introduction to the embl-ebi ontology lookup service · 2016-07-29 · the ontology of color...
TRANSCRIPT
![Page 1: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/1.jpg)
Introduction to the EMBL-EBI Ontology Lookup Service
Simon Jupp [email protected], @simonjupp
Samples, Phenotypes and Ontologies Team
European Bioinformatics Institute
Cambridge, UK.
![Page 2: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/2.jpg)
Ontologies in the life sciences
CanineDog
Different Words Same Concept
![Page 3: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/3.jpg)
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
![Page 4: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/4.jpg)
We need terminology standards
Dyschromatopsia
![Page 5: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/5.jpg)
Search PubMed for “color blindness”
![Page 6: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/6.jpg)
Search PubMed for “Dyschromatopsia”
![Page 7: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/7.jpg)
Search PubMed for "abnormality of the eye"
![Page 8: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/8.jpg)
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
![Page 9: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/9.jpg)
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
![Page 10: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/10.jpg)
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
![Page 11: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/11.jpg)
Ontologies add value
Smarter searching
Data visualisation
Data analysis
Data integration
![Page 12: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/12.jpg)
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
![Page 13: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/13.jpg)
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
![Page 14: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/14.jpg)
Live demo
• http://www.ebi.ac.uk/ols
![Page 15: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/15.jpg)
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
![Page 16: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/16.jpg)
Visualisation tools
![Page 17: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/17.jpg)
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
![Page 18: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/18.jpg)
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?
![Page 19: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/19.jpg)
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
![Page 20: Introduction to the EMBL-EBI Ontology Lookup Service · 2016-07-29 · The ontology of color blindness HP:0011518 (Eye) HP:0011518 (Dichromacy ) HP:0000551 (Abnormality of color vision](https://reader033.vdocuments.us/reader033/viewer/2022042915/5f5193b8767cd3589435dd6e/html5/thumbnails/20.jpg)
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