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Alasdair Gray, Franck Michel, Quentin Groom, and the Bioschemas Community

Alasdair J.G. Gray �Bioschemas Steering Council Chair�Heriot-Watt University – ELIXIR-UK

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Biodiversity Mini-symposium�ELIXIR All Hands, 8 June 2020

Discovering Biodiversity Resources on the Web

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Schema.org: Semantic Markup for the Web

Picture: Carole Goble, Turing Lecture 2018

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Structured data → descriptors

  • Types�(829)

What we can say about those things

  • Properties�(1351)

What we are talking about

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Bioschemas

  • Community initiative built on top of schema.org
  • Aim
    • Improve data discoverability and interoperability in Life Sciences
  • Approach
    • Add Life Science types to schema.org
    • Provide usage guidelines and examples
      • 6 Minimal properties
      • Link to domain ontologies
    • Support software

Profile over schema.org

Layer of constraints + documentation + extensions

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Specification

Data model

Minimum information

Controlled vocabularies

Cardinality

Documentation

Examples

New (properties | types)

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Bioschemas: Lightweight semantic interoperability

  • Many domain ontologies
    • Designed to model biology
  • Bioschemas focus on search!

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Findable

Accessible

Interoperable

Reusable

  • Globally unique identifiers
  • Community defined enriched metadata
  • Indexable by search engines
  • JSON-LD/RDFa
  • Link to controlled vocabularies
  • Links to other resources
  • License
  • Provenance
  • Retrievable
  • HTTP

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Bioschemas: Markup for the Life Sciences

Picture: Carole Goble, Turing Lecture 2018

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Exploiting Bioschemas Markup

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TeSS: Specialised Search

http://bioschemas.org

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29 November 2018

  • contact
  • description
  • endDate
  • eventType
  • hostInstitution
  • location
  • name
  • startDate
  • …

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Bioschemas Event:

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Data Exchange: Without an API�MarRef → BioSamples

https://github.com/EBIBioSamples/bioschemas_marref_demo/blob/master/Summary.md

Bioschemas �Scraper

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Rich snippet generation

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BMUSE: Bioschemas Markup Scraper �and Extractor

  • Directed scraper
    • List of URLs
    • Site maps
  • Extracts markup
    • JSON-LD or RDFa
    • Single page applications
  • Includes provenance of extraction
    • retrievedFrom
    • retrievedOn
  • Experimental crawl of COVID-19 markup

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https://github.com/HW-SWeL/BMUSE

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BKG Explorer

Built over Bioschemas markup crawled from 30 live deployments�20,000 pages

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Bioschemas for Biodiversity

Image: https://en.wikipedia.org/wiki/Biodiversity#/media/File:Fungi_of_Saskatchewan.JPG

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Taxon Markup

  • Taxon profile
  • Deployed at National Museum of Natural History of Paris

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Taxon Profile: https://bioschemas.org/profiles/Taxon

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Bioschemas Taxon Profile

http://bioschemas.org/profiles/Taxon/

Property

Description

Cardinality

name

Currently valid (zoological) or accepted (botanical) name for that taxon, with authorship and date information if known.

One

taxonRank

The taxonomic rank of this taxon given preferably as a URI from a controlled vocabulary (e.g. the ranks from TDWG TaxonRank ontology or equivalent Wikidata URIs)

Many

parentTaxon

Closest parent taxon of the taxon in question. Inverse property: childTaxon

Direct, most proximate higher-rank parent taxon

One

url

Link to the webpage associated to this taxon

One

additionalType

A Taxon type from a well known vocabulary, e.g. DarwinCore http://rs.tdwg.org/dwc/terms/Taxon or http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept

Many

alternativeName

Scientific name, with authorship and date information if known, of a synonym of the currently valid (zoological) or accepted (botanical) name.

Many

childTaxon

Closest child taxa of the taxon in question. Inverse property: parentTaxon

Direct, most proximate lower-rank child taxa

Many

hasCategoryCode

A Category code contained in this code set.

Many

sameAs

URL of third-party webpages describing the same taxon

Many

dwc:vernacularName

A vernacular (common) name of the taxon

Many

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BioSample Profile: https://bioschemas.org/profiles/BioSample

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BioSample Markup

  • BioSample profile
  • Deployment in development at Meise Botanical Garden, Belgium

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Bioschemas BioSample Profile

http://bioschemas.org/profiles/BioSample/

Property

Description

Cardinality

description

A description of the item.

One

identifier

The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See background notes for more details.

One

name

Currently valid (zoological) or accepted (botanical) name for that taxon, with authorship and date information if known.

One

url

Link to the webpage associated to this taxon

One

associatedDisease

Disease associated to this BioChemEntity. Such a disease can be a MedicalCondition or a URL. If you want to add an evidence supporting the association, please use PropertyValue.

Many

bioChemInteraction

A BioChemEntity that is know to interact with this item.

Many

bioChemSimilarity

A similar molecular entity, e.g., obtained by fingerprint similarity algorithm.

Many

biologicalRole

A role played by the molecular entity within a biological context.

Many

collector

The Person or Organization who collected the Sample.

Many

...

...

...

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Adding Bioschemas to a Resource

  • Identify metadata fields
  • Map metadata to�Bioschema properties
  • Generate JSON-LD
  • Embed generation�into web server

Image: Niall Beard, University of Manchester

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Bioschemas

What?

  • Exploiting schema.org to make Life Sciences resources more discoverable
    • Search engines will index and understand markup

How?

  • Extending schema.org vocabulary for life sciences
  • Provide guidelines on how to markup resources
  • Biodiversity types and profiles available

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Bioschemas Community

bioschemas.org/liveDeploys

bioschemas.org/�liveDeploys

300+

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People

17

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Types

30

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Profiles

89

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Sites

20M+

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Pages

14+

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Countries

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Acknowledgements http://bioschemas.org/people

http://bioschemas.org

Join Bioschemas: http://bioschemas.org/howtojoin/

bioschemas.org

@bioschemas

github.com/�bioschemas

Special thanks to:

  • Franck Michel
  • Quentin Groom
  • Matt Styles