AmiGO: Workflows

AmiGO workflows

name: hte1
user: high-throughput experimenter
input: list of gene ids, id format in GO database [upload gene list as flat file, or paste into search box)
output1: a list of input gene ids with corresponding GO terms [html, download as flat file, XML, Excel?]

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output2: file above mapped to a set of GO slim terms (GO slim can be chosen from set of existing GO slims or user supplied as a list of ids or a GO format slim file)

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name: hte2
user: high-throughput experimenter
input: list of gene ids, format not in GO database
output: same as above [ids invisibly converted by AmiGO using UniProt translation tables?]

name: m1
user: microarray
input: list of 'interesting' gene ids from microarray/proteomics expt, + full gene id set from expt
output1: List of significantly over-represented GO terms for 'interesting' gene set v/s full set [html, download file]

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name: ev1
user: bench scientist, genetics, genomics small-scale or high-throughput [upload as file or paste into search box. List of options - find matches via BLAST, InterProScan, others?]
input: list of sequences (protein or DNA)
output1a: BLAST results [html + file download option]. How should this be displayed? Default to top GO term, with Option for show alignments, show top 10 hits? Should we allow users to configure the hits? Should ultimately end up with a list of sequence ids with GO terms

OR

output1b: InterProScan output [we'd have to look into what their output is but, ultimately we want them to be able to download a seq id->GO term file]

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