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. | Find a paper that shows the function of a gene product or the biological process or cellular location in which it acts.<br> | ||
http://www.ncbi.nlm.nih.gov/entrez/ | http://www.ncbi.nlm.nih.gov/entrez/<br> | ||
(Should look like PMID:XXXXXXXX.) | (Should look like PMID:XXXXXXXX.) | ||
Find the accession number of the gene product, e.g. from UniProt, DDBJ or GenBank. | Find the accession number of the gene product, e.g. from UniProt, DDBJ or GenBank.<br> | ||
http://www.ebi.uniprot.org/index.shtml | http://www.ebi.uniprot.org/index.shtml<br> | ||
http://www.ncbi.nlm.nih.gov/ | http://www.ncbi.nlm.nih.gov/<br> | ||
http://www.ddbj.nig.ac.jp/ | http://www.ddbj.nig.ac.jp/ | ||
Find the GO term that is appropriate using AmiGO | Find the GO term that is appropriate using AmiGO<br> | ||
http://amigo.geneontology.org/ | http://amigo.geneontology.org/<br> | ||
(Should look like GO:XXXXXXX.) | (Should look like GO:XXXXXXX.) | ||
Choose the evidence code for the experiment that was done (e.g. IDA). | Choose the evidence code for the experiment that was done (e.g. IDA). <br> | ||
(See http://www.geneontology.org/GO.evidence.shtml and 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. | Write down the taxon id of the organism from which your gene product is derived. <br> | ||
http://www.ncbi.nlm.nih.gov/Taxonomy/ | http://www.ncbi.nlm.nih.gov/Taxonomy/<br> | ||
(Should look like Taxonomy ID: XXXX) | (Should look like Taxonomy ID: XXXX) | ||
Put these in a spreadsheet or tab-delimited file with the appropriate headings. | Put these in a spreadsheet or tab-delimited file with the appropriate headings. <br> | ||
Revision as of 10:36, 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
