Package org.intermine.bio.dataconversion

Class Summary

BioDBConverter	A DBConverter with helper methods for bio sources.
BioDirectoryConverter	A DirectoryConverter that automatically sets the dataSets collection of objects as they are stored.
BioFileConverter	A FileConverter that automatically sets the dataSets collection of objects as they are stored.
BioGridConverter	DataConverter to parse biogrid data into items Genetic interactions are labeled protein interactions, so we can't store or create any objects until all experiments and interactors are processed.
BioStoreHook	An implementation of DataConverterStoreHook that adds DataSet and DataSource references and collections to Items as they are stored.
ChadoDBConverter	DataConverter to read from a Chado database into items
ChadoProcessor	A processor for a chado module.
EntrezOrganismRetriever	Class to fill in organism information using Entrez.
EntrezPublicationsRetriever	Class to fill in all publication information from pubmed
FastaLoaderTask	A task that can read a set of FASTA files and create the corresponding Sequence objects in an ObjectStore.
FlyBaseCDSFastaLoaderTask	A fasta loader that understand the headers of FlyBase fasta CDS fasta files and can make the appropriate extra objects and references.
FlyBaseFeatureFastaLoaderTask	Code for loading fasta for flybase, setting feature attribute from the FASTA header.
FlyBaseIdResolverFactory	Create an IdResolver for Drosophila genes by querying tables in a FlyBase chado database.
FlyBaseProcessor	A converter for chado that handles FlyBase specific configuration.
FlyBaseUTRFastaLoaderTask	A fasta loader that understand the headers of FlyBase fasta UTR fasta files and can make the appropriate extra objects and references.
GenesFileProcessor	Processor of file with information about genes.
GenomeDBConverter	A ChadoDBConverter that sets the dataset and datasource for genome databases (eg.
GFF3Converter	Class to read a GFF3 source data and produce a data representation
GFF3RecordHandler	Permits specific operations to be performed when processing an line of GFF3.
GFF3SeqHandler	An interface used by GFF3Converter to choose the type of sequence Items.
GoConverter	DataConverter to parse a go annotation file into Items
HgncIdResolverFactory	Create an IdResolver for HGNC previous symbols and aliases to current symbols.
IdResolver	Hold data about primary identifiers and synonyms for a particular class in the data model and provide methods to resolved synonyms into corresponding primary identifier(s).
IdResolverFactory	Create an IdResolver.
InparanoidConverter	DataConverter to parse an INPARANOID Orthologue/Paralogue "sqltable" data file into Items
InterProConverter	DataConverter to parse InterPro data into items
KeggPathwayConverter	DataConverter to load Kegg Pathways and link them to Genes
MalariaGFF3RecordHandler	Handle special cases when converting malaria GFF3 files.
MirandaGFF3RecordHandler
MockIdResolverFactory	A mock IdResolver factory needed for testing.
ModEncodeFeatureProcessor	A processor that loads feature referred to by the modENCODE metadata.
ModEncodeMetaDataProcessor	Create items from the modENCODE metadata extensions to the chado schema.
NCBIFastaLoaderTask	A loader that works for FASTA files with an NCBI formatted header: http://www.ncbi.nlm.nih.gov/blast/fasta.shtml http://en.wikipedia.org/wiki/Fasta_format
OboConverter	Convert tree of OboTerms into Items.
PdbConverter
PsiConverter	DataConverter to parse psi data into items Experiments and interactions appear in different files, so we have to keep all experiments until all interactions are processed.
PubMedGeneConverter	DataConverter creating items from PubMed data files.
PubMedReference
ReferencesFileProcessor	File processor processing references between genes and publications from PubMed.
SequenceProcessor	A processor for the chado sequence module.
StockProcessor	A ChadoProcessor for the chado stock module.
UniprotConfig
UniprotConverter	DataConverter to parse UniProt data into items.
UniprotEntry	holder class representing an entry in uniprot xml
UniProtFastaLoaderTask	Code for loading fasta for uniprot proteins.
UniprotFilterTask	Read a set of Uniprot XML files and write out only those elements for an organism in the given set of names.
UniprotKeywordConverter	Importer to add descriptions to UniProt keywords
UniprotXmlFilter	Extract only entries for organisms of interest from UniProt XML dump files.
WormBaseChadoIdResolverFactory	Create an IdResolver for Worm genes by querying tables in a WormBase chado database.
WormBaseIdentifiersConverter	DataConverter to load WormBase gene identifiers from genes2molecular_names.txt.
WormBaseProcessor	A converter for chado that handles WormBase specific configuration.

Exception Summary

GenesProcessorException	Exception that may be thrown from GeneConvertor.
ReferencesProcessorException	Exception that may be thrown from ReferencesFileProcessor