The following functions can be used to obtain 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'.
Before running following modules, run pip install intermine in your terminal first.
from intermine import registry
registry.getMines("D. melanogaster")
FawMine FlyMine LocustMine XenMine
FawMine
FlyMine
LocustMine
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: https://www.flymine.org/flymine API Version: 30 Release Version: 49 2020 February InterMine Version: 4.1.3 Organisms: D. melanogaster Neighbours: Animals
Description: An integrated database for Drosophila genomics
URL: http://www.flymine.org/flymine
API Version: 30
Release Version: 49 2020 February
InterMine Version: 4.1.3
Organisms:
D. melanogaster
Neighbours:
Animals
Now that we are very interested after viewing information about 'flymine', getData(mine)
can be used to extract the data sets corresponding to it, the way is as follows:
registry.getData("flymine")
Name: Affymetrix array: GeneChip Drosophila Genome 2.0 Array Name: Affymetrix array: GeneChip Drosophila Genome Array Name: Alleles and phenotypes Name: Artificial deletions Name: BDGP cDNA clone data set Name: BDGP in situ data set Name: BioGRID interaction data set Name: Disease Ontology Name: Disease models Name: Drosophila species orthologues and paralogues Name: E-FLYC-6 Name: Fly Anatomy Ontology Name: Fly Development Ontology Name: FlyAtlas Name: FlyBase Contolled Vocabulary Name: FlyBase Controlled Vocabulary Name: FlyBase PubMed to gene mapping 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 fasta data set for Drosophila ananassae Name: FlyBase fasta data set for Drosophila melanogaster Name: FlyBase fasta data set for Drosophila pseudoobscura pseudoobscura Name: FlyBase fasta data set for Drosophila simulans Name: FlyBase fasta data set for Drosophila virilis Name: FlyMine intergenic regions Name: GO Name: GO Annotation data set Name: GO Annotation for Drosophila melanogaster Name: HGNC identifiers Name: HomoloGene homology predictions Name: Human gene identifiers Name: INDAC long oligo data set Name: IntAct molecular interactions Name: InterPro data set Name: InterPro domain GO annotations Name: KEGG pathways data set Name: Mouse gene identifiers Name: Mouse identifiers Name: NCBI Entrez Gene identifiers Name: NCBI PubMed to gene mapping Name: OMIM diseases Name: PSI Molecular Interactions Name: Panther orthologue and paralogue predictions Name: PubMed to gene mapping Name: REDfly Drosophila transcription factor binding sites Name: REDfly Drosophila transcriptional cis-regulatory modules Name: RNAi screen phenotypes Name: Rat gene identifiers Name: Reactome pathways data set Name: Sequence Ontology Name: Swiss-Prot data set Name: The Gene Ontology Name: The Sequence Ontology Name: The developmental transcriptome of Drosophila melanogaster. Name: TrEMBL data set Name: TreeFam data set Name: UniProt data set Name: Uniprot data set Name: WormBase gene identifiers Name: Wormbase gene identifiers Name: fly-Fish data set Name: miRBase Targets Name: microRNA Targets
Name: Affymetrix array: GeneChip Drosophila Genome 2.0 Array
Name: Affymetrix array: GeneChip Drosophila Genome Array
Name: Alleles and phenotypes
Name: Artificial deletions
Name: BDGP cDNA clone data set
Name: BDGP in situ data set
Name: BioGRID interaction data set
Name: Disease Ontology
Name: Disease models
Name: Drosophila species orthologues and paralogues
Name: E-FLYC-6
Name: Fly Anatomy Ontology
Name: Fly Development Ontology
Name: FlyAtlas
Name: FlyBase Contolled Vocabulary
Name: FlyBase Controlled Vocabulary
Name: FlyBase PubMed to gene mapping
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 fasta data set for Drosophila ananassae
Name: FlyBase fasta data set for Drosophila melanogaster
Name: FlyBase fasta data set for Drosophila pseudoobscura pseudoobscura
Name: FlyBase fasta data set for Drosophila simulans
Name: FlyBase fasta data set for Drosophila virilis
Name: FlyMine intergenic regions
Name: GO
Name: GO Annotation data set
Name: GO Annotation for Drosophila melanogaster
Name: HGNC identifiers
Name: HomoloGene homology predictions
Name: Human gene identifiers
Name: INDAC long oligo data set
Name: IntAct molecular interactions
Name: InterPro data set
Name: InterPro domain GO annotations
Name: KEGG pathways data set
Name: Mouse gene identifiers
Name: Mouse identifiers
Name: NCBI Entrez Gene identifiers
Name: NCBI PubMed to gene mapping
Name: OMIM diseases
Name: PSI Molecular Interactions
Name: Panther orthologue and paralogue predictions
Name: PubMed to gene mapping
Name: REDfly Drosophila transcription factor binding sites
Name: REDfly Drosophila transcriptional cis-regulatory modules
Name: RNAi screen phenotypes
Name: Rat gene identifiers
Name: Reactome pathways data set
Name: Sequence Ontology
Name: Swiss-Prot data set
Name: The Gene Ontology
Name: The Sequence Ontology
Name: The developmental transcriptome of Drosophila melanogaster.
Name: TrEMBL data set
Name: TreeFam data set
Name: UniProt data set
Name: Uniprot data set
Name: WormBase gene identifiers
Name: Wormbase gene identifiers
Name: fly-Fish data set
Name: miRBase Targets
Name: microRNA Targets