[Go] growth in manual GO annotation

[Doug howe]

WOW...that's way more species than I would have predicted....thanks Chris.

Chris Mungall wrote:
>
> On Apr 10, 2008, at 10:08 AM, Doug howe wrote:
>
>> Oopps...let me be more clear..I'm looking for:
>>
>> 1.  The number of distinct gene products (across all species) 
>> annotated using NON-IEA, NON-ND evidence on 1/1 of each year from 
>> 2002-2008.
>
> SELECT count(DISTINCT gene_product_id) AS num_gps
> FROM association INNER JOIN evidence ON 
> (evidence.association_id=association.id)
> WHERE code != 'IEA' AND code != 'ND';
>
> go_old_20030101
> num_gps
> 42746
>
> go_old_20040101
> num_gps
> 99116
>
> go_old_20050101
> num_gps
> 144635
>
> go_old_20060101
> num_gps
> 136734
>
> go_old_20070101
> num_gps
> 140370
>
> go_old_20080101
> num_gps
> 192535
>
>
>> 2.  The number of distinct species with any NON-IEA, NON-ND GO 
>> annotation on 1/1 of each year from 2002-2008.
>
> SELECT count(DISTINCT species_id) AS num_species
> FROM gene_product
>  INNER JOIN association ON (gene_product.id=association.gene_product_id)
>  INNER JOIN evidence ON (evidence.association_id=association.id)
> WHERE code != 'IEA' AND code != 'ND';
> go_old_20030101
> num_species
> 207
>
> go_old_20040101
> num_species
> 375
>
> go_old_20050101
> num_species
> 533
>
> go_old_20060101
> num_species
> 638
>
> go_old_20070101
> num_species
> 884
>
> go_old_20080101
> num_species
> 930
>
> (yep, these numbers are correct, there is a lot of non-MOD annotations 
> to GO)
>
>>
>> Doug howe wrote:
>>> Thanks Chris those are very useful numbers.  If you don't mind 
>>> running two more queries, it won't be necessary to open the older 
>>> stuff to Goose.
>>> I'd be interested to see:
>>> 1.  The number of distinct gene products (across all species) 
>>> annotated on 1/1 of each year from 2002-2008.
>>> 2.  The number of distinct species with any GO annotation on 1/1 of 
>>> each year from 2002-2008.
>>>
>>> -Thanks!
>>> -Doug
>>>
>>>
>>> Chris Mungall wrote:
>>>
>>>> On Apr 8, 2008, at 9:48 AM, Doug howe wrote:
>>>>
>>>>
>>>>> Does anyone have, or know how to get, historical stats on the 
>>>>> number of
>>>>> GO annotations that have been contributed to the GOC over time?  I'm
>>>>> looking for the number of non-IEA, non-ND GO annotations that existed
>>>>> for each year from 2002-2008.
>>>>>
>>>>> Midori provided me with the following numbers of GO terms for that
>>>>> period if anyone is interested:
>>>>> date            total       obsolete
>>>>> 1/1/2002    10305    152
>>>>> 1/1/2003    13339    383
>>>>> 1/1/2004    16771    725
>>>>> 1/1/2005    18219    969
>>>>> 1/1/2006    20348    992
>>>>> 1/1/2007    22928    1011
>>>>> 1/1/2008    25758    1137
>>>>>
>>>> We have historical go dbs mirrored here - we can open these to 
>>>> GOOSE if you like, or you can just request queries.
>>>>
>>>> This is what you're after:
>>>>
>>>> SELECT count(*) AS num_annots
>>>> FROM association INNER JOIN evidence ON 
>>>> (evidence.association_id=association.id)
>>>> WHERE code != 'IEA' AND code != 'ND';
>>>> go_old_20030101
>>>> num_annots
>>>> 133699
>>>>
>>>> go_old_20040101
>>>> num_annots
>>>> 386339
>>>>
>>>> go_old_20050101
>>>> num_annots
>>>> 416224
>>>>
>>>> go_old_20060101
>>>> num_annots
>>>> 469107
>>>>
>>>> go_old_20070101
>>>> num_annots
>>>> 489402
>>>>
>>>> go_old_20080101
>>>> num_annots
>>>> 580052
>>>>
>>>>
>>>> This one may also be informative: the number of terms used directly 
>>>> in annotations (all):
>>>>
>>>> SELECT count(DISTINCT term_id) AS num_terms_used_directly
>>>> FROM association;
>>>> go_old_20030101
>>>> num_terms_used_directly
>>>> 7116
>>>>
>>>> go_old_20040101
>>>> num_terms_used_directly
>>>> 9008
>>>>
>>>> go_old_20050101
>>>> num_terms_used_directly
>>>> 10134
>>>>
>>>> go_old_20060101
>>>> num_terms_used_directly
>>>> 11113
>>>>
>>>> go_old_20070101
>>>> num_terms_used_directly
>>>> 12340
>>>>
>>>> go_old_20080101
>>>> num_terms_used_directly
>>>> 13812
>>>>
>>>>
>>>>
>>>>
>>>>> -Doug
>>>>>
>>>>> _______________________________________________
>>>>> Go mailing list
>>>>> Go at geneontology.org
>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>
>>>>>
>>> _______________________________________________
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>>>
>>>
>>
>