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Re: Next step for biodiversity terms

From: Carl Boettiger <cboettig@gmail.com>
Date: Thu, 13 Feb 2020 10:49:00 -0800
Message-ID: <CAN_1p9zv3Jnkp6MeGa-Qw6EruTU21sa4WVKvJLbQE2+=x=Ca4g@mail.gmail.com>
To: "LJ.Garcia" <lj.garcia.co@gmail.com>
Cc: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>, Franck Michel <franck.michel@cnrs.fr>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>, robgur@gmail.com
Thanks!

Yes, identifiers are of course the solution, the point is that you need two
different identifiers and you need to know which is which.  Here's a quick
DarwinCore example:

 {

"taxonID": "ITIS:1000254",

"scientificName": "Rollandia micropterum",

"acceptedNameUsageID": "ITIS:562791",

"taxonomicStatus": "synonym",

"vernacularName": "Titicaca Grebe"

}



We don't need `taxonomicStatus` explicitly here, since it is implied by
seeing that the accepted ID (acceptedNameUsageID) is not the same thing as
the taxonID for this name.  But we do need two identifiers, and we need to
know which one is which.  It's not clear to me how the above would be
represented in the schema.org proposal.  (of course one could say "don't
use synonyms! but we may as well then say "don't use scientific names, just
use accepted identifiers" but we live in a world that uses scientific names
so we need these mechanism that can acknowledge some names are synonyms)

---
Carl Boettiger
http://carlboettiger.info/


On Thu, Feb 13, 2020 at 9:58 AM LJ.Garcia <lj.garcia.co@gmail.com> wrote:

> Hi Carl, Franck, all,
>
> @Carl, Franck is probably the best person to point you to
> discussions/reasons regarding the property names. I am not much aware of
> how synonyms are handled in Darwin Core so my question could be naïve
> but... having different identifiers would not help there? Identifiers in
> Bioschemas should be FAIR, so, even if the label is the same, the
> identifier should tell you better, would not it? Regarding taxonomic
> concepts, again, Franck is the one that can answer better.
> @Franck, if necessary, further properties could be included at this point
> as the submission to schema.org still will take a bit. Also, if not done
> already, I would suggest to add examples per property so people understand
> better how to use them.
>
> Kind regards,
>
> On Wed, Feb 12, 2020 at 5:18 PM Carl Boettiger <cboettig@gmail.com> wrote:
>
>> Hi Alasdair,
>>
>> Thanks for the update and your work on this.  In the spirit of
>> demonstrating adoption, I think it would be great if the recommendation
>> reflected greater alignment with existing namespaces that are widely used
>> in taxonomy, such as Darwin Core, https://dwc.tdwg.org/terms/#taxon .
>>
>> I think this would greatly facilitate adoption.  For instance, the
>> current specification provides no mechanism to disambiguate synonyms (
>> https://dwc.tdwg.org/terms/#dwc:taxonomicStatus,
>> https://dwc.tdwg.org/terms/#dwc:acceptedNameUsageID) or taxonomic
>> concepts.  I'm also unclear on the utility of `childTaxon` and
>> `hasDefinedTerm` in the current bioschemas spec.  Apologies if I've missed
>> the boat on these discussions already, but these are certainly barriers to
>> me in using bioschemas over an existing namespace like Darwin Core.  (Also
>> cc'ing Rob Guralnick on this who has far more expertise than I in this area
>> and could speak more broadly to the potential for adoption of
>> https://bioschemas.org/types/Taxon/0.3-RELEASE-2019_11_18/)
>>
>> Cheers,
>>
>> Carl
>>
>>
>>
>> ---
>> Carl Boettiger
>> http://carlboettiger.info/
>>
>>
>> On Wed, Feb 12, 2020 at 4:04 AM Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
>> wrote:
>>
>>> Hi Franck,
>>>
>>> Sorry for the slowness of my response, I have been off work for most of
>>> January and am now catching up with things.
>>>
>>> The status of getting things added to Schema.org is that we need to
>>> demonstrate usage of the deployed markup rather than just deployments of
>>> it. This is the focus of the latest ELIXIR sponsored project which will be
>>> aiming to demonstrate benefit of the markup within specific areas: rare
>>> disease, plants, intrinsically disordered proteins, and toxicology. This
>>> work will be running over the next 23 months.
>>>
>>> As such, we should not delay work on other types. So yes, we should
>>> progress the work on Taxon and TaxonName.
>>>
>>> The restructuring of the website that we conducted at the tail end of
>>> last year was motivated by making it clearer as to which profiles and types
>>> are released for general use and which are still under development.
>>>
>>> Best regards
>>>
>>> Alasdair
>>>
>>>
>>> On 11 Feb 2020, at 17:04, LJ.Garcia <lj.garcia.co@gmail.com> wrote:
>>>
>>> Hi,
>>>
>>> I am away this week so please allow me some extra days to have a look to
>>> this.
>>>
>>> Kind regards,
>>>
>>> On Saturday, February 8, 2020, Franck Michel <franck.michel@cnrs.fr>
>>> wrote:
>>>
>>>> Dear Alasdair and Leyla,
>>>>
>>>> I was wondering if you had time to check my last reply in issue 309
>>>> <https://github.com/BioSchemas/specifications/issues/309#issuecomment-576247584>.
>>>> I was suggesting that, if endorsing of the Taxon term by schema.org is
>>>> still gonna take some time, what about trying to move directly to the new
>>>> couple (Taxon, TaxonName) that we have discussed since mid-2019.
>>>>
>>>> Any thoughts on this?
>>>>
>>>> Thx,
>>>>     Franck.
>>>>
>>>> --
>>>>
>>>>
>>>> Franck MICHEL - CNRS research engineer
>>>> Université Côte d’Azur, CNRS, Inria
>>>> I3S laboratory (UMR 7271)
>>>> franck.michel@cnrs.fr - +33 (0)4 8915 4277
>>>>
>>>>
>>>
>>> --
>>> Alasdair J G Gray
>>> Associate Professor in Computer Science,
>>> School of Mathematical and Computer Sciences
>>> Heriot-Watt University, Edinburgh, UK.
>>>
>>> Email: A.J.G.Gray@hw.ac.uk <A.J.G.Gray@hw.ac.uk>
>>> Web: http://www.macs.hw.ac.uk/~ajg33
>>> ORCID: http://orcid.org/0000-0002-5711-4872
>>> Office: Earl Mountbatten Building 1.39
>>> Twitter: @gray_alasdair
>>>
>>> To arrange a meeting: http://doodle.com/ajggray
>>>
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Received on Thursday, 13 February 2020 18:49:28 UTC

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