1. Rafael Jimenez
Norman Morrison
ELIXIR Hub
Hinxton Genome
Campus
Representing the
Bioschemas.org Community
carole.goble@manchester.ac.uk
Carole Goble*
Niall Beard*
Alasdair Gray+
ELIXIR UK
*The University of Manchester
+ Heriot-Watt University

2. The FAIR Guiding Principles for scientific data management and stewardship
https://www.nature.com/articles/sdata201618 (2016)
Catalogues
Aggregators
Search

3. Structured data markup for web pages
Schema.org adds simple
structured metadata markup
to web pages & sitemaps for
harvesting, search and summary
snippet making.
Search engines often highlight
websites containing
Schema.org
Widespread commercial and
open source infrastructure
creates a low barrier to adoption

4. <div itemscope itemtype="http://schema.org/Recipe">
<h1 itemprop="name">Classic potato salad</h1>
<div itemprop="nutrition” itemscope
itemtype="http://schema.org/NutritionInformation">
Nutrition facts:
<span itemprop="calories">144 kcal</span>,
</div>
Ingredients:
- <span itemprop="recipeIngredient">800g small new potato</span>
- <span itemprop="recipeIngredient">3 shallot</span>
. . .
Structured data markup for web pages
RDFa
JSON-LD
Microdata
With markup

5. From Potato Salad to Protein Annotation
"taxon": "http://www.uniprot.org/taxonomy/9606",
"alternateName": [
{
"@language": "en",
"@value": "ABL1_HUMAN"
},
{
"@language": "en",
"@value": "Proto-oncogene c-Abl"
}
],
"description": {
"@language": "en",
"@value": "Non-receptor tyrosine-protein kinase that plays a role..."
},
"identifier": "http://www.identifiers.org/uniprot/P00519",
{
"@context": "http://schema.org",
"@type": "BiologicalEntity",
"@id":
"http://www.identifiers.org/uniprot/P00519
",
"biologicalType": "protein",
"isMentionedIn": {
"@type": "Dataset",
"@id":
"http://www.uniprot.org/news/2017/03/15/re
lease"
},
"associatedDisease": {
"@type": "MedicalCondition",
"@id":
"http://www.omim.org/entry/608232",
"name": "Leukemia, chronic myeloid
(CML)",
"code": {
"@type": "MedicalCode",
"code": "608232",
"codingSystem": "OMIM"
},
"sameAs":
"http://www.uniprot.org/diseases/DI-03735"
},
"biocoordinates": {
"@type": "QuantitativeValue",
"value": "1130"
},

6. Bioschemas.org
Data
repository
Data
repository
Training
Resource
Bioschemas Bioschemas Bioschemas
Search
engines
Registries
Data
Aggregators
Major
datasets
Smaller
datasets• Standardised
metadata
• Feed bio
registries and
aggregators
• Metadata
publish and
harvest without
APIs or special
feeds
• Commodity
• Off the Shelf
tools
• App eco-system
A community initiative built on top of Schemas.org to
improve Findability and Accessibility in Life Sciences
• Rapid markup
• Exposed to harvesting
• Find

7. Bioschemas.org
Data
repository
Data
repository
Training
Resource
Bioschemas Bioschemas Bioschemas
Search
engines
Registries
Data
Aggregators
A community initiative built on top of Schemas.org to
improve Findability and Accessibility in Life Sciences

8. First specifications target:
• Bio data infrastructure
• Repositories
• Datasets
• Bio data types
• Human beacons
• Samples
• Plant Phenotypes
• Proteins …
• Bio stuff
• Training materials
• Events
• Laboratory protocols
• Workflows andTools
Life Sciences
Bioschemas.org
A community initiative built on top of Schemas.org to
improve Findability and Accessibility in Life Sciences
Tools!!!
Specialist validators
Data providers and
consumers onboard
Notably EMBL-EBI

9. Data Repository and Datasets Descriptions
Information about repositories
with consistent structured data
Align overlapping registry efforts
around certain metadata.
Help with consistency of
metadata collected by registries
With:
omicsDI
Bioschemas.org

10. Restrictions
Constraints
Extensions
Restrictions: the few concepts to
minimally describe an entity
Constraints: cardinalities,
controlled vocabularies
Extensions: new properties and
new types, e.g. BiologicalEntity
Bioschemas.org
Adapts Schema.org

11. Bioschemas.org
Who and How?
First draft specs are out.
ELIXIR Adoptors meeting , 2-4 Oct 201,
EOSCpilot meeting, 4-5 Oct 2017
Hinxton Genome Campus, EMBL-EBI
Sponsors Supporters
Inclusion in
Schema.org
proposed for early
2018.
Additional contributors include:
Special thanks to:
Dan Brickley, Schema.org & Google Inc
Natash Noy, Google Inc
Ian Fore, NIH