Standardized Term Names

[Chris Mungall]

[cc-ing Sue, even though I suspect she is already on the development
mailing list]

Let me see if I understand

You want to just have name='oesinophil differentiation', and not bother
having exact_synonym='oesinophil cell differentiation'?

That seems very sensible, since it's not a good use of curator time to
insert these automatable synonyms. You certainly shouldn't be spending any
time on this to help an automatable parser like Obol!

Are you also saying you'd like Obol to automatically add these synonyms?
We're not really set up for this kind of dataflow at the moment. There
would be some lag, during which time users search on Amigo for "oesinophil
cell differentiation" would come back empty handed (I think this should
actually be handled at the search level rather than at the synonym level,
though again we aren't set up for this yet).

What Obol really cares about for these terms (and what I think we should
care about) is consistency with the cell ontology.

Note that the cell ontology has "eosinophil" (NOT "oesinophil"). If this
is a genuine synonym then there should be a dialog with the cell ontology
curators to introduce that synonym in the cell ontology. Synonyms for GO
can then be computed automatically for this.

Note also that the cell ontology has "chromophil cell" and "neutrophil".
Why not "chromophil" and "neutrophil cell"? If this reflects actual usage
then the term names should reflect this. If there are reasons to believe
that the cell ontology naming conventions are arbitrary, then the cell
ontology should be modified to be consistent with actual usage. The GO
should then take the cell ontology as the authorative source, and use the
corresponding naming convention.

Cheers
Chris

On Mon, 21 Feb 2005, Jennifer I Clark wrote:

> Hi Chris,
>
> I was thinking more about the cell differentiation things. I reckon your
> obol parser would be okay without the synonyms as long as I tell you a
> few more naming rules.
>
> We have the following kinds of differentiation terms:
>
> x cell differentation
> xblast differentation
> xphil differentation
>
> where the word endings 'blast' and 'phil' are synonyms for the word
> 'cell' in the first example. If I just tell you about these extra rules
> then could you add them to the pareser? That way I wouldn't need to to
> bother with the synonyms. I could add documentation to the website to
> say that where these endings are in a term we don't add the word 'cell'
> since it is redundant.
>
> Thanks,
>
> Jen
>
> Chris Mungall wrote:
>
> >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
> >>
> >>
> >>
> >>
>
>