AgriSchemas: Sharing Agrifood data
with Bioschemas
Elixir AH 2021, June 1st, 2021
Marco Brandizi <marco.brandizi@rothamsted.ac.uk>
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background source: https://www.123rf.com/photo_56576261_close-up-roots-and-soil.html

What we provide @KnetMiner and DFW

What we provide @KnetMiner and DFW
Based on publications, which genes are related to the yellow rust disease?
In which biological processes are their encoded proteins involved?
In which tissues are the genes expressed?

Why Lightweight Schemas
Based on publications,
which genes are related
to the yellow rust
disease? In which
biological processes are
their encoded proteins
involved? In which
tissues are the genes
expressed?

Schema, Bioschemas, AgriSchemas
• Ideal for:
• Heterogeneous data, sources, formats
• Informal data
• Exploratory research (including AI)
• Integration/sharing advantages
• Simple and informal, but it’s easy to integrate
• other data (eg, OBO ontologies)
• FAIR-oriented support (eg, Google Dataset
Search)
• The AgriSchemas Project
• A set of use cases modelled with
schema.org, bioschemas
• Reusable data ETL tools
• bioschemas additions and extensions

Ongoing Work
Use case Data Types Data Sources Status
Molecular Biology Gene, Protein, Pathway
encodes, participates
Via Knetminer: ENSEMBL, UniProt,
TILLING, wheat-expression.com, KEGG
Done.
Ontology Annotations Ontology Term (schema:DefinedTerm)
dc:type, schema:additionalType
Via Knetminer: GO, PO, CROP-Onto Done.
Experiments Study, agri:StudyFactor, PropertyValue EBI/GXA, GLTen, MIAPPE/BrAPI
sources, ?
GXA Done (to be published)
GLTen use case drafted
MIAPPE, use case drafted
Literature agri:ScholarlyPublication
mentions
Via Knetminer: PubMed Done
Gene Expression bioschema:expressedIn, reified
statements, agri:evidence, agri:pvalue,
agri:baseCondition
EBI/GXA, Via Knetminer: wheat-
expression.com
GXA to be published
Host-pathogen interaction Gene, Phenotype,
agri:ScholarlyPublication
agri:HostPathogenInteraction
agri:evidence
PHI-Base Use case drafted
Weather ? ? TO DO
Dataset metadata Dataset, DataCatalog
license, distribution
knetminer.org/data ongoing

References
• AgriSchemas
• https://github.com/Rothamsted/agri-schemas
• Use cases: https://github.com/Rothamsted/agri-schemas/tree/master/drafts/201904-dfw-
hackathon
• Real data & ETL tools: https://github.com/Rothamsted/agri-schemas/tree/master/dfw-dataset
• Knetminer
• Web site: http://knetminer.org
• Publication: https://doi.org/10.1111/pbi.13583
• Case study about FAIR data:
• https://knetminer.com/cases/the-power-of-standardised-and-fair-knowledge-graphs.html
• FAIR data infrastructure: https://doi.org/10.1515/jib-2018-0023
• Data endpoint: http://knetminer.org/data
• DFW
• AgriSchemas and DFW:
• https://designingfuturewheat.org.uk/dfw-and-fair-agriculture-data-the-knetminer-
experience/
• Me
• https://www.slideshare.net/mbrandizi, https://marcobrandizi.info/about-me/