- From: Ricardo Arcila <ricartomojo@gmail.com>
- Date: Mon, 11 Jun 2018 14:39:53 +0100
- To: Franck Michel <franck.michel@cnrs.fr>
- Cc: Leyla Garcia <ljgarcia@ebi.ac.uk>, 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: <CACp2UZjGKzc5jkFWdQ87UdG1XTKewnvMk3wa1NY3QPKhWW6_rA@mail.gmail.com>
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> 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. > > 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. 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. 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 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 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 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.org to 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, 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 > > > > 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 <+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 > > > > 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 <+33%204%2092%2094%2026%2080> >
Received on Monday, 11 June 2018 13:40:34 UTC