Interoperable Data for KnetMiner and DFW Use Cases
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This document discusses using AgriSchemas and schema.org to model and share interoperable agricultural data from sources like KnetMiner and DFW for use cases involving molecular biology, gene expression, literature, and experiments. AgriSchemas provides a way to formally represent heterogeneous agricultural data to support exploratory research and data integration/sharing according to FAIR principles. Examples show how gene, publication, experiment and other data from KnetMiner are modeled and made accessible via AgriSchemas and linked data formats. Ongoing work focuses on additional areas like host-pathogen interactions, weather data, and dataset metadata.
Interoperable Data for KnetMiner and DFW Use Cases
- 1. Interoperable Data for KnetMiner and DFW Use Cases Elixir BioHackathon 2021 Marco Brandizi <marco.brandizi@rothamsted.ac.uk> Find this presentation on SlideShare background source: https://alimentaciosostenible.barcelona/en/protecting-planet/urban-agriculture
- 2. Typical KnetMiner Searches Based on publications, which genes are related to the yellow rust disease? In which biological processes are their encoded proteins involved?
- 4. schema.org, 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
- 5. AgriSchemas: Molecular Biology Use Case Live: http://knetminer.org/data/rdf/resources/gene_traescs1d02g156000
- 6. AgriSchemas: Molecular Biology Use Case
- 7. AgriSchemas: Information Artifacts Live: http://knetminer.org/data/rdf/resources/publication_23105158
- 8. AgriSchemas: Gene Expression (and EBI/GXA Data) 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?
- 9. AgriSchemas: Gene Expression (and EBI/GXA Data) Live here.
- 10. AgriSchemas: Gene Expression (and EBI/GXA Data) Live here.
- 11. AgriSchemas: Ontologies and Ontology Annotations Live: http://knetminer.org/data/rdf/resources/cond_outer_pericarp
- 12. AgriSchemas: Gene Expression (and EBI/GXA Data) 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? What is the experimental evidence (ie, Field Trials) for the gene ex?
- 13. AgriSchemas: Studies/Experiments/Field Trials Live: http://knetminer.org/data/rdf/resources/exp_E-MTAB-3103 Detailed modelling about Field Trials: https://github.com/Rothamsted/agri-schemas/tree/master/doc/miappe-use-case Use case (includes study, samples, assays): https://github.com/Rothamsted/agri-schemas/blob/master/doc/miappe-use-case.ttl
- 14. 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 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 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
- 15. 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/