Table 1 An annotated example Gbrowse Moby workflow
From: Gbrowse Moby: a Web-based browser for BioMoby Services
Step | Screen | Data Type or Service (provider) | Notes |
|---|---|---|---|
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 | |
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) | |
13 | Invocation | DragonDB_Gene | Chose DEF |
14 | Search | getDragonLocusAlleles (antirrhinum.net) | |
15 | Invocation | DragonDB_Allele | Chose def-101 |
16 | Search | getDragonSimpleAnnotatedImages (antirrhinum.net) | |
17 | Invocation | SimpleAnnotatedJPEGImage | |
traverse back (with browser back button) to AGI_LocusCode:At3g54340 | |||
4a | Search | getGOTermsByAGIcode (atidb.org) | |
4b | Invocation | GO Term | |
4c | Search | getGOTermAssociations (bioinfo.icapture.ubc.ca) | |
4d | Invocation | GO Associations | |
traverse back (with browser back button) to AGI_LocusCode:At3g54340 | |||
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 | |||
4aaa | Search | getAGRISTFFamilyNameByAGI (arabidopsis.med.ohio-state.edu) | |
4aab | Invocation | AGRIS Transcription Factor Family Name |