Introduction to the EMBL-EBI Ontology Lookup Service Simon Jupp jupp@ebi.ac.uk, @simonjupp Samples, Phenotypes and Ontologies Team European Bioinformatics Institute Cambridge, UK.
Ontologies in the life sciences Different Words Same Concept Dog Canine
Building ontologies Put things into categories Biopolymer Helps organise the data Allows us to generalise over data Nucleic Acid Polypeptide Capture the relations between things Anatomical parts DNA RNA Enzyme 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:0000551 (Abnormality of color vision ) Is-a HP:0007641 (Dyschromatopsia) Disease-location Is-a HP:0011518 (Eye) HP:0011518 (Dichromacy )
The ontology of color blindness HP:0000551 (Abnormality of color vision ) Is-a synonym HP:0007641 (Dyschromatopsia) definition Is-a Disease-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. HP:0011518 (Eye) HP:0011518 (Dichromacy )
Ontologies for life sciences -Sequence types and features -Genetic Context Sequence -Protein covalent bond -Protein domain -UniProt taxonomy Proteins -Pathway ontology -Event (INOH pathway ontology) -Systems Biology -Protein-protein interaction Pathways BRENDA tissue / enzyme source -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 Anatomy Phenotype Genotype Phenotype Gene products Transcript Cell type Development Plasmodium life cycle - Molecule role - Molecular Function - Biological process - Cellular component evoc (Expressed Sequence Annotation for Humans) -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 -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 10
Ontologies add value Data analysis Smarter searching Data visualisation Data integration
Ontology Lookup Service http://www.ebi.ac.uk/ols Repository of over 150 biomedical ontologies (4.5 million terms, 11 million relations) 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
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 http://www.ebi.ac.uk/ols/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
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 ols-support@ebi.ac.uk https://github.com/ebispot/ols
Acknowledgements Sample Phenotypes and Ontologies Team - Tony Burdett, James Malone, Dani Welter, Catherine Leroy, Sira Sarntivijai, 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