Standardized Term Names--cell ontology and GO
Jennifer I Clark
jclark at ebi.ac.uk
Tue Feb 22 01:40:45 PST 2005
Hi,
In the meantime I'll fix that spelling error and leave the 'cell
differentiation' synonyms in then shall I?
Jen
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