Bio-ontologies in bioinformatics: Growing up challenges

Ontologies in Bioinformatics: Growing-up challenges

Janna Hastings1,2,3

1 Cheminformatics and Metabolism, European Bioinformatics Institute2 Swiss Center for Affective Sciences, University of Geneva

3 Swiss Institute of Bioinformatics

Robinson-Rechavi 2-day Group MeetingLausanne, June 4-5 2012

STANDARDS:RESEARCH

REPRODUCABILITY,BIOCURATION,

DATA INTEGRATION,EXCHANGE,

SEMANTIC WEB…

ANALYSIS: ENRICHMENT,

SEMANTIC SIMILARITY,…

DATABASE MANAGEMENT:

BROWSING,VISUALIZATION,CLASSIFICATION,

AUTOMATED REASONING,

…

Applications of ontologies in bioinformatics

Growing-up challenges for ontologies in bioinformatics

1. Visualization2. Moving from OBO to OWL –

tools, software3. Moving from single ontologies to multiple

ontologies (using cross-products)4. Training aimed at biologists and

bioinformaticians5. Community building

Selected ontology-related publications (JH @EBI)

• Janna Hastings et al., Structure-based classification and ontology in chemistry. Journal of Cheminformatics. 2012 Apr 5; 4:8.

• Barry Hardy, [...] Janna Hastings et al. Toxicology ontology perspectives. ALTEX 2012, 29 (2), 139.

• Janna Hastings et al. The Chemical Information Ontology: provenance and disambiguation for chemical data on the biological semantic web. PLoS ONE, 6(10).

• Melanie Courtot, […] Janna Hastings et al. Controlled vocabularies and semantics in Systems Biology. Molecular Systems Biology, 7:543.

• Janna Hastings et al., Modularization requirements in bio-ontologies: A case study of ChEBI. Frontiers in Artificial Intelligence and Applications Volume 230, p. 63--70.

• Kirill Degtyarenko, […] Janna Hastings et al., ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344-D350.

ChEBI: Chemicals of Biological Interest

1. Ontology visualization

There is a need to hide irrelevant information and concisely display relevant information

ChEBI has introduced a new heuristic for hiding redundant paths in the visualiation

See also http://ols.wordvis.com/

2. Moving from OBO to OWL

DEPRECATED

OBO-Edit is the most commonlyused bio-ontology editor, but it isno longer actively being developed

UNUSABLE

by biologist

s?

Protégé is the tool that will replace OBO-Edit, but it urgently needsinvestment in usability improvements for use by biologists and curators

APIs for programmaticaly working with OWL ontologies

• OWLTools (Java) … wrapper for, and much easier to use than, the OWL API (Java)

• OntoCat (R)• POSH (Prolog, Unix shell)• InfixOWL (Python)

Normalization of ontologies+ automated reasoning for hierarchies

FBbt

Normalized: More relationshipsMore inferred classificationsEasier to maintain but harder to navigate

Non-Normalized: Only is-a, maybe part-of relationsAll relevant relations are not asserted, onlythose found salient by the human annotators

3. Working with multiple ontologies

• Cross-products, e.g. chemicals in GO (for terms such as ‘carbohydrate metabolism’)

• No online visualization tools yet are able to display cross-products across ontologies

• Most databases don’t support annotation with composite terms, necessitating pre-composition

4. Training

5. Community building• ICBO conference• ISMB Bio-ontologies SIG

Not well attended by biologists/curators?

• Bio-curation conferenceNot well attended by ontologists?

• OBO Foundry Not very active lately?

• OntoSIB

Ontology @Pub nights Blog: www.bioontology.ch

COMPUTER SCIENCE

BIOLOGY

Thank you, AcknowledgementsChristoph SteinbeckColin BatchelorMarcus EnnisVenkatesh Muthukrishnan

Jane LomaxChris Mungall

BBSRCEU-OPENSCREEN

Barry SmithKevin MulliganWerner CeustersNicolas le NovereDavid Osumi-Sutherland

FNS (SNF)EMBL