Re: Bioschemas.org to define biodiversity-related markup

I have created an issue on GitHub for the creation of this group.
https://github.com/BioSchemas/specifications/issues/115


If you are in favour or against please use the reactions* to show this.
https://github.com/blog/2119-add-reactions-to-pull-requests-issues-and-comments


If you would like to be involved in the development, please add your name to the issue.

Best regards

Alasdair

On 10 Nov 2017, at 15:17, Franck Michel <franck.michel@cnrs.fr<mailto:franck.michel@cnrs.fr>> wrote:

Dear all,

I've just joined the Bioschemas.org<http://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<http://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<http://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<http://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<http://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 desciptionlooking 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, Fax : +33 (0)4 9294 2898


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<mailto: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










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