Data Source Library Overview
This page lists the current sources available for use in InterMine. All the sources here are found as ready-to-use JARs in the central repository, JCenter.
You can also add your own sources to load custom file formats, see Writing your own data 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. However, there are exceptions to this rule.
Core InterMine sources#
These are commonly used sources that you may want to use to load data into your own InterMine instance.
- Gene Ontology
- Homologue Data Sources
- Interactions
- Pathway data sources
- Proteins
- Publications
- NCBI - Entrez gene
- Chado
- FASTA
- GFF3
- Identifier Data Sources
- InterMine Items XML
- OMIM
- Organisms
- Sequence Ontology (SO)
- Uberon
- Data Sources
- Data Sets
- VCF files
FlyMine 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 https://github.com/intermine/flymine-bio-sources.
- affy-probes
- arbeitman-items-xml
- bdgp-clone
- bdgp-insitu
- drosdel-gff
- drosophila-homology
- fly-anatomy-ontology
- flyatlas
- flybase-alleles
- flybase-expression
- fly-development-ontology
- fly-fish
- fly-misc-cvterms
- flyreg
- long_oligo
- miranda
- redfly
- rnai
See FlyMine for more information about these datasets. Look at FlyMine's project.xml for examples of how to use these sources.
HumanMine Specific sources#
- arrayexpress-atlas
- atlas-express
- clinvar
- ensembl-hgnc
- gtex
- hgnc
- hpo
- hpo-annotation
- huge-gwas
- human-gene
- mgi-alleles
- ncbi-summaries
- orphanet
- protein-atlas
See HumanMine for more information about these datasets. Look at HumanMine's project.xml for examples on how to use these sources.