[Ontology-editors] Cell fractions
Chris Mungall
cjm at berkeleybop.org
Tue Feb 10 20:19:16 PST 2009
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&speciesdb=all&taxid=all&evcode=IMP&term_assocs=all&term=GO%3A0005792&action=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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