[Annotation] [Refgenome] Cell fractions
D'Eustachio, Peter
Peter.D'Eustachio at nyumc.org
Wed Feb 11 07:59:25 PST 2009
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)
>>>
>>>
------------------------------------------------------------------------
>>>
>>>
>>> _______________________________________________
>>> Refgenome mailing list
>>> Refgenome at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/refgenome
>>>
>>
>>
>
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