[Go] Composition of the generic GO slim

[Judith Blake]

Val,
My point really is that experiments are done in context.  A person 
studying metabolism may want to break out those terms by particular 
sub-divisions and lump other things.  One of the roles of collaborating 
GO people would be to add in the construction of particular slims if 
requested.

For example, when I have done this, the researcher provided a list of 
12-16 subdivisions that made sense for their purpose, and we constructed 
a GO_slim that subdivided the GO appropriately.  I think of it as part 
of the data analysis process.  A researcher using a generic GO_slim 
without understanding the vagaries of the annotations or of the ontology 
subtrees will neither understand the results.

my opinion.
judy

Valerie Wood wrote:
> Judy,
>
> You are correct  that no one slim is going to fit all organisms or all 
> uses.
> However it isn't simple  to create an informative slim which gives 
> complete
> (or nearly complete) coverage of all of an organisms annotations (and 
> complete
> coverage of the annotation space  is an important feature
> of a robust slim). Does the drosophila slim set cover all of the 
> annotated genes?
>
> The slim I suggested will give complete coverage for single-celled
> eukaryotes (it may need additional high level terms to cover
> muliticellular eukaryotes). This particular slim is useful for evaluating
> an organisms "cell biology". Perhaps a very generic slim, which only 
> includes
> very high level terms would be useful multicellular organisms,
> but it would not be so useful for single-celled organisms.
>
> One suggested criteria (6 in previou) suggested that terms be 
> meaningful to biologists.
> What I meant here was that the terms should be was that the terms should
> be 'biologically informative'. For cellular roles, or for a single-celled
> organism 'metabolism isn't so useful as a 'direct'  slim term ( 
> metabolic processes
> include transcription, translation, DNA replication, mRNA processing 
> etc.,
> in addition to primary and secondary metabolism). For pombe 3102 of 
> 4194 process annotated gene products are annotated to metabolism,
> so this term in a slim does not tell you very much.
>
> In addition, if metabolism is included as a 'direct' slim term, and 
> you have a gene product
> which is annotated ONLY to "metabolic process" then you really know very
> little about its biological role. This can occur as frequently as it 
> is possible to
> predict that a protein has catalytic activity, and is involved in a 
> 'metabolic process'
> but not to say anything more specific; there are many direct Interpro 
> mappings
> to these two terms.  If I was trying to assess the 'real biological 
> roles' of my organisms
> gene products, I would wish to exclude direct annotations to 
> 'metabolic process' from the slim.
>
> A GO slim provides a mechanism to filter out annotations to high level
> relatively uninformative (with respect to the biological role)  nodes 
> like
> 'metabolism, cellular  process, localization' (in the slim, they will 
> be annotated
> to  'unknown' if there is no annotation  to one of your slim terms or 
> their children).
>
> Once you exclude a term like metabolism it becomes necessary
> to include all of the child terms (or a combination of child terms ) 
> to give complete
> coverage of the parent term ( NOTE: once the slimmed terms are mapped
> to the slim ontology the  high level terms will be
> included, but their totals will only reflect the  total of the gene 
> products
> annotated via the terms in the slim).
>
> The difficult part is in building a slim is identifying the set of 
> terms which
> provides complete coverage; this is the tricky step for most biologists,
> who are not so familiar with the ontologies. It would be useful to 
> provide a
> starting slim which gives complete coverage of all annotations (using
> biologically relevant terms for common applications) which they can 
> change as necessary.
> Maybe we should provide a set of 'complete coverage' slims for common
> applications.
>
> i.e.
> suitable for multicellular organisms and very general biological roles
> suitable for single-celled eukaryotes, or evaluating basic cellular 
> processes
>
> Val
>
>
>
>
> Judith Blake wrote:
>> Val,
>> I still maintain that users need to be able to generate grouping 
>> criteria based on their usage.    I think we could go back to the fly 
>> genome paper and see the primary molecular divisions that seemed most 
>> useful to describe the genome properties.  like 'reproduction' and 
>> 'metabolism'.  Anything more granular is specific to the user.  A 
>> mapping on this basis would likely include fewer than 20 terms and 
>> would subdivide trees.
>>
>> judy
>>
>> Valerie Wood wrote:
>>> I think it is good idea for the consortium to provide an official 
>>> 'GO slim', and advise people how they may want to alter the slim to 
>>> fit their individual purpose.
>>>
>>> A useful generic GO slim has a number of qualities (I have tried to 
>>> list these below, please suggest any additional ones, I hadn't 
>>> really thought before about what the rules were I used for making a 
>>> slim so this is the first time I have documented them). Following 
>>> the 'guidelines' below I have suggested a set of process which I 
>>> think should make up the generic process slim.
>>>
>>> Perhaps we could use this as a starting point, and people can 
>>> suggest additional terms (with reasons) or terms which should be 
>>> removed. This provides good coverage of basic cellular processes but 
>>> would need extending to cover multicellular processes.
>>>
>>> GO Slim criteria
>>>
>>> 1. The generic slim should be  as organism independent as possible 
>>> (although clearly some terms will not be applicable to single celled 
>>> eukaryotes and some eukaryotic terms will not be applicable to 
>>> prokaryotes)
>>>
>>> 2. The slim should cover AS MANY genes with annotated processes as 
>>> possible
>>>
>>> 3. The slim should cover AS MANY genes with annotated processes with 
>>> the smallest number of leaf node terms (if you include too many 
>>> terms and it becomes too large and you start to loose the advantages 
>>> of a slim).
>>>
>>> 4. It might be useful to try to avoid terms with an excessively 
>>> small or large number of small number of annotations (i.e ideally 
>>> your terms will not have an extreme distributions for your histogram)
>>>
>>> 5. Preferably the slim should include  sibling terms with a large 
>>> overlaps between them. If you choose two siblings with 200 genes 
>>> annotated to each, and the majority of the annotations  overlap, it 
>>> is usually better to select the parent node (i.e replace 2 terms by 
>>> one single term). Conversely, if the child terms of a  node fall 
>>> into distinct non-overlapping subsets, it might be more informative 
>>> to include both child terms in your slim (see also point 7 below)
>>>
>>> 6. For most purposes you need to include a representative term for 
>>> all biologically relevant processes, by including terms which are 
>>> meaningful to biologists.
>>>
>>> 7. If you are using your slim for data analysis (and not just for 
>>> vizualization) you need to include terms which will allow you to 
>>> distinguish genes bases on their biological properties.
>>> For example, it is not good to lump all genes involved in transport 
>>> under transport because the genes annotated to distinct child terms; 
>>> vesicle -mediated transport, protein targeting, transmembrane 
>>> transport, are VERY different in term of their i) viability ii) 
>>> species distribution iii) number of interaction partners iv) copy 
>>> number v) expression pattern, so it does not make sense to lump them 
>>> together in your slim set.
>>>
>>> Using these criteria  this is the basic cellular process eukaryotic 
>>> slim I use (or slight variations of): The number of annotations (for 
>>> pombe obviously) is in parentheses (protein coding only).
>>>
>>> GO:0055085 transmembrane transport (278)
>>> GO:0006913 nucleocytoplasmic transport (114)
>>> GO:0006605 protein targeting (162)
>>> GO:0016192 vesicle-mediated transport (266)
>>> GO:0051186 cofactor metabolic process (139)
>>> GO:0006766 vitamin metabolic process (57)
>>> GO:0006790 sulfur metabolic process (45)
>>> GO:0006807 nitrogen compound metabolic process (224)
>>> GO:0055086 nucleobase, nucleoside and nucleotide metabolic process 
>>> (118)
>>> GO:0005975 carbohydrate metabolic process (199)
>>> GO:0006629 lipid metabolic process (201)
>>> GO:0006399 tRNA metabolic process (125)
>>> GO:0006520 amino acid metabolic process (187)
>>> GO:0006412 translation (357)
>>> GO:0006259 DNA metabolic process (296)
>>> GO:0006508 protolysis (223)
>>> GO:0005975 carbohydrate metabolic process (199)
>>> GO:0016071 mRNA metabolic process (204)
>>> GO:0043413 biopolymer glycosylation (65) possibly drop?
>>> GO:0006464 protein modification process (585)
>>> GO:0007059 chromosome segregation (186)
>>> GO:0007049 cell cycle (552)
>>> GO:0007010 cytoskeletal organization and biogenesis (236)
>>> GO:0000910 cytokinesis (145)
>>> GO:0007165 signal transduction (362)
>>> GO:0006457 protein folding (80)
>>> GO:0042254 ribosome biogenesis and assembly (223)
>>> GO:0045229 external encapsulating structure organization and 
>>> biogenesis (124)
>>> GO:xxxxxxxx general transcription (see note *1 below)
>>> GO:0032569 specific transcription from RNA polymerase II promoter (102)
>>> (total 424 for all transcription)
>>> GO:0000902 cell morphogenesis (86)
>>> GO:0006338 establishment and/or maintenance of chromatin 
>>> architecture (231)
>>> GO:reproductive process (182)
>>> GO:0007005 mitochondrion organization and biogenesis (251)
>>> GO:0006091 generation of precursor metabolites and energy (113)
>>> GO:0007031 peroxisome organization and biogenesis (20)
>>>
>>> At this point there are about ~100 pombe genes (out of the 3960 with 
>>> an annotated process term) which aren't included in the slim
>>>
>>> I could also include....
>>> vacuolar transport (91) reduces by 6 (most also annotated to protein 
>>> targeting)
>>> telomere maintenance (54) reduces by 6 (most also annotated to DNA met)
>>> snoRNA metabolic process (10) reduces by 2
>>> ...to improve coverage (very slightly)
>>>
>>> Finally I include
>>> GO:0006950 response to stress (444)
>>> this terms has overlaps with most other processes so is largely 
>>> redundant but are useful.
>>>
>>> This  leaves ~30 pombe with a process annotation unassigned to the 
>>> GO slim; these are often to terms like homeostasis and its children, 
>>> or otherwise uniformative terms
>>>
>>> For some purposes I would also include
>>> GO:0065007 biological regulation  (1021)
>>> but I don't know if this is a good term to include in a generic slim
>>>
>>> To make this work for multicellular eukaryotes, we would probably 
>>> want to add non-cellular process terms like:
>>>
>>> developmental process
>>> immune system process
>>>
>>>
>>> * Note1 it is not currently possible to retrieve genes involved in 
>>> general transcription as opposed to gene specific transcription (i.e 
>>> RNA I,II and III polymerases etc),  with a single query. This is 
>>> also important for enrichment as the genes in these 2 sets are very 
>>> different in terms of species distribution, copy number and 
>>> viability. I requested a grouping term for these processes a while 
>>> ago and hopefully this will be implemented shortly.
>>>
>>> See:
>>> https://sourceforge.net/tracker/?func=detail&aid=1590000&group_id=36855&atid=440764 
>>>
>>>
>>>
>>> Val
>>>
>>>
>>>
>>>
>>>
>>>
>>> Ben Hitz wrote:
>>>  
>>>> Emily -
>>>> I have interest in working on the generic go slim; I need it (or  
>>>> something similar) to define graphics for an interaction network.
>>>>
>>>> Ben
>>>>
>>>>
>>>> On Apr 30, 2008, at 10:03 AM, Emily Dimmer wrote:
>>>>
>>>>     
>>>>> Hi,
>>>>>
>>>>> From replying to a user request, I've just been having a quick 
>>>>> look at
>>>>> the composition of the generic GO slim, and relating the GO terms
>>>>> included to the number of annotations displayed by AmiGO.
>>>>>
>>>>> Should, for instance, the 'cell recognition' term still be 
>>>>> included in
>>>>> the generic GO slim? - it has only been annotated to 182 gene  
>>>>> products,
>>>>> whereas its sibling terms: 'cell division', 'cell cycle' and 'cell
>>>>> motility', have not been included even though they (directly or
>>>>> indirectly) have been annotated to more than 1,200 gene products 
>>>>> each.
>>>>> Similarly, the term 'cytoplasm organization and biogenesis' is in  
>>>>> the GO
>>>>> slim but only has 113 gps annotated, whereas the 'membrane  
>>>>> organisation
>>>>> and biogenesis' term has been annotated to 1,509 gps.
>>>>>
>>>>> I was just wondering what the goal of the generic GO slim is... 
>>>>> if  terms
>>>>> are selected on the basis that as many annotated gene products from
>>>>> different organisms should get mapped to descriptive GO terms before
>>>>> they are caught by the BP, MF, CC root terms (while also providing a
>>>>> full selection of terms across the whole GO vocabulary), should 
>>>>> we  think
>>>>> of reviewing its some of its composition in relation to overall
>>>>> annotation frequency? Or should the GO slim be kept as stable as  
>>>>> possible?
>>>>>
>>>>> Cheers,
>>>>> Emily
>>>>>
>>>>> -- 
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------
>>>>>
>>>>>    Emily Dimmer Ph.D.
>>>>>    GOA Coordinator
>>>>>    EMBL-EBI
>>>>>    Wellcome Trust Genome Campus
>>>>>    Hinxton
>>>>>    Cambridge CB10 1SD, U.K.
>>>>>    Tel:     +44 1223 494654
>>>>>    Fax:    +44 1223 494468
>>>>>    email:  edimmer at ebi.ac.uk
>>>>>    URL:    http://www.ebi.ac.uk/goa
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Go mailing list
>>>>> Go at geneontology.org
>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>           
>>>> -- 
>>>> Ben Hitz
>>>> Senior Scientific Programmer ** Saccharomyces Genome Database ** 
>>>> GO  Consortium
>>>> Stanford University ** hitz at genome.stanford.edu
>>>>
>>>>
>>>>
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>>>>
>>>>
>>>>       
>>>
>>>
>>>   
>>
>>
>>
>
>