Manual - Jennifer (Archived)

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.

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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