Index of /download/go

Icon  Name                                  Last modified      Size  Description
[DIR] Parent Directory                                           -   
[   ] gene_association.A_fumigatus_Af293.gz 25-Sep-2009 16:05   87K  GZIP compressed docume>
[   ] gene_association.aspgd.gz             13-Mar-2010 09:45  175K  GZIP compressed docume>
[TXT] gene_association_README.txt           11-Mar-2009 15:05  2.9K  
[DIR] go_slim/                              10-Mar-2010 11:45    -   

The download/go/ directory contains the AspGD Gene Ontology (GO) 
annotation files.

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* gene_association.aspgd.gz -- GO Annotations File

gene_association.aspgd contains the Gene Ontology (GO) curation 
from AspGD. 

This file contains GO annotations for A. nidulans genes only.

In addition to the GO annotations derived from manual GO curation, this 
file includes GO term predictions that we make based on orthology.     
The orthology mappings between A. nidulans and S. cerevisiae were made 
using the Inparanoid software developed at the Karolinska Institutet.  
In cases where an A. nidulans gene has an S. cerevisiae ortholog for 
which SGD has assigned GO terms, and these GO assignments meet our 
criteria, these GO terms are assigned to the A. nidulans gene with 
the evidence code "IEA" (Inferred from Electronic Annotation), which 
indicates that these annotations are predicted computationally, 
with no curatorial review. The criteria are as follows: Candidate 
annotations for transfer from S. cerevisiae to  A. nidulans were 
selected as those with the evidence codes IDA, IPI, IGI and IMP, as these are 
deemed to be the most reliable annotations, for which there exists experimental 
evidence. Annotations with the qualifier "NOT" are not candidates for transfer.

Please note that this file contains ALL of the AspGD GO curation, 
whereas the gene_association file that is available on the GO consortium 
(GOC) web site (ftp://ftp.geneontology.org/pub/go/gene-associations/submission/gene_association.aspgd.gz),
has been filtered according to GOC guidelines. The file contains
curation for current ORFs only.
This file is regularly updated every week.

Previous versions of the gene_association.aspgd.gz file may be retrieved from
the CVS version control system at GOC. Instructions on how to access
the GO CVS repository can be found at: ftp://ftp.geneontology.org/pub/go/www/GO.CVS.help.shtml


* gene_association_README.txt 

This README explains in detail the contents and format of the 
gene_association.aspgd file.


* gene_association.A_fumigatus_Af293.gz

gene_association.A_fumigatus_Af293.gz contains GO term predictions for 
A. fumigatus Af293, based on orthology with S. cerevisiae and A. nidulans.

To generate these data, we first used InParanoid (http://inparanoid.sbc.su.se/) 
to determine (i) orthology mappings between A. fumigatus proteins 
and S. cerevisiae proteins from SGD (details at: 
http://aspgd.org/download/homology/orthologs/Afum-Af293_Scer_by_inparanoid/),
and (ii) orthology mappings between A. fumigatus proteins and A. nidulans
proteins from AspGD (details at: 
http://aspgd.org/download/homology/orthologs/Afum-Af293_Anid_by_inparanoid).

After the ortholog mappings were generated, the set of GO annotation at
SGD and AspGD was used to make GO predictions for the A. fumigatus orthologs.
In cases where an A. fumigatus gene has an A. nidulans ortholog for which we have 
GO terms in AspGD, or a S. cerevisiae ortholog for which the Saccharomyces Genome 
Database has assigned GO terms, and these GO assignments meet our criteria, these 
terms are assigned to the A. fumigatus gene with the evidence code "IEA" (Inferred 
from Electronic Annotation), which indicates that these annotations are predicted 
computationally, with no curatorial review. The criteria are as follows: Candidate 
annotations for transfer from S. cerevisiae or A. nidulans to A. fumigatus were 
selected as those with the evidence codes IDA, IPI, IGI and IMP, as these are 
deemed to be the most reliable annotations, for which there exists experimental 
evidence. Annotations with the qualifier "NOT" are not candidates for transfer.

The GO annotations listed in this file are a collection of those transferred from 
S. cerevisiae and A. nidulans.  All of the predictions are included; if the same 
GO term is predicted based on orthology to both S. cerevisiae and A. nidulans, 
both of these predictions are included in the file (i.e., redundant annotations 
have not been filtered in any way).


Please see http://aspgd.org/download/homology/orthologs/Afum-Af293_Scer_by_inparanoid/
and http://aspgd.org/download/homology/orthologs/Afum-Af293_Anid_by_inparanoid/
for more details about the generation of these predictions.

gene_association.A_fumigatus_Af293.gz is in a format very close to "gene_association format", 
described at http://www.aspgd.org/download/go/gene_association_README.txt.  
The difference from a "true" gene_association
format file is that this file contains no data in Column 2 (DB_Object_ID) 
or in Column 6 (DB:Reference [|DB:Reference], the reference associated with the GO annotation). 
These columns are required to be populated in a "true" gene_association format file.

This file is not submitted to the GO Consortium repository because all the GO assignments are
computationally predicted and the file format is not strictly compliant with the format requirements.

At this time (September 2009), this file is not scheduled to be updated routinely.  
Please contact us at aspergillus-curator@genome.stanford.edu
if regular (for example, quarterly) updates to these predictions would be useful to you.


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/go_slim/

This directory contains files related to Aspergillus GO Slim.

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