introduction to the embl-ebi ontology lookup service · 2016-07-29 · the ontology of color...

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

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

• ols-support@ebi.ac.uk

• 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