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Re: Bioschemas.org to define biodiversity-related markup

From: LJ Garcia Castro <ljgarcia@ebi.ac.uk>
Date: Mon, 11 Jun 2018 14:46:04 +0100
To: Ricardo Arcila <ricartomojo@gmail.com>, Franck Michel <franck.michel@cnrs.fr>
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: <68829495-ab4c-9885-494c-e426decc3b07@ebi.ac.uk>
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.


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.>
>>>>>>>>>     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.>
>>>>>>>>>>     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 Monday, 11 June 2018 13:46:36 UTC

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