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Bioschemas: �Marking up biodiversity websites to improve �data discovery and web-scale integration

* Wimmics: AI in bridging social semantics and formal semantics on the Web

TDWG Webinar, 2021-03-10

Franck MICHEL*

Bioschemas Community http://bioschemas.org/people/

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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Semantic markup for web pages

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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: semantic markup for resources on the internet

Collaborative community project founded in 2011 by

​

Define a common vocabulary to markup resources on the internet

  • Structured data makes resources understandable to search engines
  • Improve ranking, discoverability
  • Provide informative summarizations

​

schema.org

Microdata

RDFa

Microformats

Markup formats

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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: semantic markup for resources on the internet

Collaborative community project founded in 2011 by

​

Define a common vocabulary to markup resources on the internet

  • Structured data makes resources understandable to search engines
  • Improve ranking, discoverability
  • Provide informative summarizations

​

Microdata

RDFa

Microformats

schema.org

Source: https://w3techs.com/technologies/history_overview/structured_data/all

Markup formats

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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: semantic markup for resources on the internet

What we are �talking about: �types (778)

What we can say about those things: �properties (1369)

schema.org

http://schema.org/Person

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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How to share your biodiversity data?

Webpages

Web API�Linked Data KG

Integrative approach GBIF, EoL, iDigBio…

simple

sophisticated

Flat files

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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How to share your biodiversity data?

Web API�Linked Data KG

Integrative approach GBIF, EoL, iDigBio…

simple

sophisticated

Webpages

Flat files

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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Bioschemas: schema.org extension for Life Sciences

Community initiative built on top of Schema.org

Aim

Help search engines understand and index webpages

Improve resources discoverability and interoperability

Approach

Reuse/extend Schema.org for life sciences

Keep it simple (no complex domain ontology)

Provide guidelines on how to markup resources

      • Minimum/recommended/optional properties
      • Link to other vocabularies & domain ontologies

Flexibility: recommandations, not constraints

Support software

Specification

Data model

Minimum information

Controlled vocabularies

Cardinality

Documentation

Examples

New (properties | types)

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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Bioschemas: schema.org extension for Life Sciences

Currently defined terms

  • ChemicalSubstance
  • DataCatalog
  • Dataset
  • Gene
  • MolecularEntity
  • Protein
  • Sample
  • Taxon

More terms to come

  • BioSample
  • ComputationalTool
  • ComputationalWorkflow
  • LabProtocol
  • Phenotype
  • ProteinStructure
  • RNA
  • TaxonName
  • …

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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Taxon

Type: https://bioschemas.org/types/Taxon meant to become http://schema.org/Taxon

Profile: https://bioschemas.org/profiles/Taxon provides usage recommendations

dwc:vernacularName

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Example markup of a page about taxon Delphinapterus leucas

<script type="application/ld+json">

{

"@context": "http://schema.org",

"@type" : "Taxon",

"name": "Delphinapterus leucas (Pallas, 1776)",

"taxonRank": "species"

}

</script>

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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Example markup of a page about taxon Delphinapterus leucas

<script type="application/ld+json">

{

"@context": [

"http://schema.org",

{ "dwc": "http://rs.tdwg.org/dwc/terms/",

"dwc:vernacularName": { "@container": "@language" }

}

],

"@type" : "Taxon",

"additionalType": "dwc:Taxon",

"taxonRank": ["species", "http://www.wikidata.org/entity/Q7432" ],

"name": "Delphinapterus leucas (Pallas, 1776)",

"alternateName": [ "Balaena albicans Muller, 1776", "Beluga catodon Gray, 1846" ],

"dwc:vernacularName": [

{ "@language": "en", "@value": "Beluga Whale" },

{ "@language": "fr", "@value": "Bélouga" }

],

​

"parentTaxon": {

"@type": "Taxon",

"name": "Delphinapterus Lacépède, 1804",

"mainEntityOfPage": "https://inpn.mnhn.fr/espece/cd_nom/191588?lg=en",

"taxonRank" : "genus"

},

"image": "https://inpn.mnhn.fr/photos/uploads/webtofs/inpn/3/181473.jpg"

}

</script>

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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Example markup of a page about taxon Delphinapterus leucas

<script type="application/ld+json">

{

...

"sameAs": [

"http://doris.ffessm.fr/Especes/Delphinapterus-leucas-Beluga-868",

"http://www.marinespecies.org/aphia.php?p=taxdetails&id=137115",

"http://www.iucnredlist.org/details/6335"

],

​

"identifier": [

"60932",

{ "@type": "PropertyValue",

"name": "WoRMS id",

"propertyID": "http://www.wikidata.org/entity/P850", # WoRMS id

"value": "137115"

}

],

}

</script>

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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What about names registries such as�IPNI, Zoobank, Mycobank?

Photo: https://commons.wikimedia.org/wiki/File:Name_label.JPG

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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TaxonName

Taxon vs. TaxonName, discussion:

https://github.com/BioSchemas/specifications/issues/309

Taxon

Type: https://bioschemas.org/types/TaxonName meant to become http://schema.org/TaxonName

Profile: https://bioschemas.org/profiles/TaxonName provides usage recommendations

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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Example markup of a page about name Delphinapterus leucas

<script type="application/ld+json">

{

"@context": "http://schema.org",

​

"@type" : "Taxon",

"taxonRank": "species“,

​

"scientificName": {

"@type" : "TaxonName",

"name": "Delphinapterus leucas",

"author": "(Pallas, 1776)",

"taxonRank": "species"

},

​

"alternateScientificName": [

{ "@type" : "TaxonName",

"name": "Balaena albicans",

"author": "Muller, 1776",

"taxonRank": "species"

},

{ "@type" : "TaxonName",

"name": "Beluga catodon",

"author": "Gray, 1846",

"taxonRank": "species"

}

]

}

</script>

<script type="application/ld+json">

{

"@context": "http://schema.org",

​

"@type" : "TaxonName",

"name": "Delphinapterus leucas",

"author": "(Pallas, 1776)",

"taxonRank": "species"

}

</script>

Taxon with TaxonName

TaxonName alone

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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Live �deployments

Photo: https://www.flickr.com/photos/35034363287@N01/2284904309

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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Early deployment at NMNH Paris

https://search.google.com/structured-data/testing-tool

180,000+ pages marked up with �Taxon & TaxonName types

https://inpn.mnhn.fr/espece/cd_nom/60932

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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Early deployments

NMNH Paris

Taxon & TaxonName, 180K pages

GBIF

Taxon & TaxonName, 3M pages

Scholia

Taxon, 2.7M pages�Scientific bibliographic information based on Wikidata

PIPPA

PSB Int. for Plant Phenotype Analysis

Taxon ↔ BioChemEntity

OpaleSurfCasting.net

Taxon�French leisure sea fishing legislation.

Why do early deployments matter?

  • A way for the community to show its interest in having these terms
  • Necessary for Schema.org to endorse new types
  • First step to foster novel applications (chicken & egg)

https://bioschemas.org/liveDeploys/

https://scholia.toolforge.org

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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Next steps

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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Bioschemas work on biodiversity

Currently:

Taxon, TaxonName�Links to DwC terms

Future

Specimen �Links to ABCD, openDS, MIDS?

Traits �Links to traits ontologies?

Occurrence �Links to DwC occurrences?

…

​

​

https://bioschemas.org/groups/Biodiversity/

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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Marking up biodiversity resources… at scale

GBIF, EoL, CoL, iDigBio, DiSSCo…

Museum collections,

Literature (BHL, Plazi…),

Citizen science platforms,

Independent institutions,

Associations,

…

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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Take-aways

Marking up webpages

Let’s have search engines �do the job for us!

    • Connect pieces of data at web scale
    • First step for data integration is discovery
    • Dataset search engines
    • What about a Species Search Engine?
    • …
    • Increases data visibility and discoverability
    • Relatively inexpensive
    • Connect unconnected pieces of data,�e.g. “grey literature”

​

Not the magic bullet

    • Names discrepancies
    • Compliance with nomenclature
    • How to name taxonomic ranks
    • …

​

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France

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https://bioschemas.org/�https://github.com/BioSchemas/specifications/wiki

Questions?

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Franck MICHEL - Université Côte d’Azur, CNRS, Inria, I3S, France