Re: Next step for biodiversity terms

Hi all,

@Franck Michel <franck.michel@cnrs.fr> could you please pick up this
two-identifier requirement raised by Carl? If needed, either ask Carl to
create a GitHub issue or go ahead and do it yourself.

Regards,

On Thu, Feb 13, 2020 at 7:49 PM Carl Boettiger <cboettig@gmail.com> wrote:

> 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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