Jargon bad, controlled vocabulary good

A post over at Omics! Omics! discusses The gene and the genon concept: a functional and information-theoretic analysis, published in Molecular Systems Biology. This article points out that “gene” is a poorly-defined word and then proposes some new terms: genon (with pre-, proto- and transgenons), P-, R-, s- and c-genes with various combinations thereof and a whole bunch of other jargon. It reminded me of a similar debate that I read recently in Genome Biology on the use of the words “ortholog” and “paralog” – and whether we need additional terms such as “metalog” or “xenolog”.

I find these papers fun but unhelpful and I think they demonstrate another case where a journal article is not an appropriate forum. When articles like these appear out of the blue it’s easy to form the impression, rightly or wrongly, that rather than an honest proposal to improve the situation, it’s an attempt to push a personal agenda. My first thought is always “hey, some crazy people have invented their own language and they want us all to use it!”

We do need to define concepts in biology, but as a community. Can it be so hard for a panel of experts to get together, think about what makes up a complete biological “parts list” and define a controlled vocabulary and an ontology? I know that there are projects like this. Furthermore, can they do it in a visible, public forum where we can all contribute and comment? That way we might end with some useful definitions and tools.

One thought on “Jargon bad, controlled vocabulary good

  1. Can it be so hard for a panel of experts to get together

    Getting the panel together is the easy part. Getting them to agree to a set of standards and have meaningful dialog on the other hand, that’s another story.

    There have been some success stories, but for each success story, there are probably ten more failures. Scientists (I suppose all people) are good at talking about things, but not half as good as taking action.

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