Manual - Jennifer (Archived): Difference between revisions
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Find a paper that shows the function of a gene product or the biological process or cellular location in which it acts. | |||
http://www.ncbi.nlm.nih.gov/entrez/ | |||
(Should look like PMID:XXXXXXXX.) | |||
Find the accession number of the gene product, e.g. from UniProt, DDBJ or GenBank. | |||
http://www.ebi.uniprot.org/index.shtml | |||
http://www.ncbi.nlm.nih.gov/ | |||
http://www.ddbj.nig.ac.jp/ | |||
Find the GO term that is appropriate using AmiGO | |||
http://amigo.geneontology.org/ | |||
(Should look like GO:XXXXXXX.) | |||
Choose the evidence code for the experiment that was done (e.g. IDA). | |||
http://www.geneontology.org/GO.evidence.codes.shtml) | (See http://www.geneontology.org/GO.evidence.shtml and http://www.geneontology.org/GO.evidence.codes.shtml) | ||
Write down the taxon id of the organism from which your gene product is derived. | |||
http://www.ncbi.nlm.nih.gov/Taxonomy/ | |||
(Should look like Taxonomy ID: XXXX) | |||
Put these in a spreadsheet or tab-delimited file with the appropriate headings. | |||
Here is my first draft powerpoint image | Here is my first draft powerpoint image |
Revision as of 10:35, 28 February 2007
Here are the steps that I can think of in doing manual literature-based annotation:
Find a paper that shows the function of a gene product or the biological process or cellular location in which it acts.
http://www.ncbi.nlm.nih.gov/entrez/
(Should look like PMID:XXXXXXXX.)
Find the accession number of the gene product, e.g. from UniProt, DDBJ or GenBank. http://www.ebi.uniprot.org/index.shtml http://www.ncbi.nlm.nih.gov/ http://www.ddbj.nig.ac.jp/
Find the GO term that is appropriate using AmiGO http://amigo.geneontology.org/ (Should look like GO:XXXXXXX.)
Choose the evidence code for the experiment that was done (e.g. IDA). (See http://www.geneontology.org/GO.evidence.shtml and http://www.geneontology.org/GO.evidence.codes.shtml)
Write down the taxon id of the organism from which your gene product is derived. http://www.ncbi.nlm.nih.gov/Taxonomy/ (Should look like Taxonomy ID: XXXX)
Put these in a spreadsheet or tab-delimited file with the appropriate headings.
Here is my first draft powerpoint image
wondered if you would find it useful..Evelyn