=Paper=
{{Paper
|id=None
|storemode=property
|title=Modular Extensions to the ChEBI Ontology
|pdfUrl=https://ceur-ws.org/Vol-897/poster_7.pdf
|volume=Vol-897
|dblpUrl=https://dblp.org/rec/conf/icbo/HastingsMDEMTOS12
}}
==Modular Extensions to the ChEBI Ontology==
https://ceur-ws.org/Vol-897/poster_7.pdf
Modular Extensions to the ChEBI Ontology
Janna Hastings∗, Paula de Matos, Adriano Dekker, Marcus Ennis, Venkatesh
Muthukrishnan, Steve Turner, Gareth Owen and Christoph Steinbeck
Cheminformatics and Metabolism, European Bioinformatics Institute, Hinxton, UK
ABSTRACT from the core database content. The mapping to BFO is made
ChEBI is an ontology of chemical entities of biological interest. It available as one such modular extension, chebi-in-bfo.owl.
includes a structure-based and a role-based classification of chemical Another extension, available as chebi-disjoints.owl,
entities including molecules, ions and salts. This poster showcases includes axioms about disjointness between entities in the onto-
recent developments and forthcoming enhancements to the ontology, logy. Many of the classes in the chemical entity ontology are not
focusing on modular extensions of the content. These extensions disjoint, because chemical classification is compositional (Hastings
are being developed in support of error detection and consistency et al., 2012). Annotating those pairs of classes that are disjoint thus
checking and to improve the capability for automated reasoning about allows for better error detection, as a reasoner is able to raise an error
the biological context of chemicals. if anything is accidentally classified beneath both of the two clas-
ses that should be disjoint. In an ontology the size of ChEBI, such
1 INTRODUCTION automated assistance with the detection of errors is essential. For
example, group (CHEBI:24433) is disjoint from molecular entity
ChEBI is an ontology of chemical entities of biological interest
(CHEBI:23367). Introducing this axiom allowed us to detect and
(de Matos et al., 2010). It includes a structure-based and a role-
correct an incorrect classification of the ion 3-D-glucuronosyl-N2,6-
based classification of chemical entities, such as molecules, ions
disulfonato-beta-D-glucosamine(3-) (CHEBI:58150) as a group.
and salts. Within the structure-based classification, chemical enti-
ties are organised according to shared structural features, such as
skeletons and functional groups. In addition to taxonomic classi- 4 THE BIOLOGICAL CONTEXT OF CHEMICALS
fication, structure-based relationships capture biologically relevant ChEBI is also being extended in order to explicitly represent the
associations between compounds, such as tautomers, enantiomers biological context of the chemicals as semantic relationships to bio-
and conjugate bases and acids. Within the role classification, the logical entities in external ontologies, as described in (Batchelor
various ways that chemical entities can be active in biological and et al., 2010). One example of such is the explicit annotation of spe-
chemical contexts are organised, such as by inhibiting the activity of cies and tissue for metabolites (natural products). Another is the
enzymes, acting as hormones, being used as insecticides, and being explicit annotation of diseases in the case of drugs used to treat the
used as solvents. Chemical entities are linked to roles with the has diseases and in the case of metabolites that are markers for certain
role relationship. diseases. Cross-references and annotations of ChEBI identifiers in
ChEBI includes just over 28,000 annotated entities as of the biological databases will be used as sources for this effort, which
May 2012 release. The ontology is available for browsing at will then be checked by ChEBI curators.
http://www.ebi.ac.uk/chebi/ and is fully downloadable Relationships from the RO and other ontologies from the OBO
in several formats including OBO and OWL. Foundry effort will be used in all cases.
2 RECENT DEVELOPMENTS ACKNOWLEDGEMENTS
ChEBI recently completed a large annotation push to make the onto- ChEBI is funded by the BBSRC, grant agreement BB/G022747/1
logy fully is-a complete, that is, to ensure that each entity has at within the ‘Bioinformatics and biological resources’ fund.
least one taxonomic parent. (Previously, due to historical legacy,
there were some entities that were only classified using structural REFERENCES
relationships such as has functional parent.) Furthermore, ChEBI is Batchelor, C., Hastings, J., and Steinbeck, C. (2010). Ontological dependence, dispo-
now aligned with BFO, as described in (Hastings et al., 2011) and sitions and institutional reality in chemistry. In A. Galton and R. Mizoguchi,
work is well underway in alignment with the Gene Ontology (The editors, Proceedings of the 6th Formal Ontology in Information Systems conference,
Toronto, Canada.
Gene Ontology Consortium, 2000). Another recent development is
de Matos, P., Alcántara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., Spiteri, I.,
the provision of a new graph-based visualisation of the ontology. Turner, S., and Steinbeck, C. (2010). Chemical Entities of Biological Interest: an
update. Nucleic Acids Research, 38, D249–D254.
3 EXTENSIONS FOR ERROR DETECTION Hastings, J., de Matos, P., Dekker, A., Ennis, M., Haug, K., Josephs, Z., Owen, G.,
Turner, S., and Steinbeck, C. (2011). Recent developments in the ChEBI ontology.
ChEBI is being enhanced with modular extensions to the onto- In Proceedings of the International Conference on Biomedical Ontology (ICBO),
logy in support of error detection and consistency checking. These CEUR-WS volume 833.
extensions are being annotated in separate OWL module files which Hastings, J., Magka, D., Batchelor, C., Duan, L., Stevens, R., Ennis, M., and Steinbeck,
C. (2012). Structure-based classification and ontology in chemistry. Journal of
extend the main ontology file that is generated on a monthly basis
Cheminformatics, 4(1), 8.
The Gene Ontology Consortium (2000). Gene ontology: tool for the unification of
∗ To whom correspondence should be addressed: hastings@ebi.ac.uk biology. Nat. Genet., 25, 25–9.
1