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An annotated example Gbrowse Moby workflow |
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| Step |
Screen |
Data Type or Service (provider) |
Notes |
|
|
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| 1 |
Initialization |
Namespace: Global_keyword ID: apetala3 |
Select namespace and type in the ID |
| 2 |
Search |
GetAGILocusCodes (mips.gsf.de) |
|
| 3 |
Invocation |
AGI_LocusCode:At3g54340 |
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| 4 |
Search |
getEmblDNASequence (mips.gsf.de) |
|
| 5 |
Invocation |
CommentedDNASequence |
type FASTA into the desired output object field and Re-initialize |
| 6 |
Search |
GenericSequence2FASTA (bioinfo.icapture.ubc.ca) |
|
| 7 |
Invocation |
FASTA |
Switch the authority to antirrhinum.net to limit to the Snapdragon database. Switch semantic searching OFF to limit to services that specifically consume FASTA files. |
| 8 |
Search |
getDragonBlastText (antirrhinum.net) |
|
| 9 |
Invocation |
NCBI_Blast_Text |
keep the authority as antirrhinum.net and resubmit |
| 10 |
Search |
parseDragonDBBlastText (antirrhinum.net) |
|
| 11 |
Invocation |
DragonDB_Sequence |
Chose EM:AMDEFA |
| 12 |
Search |
getDragonSequenceLocus (antirrhinum.net) |
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| 13 |
Invocation |
DragonDB_Gene |
Chose DEF |
| 14 |
Search |
getDragonLocusAlleles (antirrhinum.net) |
|
| 15 |
Invocation |
DragonDB_Allele |
Chose def-101 |
| 16 |
Search |
getDragonSimpleAnnotatedImages (antirrhinum.net) |
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| 17 |
Invocation |
SimpleAnnotatedJPEGImage |
|
| traverse back (with browser back button) to AGI_LocusCode:At3g54340 |
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| 4a |
Search |
getGOTermsByAGIcode (atidb.org) |
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| 4b |
Invocation |
GO Term |
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| 4c |
Search |
getGOTermAssociations (bioinfo.icapture.ubc.ca) |
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| 4d |
Invocation |
GO Associations |
|
| traverse back (with browser back button) to AGI_LocusCode:At3g54340 |
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| 4aa |
Search |
getNASC_codebyAGI_locus (arabidopsis.info) |
|
| 4ab |
Invocation |
NASC_Code |
note all of the cross-references, all clickable to reinitialize the browsing session |
| traverse back (with browser back button) to AGI_LocusCode:At3g54340 |
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| 4aaa |
Search |
getAGRISTFFamilyNameByAGI (arabidopsis.med.ohio-state.edu) |
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| 4aab |
Invocation |
AGRIS Transcription Factor Family Name |
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Steps in the browsing session are enumerated, sequentially. Numbers with suffixes (e.g. 4a) indicate an alternate path (a) starting from step 4. The column labeled Screen indicates which Gbrowse Moby screen is visible at any given step. The middle column indicates which Moby Service (for the Search screen) should be selected, or which output data-type (for the Initialization and Invocation screens) is being displayed on the screen. The Notes column provides browsing hints and/or observations that can be made at any given step. | |||
Wilkinson Source Code for Biology and Medicine 2006 1:4 doi:10.1186/1751-0473-1-4 |
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