Standardized Term Names--cell ontology and GO
Chris Mungall
cjm at fruitfly.org
Tue Feb 22 11:03:26 PST 2005
Hi Sue
I will do this. Perhaps there should be a cell ontology mailing list on
obo.sf.net? It's easy to set up and administer, I can show you how to do
this or even do it myself.
Cheers
Chris
On Mon, 21 Feb 2005, Sue Rhee wrote:
> I agree with both Chris and Alexander's views. While the cell ontology is
> much smaller effort than GO, Michael, Jonathan, and I are interested and
> somewhat committed to improving the cell ontology to use
> community-accepted terminology. May I suggest that you include Michael
> Ashburner, Jonathan Bard, and myself in the recipients of the obol run and
> we will try to resolve the name conflicts? Also, if anyone has any other
> term-related issues relevant to cell ontology such as those brought up by
> Alex in the thread below, please send them to Michael Ashburner, who is
> the official curator of cell ontology.
>
> Many thanks,
> Sue
>
> On Mon, 21 Feb 2005, Chris Mungall wrote:
>
> >
> > Hi Alex - I agree completely. I will create a specific cell ontology
> > alignment report next obol run
> >
> > On Mon, 21 Feb 2005, Alexander Diehl wrote:
> >
> > > Chris,
> > >
> > > While I would like to see the cell ontology continued to be improved,
> > > I think that its use in constructing GO terms cannot be forced at
> > > this time for the reasons I mentioned previously. In particular, I
> > > don't feel the cell ontology can be considered authoritative at this
> > > time and its naming conventions differ significantly from the GO.
> > > Nevertheless, it would be useful for interested parties to compare
> > > the cell ontology with the implicit GO cell ontology either
> > > computationally or by hand to look for discrepancies between the two
> > > and add appropriate synonyms where needed. I would also suggest the
> > > GO editors at EBI could make a point of comparing the two ontologies
> > > whenever a GO term containing a cell type name is being coined or
> > > modified in order to ensure the two ontologies are more in harmony by
> > > suggesting changes to one or the other ontology.
> > >
> > > -- Alex
> > >
> > >
> > > At 11:46 AM -0800 2/21/05, Chris Mungall wrote:
> > > >Alexander,
> > > >
> > > >The cell ontology is still young and not yet seeing much active use, so
> > > >it's not surprising it's incomplete and has problems. I had envisioned one
> > > >of the main users of the cell ontology as being the GO curators. It seems
> > > >that instead GO curators are focusing their energies on getting the
> > > >implicit cell ontology within GO correct, and ignoring the cell ontology
> > > >(I may be mischaracterizing here, I don't know to what extent annotators
> > > >are doing curation).
> > > >
> > > >I guess this is perfectly understandable, given that this is the GO
> > > >consortium and not the cell ontology consortium. However, I think it is
> > > >extremely counterproductive in the long run.
> > > >
> > > >If we can somehow divert more energy to getting the cell ontology correct,
> > > >then we can use this for automatic correction in GO.
> > > >
> > > >I realise this may seem quite daunting. There are indeed glaring
> > > >inconsistencies. I'm not suggesting anyone sits down and manually sorts
> > > >these out. The technology is there to automate this task. Obol currently
> > > >reports inconsistencies, and obol is also capable of exporting the
> > > >implicit cell (or anatomy or chemical or protein) ontology from GO.
> > > >
> > > >Soon we will have the ability to make genuine cross products between GO
> > > >and CellOnt, with the cross-product recorded in the obo file. This will
> > > >allow OBO-Edit to automatically flag inconsistencies (rather than having
> > > >the curator examine a seperate text report).
> > > >
> > > >Of course, if this approach is to succeed, then it would require a slight
> > > >shift in working practice. There would have to be more cross-talk between
> > > >the cell ontology and GO. GO curators would still of course be free to
> > > >define their 'own' cell ontology within GO that need not be consistent
> > > >with the cell ontology (in either DAG structure, synonyms or spelling),
> > > >but this would be deeply counterproductive. The correct approach would be
> > > >to correct the cell ontology and have this automatically propagate into
> > > >GO.
> > > >
> > > >Does this sound reasonable?
> > > >
> > > >Cheers
> > > >Chris
> > > >
> > > >On Mon, 21 Feb 2005, Alexander Diehl wrote:
> > > >
> > > >> The correct spelling is "eosinophil," which gets about 225000 hits in
> > > >> Google. "Oesinophil" seems to be a mispelling, and gets about 30
> > > >> hits in Google.
> > > >>
> > > >> As currently constituted, I would have a lot of problems with using
> > > >> the cell ontology as a source for correct nomenclature for cell types
> > > >> in the GO. The cell ontology differs from standard usage for many
> > > >> terms and is far from complete. It also lacks definitions for its
> > > >> terms as well as many commonly used synonyms. There are glaring
> > > >> discrepancies between cell types in the GO and cell ontology terms,
> > > >> such as the use of T-cell in the GO and T_lymphocyte in the cell
> > > >> ontology, with no synonyms in either place to provide a mapping
> > > >> between the two terms. All in all, one could probably construct an
> > > > > equally valid cell type ontology by deconstructing GO terms.
> > > >> Nevertheless, I do use the cell ontology in annotation notes to
> > > >> provide clarifying information when the GO term is inadequate, and I
> > > >> welcome its continued development.
> > > >>
> > > >> GO term names should reflect actual usage and proper English, which
> > > >> was the source of my initial complaint.
> > > >>
> > > >> -- Alex
> > > >>
> > > >> At 10:05 AM -0800 2/21/05, Chris Mungall wrote:
> > > >> >[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
> > >
> > >
> >
>
> -----------------------------------------------------------------------------
> Sue Rhee rhee at acoma.stanford.edu
> The Arabidopsis Information Resource URL: www.arabidopsis.org
> Carnegie Institution of Washington FAX: +1-650-325-6857
> Department of Plant Biology Tel: +1-650-325-1521 ext. 251
> 260 Panama St.
> Stanford, CA 94305
> U.S.A.
> -----------------------------------------------------------------------------
>
>
>
>
More information about the Development
mailing list