SRI InternationalBioinformatics

Data Import / Export

Markus Krummenacker

Bioinformatics Research Group

SRI, International

Q3 2012

SRI InternationalBioinformatics

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 http://bioinformatics.ai.sri.com/biowarehouse/

SRI InternationalBioinformatics

Import/Export of Pathways, etc.

Export selected pathways (and related objects) as a file

Import this file into a different PGDBCan be used for submitting pathways to MetaCyc.

See http://metacyc.org/MetaCycPosting.shtmlVisit page of pathway (or object), and right-click

choose Edit->Add Object to File Export List

File->Export->Selected Objects to Lisp-Format FileFile->Import->Frames from Lisp-Format File

SRI InternationalBioinformatics

Dump PGDB into Flatfiles

Export of entire PGDB as Flatfiles Format Description:

http://bioinformatics.ai.sri.com/ptools/flatfile-format.html 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

SRI InternationalBioinformatics

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

SRI InternationalBioinformatics

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