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SRI International Bioinformatics Data Import / Export Markus Krummenacker Bioinformatics Research Group SRI, International Q3 2012.

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Presentation on theme: "SRI International Bioinformatics Data Import / Export Markus Krummenacker Bioinformatics Research Group SRI, International Q3 2012."— Presentation transcript:

1 SRI International Bioinformatics Data Import / Export Markus Krummenacker Bioinformatics Research Group SRI, International Q3 2012

2 SRI International Bioinformatics Data Exchange Overview Java API and Perl API : read & modify BioPAX Export: since Pathway Tools 9.0 Biopax.org Export of entire PGDB as a set of Flatfiles Export of Reactions as SBML -- sbml.org Import/Export of Pathways: between PGDBs Import/Export of Selected Frames, for Spreadsheets Import/Export of Compounds as Molfile, CML Registering/Publishing PGDBs on WWW Export PGDB as Genbank BioWarehouse : Loader for Flatfiles, SQL access

3 SRI International Bioinformatics Import/Export of Pathways, etc. Export selected pathways (and related objects) as a file Import this file into a different PGDB Can be used for submitting pathways to MetaCyc. See Visit page of pathway (or object), and right-click choose Edit->Add Object to File Export List File->Export->Selected Objects to Lisp-Format File File->Import->Frames from Lisp-Format File

4 SRI International Bioinformatics Dump PGDB into Flatfiles Export of entire PGDB as Flatfiles Format Description: Column delimited: 1 line per frame Attribute-value: 1 record per frame Multiple slot values: Column delimited: several values per column Attribute-value: several lines for several values

5 SRI International Bioinformatics Frame Import/Export Import/Export of Selected Frames, for Spreadsheets Allows external editing of frames, and also frame creation Detailed Description: UG section 5.6 Export: GUI for Frame selection, Slot selection Slots depend on selected class Caveat: value annots in slots get lost ! Direct or all instances under class can be exported Import: Many choices for merging or replacing data values File Format Choices like the Flatfiles: Column delimited: 1 line per frame Attribute-value: 1 record per frame Multiple slot values: Column delimited: several values per column Attribute-value: several lines for several values

6 SRI International Bioinformatics Misc. Export of a replicon as a Genbank file Pathologic is the inverse, “Import” But: information loss, e.g. gene product comments have no feature qualifier in Genbank Importing protein features from UniProt Connection to MySQL BioWarehouse needed See UG section 5.8 Importing Citations from PubMed


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