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Introduction to the EMBL-EBI Ontology Lookup Service
Simon Jupp [email protected], @simonjupp
Samples, Phenotypes and Ontologies Team
European Bioinformatics Institute
Cambridge, UK.
Ontologies in the life sciences
CanineDog
Different Words Same Concept
Building ontologies
• Put things into categories
• Helps organise the data
• Allows us to generalise over data
• Capture the relations between things
• Anatomical parts
Biopolymer
Nucleic Acid Polypeptide
EnzymeDNA RNA
tRNA mRNA smRNA
We need terminology standards
Dyschromatopsia
Search PubMed for “color blindness”
Search PubMed for “Dyschromatopsia”
Search PubMed for "abnormality of the eye"
The ontology of color blindness
HP:0011518 (Dichromacy )HP:0011518 (Eye)
HP:0000551 (Abnormality of color vision )
HP:0007641 (Dyschromatopsia)
Is-a
Is-aDisease-location
The ontology of color blindness
HP:0011518 (Dichromacy )HP:0011518 (Eye)
HP:0000551 (Abnormality of color vision )
HP:0007641 (Dyschromatopsia)
Is-a
Is-aDisease-location
“Colorblindness”
“A form of colorblindness in which only two of the three fundamental colors can be distinguished due to a lack of one of the retinal cone pigments.”
synonym
definition
10
Genotype Phenotype
SequenceProteins
Gene products Transcript
Pathways
Cell type
BRENDA tissue / enzyme source
Development
AnatomyPhenotype
Plasmodium life cycle
-Sequence types and features-Genetic Context
- Molecule role - Molecular Function- Biological process - Cellular component
-Protein covalent bond -Protein domain -UniProt taxonomy
-Pathway ontology -Event (INOH pathway ontology) -Systems Biology -Protein-protein interaction
-Arabidopsis development -Cereal plant development -Plant growth and developmental stage -C. elegans development -Drosophila development FBdv fly development.obo OBO yes yes -Human developmental anatomy, abstract version -Human developmental anatomy, timed version
-Mosquito gross anatomy-Mouse adult gross anatomy -Mouse gross anatomy and development -C. elegans gross anatomy-Arabidopsis gross anatomy -Cereal plant gross anatomy -Drosophila gross anatomy -Dictyostelium discoideum anatomy -Fungal gross anatomy FAO -Plant structure -Maize gross anatomy -Medaka fish anatomy and development -Zebrafish anatomy and development
-NCI Thesaurus -Mouse pathology -Human disease -Cereal plant trait -PATO PATO attribute and value.obo-Mammalian phenotype - Human phenotype-Habronattus courtship -Loggerhead nesting -Animal natural history and life history
eVOC (Expressed Sequence Annotation for Humans)
Ontologies for life sciences
Ontologies add value
Smarter searching
Data visualisation
Data analysis
Data integration
Ontology Lookup Service
• Search for terms based on id or labels
• Browse and visualise ontologies as a tree or a graph
• Powerful RESTful API and third party libraries (Java, Python, R) for programmatic access
• Open source project
• Generic infrastructure (can load any ontology represented in OWL)
https://github.com/EBISPOT/OLS
Repository of over 150 biomedical ontologies (4.5 million terms, 11 million relations)
http://www.ebi.ac.uk/ols
What’s in OLS?
• All Open Biomedical Ontology (OBO) ontologies
• http://obofoundry.org
• Community of interoperable ontologies for the life science and medical domain
• Other ontologies relevant for EBI data
• E.g. Experimental Factor Ontology
• Can load any OBO or OWL formatted ontology
• Many domains covered
• Anatomy, cell type, cell lines, disease, taxonomy, gene function, biological processes
Live demo
• http://www.ebi.ac.uk/ols
REST API
• Crawlable API - Hypermedia drivel (HAL)
• Get ontology and term meta data • /ontologies• /ontologies/{name}• /ontologies/{name}/terms• /ontologies/{name}/terms/{termid}
• Get related terms and navigate ontology structure• /ontologies/{name}/terms/{termid}/parent• /ontologies/{name}/terms/{termid}/children• /ontologies/{name}/terms/{termid}/descendants• /ontologies/{name}/terms/{termid}/ancestors• /ontologies/{name}/terms/{termid}/{relation} e.g. part_of
http://www.ebi.ac.uk/ols/api
Visualisation tools
Third part libs
• OLS Java client
• https://github.com/PRIDE-Utilities/ols-client
• OLS python library
• https://github.com/LLTommy/biopython-EBI-Resources/tree/master/EBI-ontologies
• OLS R (rols)
• https://github.com/lgatto/rols
What’s next for Ontology services?
• Data annotation
• Extend Zooma to support all ontologies in OLS
• Automatically map your data to existing ontologies based on curated data we’ve seen before
• Ontology mapping service
• Getting access to disease terminology cross-references (UMLS, SNOMED-CT, ICD 9/10, NCI, OMIM, MeSH)
• What would you likes to see?
Further information
• OLS http://www.ebi.ac.uk/ols
• OBO foundry http://www.obofoundry.org
• Ontogenesis http://ontogenesis.knowledgeblog.org
Contact us
• https://github.com/EBISPOT/OLS
Acknowledgements
• Sample Phenotypes and Ontologies Team - Tony Burdett, James Malone, Dani Welter, Catherine Leroy, SiraSarntivijai, Ilinca Tudose, Helen Parkinson
• Matt Pearce – Flax (BioSOLR project)
• Michal Bachman and GraphAware team (Neo4j training)
• Funding
• European Molecular Biology Laboratory (EMBL)
• European Union projects: DIACHRON, BioMedBridges and CORBEL