[Annotation] [Refgenome] Cell fractions
Harold Drabkin
hjd at informatics.jax.org
Wed Feb 11 08:30:50 PST 2009
I just feel that mapping them to a "real" cc makes an implication the
original authors did not make. And maybe a "fraction" assignment from
one paper who used liver as the source may give results that differ from
someone in another paper using immunolocalization but is looking in
lung. That kind of thing even happens when the same assay is applied.
Again, I would just as soon leave them as is.
hd
D'Eustachio, Peter wrote:
> I'm not getting the distinction. Dangerous, yes, because authors
> convince themselves that their fractionation schemes are completely
> effective and the tube labeled "cell_component" really contains only
> that cell component. But they also convince themselves that their
> antibodies are only reactive with a single, uniquely localized antigen
> and thus reason their way to a cell_component term based on
> immunofluoresence that can be fully as wrong as the one based on
> centrifugal fractions.
>
> Peter
>
> -----Original Message-----
> From: annotation-bounces at genome.stanford.edu
> [mailto:annotation-bounces at genome.stanford.edu] On Behalf Of Harold
> Drabkin
> Sent: Wednesday, February 11, 2009 10:03 AM
> To: pgaudet at northwestern.edu
> Cc: Refgenome List; GO Annotation list
> Subject: Re: [Annotation] [Refgenome] Cell fractions
>
> Again, dangerous because of different methods of preparation. I still
> think the easiest thing to do is that if there is no better or other
> localization data, leave them. I would not "map" them. They are
> suggestions as to where one might look with other methods. The placement
>
> of the graph for these terms holds true, I would hope , that they are in
>
> the cell (cell part).
>
>
> hjd
>
>
> Pascale Gaudet wrote:
>
>> Hi Alex and everyone,
>>
>> I made a list of suggested mappings:
>>
>>
> http://wiki.geneontology.org/index.php/RefGenome10Feb09_Phone_Conference
> #Fraction_terms
>
>> For example 'membrane fraction' can possibly be mapped to 'membrane' ?
>>
>
>
>> All those fraction terms describe is the assay that was used to
>> determine the cellular component.
>>
>> Pascale
>>
>>
>> Alexander Diehl wrote:
>>
>>> [switched from ontology-editors to GO annotation list]
>>>
>>> Chris,
>>>
>>> I would justify ISS annotations for cell fraction based on the
>>> assumption that physiochemical properties of proteins that determine
>>> their fractionation are highly sequence dependent, and presumably
>>> protein homologs/orthologs have a high degree of sequence similarity,
>>>
>
>
>>> including the presence or absence of transmembrane domains, which
>>> determines the protein's behavior in cell fractionation procedures in
>>>
>
>
>>> most cases.
>>>
>>> Also the argument can be made, that a term like "membrane fraction"
>>> represents the unity of all membrane types in the cell (although this
>>>
>
>
>>> may depend on the fractionation procedure in practice), and if we
>>> believe ISS can be used to transfer, for instance, "plasma membrane"
>>> annotations between species, why not "membrane fraction" annotations?
>>>
>>> IMP annotations are similarly straight-forward. If one assays for an
>>>
>
>
>>> enzyme activity in the soluble franction, and fails to find that
>>> activity in the soluble fraction of cells of the same cell type from
>>> a KO mouse with the putative enzyme missing, then an IMP annotation
>>> is entirely appropriate. In particular this applies in cases where
>>> several genes may have similar catalytic activity, but different
>>> cellular expression patterns. Otherwise, depending on the strength
>>> of the data, one could argue for an IDA here as well.
>>>
>>> Harold may respond about the particular MGI IMP annotations you refer
>>>
>
>
>>> to.
>>>
>>> IPI annotations are a type of IDA in any case, and NAS and TAS
>>> annotations should ideally be replaces at some point.
>>>
>>> Thanks,
>>>
>>> Alex
>>>
>>>
>>> Chris Mungall wrote:
>>>
>>>> Following on from our call this morning - it seems the cell fraction
>>>>
>
>
>>>> terms may be around for a while yet. However, I was wondering what
>>>> people's opinions were on evidence codes for fraction terms. I'm not
>>>>
>
>
>>>> really sure how valid it is to make an ISS to a fraction term. Or an
>>>>
>
>
>>>> IMP. Shouldn't IDA be the only code allowed?
>>>>
>>>> Here are some IMPs for microsome:
>>>>
>>>>
>>>>
> http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?gptype=all&sp
> eciesdb=all&taxid=all&evcode=IMP&term_assocs=all&term=GO%3A0005792&actio
> n=filter
>
> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?gptype=all&s
> peciesdb=all&taxid=all&evcode=IMP&term_assocs=all&term=GO%3A0005792&acti
> on=filter>
>
>>>> I followed up the mouse one and am not really sure how the IMP is
>>>> justified
>>>>
>>>> Here are some numbers for the genes annotated to cell fractions
>>>> using different evidence codes
>>>>
>>>>
> +------------+---------------------------------------------+------------
> --------+------+---------+
>
>>>>>> | acc | name |
>>>>>> term_type | code | n_genes |
>>>>>>
>>>>>>
> +------------+---------------------------------------------+------------
> --------+------+---------+
>
>>>>>> | GO:0000267 | cell fraction |
>>>>>> cellular_component | IDA | 3 | | GO:0000267 | cell
>>>>>> fraction | cellular_component | NAS
>>>>>>
>
>
>>>>>> | 1 | | GO:0000299 | integral to membrane of membrane
>>>>>> fraction | cellular_component | IDA | 27 | | GO:0000299 |
>>>>>> integral to membrane of membrane fraction | cellular_component |
>>>>>>
>
>
>>>>>> IPI | 2 | | GO:0000299 | integral to membrane of membrane
>>>>>> fraction | cellular_component | ISA | 1 | | GO:0000299 |
>>>>>> integral to membrane of membrane fraction | cellular_component |
>>>>>>
>
>
>>>>>> ISO | 2 | | GO:0000299 | integral to membrane of membrane
>>>>>> fraction | cellular_component | ISS | 16 | | GO:0000299 |
>>>>>> integral to membrane of membrane fraction | cellular_component |
>>>>>>
>
>
>>>>>> NAS | 1 | | GO:0000299 | integral to membrane of membrane
>>>>>> fraction | cellular_component | TAS | 3 | | GO:0000300 |
>>>>>> peripheral to membrane of membrane fraction | cellular_component |
>>>>>>
>
>
>>>>>> IDA | 28 | | GO:0000300 | peripheral to membrane of membrane
>>>>>>
>
>
>>>>>> fraction | cellular_component | IPI | 1 | | GO:0000300 |
>>>>>> peripheral to membrane of membrane fraction | cellular_component |
>>>>>>
>
>
>>>>>> ISA | 1 | | GO:0000300 | peripheral to membrane of membrane
>>>>>>
>
>
>>>>>> fraction | cellular_component | ISO | 3 | | GO:0000300 |
>>>>>> peripheral to membrane of membrane fraction | cellular_component |
>>>>>>
>
>
>>>>>> ISS | 6 | | GO:0005624 | membrane
>>>>>> fraction | cellular_component | IDA
>>>>>> | 615 | | GO:0005624 | membrane
>>>>>> fraction | cellular_component | IGI
>>>>>> | 1 | | GO:0005624 | membrane
>>>>>> fraction | cellular_component | IMP
>>>>>> | 5 | | GO:0005624 | membrane
>>>>>> fraction | cellular_component | ISA
>>>>>> | 4 | | GO:0005624 | membrane
>>>>>> fraction | cellular_component | ISO
>>>>>> | 19 | | GO:0005624 | membrane
>>>>>> fraction | cellular_component | ISS
>>>>>> | 280 | | GO:0005624 | membrane
>>>>>> fraction | cellular_component | NAS
>>>>>> | 17 | | GO:0005624 | membrane
>>>>>> fraction | cellular_component | RCA
>>>>>> | 2 | | GO:0005624 | membrane
>>>>>> fraction | cellular_component | TAS
>>>>>> | 249 | | GO:0005625 | soluble
>>>>>> fraction | cellular_component | IDA
>>>>>> | 428 | | GO:0005625 | soluble
>>>>>> fraction | cellular_component | IMP
>>>>>> | 2 | | GO:0005625 | soluble
>>>>>> fraction | cellular_component | ISA
>>>>>> | 1 | | GO:0005625 | soluble
>>>>>> fraction | cellular_component | ISO
>>>>>> | 8 | | GO:0005625 | soluble
>>>>>> fraction | cellular_component | ISS
>>>>>> | 99 | | GO:0005625 | soluble
>>>>>> fraction | cellular_component | NAS
>>>>>> | 10 | | GO:0005625 | soluble
>>>>>> fraction | cellular_component | TAS
>>>>>> | 135 | | GO:0005626 | insoluble
>>>>>> fraction | cellular_component | IDA
>>>>>> | 65 | | GO:0005626 | insoluble
>>>>>> fraction | cellular_component | ISO
>>>>>> | 1 | | GO:0005626 | insoluble
>>>>>> fraction | cellular_component | ISS
>>>>>> | 32 | | GO:0005626 | insoluble
>>>>>> fraction | cellular_component | TAS
>>>>>> | 5 | | GO:0005792 |
>>>>>> microsome | cellular_component |
>>>>>>
>
>
>>>>>> IDA | 240 | | GO:0005792 |
>>>>>> microsome | cellular_component |
>>>>>>
>
>
>>>>>> IMP | 5 | | GO:0005792 |
>>>>>> microsome | cellular_component |
>>>>>>
>
>
>>>>>> IPI | 3 | | GO:0005792 |
>>>>>> microsome | cellular_component |
>>>>>>
>
>
>>>>>> ISA | 2 | | GO:0005792 |
>>>>>> microsome | cellular_component |
>>>>>>
>
>
>>>>>> ISO | 4 | | GO:0005792 |
>>>>>> microsome | cellular_component |
>>>>>>
>
>
>>>>>> ISS | 105 | | GO:0005792 |
>>>>>> microsome | cellular_component |
>>>>>>
>
>
>>>>>> NAS | 97 | | GO:0005792 |
>>>>>> microsome | cellular_component |
>>>>>>
>
>
>>>>>> RCA | 1 | | GO:0005792 |
>>>>>> microsome | cellular_component |
>>>>>>
>
>
>>>>>> TAS | 40 | | GO:0019717 |
>>>>>> synaptosome | cellular_component |
>>>>>>
>
>
>>>>>> IDA | 77 | | GO:0019717 |
>>>>>> synaptosome | cellular_component |
>>>>>>
>
>
>>>>>> IEP | 1 | | GO:0019717 |
>>>>>> synaptosome | cellular_component |
>>>>>>
>
>
>>>>>> ISA | 1 | | GO:0019717 |
>>>>>> synaptosome | cellular_component |
>>>>>>
>
>
>>>>>> ISO | 5 | | GO:0019717 |
>>>>>> synaptosome | cellular_component |
>>>>>>
>
>
>>>>>> ISS | 34 | | GO:0019717 |
>>>>>> synaptosome | cellular_component |
>>>>>>
>
>
>>>>>> NAS | 2 | | GO:0019718 | rough
>>>>>> microsome | cellular_component | IDA
>>>>>> | 5 | | GO:0019719 | smooth
>>>>>> microsome | cellular_component | IDA
>>>>>> | 1 | | GO:0042598 | vesicular
>>>>>> fraction | cellular_component | IDA
>>>>>> | 12 | | GO:0042598 | vesicular
>>>>>> fraction | cellular_component | ISS
>>>>>> | 7 |
>>>>>>
>>>>>>
> +------------+---------------------------------------------+------------
> --------+------+---------+
>
>>>>>> 53 rows in set (36.97 sec)
>>>>>>
>>>>
> ------------------------------------------------------------------------
>
>
>>>> _______________________________________________
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>>>>
>>>>
>>>
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>
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