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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 (  
3 Invocation AGI_LocusCode:At3g54340  
4 Search getEmblDNASequence (  
5 Invocation CommentedDNASequence type FASTA into the desired output object field and Re-initialize
6 Search GenericSequence2FASTA (  
7 Invocation FASTA Switch the authority to to limit to the Snapdragon database. Switch semantic searching OFF to limit to services that specifically consume FASTA files.
8 Search getDragonBlastText (  
9 Invocation NCBI_Blast_Text keep the authority as and resubmit
10 Search parseDragonDBBlastText (  
11 Invocation DragonDB_Sequence Chose EM:AMDEFA
12 Search getDragonSequenceLocus (  
13 Invocation DragonDB_Gene Chose DEF
14 Search getDragonLocusAlleles (  
15 Invocation DragonDB_Allele Chose def-101
16 Search getDragonSimpleAnnotatedImages (  
17 Invocation SimpleAnnotatedJPEGImage  
    traverse back (with browser back button) to AGI_LocusCode:At3g54340
4a Search getGOTermsByAGIcode (  
4b Invocation GO Term  
4c Search getGOTermAssociations (  
4d Invocation GO Associations  
    traverse back (with browser back button) to AGI_LocusCode:At3g54340
4aa Search getNASC_codebyAGI_locus (  
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 (  
4aab Invocation AGRIS Transcription Factor Family Name  
  1. 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.