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Re: [SUSPECTED SPAM] Re: Bioschemas.org to define biodiversity-related markup

From: Franck Michel <franck.michel@cnrs.fr>
Date: Tue, 12 Jun 2018 11:02:03 +0200
To: LJ Garcia Castro <ljgarcia@ebi.ac.uk>, Ricardo Arcila <ricartomojo@gmail.com>
Cc: public-bioschemas@w3.org, "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>, "Rafael C. Jimenez" <rafael.jimenez@elixir-europe.org>, "Carole Goble (carole.goble@manchester.ac.uk)" <carole.goble@manchester.ac.uk>
Message-ID: <7847bbfe-4b8b-50bc-c5e2-6fa8a0dcc78d@cnrs.fr>
Dear Ricardo and Leyla,

I just made a pull request, and I created a Biodiversity specification 
folder on Google drive. Let me know if anything is not right. I've set 
myself as the group leader, but I would feel more comfortable if someone 
of the community would join me in this role. And obviously, you are most 
welcome to join the group!

 > will be Taxon a BioChemEntity? I am asking because in UniProt we have 
proteins link to what is defined as an "unknown" taxon in NCBI 
taxonomy/UniProt taxonmy. I guess, even if iwe have this "unknown" case, 
we could still use BiochemEntity and suppose any "unknow" will be 
eventually resolve to an actual entity. Happy to chat about it.
I agree, the large definition of BioChemEntity makes it appropriate as 
the root of Taxon. So far, I think of Taxon as a profile more than a 
type of its own. I'll read the wiki and start drafting something. I let 
you know if (most probably when) I have any question. ;)

Regards,
     Franck.

Le 11/06/2018 à 15:46, LJ Garcia Castro a écrit :
>
> Hello Franck,
>
> The taxon profile has been mentioned as one we need before but there 
> was no group for it. Wonderful you are starting one now! Please ask 
> whenever you have a doubt about the process or the different 
> approaches (third-party vocabs or additionalProperty) to deal with 
> properties not covered by BioChemEntity.
>
> By the way, will be Taxon a BioChemEntity? I am asking because in 
> UniProt we have proteins link to what is defined as an "unknown" taxon 
> in NCBI taxonomy/UniProt taxonmy. I guess, even if iwe have this 
> "unknown" case, we could still use BiochemEntity and suppose any 
> "unknow" will be eventually resolve to an actual entity. Happy to chat 
> about it.
>
> Regards,
>
>
>
> On 11/06/2018 14:39, Ricardo Arcila wrote:
>> Hello Franck,
>>
>> It is a good idea to start by creating the group. You can do it by 
>> creating a pull request on the bioschemas groups repository 
>> <https://github.com/BioSchemas/bioschemas.github.io/tree/master/_groups>. 
>> Then you can add yourself on the people repository 
>> <https://github.com/BioSchemas/bioschemas.github.io/tree/master/_people>. 
>> I will be happy to help you in this process and if you'd like I could 
>> be part of the group as well.
>>
>> In order to start a draft specification for Taxon you should create a 
>> folder with the profile name on the specifications drive folder 
>> <https://drive.google.com/drive/folders/0Bw_p-HKWUjHoNThZOWNKbGhOODg?usp=sharing>. 
>> This process its detailed on the bioschemas github wiki 
>> <https://github.com/BioSchemas/specifications/wiki/Bioschemas-Specification-Process>.
>>
>> Please let me know if you have any question or doubt about the 
>> process, I will be most happy to help.
>>
>>
>> Best regards,
>> Ricardo Arcila
>>
>>
>> On Thu, Jun 7, 2018 at 9:54 AM Franck Michel <franck.michel@cnrs.fr 
>> <mailto:franck.michel@cnrs.fr>> wrote:
>>
>>     Hi all,
>>
>>     I'm catching up with the discussions on the list, and I'm happy
>>     to see that things are moving on with the submission of new types
>>     to schema.org <http://schema.org>.
>>
>>     At the same time, I realize that we did not really go ahead about
>>     the biodiversity topic. As I will present a poster about
>>     Bioschemas.org at the Biodiversity Information Standard in
>>     August, that would maybe be a good thing to initiate the work on
>>     this by this date. How do we go on? I suggested the creation of a
>>     a Taxon profile, but we may have to start with the creation of a
>>     group?
>>     Could you please guide me/us in this process?
>>
>>     Thx,
>>         Franck.
>>
>>     Le 23/01/2018 à 11:09, Leyla Garcia a écrit :
>>>     Hello Bioschemas governance team,
>>>
>>>     What do you think about going ahead with the Biodiversity
>>>     schemas? Do we have a heads up?
>>>
>>>     @Franck, I am not really aware of those organizations but I am
>>>     happy to guide you through the work we have done for Bioschemas
>>>     so far. I worked a bit on a biodiversity project but that was
>>>     some years ago. Still, I like the subject!
>>>
>>>     Let's wait to see what Carole, Rafael and Alasdair suggest.
>>>
>>>     Regards,
>>>
>>>     On 23/01/2018 08:47, Franck Michel wrote:
>>>>     Dear Leyla and all,
>>>>
>>>>     I understand that your response stands for a GO. Right?
>>>>
>>>>     I've not been involved yet in the specification of the
>>>>     Bioschemas.org profiles. So indeed, I shall need help and
>>>>     guidance as to how things are going on, the tools, the process,
>>>>     the expected outcomes, etc.
>>>>
>>>>     As I proposed, we could start with contacting people that would
>>>>     potentially be interested in taking part into this. I'm
>>>>     thinking about Encyclopedia of Life, Catalogue of Life, GBIF.
>>>>     If you already know contacts in these organizations, that would
>>>>     certainly be helpful.
>>>>
>>>>     Franck.
>>>>
>>>>     Le 22/01/2018 à 11:37, Leyla Garcia a écrit :
>>>>>     Hi Franck,
>>>>>
>>>>>     Great news!
>>>>>
>>>>>     Do you need any help/guides for the start-up?
>>>>>
>>>>>     Cheers,
>>>>>
>>>>>
>>>>>     On 17/01/2018 15:24, Franck Michel wrote:
>>>>>>     Dear all,
>>>>>>
>>>>>>     I'm following up on this suggestion about creating a
>>>>>>     biodiversity-related group in Bioschemas.org.
>>>>>>
>>>>>>     The proposition received four +1's. I'm not sure if there is
>>>>>>     a "minimum score" to attest of sufficient consensus.
>>>>>>
>>>>>>     As we discussed, if we go for the creation of this group, it
>>>>>>     would be beneficial to involve at least EoL folks, possibly
>>>>>>     other people from the biodiversity community. I can try to
>>>>>>     initiate this, yet before I would like to have an official GO
>>>>>>     from our community.
>>>>>>
>>>>>>     Let me know how this usually works, and what you think about
>>>>>>     this.
>>>>>>
>>>>>>     Regards,
>>>>>>         Franck.
>>>>>>
>>>>>>     Le 17/11/2017 à 16:40, Franck Michel a écrit :
>>>>>>>     Hi Mélanie, hi all,
>>>>>>>
>>>>>>>     To go a bit further I've tried to somewhat extend the
>>>>>>>     example I've initiated. There it is:
>>>>>>>     https://github.com/frmichel/taxref-ld/tree/master/bioschemas-org
>>>>>>>     The README gives details as to how the example file is
>>>>>>>     organized, and more importantly it lists some of the issues
>>>>>>>     and questions that we shall have to tackle if we officially
>>>>>>>     start the group.
>>>>>>>
>>>>>>>     @Alasdair, Carole, Rafael: as discussed in the thread, at
>>>>>>>     some point it shall be beneficial to to invite people from
>>>>>>>     EoL and TDWG. Is there some sort of "official" channel for
>>>>>>>     the community to do that?
>>>>>>>
>>>>>>>     Have a nice week-end,
>>>>>>>         Franck.
>>>>>>>
>>>>>>>     Le 17/11/2017 à 10:19, Melanie Courtot a écrit :
>>>>>>>>     Hi Frank, all,
>>>>>>>>
>>>>>>>>     On 16/11/2017 09:37, Franck Michel wrote:
>>>>>>>>>     Hi Meanie, hi all,
>>>>>>>>>
>>>>>>>>>     EoL provides an API that returns species descriptions as
>>>>>>>>>     JSON-LD based on schemas.org <http://schemas.org>. Beluga
>>>>>>>>>     example: http://eol.org/api/traits/328541
>>>>>>>>>     It is unclear who consumes this data, but at least, as you
>>>>>>>>>     already saw, they embed it at the end of their own web
>>>>>>>>>     pages such as http://eol.org/pages/328541/data.
>>>>>>>>     BioSamples does the same - an API to retrieve JSON and we
>>>>>>>>     embed it in our webpages for crawler as well.
>>>>>>>>>
>>>>>>>>>     As you also noticed, the JSON-LD they provide is not
>>>>>>>>>     valid. I didn't know about that EOL Github issue, but I
>>>>>>>>>     recently discussed it with Rod Page from the Biodiversity
>>>>>>>>>     Information Standards (aka TDWG), who replied on the
>>>>>>>>>     Github issue. The Google structured data testing tool
>>>>>>>>>     gives more details on that: https://frama.link/xJm0AAto
>>>>>>>>>     Besides, other errors are not reported (well, I think
>>>>>>>>>     these are errors): property scienfiticName without any
>>>>>>>>>     namespace is invalid, that should be dwc:scientificName
>>>>>>>>>     since this does not exist in schema.org
>>>>>>>>>     <http://schema.org>. Same issue for vernacularName,
>>>>>>>>>     traits, units...
>>>>>>>>>
>>>>>>>>>     But whatever, this JSON-LD has lots of issues, but it's a
>>>>>>>>>     start. 
>>>>>>>>
>>>>>>>>     Yes. Only mentioned the tweaks in case someone wanted to
>>>>>>>>     give it a try as well.
>>>>>>>>
>>>>>>>>>     The assumption is that there is some sort of specific
>>>>>>>>>     (one-to-one) agreement between EoL and Google, and that
>>>>>>>>>     Google harvests this data despite the invalid JSON-LD. But
>>>>>>>>>     I have no confirmation of that
>>>>>>>>
>>>>>>>>     It'd be interesting to clarify this. It seems a little bit
>>>>>>>>     counter intuitive that EoL would mark their pages up with
>>>>>>>>     JSON for Google to read it but then Google couldn't do so
>>>>>>>>     without a special adapter? We're probably missing a piece
>>>>>>>>     of the story.
>>>>>>>>>
>>>>>>>>>     > - the measurement type points to
>>>>>>>>>     http://purl.obolibrary.org/obo/VT_0001256, which is body
>>>>>>>>>     length. The schema.org/predicate
>>>>>>>>>     <http://schema.org/predicate> value is also "body length
>>>>>>>>>     (VT)". How is this understood and displayed as Length on
>>>>>>>>>     the Google result?
>>>>>>>>>     - Similar question for the actual value and units, which
>>>>>>>>>     are "4249.83" and "mm" respectively. Is Google doing some
>>>>>>>>>     sort of unit conversion/roundup for display?
>>>>>>>>>
>>>>>>>>>     Good question. Typically about the unit "mm":
>>>>>>>>>     - "units": "mm" => there is no such thing as
>>>>>>>>>     http://schema.org/units
>>>>>>>>>     - "dwc:measurementUnit":
>>>>>>>>>     "http://purl.obolibrary.org/obo/UO_0000016"
>>>>>>>>>     <http://purl.obolibrary.org/obo/UO_0000016> => this seems
>>>>>>>>>     to be the only reliable property, but then Google knows
>>>>>>>>>     the Darwin Core vocabulary and interprets it.
>>>>>>>>>     My assumption is that Google performs some treatment on
>>>>>>>>>     the values. Possibly, they developed a specific connector
>>>>>>>>>     to cope with EoL JSON-LD and translate this body size to
>>>>>>>>>     "4.2 m".
>>>>>>>>>     Besides, the snippet mentions "4.2 m *(Adult)*", so they
>>>>>>>>>     also presumably consider this property:
>>>>>>>>>     eol:traitUri"http://eol.org/resources/704/measurements/adultheadbodylen27"
>>>>>>>>>     <http://eol.org/resources/704/measurements/adultheadbodylen27>
>>>>>>>>>     to know that this is the size of an adult.
>>>>>>>>>
>>>>>>>>>     With proper Bioschemas.org profiles, I think we could
>>>>>>>>>     annotate pages from many other institutions, such as the
>>>>>>>>>     Beluga page
>>>>>>>>>     <https://inpn.mnhn.fr/espece/cd_nom/60932?lg%3Den> on the
>>>>>>>>>     french National Museum of Natural History, and in turn,
>>>>>>>>>     enable search engines to harvest data from complimentary
>>>>>>>>>     pages and produce mashups of related pages, etc.
>>>>>>>>     That sounds like a great idea and entirely within the scope
>>>>>>>>     of Bioschemas.
>>>>>>>>>
>>>>>>>>>     At this point, I think we should involve people from EoL,
>>>>>>>>>     and from the TDWG community (Rod Page would certainly be
>>>>>>>>>     of great added value in this respect). What do you think?
>>>>>>>>>     Is there a procedure for inviting people "officially"?
>>>>>>>>     I think we could benefit from their experience indeed; it
>>>>>>>>     seems they were able to deploy markup, add additional
>>>>>>>>     properties and then get this to be interpreted by Google
>>>>>>>>     which seems to match our use case pretty well!
>>>>>>>>     I +1'd the issue at
>>>>>>>>     https://github.com/BioSchemas/specifications/issues/115
>>>>>>>>
>>>>>>>>     Cheers,
>>>>>>>>     Melanie
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>>     Franck.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>     Le 15/11/2017 à 17:57, Melanie Courtot a écrit :
>>>>>>>>>>     Hi Frank,
>>>>>>>>>>
>>>>>>>>>>     This looks really interesting, thanks for bringing it up.
>>>>>>>>>>     I was trying to find out how the interaction between EoL
>>>>>>>>>>     and schema.org <http://schema.org> was working and am
>>>>>>>>>>     wondering if you (or someone else!) could shed some light
>>>>>>>>>>     on this?
>>>>>>>>>>
>>>>>>>>>>     As you suggested in the below, I checked the google
>>>>>>>>>>     beluga
>>>>>>>>>>     <https://www.google.fr/search?dcr=0&ei=ml74WajPMMzWUabjqvAF&q=beluga&oq=beluga&gs_l=psy-ab.3...19519.20929.0.20945.6.3.0.0.0.0.93.93.1.1.0....0...1.1.64.psy-ab..5.1.92...0j0i131k1.0.AGNziTItYzc>
>>>>>>>>>>     search result and do see the line "Length: 4.2 m (Adult)
>>>>>>>>>>     Encyclopedia of Life"
>>>>>>>>>>
>>>>>>>>>>     If I try to find where that info comes from, and head to
>>>>>>>>>>     EoL, I can reach the page
>>>>>>>>>>     http://eol.org/pages/328541/overview, and follow the "see
>>>>>>>>>>     all traits" link to http://eol.org/pages/328541/data
>>>>>>>>>>     which contains the JSON-LD.
>>>>>>>>>>
>>>>>>>>>>     I trimmed it down to extract the relevant bit, updated
>>>>>>>>>>     the id to be a string as per
>>>>>>>>>>     https://github.com/EOL/tramea/issues/352, and pasted it
>>>>>>>>>>     in the JSON playground mostly to make sure it was working
>>>>>>>>>>     as expected: http://tinyurl.com/yadam6nj
>>>>>>>>>>
>>>>>>>>>>     I am missing the link of how the following happens:
>>>>>>>>>>     - the measurement type points to
>>>>>>>>>>     http://purl.obolibrary.org/obo/VT_0001256, which is body
>>>>>>>>>>     length. The schema.org/predicate
>>>>>>>>>>     <http://schema.org/predicate> value is also "body length
>>>>>>>>>>     (VT)". How is this understood and displayed as Length on
>>>>>>>>>>     the Google result?
>>>>>>>>>>     - Similar question for the actual value and units, which
>>>>>>>>>>     are "4249.83" and "mm" respectively. Is Google doing some
>>>>>>>>>>     sort of unit conversion/roundup for display?
>>>>>>>>>>     - Trophic level on EoL is "carnivore", but Google
>>>>>>>>>>     displays "Carnivorous"
>>>>>>>>>>     etc
>>>>>>>>>>
>>>>>>>>>>     Or am I looking at the wrong source for the markup?
>>>>>>>>>>
>>>>>>>>>>     Cheers,
>>>>>>>>>>     Melanie
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>     On 10/11/2017 15:17, Franck Michel wrote:
>>>>>>>>>>>     Dear all,
>>>>>>>>>>>
>>>>>>>>>>>     I've just joined the Bioschemas.org community following
>>>>>>>>>>>     some discussions I had with Alasdair Gray whom I met at
>>>>>>>>>>>     ISWC in Vienna, and I'd like to start a new discussion
>>>>>>>>>>>     thread.
>>>>>>>>>>>
>>>>>>>>>>>     So, just to start, a few words about me. I'm a CNRS
>>>>>>>>>>>     research engineer, I work at the I3S laboratory in
>>>>>>>>>>>     France, in particular with the Wimmics research team led
>>>>>>>>>>>     by Fabien Gandon. I'm currently involved in some
>>>>>>>>>>>     activities related to the publication of taxonomic
>>>>>>>>>>>     information as Linked Data [1]. In this context, I've
>>>>>>>>>>>     met the Biodiversity Information Standards community
>>>>>>>>>>>     (TDWG) that is increasingly considering SW standards, LD
>>>>>>>>>>>     publication and web pages markup. This is a domain
>>>>>>>>>>>     where, I think, it would be relevant for
>>>>>>>>>>>     Bioschemas.orgto get involved.
>>>>>>>>>>>
>>>>>>>>>>>     There exist lots of web portals reporting observations,
>>>>>>>>>>>     traits and other data about all sorts of living
>>>>>>>>>>>     organisms. Encyclopedia of Life <http://eol.org/> (EoL)
>>>>>>>>>>>     and the Global Biodiversity Information Facility
>>>>>>>>>>>     <https://www.gbif.org/> (GBIF) are some of the most well
>>>>>>>>>>>     known. Markup questions are actively considered in this
>>>>>>>>>>>     field, for instance EoL web pages embed
>>>>>>>>>>>     schemas.org-based JSON-LD descriptions that Google
>>>>>>>>>>>     leverages to enrich their snippets: e.g. if you google
>>>>>>>>>>>     beluga
>>>>>>>>>>>     <https://www.google.fr/search?dcr=0&ei=ml74WajPMMzWUabjqvAF&q=beluga&oq=beluga&gs_l=psy-ab.3...19519.20929.0.20945.6.3.0.0.0.0.93.93.1.1.0....0...1.1.64.psy-ab..5.1.92...0j0i131k1.0.AGNziTItYzc>
>>>>>>>>>>>     you shall see 'Encyclopedia of Life' mentions in the
>>>>>>>>>>>     snippet providing average weight and size data. For now,
>>>>>>>>>>>     this seems to be an "individual" initiative between EoL
>>>>>>>>>>>     and Google/schemas.org <http://schemas.org>, but it
>>>>>>>>>>>     would make sense if this was part of a broader
>>>>>>>>>>>     reflection led by Bioschemas.org.
>>>>>>>>>>>
>>>>>>>>>>>     My opinion is that fostering the use of common markup by
>>>>>>>>>>>     these portals could be very effective in helping the
>>>>>>>>>>>     biodiversity community to discover information and
>>>>>>>>>>>     figure out new data integration scenarios.Within
>>>>>>>>>>>     Bioschemas.org, we could define profiles to account for
>>>>>>>>>>>     biodiversity-related information.Taxonomic registers are
>>>>>>>>>>>     used as the backbone of many web portals, apps and
>>>>>>>>>>>     databases related to biodiversity, agronomy and
>>>>>>>>>>>     agriculture.For instance, EoL and GBIF both rely on the
>>>>>>>>>>>     Catalog of Life <http://www.catalogueoflife.org/>
>>>>>>>>>>>     taxonomy. Therefore, we could start with the definition
>>>>>>>>>>>     of a profile to describe a taxon and the related
>>>>>>>>>>>     scientific and vernacular names thereof. Then, this
>>>>>>>>>>>     could be extended with the representation of traits
>>>>>>>>>>>     (characteristics of biological organisms), observations,
>>>>>>>>>>>     occurrence data, conservation status (e.g. endangered)
>>>>>>>>>>>     etc. There already exist vocabularies for such data such
>>>>>>>>>>>     as the well-adopted Darwin Core terms.
>>>>>>>>>>>
>>>>>>>>>>>     As a quick example, consider the web page describing the
>>>>>>>>>>>     common dolphin on the web site of the french Museum of
>>>>>>>>>>>     Natural History:
>>>>>>>>>>>     https://inpn.mnhn.fr/espece/cd_nom/60878?lg=en. This
>>>>>>>>>>>     page could come with a JSON-LD desciption looking like
>>>>>>>>>>>     this:
>>>>>>>>>>>     https://github.com/frmichel/taxref-ld/blob/master/bioschemas-org-example.json
>>>>>>>>>>>     This example is naive and very succinct, and there are
>>>>>>>>>>>     lots of things to discuss and decide. Besides, I've just
>>>>>>>>>>>     registered on the mailing yesterday, so it may not fit
>>>>>>>>>>>     with good practices that you guys have already agreed
>>>>>>>>>>>     upon. Sorry if this is the case. Nevertheless, my point
>>>>>>>>>>>     is basically to bootstrap the discussion and see if the
>>>>>>>>>>>     community is willing to endorse this initiative. If this
>>>>>>>>>>>     is the case, we should probably involve people from the
>>>>>>>>>>>     biodiversity community: Darwin Core experts, EoL/GBIF
>>>>>>>>>>>     representatives etc. But that will come in time.
>>>>>>>>>>>
>>>>>>>>>>>     I look forward to further discussions.
>>>>>>>>>>>     Regards,
>>>>>>>>>>>        Franck.
>>>>>>>>>>>
>>>>>>>>>>>     [1] Michel F., Gargominy O., Tercerie S. & Faron-Zucker
>>>>>>>>>>>     C. (2017). A Model to Represent Nomenclatural and
>>>>>>>>>>>     Taxonomic Information as Linked Data. Application to the
>>>>>>>>>>>     French Taxonomic Register, TAXREF. In Proceedings of the
>>>>>>>>>>>     2nd International Workshop on Semantics for Biodiversity
>>>>>>>>>>>     (S4BioDiv) co-located with ISWC 2017 vol. 1933. Vienna,
>>>>>>>>>>>     Austria. CEUR.
>>>>>>>>>>>
>>>>>>>>>>>     -- 
>>>>>>>>>>>     	
>>>>>>>>>>>     Franck MICHEL
>>>>>>>>>>>     CNRS research engineer
>>>>>>>>>>>     	+33 (0)492 96 5004
>>>>>>>>>>>     franck.michel@cnrs.fr <mailto:franck.michel@cnrs.fr>
>>>>>>>>>>>
>>>>>>>>>>>     	
>>>>>>>>>>>
>>>>>>>>>>>     Université Côte d’Azur, CNRS, *Inria* - I3S - UMR 7271
>>>>>>>>>>>     930 route des Colles - Bât. Les Templiers
>>>>>>>>>>>     BP 145 - 06903 Sophia Antipolis CEDEX - France
>>>>>>>>>>>     Tel. +33 (0)4 9294 2680
>>>>>>>>>>>     <tel:+33%204%2092%2094%2026%2080>, Fax : +33 (0)4 9294 2898
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>     -- 
>>     	
>>     Franck MICHEL
>>     CNRS research engineer
>>     	+33 (0)4 8915 4277
>>     franck.michel@cnrs.fr <mailto:franck.michel@cnrs.fr>
>>
>>     	
>>
>>     Université Côte d’Azur, CNRS- I3S - UMR 7271
>>     930 route des Colles
>>     <https://maps.google.com/?q=930+route+des+Colles&entry=gmail&source=g>
>>     - Bât. Les Templiers
>>     BP 145 - 06903 Sophia Antipolis CEDEX - France
>>     Tel. +33 (0)4 9294 2680 <tel:+33%204%2092%2094%2026%2080>
>>
>
Received on Tuesday, 12 June 2018 09:02:35 UTC

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