- From: ljgarcia <ljgarcia@ebi.ac.uk>
- Date: Tue, 26 Jun 2018 18:36:04 +0100
- To: Franck Michel <fmichel@i3s.unice.fr>
- Cc: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>, Ricardo Arcila <arcila@ebi.ac.uk>, public-bioschemas@w3.org
Hi Franck, Just added some comments to the document. I would say we just started the Taxon cross-walk, first step for new specifications. Great start! Cheers, On 2018-06-20 22:47, Franck Michel wrote: > Hi all, > > It seems like I've had email issues lately. I just discovered > Ricardo's and Alasdair's answers in the flow below. > > Also, I thought I had submitted a pull request for the creation of a > _groups/Biodiversity.md file that I had carefully written, but it > never reached out to Ricardo (and I can't find any trace of it on > Gihub ;)). Anyway, my idea was to create a Biodiversity group (instead > of a Taxon group), whose first task would be to define the Taxon > profile. There may be other profiles defined by this group later on. > Are you ok with that? > > @Leyla: as a starting point, maybe we can interact through the > discussion document I associated with the mapping (in the Taxon folder > [30])? > > Franck. > > Le 20/06/2018 à 19:49, LJ Garcia Castro a écrit : > >> Hi Franck, >> >> We associate proteins to taxa so I am happy to help. Please add me >> to the loop and let us know what would be the best approach to >> contribute, i.e., email, comments via gdrive, issues via github, >> etc. >> >> Regards, >> >> On 15/06/2018 13:10, Gray, Alasdair J G wrote: >> Hi All >> >> I’m happy for the taxon group to be created with Franck as the >> initial group lead. Is there someone willing to support Franck in >> this role? >> >> Alasdair >> >> On 15 Jun 2018, at 12:58, Ricardo Arcila <arcila@ebi.ac.uk> wrote: >> >> Hello Franck, >> >> I have taken the liberty to create a branch [1] with the draft of >> the group Taxons, please feel free to adjust it as you see fit. >> >> Kind regards, >> Ricardo >> >> On 12 Jun 2018, at 10:02, Franck Michel <franck.michel@cnrs.fr> >> wrote: >> >> 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 [2]. >> Then you can add yourself on the people repository [3]. 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 >> [4]. This process its detailed on the bioschemas github wiki [5]. >> >> 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 [6]. >> >> 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 [7] 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 [7] 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 [7]. >> >> 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 [8] >> 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 [9]. Beluga example: >> http://eol.org/api/traits/328541 [10] >> 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 [11]. >> 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 [12] >> 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 [6]. 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 [13], which is body >> length. The schema.org/predicate [14] 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 >> [15] >> - "dwc:measurementUnit": "http://purl.obolibrary.org/obo/UO_0000016" >> [16] => 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" [17] >> to know that this is the size of an adult. >> >> With proper Bioschemas.org [7] profiles, I think we could annotate >> pages from many other institutions, such as the Beluga page [18] 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 [19] >> >> 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 >> [6] 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 [20] >> 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 [21], and follow >> the "see all traits" link to http://eol.org/pages/328541/data [11] >> 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 [22], and >> pasted it in the JSON playground mostly to make sure it was working >> as expected: http://tinyurl.com/yadam6nj [23] >> >> I am missing the link of how the following happens: >> - the measurement type points to >> http://purl.obolibrary.org/obo/VT_0001256 [13], which is body >> length. The schema.org/predicate [14] 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 [7] 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 [7] to get involved. >> >> There exist lots of web portals reporting observations, traits and >> other data about all sorts of living organisms. Encyclopedia of Life >> [24] (EoL) and the Global Biodiversity Information Facility [25] >> (GBIF) are some of the most well known. Markup questions are >> actively considered in this field, for instance EoL web pages embed >> schemas.org [9]-based JSON-LD descriptions that Google leverages to >> enrich their snippets: e.g. if you google beluga [20] 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 [9], but it would make >> sense if this was part of a broader reflection led by Bioschemas.org >> [7]. >> >> 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 [7], 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 [26] >> 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 [27]. This page could >> come with a JSON-LD desciption looking like this: >> > https://github.com/frmichel/taxref-ld/blob/master/bioschemas-org-example.json >> [28] >> 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 [29], 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 [31] - Bât. Les Templiers > BP 145 - 06903 Sophia Antipolis CEDEX - France > Tel. +33 (0)4 9294 2680 [29] > > Alasdair J G Gray > > Fellow of the Higher Education Academy > Assistant Professor in Computer Science, > School of Mathematical and Computer Sciences > (Athena SWAN Bronze Award) > Heriot-Watt University, Edinburgh UK. > > Email: A.J.G.Gray@hw.ac.uk > Web: http://www.macs.hw.ac.uk/~ajg33 [32] > ORCID: http://orcid.org/0000-0002-5711-4872 > Office: Earl Mountbatten Building 1.39 > Twitter: @gray_alasdair > > Untitled Document > > ------------------------- > > _HERIOT-WATT UNIVERSITY IS THE TIMES & THE SUNDAY TIMES INTERNATIONAL > UNIVERSITY OF THE YEAR 2018_ > > Founded in 1821, Heriot-Watt is a leader in ideas and solutions. 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If you are > not the intended recipient of this e-mail, any disclosure, copying, > distribution or use of its contents is strictly prohibited, and you > should please notify the sender immediately and then delete it > (including any attachments) from your system. > > > > Links: > ------ > [1] > https://github.com/BioSchemas/bioschemas.github.io/tree/ric/feat/taxons-group > [2] > https://github.com/BioSchemas/bioschemas.github.io/tree/master/_groups > [3] > https://github.com/BioSchemas/bioschemas.github.io/tree/master/_people > [4] > https://drive.google.com/drive/folders/0Bw_p-HKWUjHoNThZOWNKbGhOODg?usp=sharing > [5] > https://github.com/BioSchemas/specifications/wiki/Bioschemas-Specification-Process > [6] http://schema.org/ > [7] http://bioschemas.org/ > [8] https://github.com/frmichel/taxref-ld/tree/master/bioschemas-org > [9] http://schemas.org/ > [10] http://eol.org/api/traits/328541 > [11] http://eol.org/pages/328541/data > [12] https://frama.link/xJm0AAto > [13] http://purl.obolibrary.org/obo/VT_0001256 > [14] http://schema.org/predicate > [15] http://schema.org/units > [16] http://purl.obolibrary.org/obo/UO_0000016 > [17] http://eol.org/resources/704/measurements/adultheadbodylen27 > [18] https://inpn.mnhn.fr/espece/cd_nom/60932?lg%3Den > [19] https://github.com/BioSchemas/specifications/issues/115 > [20] > 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 > [21] http://eol.org/pages/328541/overview > [22] https://github.com/EOL/tramea/issues/352 > [23] http://tinyurl.com/yadam6nj > [24] http://eol.org/ > [25] https://www.gbif.org/ > [26] http://www.catalogueoflife.org/ > [27] https://inpn.mnhn.fr/espece/cd_nom/60878?lg=en > [28] > https://github.com/frmichel/taxref-ld/blob/master/bioschemas-org-example.json > [29] tel:+33%204%2092%2094%2026%2080 > [30] > https://drive.google.com/drive/u/0/folders/1Fp2AKbb07So7rVvUhnQIjpl8HLPSwpbP > [31] > https://maps.google.com/?q=930+route+des+Colles&entry=gmail&source=g > [32] http://www.macs.hw.ac.uk/%7Eajg33
Received on Tuesday, 26 June 2018 17:36:35 UTC