The following functions can be used to optain some useful information about a mine or an organism. Assuming you are inside intermine-ws-python folder:
getMines(organism)
fetches the mine(s) of a particular organism, say 'D. melanogaster'.
from intermine import registry
registry.getMines("D. melanogaster")
FlyMine
FlyMine Beta
XenMine
Now that we have the mines, we can use getInfo(mine)
to fetch all the information about a particular mine ie its description, version, organisms associated etc. Suppose we want to know more about flymine, here's what we do:
registry.getInfo("flymine")
Description: An integrated database for Drosophila genomics
URL: http://www.flymine.org/flymine
API Version: 25
Release Version: 45.1 2017 August
InterMine Version: 1.8.5
Organisms:
D. melanogaster
Neighbours:
MODs
Now that I am very interested after viewing information about 'flymine', getData(mine)
can be used to extract the data sets corresponding to it:
registry.getData("flymine")
Name: Affymetrix array: Drosophila1
Name: Affymetrix array: Drosophila2
Name: Affymetrix array: GeneChip Drosophila Genome 2.0 Array
Name: Affymetrix array: GeneChip Drosophila Genome Array
Name: Anoph-Expr data set
Name: BDGP cDNA clone data set
Name: BDGP in situ data set
Name: BioGRID interaction data set
Name: Department of Genetics tiling path
Name: DrosDel P-element and Deletion collection
Name: Drosophila 12 Genomes Consortium homology
Name: E-FLYC-6
Name: Ensembl Anopheles gambiae [AgamP3.4]
Name: FlyAtlas
Name: FlyBase
Name: FlyBase data set for Drosophila ananassae
Name: FlyBase data set for Drosophila erecta
Name: FlyBase data set for Drosophila grimshawi
Name: FlyBase data set for Drosophila melanogaster
Name: FlyBase data set for Drosophila mojavensis
Name: FlyBase data set for Drosophila persimilis
Name: FlyBase data set for Drosophila pseudoobscura pseudoobscura
Name: FlyBase data set for Drosophila sechellia
Name: FlyBase data set for Drosophila simulans
Name: FlyBase data set for Drosophila virilis
Name: FlyBase data set for Drosophila willistoni
Name: FlyBase data set for Drosophila yakuba
Name: FlyBase expression data
Name: FlyBase fasta data set for Drosophila ananassae
Name: FlyBase fasta data set for Drosophila erecta
Name: FlyBase fasta data set for Drosophila grimshawi
Name: FlyBase fasta data set for Drosophila melanogaster
Name: FlyBase fasta data set for Drosophila mojavensis
Name: FlyBase fasta data set for Drosophila persimilis
Name: FlyBase fasta data set for Drosophila pseudoobscura pseudoobscura
Name: FlyBase fasta data set for Drosophila sechellia
Name: FlyBase fasta data set for Drosophila simulans
Name: FlyBase fasta data set for Drosophila virilis
Name: FlyBase fasta data set for Drosophila willistoni
Name: FlyBase fasta data set for Drosophila yakuba
Name: FlyMine intergenic regions
Name: FlyReactome data set
Name: FlyReg data set
Name: GO Annotation from BHF-UCL
Name: GO Annotation from CACAO
Name: GO Annotation from FlyBase
Name: GO Annotation from FlyBase
Name: GO Annotation from GO_Central
Name: GO Annotation from InterPro
Name: GO Annotation from ParkinsonsUK-UCL
Name: GO Annotation from UniProt
Name: GO Annotation from YeastFunc
Name: GenomeRNAi data set
Name: HGNC identifiers
Name: HomoloGene data set
Name: INDAC long oligo data set
Name: IntAct interactions data set
Name: InterPro GO Annotation data set
Name: InterPro data set
Name: KEGG pathways data set
Name: MGI identifiers
Name: NCBI Entrez Gene identifiers
Name: OMIM diseases
Name: PDB dmel data set
Name: Panther data set
Name: PubMed to gene mapping
Name: REDfly Drosophila transcription factor binding sites
Name: REDfly Drosophila transcriptional cis-regulatory modules
Name: RGD gene identifiers
Name: Reactome pathways data set
Name: Swiss-Prot data set
Name: TrEMBL data set
Name: TreeFam data set
Name: UniProt data set
Name: UniProt keywords data set
Name: VectorBase AnoEST clusters
Name: VectorBase Anopheles
Name: WormBase genes
Name: fly-Fish data set
Name: miRBase Targets