Standardized Term Names

[Chris Mungall]

Whichever way we do it, I don't think we should mark up things in the
ontology just to suit a particular piece of software.

We should only do this if it doesn't impact curation time and if the
notion of a 'formal' synonym for a term is useful to humans.

Here are the criteria for a formal synonym:

- it must be an exact synonym
  [ and would still be designated as such in the obo file, it
    would just have an additional qualifier ]

- the existing term name is some kind of colloquial shorthand
  that is readily recognised by most biologists, yet the naming
  style of the shorthand is different from the consistent naming
  style employed for similar terms

- the existence of the synonym is a genuine rephrasing of the
  term name, and does not exist by virtue of alternate spellings
  of words.

- the formal synonym must employ canonical spellings

Why would this be useful to humans too? Well, sometimes it may be useful
to organise a set of terms such that either the formal synonym (or just
the name if there is no designated formal synonym) is used as the primary
label. Thus the term with name "methanogenesis" will be listed as "methane
biosynthesis" and will have consistent labeling style with other "X
biosynthesis" terms.

If this isn't useful then we shouldn't bother.

If we don't, then what I do think will be useful (and what will be quite
sufficient for obol) is to separate the useful exact_synonyms from the
exact_synonyms that are derivable from the exact_synonyms of sub-terms.

An example is "sulfite reduction/sulphite reduction". This is only useful
for the purposes of searching, and could be handled automatically.
Displaying this synonym is of no use to the user.

Cheers
Chris

On Fri, 18 Feb 2005, John Day-Richter wrote:

> J Clark wrote:
>
> > If there was a way to mark the 'obol' synonym then I could easily
> > assign the synonym type to that as I went along. Might this be a
> > possibility with DAG-Edit John?
>
> We have synonym types in OBO-Edit... just hang on! A beta-version will
> be out soon (of course, you won't be able to save your changes to the
> repository for a while after that, because everyone else will still be
> using DAG-Edit).
>
> For now, I suggest you add a synonym dbxref to the OBO synonyms (like
> "syntype:obol"). Once we move to full-fledged synonym types, we can do a
> quick search-and-replace to change those dbxrefs into synonym category
> identifiers.
>
>     -John
>
>