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Watson’s law of bioinformatics ontologies

Modeled very much on Godwin’s law, “Watson’s law of bioinformatics ontologies” was first coined at TGAC during an ELIXIR/GOBLET workshop.

The law simply states:

"As the discussion regarding a particular bioinformatics topic gets longer, 
the probability that someone will suggest the group develops an ontology for 
that topic approaches 1"

Bioinformatics is awash with ontologies, including the sequence ontology and the gene ontology.  There is at least anecdotal evidence that neither is actually a true ontology.  There is also the suggestion that the gene ontology should only have two terms: “encodes for a protein”; and “encodes for an RNA”.  Function would then be defined by a Protein Ontology (PO) and RNA ontology (RO).

The particular discussion that inspired the “Watson’s law of bioinformatics ontologies” was around SASI, an ontology to describe events/announcements in the life sciences.

I would also like to suggest the very beginnings of a controlled vocabulary, possibly to be developed into an ontology, to describe bioinformaticians themselves.  The first two terms may be:

  • “has an interest in ontologies”
  • “has no interest in ontologies”

Comments welcome 🙂

6 Comments

  1. I know it might sound naive, but the worst is not the ontology per se, but the amount of time people waste in reaching an agreement to develop the ontology. And it is sadder, that amount of time is inversely proportional to the amount of people that will actually use it!

  2. I think you have misunderstood the Gene Ontology; it is a controlled vocabulary of terms to capture the processes a gene or gene product participates in, and the cellular locations in which it is found (see http://geneontology.org for more info). People used to add a disclaimer to their GO presentations to say that the project was not about genes, and was definitely not an ontology of genes. The name just stuck!

  3. PS: you shouldn’t use negative terms in ontologies. Your bioinformatician ontology would be better structured thus (where [i] represents an ‘is a’ relationship to the parent term):

    bioinformatician
    [i] bioinformatician interested in ontologies

    But then you’d probably want to make your ontology a bit more generic so you could cover others who use ontologies (e.g. computer scientists; philosophers; professional pedants) and other interests. I’d elaborate more, but I’m fairly sure there’s a paper in this…

  4. The “Gene Ontology” is a misnomer; it is really the “Gene Product” ontology.
    It’s a little unfortunate, but is demonstrates a point well known by
    ontologies: names are hard.

    Having said this ontologies can be useful. A question like “which kind of
    genes are upregulated in this microarray/proteomics/next-gen dataset” is hard
    without the gene ontology. Likewise, bibtex
    file is possible because of a small ontology; you did know that your web page
    contains an ontology?

    Having said that, I think that there is a problem. Within the bio-ontologies
    community (where I guess I am), I think there is currently too much focus on
    the ontology as end product, and too little focus on applications. Funnily,
    enough you encapsulate the problem in your post: “There is at least anecdotal evidence that neither is
    actually a true ontology.” Ontologists can get very exicted about what what is
    or is not a “true” ontology; mission-creep, and the desire to model the entire
    world, is all too common. Indeed, some even make the mistake that this desire
    defines what is a good ontology. It’s corrosive and problematic.

    You don’t say which category you are in: if you are “have no interest in
    ontologies”, then I think you are wrong; but I also think its up to me to
    prove that you are wrong. It is something that we could do a much better job
    of.

  5. Negative terms are fine, and have a clearly defined semantics. Your ontology cannot differentiate between bioinformaticians not interested in ontologies, and bioinformaticians who interest level we do not know.

  6. I’m thinking in GO mode, where you’d use the ‘NOT’ qualifier to annotate someone who wasn’t interested in ontologies.
    With conversations like this, it’s difficult to see how anyone could fail to be interested in ontologies! ;^)

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