InterMine Bio sources

This page lists the current sources available for use in InterMine. All the sources here are found in bio/sources. Look at flymine/project.xml for examples of how to use them.

You can also add your own sources to load custom file formats, see How to create a source for more information. In addition, the tutorial contains detailed steps on creating sources for a variety of different data formats.

Most of the configuration done in the config files is optional, if no config entry exists the default behaviour is followed. For instance, if no chromosomes are specified in ensembl_config.properties, then all chromosomes are processed. There are exceptions to this rule, however.

Common sources

These are commonly used sources that you may want to use to load data into your own InterMine instance.

source	data	model	config	project.xml
biogrid	Loads genetic and protein interaction data from  BioGRID. These data include both high-throughput studies and conventional focused studies and have been curated from the literature.	genes, proteins, interactions	biogrid_config.properties - which gene identifiers are populated.	All files specified in project.xml will be processed.
biopax	Loads data from files in  BioPAX level 2 format	pathways, proteins, genes	biopax_config.properties- which gene identifiers are populated.	See Reactome
chado-db	Loads data from a  Chado database.	Any chado features, eg. chromosome location, genes, proteins.	none	See chado-db docs
ensembl	Load  ensembl data from a downloaded mysql database or access via script using their API	chromosomes, genes, transcripts, exons, protein sequences, CDSs, SNPs	ensembl_config.properties - which chromosomes are processed.	See Ensembl
ensembl-compara	Load  ensembl compara data from public BioMart?	homologues	See EnsemblCompara
entrez-organism	All other sources refer to organisms only by their  NCBI taxonomy id. This source should be included at the end of the build. It will select the taxonIds loaded into the Organism class, fetch details via the Entrez web service and fill in the organism names in the database.	updates fields for organism created by other sources	none
fasta	Load features and their sequences. Will create a feature for each entry in a fasta file and set the sequence, the class of the feature to create is set for the whole file.	protein, sequence	none	See FASTA
gff	This isn't a source itself but genome annotation from gff files can be loaded easily by creating a new source of type gff. See redfly, malaria-gff and tiffin for examples.	features	Configuration is added to the project.properties file and an optional handler can be added to deal with data in the attributes section of the gff file.	See GFF
go-annotation	Load  gene association files that link GO terms to genes or proteins.	genes, go terms	go-annotation_config.properties - determines type of object annotated and which identifiers are created. Note: Currently we require that the gene_association file is sorted by the 'product' (gene/protein/etc) identifier in column 2. This is to save memory while loading. If your file isn't already sorted by column 2 you can use this command > sort -k 2,2 input_file > output_file
go	Load the  Gene Ontology term ids, names and definitions, and the relationships between terms. Should be loaded if the go-annotation source is used.	go terms	none
intact	Load interactions data from  IntAct.	genes, interactions	psi-intact_config.properties - which gene identifiers are set	organisms - If none are configured, all interactions are stored.
intermine-items-xml-file	Use this source to load Items XML conforming to the data model directly into the production database.	any	none
intermine-items-large-xml-file	Use this source to load Items XML conforming to the data model into the production database, this uses an intermediate database to allow it to cope with very large files that would otherwise cause memory problems.	any	none
interpro	Data from  interpro	protein domains	none
kegg-orthologues	Load homologues from  KEGG	homologues, genes	kegg_config.properties - which gene identifier fields are populated, mapping from organism taxonId to abbreviation	only taxonIds specified in project.xml file are downloaded, if no taxonIds are configured, all are loaded.
kegg-pathway	Link genes to  KEGG pathways that they operate in.	pathways, genes	kegg_config.properties - which gene identifier fields are populated, mapping from organism taxonId to abbreviation	only taxonIds specified in project.xml file are downloaded, if no taxonIds are configured, all are loaded.
miranda	miRBase Targets from the Sanger Institute	MiRNATargets, MRNAs, genes	Configuration is added to the project.properties file and an optional handler can be added to deal with data in the attributes section of the gff file.	See GFF
pdb	Data from  PDB	proteins, protein structures	none	each structure is its own PDB file. PDB file doesn't contain taxonId, so files must live in taxonId-specific directories, eg /7227. converter processes directories specified in project.xml. if nothing configured, processes all directories
psi-mi-ontology	Include this source when loading psi data to fill in details of ontology terms used. Loads the file  psi-mi.obo file.	ontology terms	none
pubmed	data from pubmed	publications	none	entire file is downloaded, only taxonIDs set in project.xml will be loaded. if nothing configured, processes all entries.
reactome	flat file from Reactome mart	pathways and genes	none	See Reactome
so	This source loads no data but adds a class in the data model for every term in SOFA - a reduced version of the  sequence ontology. SO terms represent biological features such as gene, exon, 3' UTR. The version of SOFA we use is a little out of date. You should include it if you are loading genome annotation.	see the SO file for complete list.	none
snp	Load SNP data from a downloaded mysql database	SNPs, chromosomes	none	See Ensembl
treefam	Loads homologue data from  TreeFam See TreeFam	genes, homologues	treefam_config.properties - which gene identifiers are set	geneFile - location of gene file, organisms - taxonIds or organisms to process See TreeFam
uniprot	Loads protein information from  UniProtKB XML files.	protein sequences, lengths and molecular weights, links between proteins and genes, features located on proteins, UniProt keywords, references and comments. This source can optionally load InterPro protein domains and GO terms	uniprot_config.properties - where to get identifiers for genes and which field should be unique	See UniProt
uniprot-fasta	Loads sequences for proteins loaded in UniProt source	sequences	none	See UniProt
uniprot-keywords	Load definitions of UniProtKB keywords, should be included if loading data from uniprot.	updates uniprot keyword definitions	none	See UniProt
update-publications	All publications are referred to by PubMed id by other sources. This source should be included at the end of the build. It will query all PubMed ids from the database, fetch details from the Entrez web service and fill in Publication objects.	updates publications loaded by other sources	none

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Specific sources

These are sources that load Drosophila specific data sets into FlyMine, we don't expect you will re-use these unless you are creating a Drosophila warehouse. All of these sources are located in bio/sources/flymine.

• affy-probes
• anoest
• anopheles-identifiers
• anoph-expr
• arbeitman-items-xml
• bdgp-clone
• bdgp-insitu
• drosdel-gff
• drosophila-homology
• fly-anatomy-ontology
• flyatlas
• fly-development-ontology
• fly-fish
• fly-misc-cvterms
• flyreg
• flyrnai-screens
• homophila
• long_oligo
• protein_structure
• redfly
• rnai
• tiffin
• tiffin-expression
• tiling_path

See  FlyMine for more information about these datasets. Look at flymine/project.xml for examples of how to use these sources.

Other loaders

These loaders were written by InterMine users.

• CHEBI
• Disease ontology
• haem-atlas
• HGNC
• HuGE
• Mammalian phenotypes
• pride
• stitch