AmiGO: Workflows: Difference between revisions
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== AmiGO workflows == | == AmiGO workflows == | ||
*name: hte1 | |||
*user: high-throughput experimenter | *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) | *input: list of gene ids, id format in GO database [upload gene list as flat file, or paste into search box) | ||
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-------- | -------- | ||
*name: hte2 | |||
*user: high-throughput experimenter | *user: high-throughput experimenter | ||
*input: list of gene ids, format not in GO database | *input: list of gene ids, format not in GO database | ||
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-------- | -------- | ||
*name: m1 | |||
*user: microarray | *user: microarray | ||
*input: list of 'interesting' gene ids from microarray/proteomics expt, + full gene id set from expt | *input: list of 'interesting' gene ids from microarray/proteomics expt, + full gene id set from expt | ||
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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?] | *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) | *input: list of sequences (protein or DNA) | ||
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--------- | --------- | ||
*name: brb1 | |||
*user: bench research biologist | *user: bench research biologist | ||
*input: single gene id, format in GO database | *input: single gene id, format in GO database | ||
| Line 47: | Line 52: | ||
--------- | --------- | ||
*name brb2 | |||
*user: bench research biologist | *user: bench research biologist | ||
*input: single gene id, format not in GO database | *input: single gene id, format not in GO database | ||
*output: as above, but we need to convert id behind the scenes | *output: as above, but we need to convert id behind the scenes | ||
Revision as of 17:50, 12 December 2006
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?]
V
- 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)
V
- output3: A chart representation of the above slimmed file
- 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]
V
- output2: slimmed version of above file [as before]
V
- output3: chart of above [as before]
- 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]
V
- output2: slimmed version of above file [as before]
V
- output3: A chart representation of the above slimmed file [as before]
- name: brb1
- user: bench research biologist
- input: single gene id, format in GO database
- output: all annotations for that term [as it is now]
- name brb2
- user: bench research biologist
- input: single gene id, format not in GO database
- output: as above, but we need to convert id behind the scenes