This very short tutorial will talk about how you can access your saved templates and lists if you have your login information (username and password). If you don't have an account, you can create one at http://www.flymine.org/
Once, you have made an account, you can use the web service to create a query of your choice and save it as a template. This template can be used through the Python API or through the web service.
To login and access your templates through Python, you can provide your login information as shown below. Note that the code shown below is in comments because it needs to be specific to your account. Change the username and password to match yours, uncomment the code, and then run it.
from intermine.webservice import Service
from intermine import query
# service=Service("www.flymine.org/flymine/service",username="Enter username",password="Enter password")
#template=service.get_template("Name of a saved template")
You can then play around with this saved template like any of the existing templates on Flymine.
To view the names of all the available templates you can view the templates dictionary and iterate through it. This can be done as follows.
service = Service("https://www.flymine.org/flymine/service")
templates=service.templates
for name in templates.keys():
print(name)
Gene_RegionLocation AlleleClass_Allele FlyFish_Genes Organism_Sequence GOterm_GenesInsertions Gene_BDGP Pathway_Genes AllGene_Chromosome Gene_IntronChromosome RNA_seq_Genes protein_interactions Gene_GOAll Gene_Interactions2 RNAiScreen_genes Gene_CDSs OrganismGO_GenePointMutation Gene_Publications Protein_GeneChromosomeLength protein_domains2 GO_Gene Gene_Pathway All_Genes_In_Organism_To_Publications Organism_NaturalTransposableElements Organism_Protein Tissue_Flyatlas PhenotypeType_Alleles TranscriptionFactor_Genes ChromLocation_GeneTranscriptExon Gene_PointMutationLocation AnatomyTerm_Region Gene_Protein Gene_transposableElementsOverlappingExons Gene_OverlapppingGenes Transcriptionfactor_TFBindingSiteGene Gene_RNAi Gene_TimeCourseExpression CRM _AnatomyTerm protein_domain ChromLocation_Gene Chromosome_Gene Gene_GO Organism_transposableElementInsertionSites ChromLocation_CRM Gene_AdjacentGenes Organism_3UTR Gene_overlapping2 Gene_Orth_seq Gene_disease Protein_PublicationAll Intron_regulatoryRegions Disease_gene2 FlyRegBindingSite_TranscriptionFactor organism_allmiRNA Gene_FlyAtlas_TissueList Gene_RegulatoryRegion Gene_proteindomain ChromLocation_RegulatoryRegion Probe_Gene BDGP_Gene geneInteractiongene modENCODE_RNA_seq_Tissues Gene_AlleleStocks Publication_Genes Transcript_INDAC Pathway_GenesOrthol_new2 Test_for_Julianne Gene_TranscriptExonLocation ChromLocation_TFBindingSiteLocationGeneFactor Gene_upstreamRegulatoryRegions GOterm_genesDrosDelDeletion Gene_Insertion Stage_FlyFishBDGP Organism_5UTR organismGenes_GOterms Intergenic_RegRegion Organism_GenesTranscriptsExonsIntrons ChromLocation_CRMOverlappingTFBindingsite Gene_enhancer Gene_AdjacentGene_FlyAtlas_upstream MeSH_Publication Gene_Location Gene_Probe Gene_ExonLocation2 ChromLocation_GeneTranscriptINDAC Gene_RNA_seq Gene_INDAC PointMutation_Gene_Chromosome Clone_gene TimeCourseData_Gene Chromosome_IntergenicSequence Gene_AdjacentGene_FlyAtlas_downstream Gene_1CDSsequence Gene_DrosophilaOrthologues NaturalTransposableElement_InsertedElements Organism_Intergenic Gene_pathway_interactions Organism_NaturalTransposableElementsandSites GeneTissue_FlyAtlas Gene_TranscriptOrthologue Gene_FlyAtlas Mutagen_Allele AnatomyTerm_Alleles ECnumber_gene_protein miRNA_Targets Organism_GOtermsOrthologues Dataset_TF_BindingSites Chromosome_CRMOverlappingInsertion DrosDel_GeneLocation Genes_Publications miRNAtargetGene_miRNAgene ProbeSet_FlyAtlas ListPathway INDAC_GeneLocation Gene_transcriptionFactors Gene_FlyFish Gene_AdjacentGenesLocations Protein_GOterms_1 Disease_gene_orthologue Protein_Publication InterPro_Domain_Family Gene_Alleles Gene_Orth organism_allGenes GO_GeneOrthologues Chromosome_GeneInsertionLocation Gene_BDGPFlyFish Protein_DomainGO
This dictionary contains all the information about all the available templates, including the exact name and description. If you now want to view the details about a particular template name, this can be done as shown below.
templates["Gene_RNAi"]
'<template comment="" name="Gene_RNAi" title="Gene --> RNAi phenotypes"><query longDescription="Show RNAi phenotypes for a specified gene or genes." model="genomic" name="Gene_RNAi" sortOrder="Gene.primaryIdentifier asc" view="Gene.primaryIdentifier Gene.symbol Gene.rnaiResults.phenotype Gene.rnaiResults.score Gene.rnaiResults.rnaiScreen.scoreType Gene.rnaiResults.reagentId Gene.rnaiResults.conditions Gene.rnaiResults.rnaiScreen.publication.pubMedId Gene.rnaiResults.rnaiScreen.name Gene.rnaiResults.rnaiScreen.assay Gene.rnaiResults.rnaiScreen.bioSourceName Gene.rnaiResults.rnaiScreen.bioSourceType Gene.rnaiResults.rnaiScreen.method"><constraint description="Show RNAi phenotypes for the following gene:" editable="true" extraValue="D. melanogaster" op="LOOKUP" path="Gene" value="eve"/></query></template>'
If you don't feel comfortable with viewing this dictionary, you can also view the templates on: http://beta.flymine.org/beta/templates.do and https://www.flymine.org/flymine/templates.do You can scroll through the list of templates. If you find an interesting template, click on the template and click on the Python tab (in blue). This would show you how to call the template in Python using the exact name.