Standardized Term Names--cell ontology and GO

[Jennifer I Clark]

Hi,

I think someone must have got there first since that synonym is spelt 
correctly.

Jen

Jennifer I Clark wrote:

> 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.
>> ----------------------------------------------------------------------------- 
>>
>>
>>
>>
>>  
>>
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