O'Really?

June 4, 2009

Improving the OBO Foundry Principles

The Old Smithy Pub by loop ohThe Open Biomedical Ontologies (OBO) are a set of reference ontologies for describing all kinds of biomedical data, see [1-5] for examples. Every year, users and developers of these ontologies gather from around the globe for a workshop at the EBI near Cambridge, UK. Following on from the first workshop last year, the 2nd OBO workshop 2009 is fast approaching.

In preparation, I’ve been revisiting the OBO Foundry documentation, part of which establishes a set of principles for ontology development. I’m wondering how they could be improved because these principles are fundamental to the whole effort. We’ve been using one of the OBO ontologies (called Chemical Entities of Biological Interest (ChEBI)) in the REFINE project to mine data from the PubMed database. OBO Ontologies like ChEBI and the Gene Ontology are really crucial to making sense of the massive data which are now common in biology and medicine – so this is stuff that matters.

The OBO Foundry Principles, a sort of Ten Commandments of Ontology (or Obology if you prefer) currently look something like this (copied directly from obofoundry.org/crit.shtml):

  1. The ontology must be open and available to be used by all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed under the original name or with the same identifiers.The OBO ontologies are for sharing and are resources for the entire community. For this reason, they must be available to all without any constraint or license on their use or redistribution. However, it is proper that their original source is always credited and that after any external alterations, they must never be redistributed under the same name or with the same identifiers.
  2. The ontology is in, or can be expressed in, a common shared syntax. This may be either the OBO syntax, extensions of this syntax, or OWL. The reason for this is that the same tools can then be usefully applied. This facilitates shared software implementations. This criterion is not met in all of the ontologies currently listed, but we are working with the ontology developers to have them available in a common OBO syntax.
  3. The ontologies possesses a unique identifier space within the OBO Foundry. The source of a term (i.e. class) from any ontology can be immediately identified by the prefix of the identifier of each term. It is, therefore, important that this prefix be unique.
  4. The ontology provider has procedures for identifying distinct successive versions.
  5. The ontology has a clearly specified and clearly delineated content. The ontology must be orthogonal to other ontologies already lodged within OBO. The major reason for this principle is to allow two different ontologies, for example anatomy and process, to be combined through additional relationships. These relationships could then be used to constrain when terms could be jointly applied to describe complementary (but distinguishable) perspectives on the same biological or medical entity. As a corollary to this, we would strive for community acceptance of a single ontology for one domain, rather than encouraging rivalry between ontologies.
  6. The ontologies include textual definitions for all terms. Many biological and medical terms may be ambiguous, so terms should be defined so that their precise meaning within the context of a particular ontology is clear to a human reader.
  7. The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the OBO Relation Ontology.
  8. The ontology is well documented.
  9. The ontology has a plurality of independent users.
  10. The ontology will be developed collaboratively with other OBO Foundry members.

ResearchBlogging.orgI’ve been asking all my frolleagues what they think of these principles and have got some lively responses, including some here from Allyson Lister, MĂ©lanie Courtot, Michel Dumontier and Frank Gibson. So what do you think? How could these guidelines be improved? Do you have any specific (and preferably constructive) criticisms of these ambitious (and worthy) goals? Be bold, be brave and be polite. Anything controversial or “off the record” you can email it to me… I’m all ears.

CC-licensed picture above of the Old Smithy (pub) by Loop Oh. Inspired by Michael Ashburner‘s standing OBO joke (Ontolojoke) which goes something like this: Because Barry Smith is one of the leaders of OBO, should the project be called the OBO Smithy or the OBO Foundry? 🙂

References

  1. Noy, N., Shah, N., Whetzel, P., Dai, B., Dorf, M., Griffith, N., Jonquet, C., Rubin, D., Storey, M., Chute, C., & Musen, M. (2009). BioPortal: ontologies and integrated data resources at the click of a mouse Nucleic Acids Research DOI: 10.1093/nar/gkp440
  2. Côté, R., Jones, P., Apweiler, R., & Hermjakob, H. (2006). The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries BMC Bioinformatics, 7 (1) DOI: 10.1186/1471-2105-7-97
  3. Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L., Eilbeck, K., Ireland, A., Mungall, C., Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S., Scheuermann, R., Shah, N., Whetzel, P., & Lewis, S. (2007). The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration Nature Biotechnology, 25 (11), 1251-1255 DOI: 10.1038/nbt1346
  4. Smith, B., Ceusters, W., Klagges, B., Köhler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A., & Rosse, C. (2005). Relations in biomedical ontologies Genome Biology, 6 (5) DOI: 10.1186/gb-2005-6-5-r46
  5. Bada, M., & Hunter, L. (2008). Identification of OBO nonalignments and its implications for OBO enrichment Bioinformatics, 24 (12), 1448-1455 DOI: 10.1093/bioinformatics/btn194

May 13, 2009

XML Summer School, Oxford

XML Summer School, Oxford, U.K.After a brief absence, it is good to see the XML Summer School is back again this September (20th-25th) at St. Edmund Hall, Oxford. This is  “a unique event for everyone using, designing or implementing solutions using XML and related technologies.” I’ve been both a delegate and a speaker here over the years; back in 2005, with Nick Drummond we presented the ProtĂ©gĂ© and OWL tutorial which was good fun.  So here is what I.M.H.O. makes the XML summer school worth a look: (more…)

May 22, 2008

First ChEBI workshop, Day Two

Filed under: informatics — Duncan Hull @ 2:49 pm
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Chemist Margaret Thatcher stays at the Crowne House Hotel, Great Chesterford, England
Some rough and ready notes from day two of the first ChEBI workshop, 20th May 2008. There were two talks, one from Kirill Degtyarenko (European Patent Office) and the other from Janna Hastings (EBI), followed by a discussion.

Kirill Degtyarenko: Good annotation practice for chemical data, ChEBI experience

Kirill’s talk described how to give the most appropriate names, especially since “biologists don’t name things properly, if at all” (!). Systematic (IUPAC) names are usually better than common names except for “the unprounounceables” for example, an antibiotic called (E)-roxithromycin (ChEBI:48935) has the IUPAC name:

(3R,4S,5S,6R,7R,9R,10E,11S,12R,13S,14R)-4-(2,6-dideoxy-3-C-methyl-3-O-methyl-α-L-ribo-hexopyranosyloxy)-14-ethyl-7,12,13-trihydroxy-10-{[(2-methoxyethoxy)methoxy]imino}-6-[3,4,6-trideoxy-3-(dimethylamino)-β-D-xylo-hexopyranosyloxy]-3,5,7,9,11,13-hexamethyloxacyclotetradecan-2-one

…which just trips of the tongue (and fits beautifully, without line breaks onto regular computer screens). Fortunately, the curator can draw the chemical (note the wavy bond, unknown stereochemistry), using the curator tools, then the inchi and smiles strings are generated from the drawing. Currently they use something called ACD/Name which can generate PubChem links automatically. As of May 2008 14,000 chebi ids translates to around 11,000 CIDs in PubChem, which is structures only.
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May 21, 2008

First ChEBI workshop, Day one



Great Chesterford
Some notes from day one of the first ChEBI workshop, 19th May 2008. There were four talks from Colin Batchelor (Royal Society of Chemistry), Ulrike Witting (EML Research GmbH Hiedelberg), Giles Weaver (Unilever) and Paula de Matos (EBI). Christoph Steinbeck has already written some ChEBI notes, these just add a little more detail. (more…)

May 15, 2008

BBC: Building a Better ChEBI

Filed under: semweb — Duncan Hull @ 4:09 pm
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molecule by vabellon, on FlickrChemical Entitites of Biological Interest, ChEBI, is a freely available dictionary [1] of molecular entities, especially small chemical compounds. Like all big dictionaries and ontologies, it has its own unique challenges. Fortunately, those nice people at the EBI are holding a workshop to discuss future developments in ChEBI. In preparation for the workshop, here are some brief notes on how ChEBI could be made better. [Disclaimer: I’m fairly new to ChEBI and “thinking out loud” here, add comments below if I’ve said anything stupid or wrong]

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March 5, 2008

Cheminformatics 2.0

Some brief notes on and links to presentations from the MCISB / NaCTeM workshop on Chemical Informatics and Data-driven Science, held at the MIB in Manchester, 4th March 2008. (more…)

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