistes caeruleus", - which, further, was
>> authored (P405) by Lnnaeus (item Q1043) in the year (P574) 1758.
>>
>> Or is that not what you meant?
>>
>> Anyone wanting to know more, or to contribute, may do so at:
>>
>> https://www.wikidata.org/wiki/Wikidata:WikiProject_Taxonomy [4]
>>
>> --
>> Andy Mabbett
>> @pigsonthewing
>> http://pigsonthewing.org.uk [5]
>>
>> On 25 October 2015 at 12:08, Roderic Page <Roderic.Page at glasgow.ac.uk> wrote:
>>
>>> 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).
>>
>> On the contrary, I think it does.
>>
>> https://www.wikidata.org/wiki/Q25404 [3] is a Wikidata item representing a
>> species (taxon). One property of that item is that it is known by the
>> taxon name (P225) "Cyanistes caeruleus", - which, further, was
>> authored (P405) by Lnnaeus (item Q1043) in the year (P574) 1758.
>>
>> Or is that not what you meant?
>>
>> Anyone wanting to know more, or to contribute, may do so at:
>>
>> https://www.wikidata.org/wiki/Wikidata:WikiProject_Taxonomy [4]
>>
>> --
>> Andy Mabbett
>> @pigsonthewing
>> http://pigsonthewing.org.uk [5]
>> _______________________________________________
>> Taxacom Mailing List
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>>
>> Celebrating 28 years of Taxacom in 2015.
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>>
>> Celebrating 28 years of Taxacom in 2015.
>
>
>
> Links:
> ------
> [1] https://m.wikidata.org/wiki/Q272518
> [2] http://aka.ms/Ox5hz3
> [3] https://www.wikidata.org/wiki/Q25404
> [4] https://www.wikidata.org/wiki/Wikidata:WikiProject_Taxonomy
> [5] http://pigsonthewing.org.uk
> [6] http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> [7] http://taxacom.markmail.org
> _______________________________________________
> Taxacom Mailing List
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>
> Celebrating 28 years of Taxacom in 2015.



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