Variant annotation: Difference between revisions

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==Homo sapiens==
==Homo sapiens==
==Mus musculus==
==Mus musculus==
For each annotation, MGI has a "notes field" that is not available to the public. That note has a structure as follows:
evidence:
anatomy:
cell type:
gene product:
qualifier:
target:
external ref:
text:
If a paper actually specifies a specific isoform, the appropriate refseq is entered into the "gene_product" field
eg, For the annotation of MGI:1341722, Kcnh2, to GO:0005886,plasma membrane, by IDA, the
field would look like:
gene_product:SPKW:O35219-1
We presently only have about 300 of these with experimental evidence codes, annotated after the adoption of the structured notes. So QC has to be done for some. Annotations done prior to that will not have any entry, as we had no way of capturing the data.
We are looking at ways to "back annotate" by identifying having multiple isoforms identified in references that have been used for GO annotation at MGI.
==Rattus norvegicus==
==Rattus norvegicus==
==Saccharomyces cerevisiae==
==Saccharomyces cerevisiae==
==Schizosaccharomyces pombe==
==Schizosaccharomyces pombe==

Revision as of 15:42, 10 October 2007

Arabidopsis thaliana

Caenorhabditis elegans

Danio rerio

We almost never have enough info to curate to the level of a splice variant. Our annotations are applied at the level of the gene.

Dictyostelium discoideum

So far we only have a few genes and publications that described splice variants, and the papers never described different functions for the different variants. Hence, we currently don't capture annotations to different variants of gene products.

Drosophila melanogaster

Escherichia coli

Gallus gallus

Homo sapiens

Mus musculus

For each annotation, MGI has a "notes field" that is not available to the public. That note has a structure as follows:

evidence: anatomy: cell type: gene product: qualifier: target: external ref: text:

If a paper actually specifies a specific isoform, the appropriate refseq is entered into the "gene_product" field eg, For the annotation of MGI:1341722, Kcnh2, to GO:0005886,plasma membrane, by IDA, the field would look like:

gene_product:SPKW:O35219-1

We presently only have about 300 of these with experimental evidence codes, annotated after the adoption of the structured notes. So QC has to be done for some. Annotations done prior to that will not have any entry, as we had no way of capturing the data. We are looking at ways to "back annotate" by identifying having multiple isoforms identified in references that have been used for GO annotation at MGI.

Rattus norvegicus

Saccharomyces cerevisiae

Schizosaccharomyces pombe