Manual - Jennifer (Archived): Difference between revisions
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*IC: Inferred by Curator | *IC: Inferred by Curator | ||
Now fill in the column with " [from <GO:id>]" | Now fill in the column with " [from <GO:id>]"<br> | ||
goto stuff about this. | goto stuff about this. | ||
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*IGI: Inferred from Genetic Interaction | *IGI: Inferred from Genetic Interaction | ||
Now fill in the column " [with <database:gene_symbol[allele_symbol]>]" | Now fill in the column " [with <database:gene_symbol[allele_symbol]>]"<br> | ||
(goto stuff about this.) | (goto stuff about this.) | ||
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*IPI: Inferred from Physical Interaction | *IPI: Inferred from Physical Interaction | ||
Now fill in the column with "[with <database:protein_name>]" | Now fill in the column with "[with <database:protein_name>]"<br> | ||
(goto stuff about this.) | (goto stuff about this.) | ||
Revision as of 09:44, 6 February 2007
Here are the steps that I can think of in doing manual annotation:
1) Find a paper that shows the function of a gene product or the biological process or cellular location in which it acts.
2) Find the accession number of the gene product, e.g. from UniProt or GenBank.
3) Find the GO term that is appropriate using AmiGO (e.g. GO:0048256).
4) 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)
[At this point in the flowchart we could have a list of evidence codes and have the flowchart branch off and say what different fields are needed for which evidence codes.)
The branches are down below in this page.
5) Note down the pubmed id for the paper. (e.g. PMID: 17277778)
(See http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed)
6) Put these in a spreadsheet with the appropriate headings.
Or put them in a tab-delimited file.
(See http://www.geneontology.org/GO.annotation.shtml#fields)
7) Send to the GO Consortium.
This is the list of branches that happen at the evidence code stage:
- IC: Inferred by Curator
Now fill in the column with " [from <GO:id>]"
goto stuff about this.
- IDA: Inferred from Direct Assay
- IEA: Inferred from Electronic Annotation
See Electronic annotation guide.
- IEP: Inferred from Expression Pattern
- IGC: Inferred from Genomic Context
- IGI: Inferred from Genetic Interaction
Now fill in the column " [with <database:gene_symbol[allele_symbol]>]"
(goto stuff about this.)
- IMP: Inferred from Mutant Phenotype
- IPI: Inferred from Physical Interaction
Now fill in the column with "[with <database:protein_name>]"
(goto stuff about this.)
- ISS: Inferred from Sequence or Structural Similarity
See sequence similarity annotation guide.
- NAS: Non-traceable Author Statement
- ND: No biological Data available
- RCA: inferred from Reviewed Computational Analysis
- TAS: Traceable Author Statement
- NR: Not Recorded