Dipper
autodoc
Installation
Getting started with Dipper
Notebooks
Downloads
Ingest status
Applications
Working with graphs
Working with the models API
Writing ingests with the source API
Testing ingests
Configuring dipper with keys and passwords
Schemas
API Docs
Source APIs
Dipper
Docs
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Index
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Index
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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Z
A
add_agent_to_graph() (dipper.models.Provenance.Provenance method)
add_assay_to_graph() (dipper.models.Provenance.Provenance method)
add_assertion() (dipper.models.Provenance.Provenance method)
add_association_to_graph() (dipper.models.assoc.Association.Assoc method)
(dipper.models.assoc.D2PAssoc.D2PAssoc method)
(dipper.models.assoc.G2PAssoc.G2PAssoc method)
add_common_files_to_file_list() (dipper.sources.HPOAnnotations.HPOAnnotations method)
add_data_individual() (dipper.models.Evidence.Evidence method)
add_date() (dipper.models.assoc.Association.Assoc method)
add_date_created() (dipper.models.Provenance.Provenance method)
add_evidence() (dipper.models.assoc.Association.Assoc method)
(dipper.models.Evidence.Evidence method)
add_gene_family_to_graph() (dipper.models.assoc.OrthologyAssoc.OrthologyAssoc method)
add_orthologs_by_gene_group() (dipper.sources.NCBIGene.NCBIGene method)
add_predicate_object() (dipper.models.assoc.Association.Assoc method)
add_property_axioms() (dipper.utils.GraphUtils.GraphUtils static method)
add_property_to_graph() (dipper.utils.GraphUtils.GraphUtils static method)
add_protein_to_graph (dipper.sources.OrthoXML.OrthoXML attribute)
add_provenance() (dipper.models.assoc.Association.Assoc method)
add_relation() (dipper.sources.MyChem.MyChem static method)
add_source() (dipper.models.assoc.Association.Assoc method)
(dipper.models.Evidence.Evidence method)
add_study_measure() (dipper.models.Provenance.Provenance method)
add_study_parts() (dipper.models.Provenance.Provenance method)
add_study_to_measurements() (dipper.models.Provenance.Provenance method)
add_supporting_data() (dipper.models.Evidence.Evidence method)
add_supporting_evidence() (dipper.models.Evidence.Evidence method)
add_supporting_publication() (dipper.models.Evidence.Evidence method)
addAffectedLocus() (dipper.models.Genotype.Genotype method)
addAllele() (dipper.models.Genotype.Genotype method)
addAlleleOfGene() (dipper.models.Genotype.Genotype method)
addAuthor() (dipper.models.Reference.Reference method)
addBlankNodeAnnotation() (dipper.models.Model.Model method)
addChromosome() (dipper.models.Genotype.Genotype method)
addChromosomeClass() (dipper.models.Genotype.Genotype method)
addChromosomeInstance() (dipper.models.Genotype.Genotype method)
addClassToGraph() (dipper.models.Model.Model method)
addComment() (dipper.models.Model.Model method)
addComponentAttributes() (dipper.models.Environment.Environment method)
addComponentToEnvironment() (dipper.models.Environment.Environment method)
addComponentToPathway() (dipper.models.Pathway.Pathway method)
addConstruct() (dipper.models.Genotype.Genotype method)
addDefinition() (dipper.models.Model.Model method)
addDepiction() (dipper.models.Model.Model method)
addDeprecatedClass() (dipper.models.Model.Model method)
addDeprecatedIndividual() (dipper.models.Model.Model method)
addDerivesFrom() (dipper.models.Genotype.Genotype method)
addDescription() (dipper.models.Model.Model method)
addEnvironment() (dipper.models.Environment.Environment method)
addEnvironmentalCondition() (dipper.models.Environment.Environment method)
addEquivalentClass() (dipper.models.Model.Model method)
addFeatureEndLocation() (dipper.models.GenomicFeature.Feature method)
addFeatureProperty() (dipper.models.GenomicFeature.Feature method)
addFeatureStartLocation() (dipper.models.GenomicFeature.Feature method)
addFeatureToGraph() (dipper.models.GenomicFeature.Feature method)
addGene() (dipper.models.Genotype.Genotype method)
addGeneProduct() (dipper.models.Genotype.Genotype method)
addGeneTargetingReagent() (dipper.models.Genotype.Genotype method)
addGeneTargetingReagentToGenotype() (dipper.models.Genotype.Genotype method)
addGeneToPathway() (dipper.models.Pathway.Pathway method)
addGenome() (dipper.models.Genotype.Genotype method)
addGenomicBackground() (dipper.models.Genotype.Genotype method)
addGenomicBackgroundToGenotype() (dipper.models.Genotype.Genotype method)
addGenotype() (dipper.models.Genotype.Genotype method)
addIndividualToGraph() (dipper.models.Model.Model method)
addLabel() (dipper.models.Model.Model method)
addMember() (dipper.models.Family.Family method)
addMemberOf() (dipper.models.Family.Family method)
addMemberOfPopulation() (dipper.models.Genotype.Genotype method)
addOntologyDeclaration() (dipper.models.Model.Model method)
addOWLPropertyClassRestriction() (dipper.models.Model.Model method)
addOWLVersionInfo() (dipper.models.Model.Model method)
addOWLVersionIRI() (dipper.models.Model.Model method)
addPage() (dipper.models.Reference.Reference method)
addParts() (dipper.models.Genotype.Genotype method)
addPartsToVSLC() (dipper.models.Genotype.Genotype method)
addPathway() (dipper.models.Pathway.Pathway method)
addPerson() (dipper.models.Model.Model method)
addPolypeptide() (dipper.models.Genotype.Genotype method)
addPositionToGraph() (dipper.models.GenomicFeature.Feature method)
addReagentTargetedGene() (dipper.models.Genotype.Genotype method)
addReferenceGenome() (dipper.models.Genotype.Genotype method)
addRefToGraph() (dipper.models.Reference.Reference method)
addRegionPositionToGraph() (dipper.models.GenomicFeature.Feature method)
addSameIndividual() (dipper.models.Model.Model method)
addSequenceAlteration() (dipper.models.Genotype.Genotype method)
addSequenceAlterationToVariantLocus() (dipper.models.Genotype.Genotype method)
addSequenceDerivesFrom() (dipper.models.Genotype.Genotype method)
addSubClass() (dipper.models.Model.Model method)
addSubsequenceOfFeature() (dipper.models.GenomicFeature.Feature method)
addSynonym() (dipper.models.Model.Model method)
addTargetedGeneComplement() (dipper.models.Genotype.Genotype method)
addTargetedGeneSubregion() (dipper.models.Genotype.Genotype method)
addTaxon() (dipper.models.Genotype.Genotype method)
addTaxonToFeature() (dipper.models.GenomicFeature.Feature method)
addTitle() (dipper.models.Reference.Reference method)
addTriple() (dipper.graph.Graph.Graph method)
(dipper.graph.RDFGraph.RDFGraph method)
(dipper.graph.StreamedGraph.StreamedGraph method)
(dipper.models.Model.Model method)
addType() (dipper.models.Model.Model method)
addVSLCtoParent() (dipper.models.Genotype.Genotype method)
addXref() (dipper.models.Model.Model method)
AnimalQTLdb (class in dipper.sources.AnimalQTLdb)
annotation_properties (dipper.models.assoc.Association.Assoc attribute)
(dipper.models.Environment.Environment attribute)
(dipper.models.GenomicFeature.Feature attribute)
(dipper.models.Genotype.Genotype attribute)
(dipper.models.Model.Model attribute)
(dipper.models.Reference.Reference attribute)
Assoc (class in dipper.models.assoc.Association)
assoc_types (dipper.models.assoc.Association.Assoc attribute)
B
BENCHMARK_BASE (dipper.sources.OMA.OMA attribute)
Bgee (class in dipper.sources.Bgee)
BGEE_FTP (dipper.sources.Bgee.Bgee attribute)
bind_all_namespaces() (dipper.graph.RDFGraph.RDFGraph method)
BioGrid (class in dipper.sources.BioGrid)
biogrid_ids (dipper.sources.BioGrid.BioGrid attribute)
build_measurement_description() (dipper.sources.MPD.MPD static method)
C
check_header() (dipper.sources.MPD.MPD static method)
check_uniprot() (dipper.sources.MyChem.MyChem static method)
checkIfRemoteIsNewer() (dipper.sources.Bgee.Bgee method)
(dipper.sources.MyDrug.MyDrug method)
(dipper.sources.Source.Source method)
Chem2DiseaseAssoc (class in dipper.models.assoc.Chem2DiseaseAssoc)
chunks() (dipper.sources.MyChem.MyChem static method)
clean_db_prefix() (dipper.sources.GeneOntology.GeneOntology method)
clean_protein_id() (dipper.sources.OrthoXML.OrthoXML method)
clean_up_omim_genes() (dipper.sources.OMIA.OMIA method)
ClinVar (class in dipper.sources.ClinVar)
compare_checksums() (dipper.sources.IMPC.IMPC method)
compare_local_remote_bytes() (dipper.sources.Source.Source method)
conf (in module dipper.config)
Coriell (class in dipper.sources.Coriell)
create_books() (dipper.sources.GeneReviews.GeneReviews method)
CTD (class in dipper.sources.CTD)
curie_util (dipper.graph.RDFGraph.RDFGraph attribute)
(dipper.graph.StreamedGraph.StreamedGraph attribute)
CurieUtil (class in dipper.utils.CurieUtil)
D
d2p_object_properties (dipper.models.assoc.D2PAssoc.D2PAssoc attribute)
D2PAssoc (class in dipper.models.assoc.D2PAssoc)
data_properties (dipper.models.GenomicFeature.Feature attribute)
data_property (dipper.models.Evidence.Evidence attribute)
data_types (dipper.models.Evidence.Evidence attribute)
Dataset (class in dipper.models.Dataset)
datatype_properties (dipper.models.assoc.Association.Assoc attribute)
(dipper.models.Model.Model attribute)
Decipher (class in dipper.sources.Decipher)
declareAsOntology() (dipper.sources.Source.Source method)
default_node_list() (dipper.sources.OrthoXML.OrthoXMLParser method)
DEFAULT_TAXA (dipper.sources.Bgee.Bgee attribute)
(dipper.sources.StringDB.StringDB attribute)
digest_id() (dipper.utils.GraphUtils.GraphUtils method)
dipper (module)
dipper.config (module)
dipper.curie_map (module)
dipper.graph (module)
dipper.graph.Graph (module)
dipper.graph.RDFGraph (module)
dipper.graph.StreamedGraph (module)
dipper.models (module)
dipper.models.assoc (module)
dipper.models.assoc.Association (module)
dipper.models.assoc.Chem2DiseaseAssoc (module)
dipper.models.assoc.D2PAssoc (module)
dipper.models.assoc.DispositionAssoc (module)
dipper.models.assoc.G2PAssoc (module)
dipper.models.assoc.InteractionAssoc (module)
dipper.models.assoc.OrthologyAssoc (module)
dipper.models.Dataset (module)
dipper.models.Environment (module)
dipper.models.Evidence (module)
dipper.models.Family (module)
dipper.models.GenomicFeature (module)
dipper.models.Genotype (module)
dipper.models.Model (module)
dipper.models.Pathway (module)
dipper.models.Provenance (module)
dipper.models.Reference (module)
dipper.sources (module)
dipper.sources.AnimalQTLdb (module)
dipper.sources.Bgee (module)
dipper.sources.BioGrid (module)
dipper.sources.ClinVar (module)
dipper.sources.Coriell (module)
dipper.sources.CTD (module)
dipper.sources.Decipher (module)
dipper.sources.Ensembl (module)
dipper.sources.EOM (module)
dipper.sources.FlyBase (module)
dipper.sources.GeneOntology (module)
dipper.sources.GeneReviews (module)
dipper.sources.GWASCatalog (module)
dipper.sources.HGNC (module)
dipper.sources.HPOAnnotations (module)
dipper.sources.IMPC (module)
dipper.sources.KEGG (module)
dipper.sources.MGI (module)
dipper.sources.MGISlim (module)
dipper.sources.MMRRC (module)
dipper.sources.Monarch (module)
dipper.sources.Monochrom (module)
dipper.sources.MPD (module)
dipper.sources.MyChem (module)
dipper.sources.MyDrug (module)
dipper.sources.NCBIGene (module)
dipper.sources.OMA (module)
dipper.sources.OMIA (module)
dipper.sources.OMIM (module)
dipper.sources.Orphanet (module)
dipper.sources.OrthoXML (module)
dipper.sources.Panther (module)
dipper.sources.PostgreSQLSource (module)
dipper.sources.Reactome (module)
dipper.sources.RGD (module)
dipper.sources.SGD (module)
dipper.sources.Source (module)
dipper.sources.StringDB (module)
dipper.sources.UCSCBands (module)
dipper.sources.UDP (module)
dipper.sources.WormBase (module)
dipper.sources.ZFIN (module)
dipper.sources.ZFINSlim (module)
dipper.utils (module)
dipper.utils.CurieUtil (module)
dipper.utils.DipperUtil (module)
dipper.utils.GraphUtils (module)
dipper.utils.pysed (module)
dipper.utils.romanplus (module)
dipper.utils.TestUtils (module)
DipperUtil (class in dipper.utils.DipperUtil)
DispositionAssoc (class in dipper.models.assoc.DispositionAssoc)
E
eco_dict (dipper.sources.HPOAnnotations.HPOAnnotations attribute)
Ensembl (class in dipper.sources.Ensembl)
Environment (class in dipper.models.Environment)
environment_parts (dipper.models.Environment.Environment attribute)
EOM (class in dipper.sources.EOM)
Evidence (class in dipper.models.Evidence)
evidence_types (dipper.models.Evidence.Evidence attribute)
execute_query() (dipper.sources.MyChem.MyChem static method)
extract_pairwise_relations() (dipper.sources.OrthoXML.OrthoXMLParser method)
extract_taxon_info() (dipper.sources.OrthoXML.OrthoXML method)
F
Family (class in dipper.models.Family)
Feature (class in dipper.models.GenomicFeature)
fetch() (dipper.sources.AnimalQTLdb.AnimalQTLdb method)
(dipper.sources.Bgee.Bgee method)
(dipper.sources.BioGrid.BioGrid method)
(dipper.sources.CTD.CTD method)
(dipper.sources.ClinVar.ClinVar method)
(dipper.sources.Coriell.Coriell method)
(dipper.sources.Decipher.Decipher method)
(dipper.sources.EOM.EOM method)
(dipper.sources.Ensembl.Ensembl method)
(dipper.sources.FlyBase.FlyBase method)
(dipper.sources.GWASCatalog.GWASCatalog method)
(dipper.sources.GeneOntology.GeneOntology method)
(dipper.sources.GeneReviews.GeneReviews method)
(dipper.sources.HGNC.HGNC method)
(dipper.sources.HPOAnnotations.HPOAnnotations method)
(dipper.sources.IMPC.IMPC method)
(dipper.sources.KEGG.KEGG method)
(dipper.sources.MGI.MGI method)
(dipper.sources.MGISlim.MGISlim method)
(dipper.sources.MMRRC.MMRRC method)
(dipper.sources.MPD.MPD method)
(dipper.sources.Monarch.Monarch method)
(dipper.sources.Monochrom.Monochrom method)
(dipper.sources.MyChem.MyChem method)
(dipper.sources.MyDrug.MyDrug method)
(dipper.sources.NCBIGene.NCBIGene method)
(dipper.sources.OMIA.OMIA method)
(dipper.sources.OMIM.OMIM method)
(dipper.sources.Orphanet.Orphanet method)
(dipper.sources.OrthoXML.OrthoXML method)
(dipper.sources.Panther.Panther method)
(dipper.sources.RGD.RGD method)
(dipper.sources.Reactome.Reactome method)
(dipper.sources.SGD.SGD method)
(dipper.sources.Source.Source method)
(dipper.sources.StringDB.StringDB method)
(dipper.sources.UCSCBands.UCSCBands method)
(dipper.sources.UDP.UDP method)
(dipper.sources.WormBase.WormBase method)
(dipper.sources.ZFIN.ZFIN method)
(dipper.sources.ZFINSlim.ZFINSlim method)
fetch_from_mychem() (dipper.sources.MyChem.MyChem method)
fetch_from_pgdb() (dipper.sources.PostgreSQLSource.PostgreSQLSource method)
fetch_from_url() (dipper.sources.Source.Source method)
fetch_protein_gene_map() (dipper.sources.Ensembl.Ensembl method)
fetch_protein_list() (dipper.sources.Ensembl.Ensembl method)
fetch_query_from_pgdb() (dipper.sources.PostgreSQLSource.PostgreSQLSource method)
fetch_transgene_genes_from_db() (dipper.sources.MGI.MGI method)
fetch_uniprot_gene_map() (dipper.sources.Ensembl.Ensembl method)
file_len() (dipper.sources.Source.Source method)
files (dipper.sources.AnimalQTLdb.AnimalQTLdb attribute)
(dipper.sources.Bgee.Bgee attribute)
(dipper.sources.BioGrid.BioGrid attribute)
(dipper.sources.CTD.CTD attribute)
(dipper.sources.ClinVar.ClinVar attribute)
(dipper.sources.Coriell.Coriell attribute)
(dipper.sources.Decipher.Decipher attribute)
(dipper.sources.EOM.EOM attribute)
(dipper.sources.Ensembl.Ensembl attribute)
(dipper.sources.FlyBase.FlyBase attribute)
(dipper.sources.GWASCatalog.GWASCatalog attribute)
(dipper.sources.GeneOntology.GeneOntology attribute)
(dipper.sources.GeneReviews.GeneReviews attribute)
(dipper.sources.HGNC.HGNC attribute)
(dipper.sources.HPOAnnotations.HPOAnnotations attribute)
(dipper.sources.IMPC.IMPC attribute)
(dipper.sources.KEGG.KEGG attribute)
(dipper.sources.MMRRC.MMRRC attribute)
(dipper.sources.MPD.MPD attribute)
(dipper.sources.Monochrom.Monochrom attribute)
(dipper.sources.MyDrug.MyDrug attribute)
(dipper.sources.NCBIGene.NCBIGene attribute)
(dipper.sources.OMA.OMA attribute)
(dipper.sources.OMIA.OMIA attribute)
(dipper.sources.OMIM.OMIM attribute)
(dipper.sources.Orphanet.Orphanet attribute)
(dipper.sources.OrthoXML.OrthoXML attribute)
(dipper.sources.Panther.Panther attribute)
(dipper.sources.RGD.RGD attribute)
(dipper.sources.Reactome.Reactome attribute)
(dipper.sources.SGD.SGD attribute)
(dipper.sources.Source.Source attribute)
(dipper.sources.UCSCBands.UCSCBands attribute)
(dipper.sources.UDP.UDP attribute)
(dipper.sources.WormBase.WormBase attribute)
(dipper.sources.ZFIN.ZFIN attribute)
(dipper.sources.ZFINSlim.ZFINSlim attribute)
filter_keep_phenotype_entry_ids() (in module dipper.sources.OMIM)
FlyBase (class in dipper.sources.FlyBase)
format_actions() (dipper.sources.MyChem.MyChem static method)
fromRoman() (in module dipper.utils.romanplus)
G
g2p_types (dipper.models.assoc.G2PAssoc.G2PAssoc attribute)
G2PAssoc (class in dipper.models.assoc.G2PAssoc)
GeneOntology (class in dipper.sources.GeneOntology)
GeneReviews (class in dipper.sources.GeneReviews)
genoparts (dipper.models.Genotype.Genotype attribute)
Genotype (class in dipper.models.Genotype)
get() (in module dipper.curie_map)
get_association_id() (dipper.models.assoc.Association.Assoc method)
get_base() (dipper.utils.CurieUtil.CurieUtil method)
(in module dipper.curie_map)
get_children() (dipper.sources.OrthoXML.OrthoXMLParser method)
get_common_files() (dipper.sources.HPOAnnotations.HPOAnnotations method)
get_config() (in module dipper.config)
get_curie() (dipper.utils.CurieUtil.CurieUtil method)
get_curie_prefix() (dipper.utils.CurieUtil.CurieUtil method)
get_doid_ids_for_unpadding() (dipper.sources.HPOAnnotations.HPOAnnotations method)
get_drug_record() (dipper.sources.MyChem.MyChem static method)
get_eco_map() (dipper.sources.Source.Source static method)
get_feature_type_by_class_and_biotype() (dipper.sources.WormBase.WormBase method)
get_file_md5() (dipper.sources.Source.Source method)
get_files() (dipper.sources.Source.Source method)
get_homologene_by_gene_num() (dipper.utils.DipperUtil.DipperUtil static method)
get_inchikeys() (dipper.sources.MyChem.MyChem static method)
get_license() (dipper.models.Dataset.Dataset method)
get_local_file_size() (dipper.sources.Source.Source method)
get_ncbi_id_from_symbol() (dipper.utils.DipperUtil.DipperUtil static method)
get_ncbi_taxon_num_by_label() (dipper.utils.DipperUtil.DipperUtil static method)
get_omim_id_from_entry() (in module dipper.sources.OMIM)
get_orthology_evidence_code() (dipper.sources.ZFIN.ZFIN method)
get_orthology_sources_from_zebrafishmine() (dipper.sources.ZFIN.ZFIN method)
get_properties() (dipper.models.assoc.Association.Assoc method)
get_properties_from_graph() (dipper.utils.GraphUtils.GraphUtils static method)
get_remote_content_len() (dipper.sources.Source.Source method)
get_symbol_id_map() (dipper.sources.HGNC.HGNC method)
get_uniprot_entrez_id_map() (dipper.sources.GeneOntology.GeneOntology method)
get_uri() (dipper.utils.CurieUtil.CurieUtil method)
getChrPartTypeByNotation() (in module dipper.sources.Monochrom)
getGraph() (dipper.models.Dataset.Dataset method)
getTestSuite() (dipper.sources.AnimalQTLdb.AnimalQTLdb method)
(dipper.sources.BioGrid.BioGrid method)
(dipper.sources.CTD.CTD method)
(dipper.sources.ClinVar.ClinVar method)
(dipper.sources.Coriell.Coriell method)
(dipper.sources.EOM.EOM method)
(dipper.sources.Ensembl.Ensembl method)
(dipper.sources.FlyBase.FlyBase method)
(dipper.sources.GWASCatalog.GWASCatalog method)
(dipper.sources.GeneOntology.GeneOntology method)
(dipper.sources.GeneReviews.GeneReviews method)
(dipper.sources.HGNC.HGNC method)
(dipper.sources.HPOAnnotations.HPOAnnotations method)
(dipper.sources.IMPC.IMPC method)
(dipper.sources.KEGG.KEGG method)
(dipper.sources.MGI.MGI method)
(dipper.sources.MMRRC.MMRRC method)
(dipper.sources.MPD.MPD method)
(dipper.sources.Monochrom.Monochrom method)
(dipper.sources.NCBIGene.NCBIGene method)
(dipper.sources.OMA.OMA method)
(dipper.sources.OMIA.OMIA method)
(dipper.sources.OMIM.OMIM method)
(dipper.sources.Orphanet.Orphanet method)
(dipper.sources.Panther.Panther method)
(dipper.sources.Source.Source method)
(dipper.sources.UCSCBands.UCSCBands method)
(dipper.sources.WormBase.WormBase method)
(dipper.sources.ZFIN.ZFIN method)
Graph (class in dipper.graph.Graph)
GraphUtils (class in dipper.utils.GraphUtils)
GWASCatalog (class in dipper.sources.GWASCatalog)
GWASFILE (dipper.sources.GWASCatalog.GWASCatalog attribute)
GWASFTP (dipper.sources.GWASCatalog.GWASCatalog attribute)
H
hash_id() (dipper.sources.Source.Source static method)
HGGP (dipper.sources.UCSCBands.UCSCBands attribute)
HGNC (class in dipper.sources.HGNC)
HPOAnnotations (class in dipper.sources.HPOAnnotations)
I
IMPC (class in dipper.sources.IMPC)
interaction_object_properties (dipper.models.assoc.InteractionAssoc.InteractionAssoc attribute)
InteractionAssoc (class in dipper.models.assoc.InteractionAssoc)
InvalidRomanNumeralError
is_internal_node() (dipper.sources.OrthoXML.OrthoXMLParser method)
is_leaf() (dipper.sources.OrthoXML.OrthoXMLParser method)
is_omim_disease() (dipper.utils.DipperUtil.DipperUtil static method)
K
KEGG (class in dipper.sources.KEGG)
L
leaf_label() (dipper.sources.OrthoXML.OrthoXMLParser method)
M
make_allele_by_consequence() (dipper.sources.Decipher.Decipher method)
make_apo_map() (dipper.sources.SGD.SGD static method)
make_association() (dipper.sources.RGD.RGD method)
(dipper.sources.SGD.SGD method)
make_association_id() (dipper.models.assoc.Association.Assoc static method)
make_breed_id() (dipper.sources.OMIA.OMIA method)
make_c2p_assoc_id() (dipper.models.assoc.Chem2DiseaseAssoc.Chem2DiseaseAssoc method)
make_d2p_id() (dipper.models.assoc.D2PAssoc.D2PAssoc method)
make_experimental_model_with_genotype() (dipper.models.Genotype.Genotype method)
make_g2p_id() (dipper.models.assoc.G2PAssoc.G2PAssoc method)
make_id() (dipper.sources.Source.Source static method)
make_parent_bands() (dipper.sources.Monochrom.Monochrom method)
make_reagent_targeted_gene_id() (dipper.sources.WormBase.WormBase method)
make_targeted_gene_id() (dipper.sources.ZFIN.ZFIN static method)
make_triples() (dipper.sources.MyChem.MyChem method)
make_variant_locus_label() (dipper.models.Genotype.Genotype method)
make_vslc_label() (dipper.models.Genotype.Genotype method)
makeChromID() (in module dipper.models.GenomicFeature)
makeChromLabel() (in module dipper.models.GenomicFeature)
makeGenomeID() (dipper.models.Genotype.Genotype method)
makeLeader() (dipper.models.Model.Model method)
map_files (dipper.sources.GeneOntology.GeneOntology attribute)
(dipper.sources.IMPC.IMPC attribute)
(dipper.sources.Reactome.Reactome attribute)
(dipper.sources.UDP.UDP attribute)
map_omia_group_category_to_ontology_id() (dipper.sources.OMIA.OMIA method)
map_type_of_gene() (dipper.sources.NCBIGene.NCBIGene static method)
map_type_of_region() (dipper.sources.Monochrom.Monochrom method)
mgd_agent_id (dipper.sources.MPD.MPD attribute)
mgd_agent_label (dipper.sources.MPD.MPD attribute)
mgd_agent_type (dipper.sources.MPD.MPD attribute)
MGI (class in dipper.sources.MGI)
MGISlim (class in dipper.sources.MGISlim)
MMRRC (class in dipper.sources.MMRRC)
Model (class in dipper.models.Model)
Monarch (class in dipper.sources.Monarch)
Monochrom (class in dipper.sources.Monochrom)
MPD (class in dipper.sources.MPD)
MPDDL (dipper.sources.MPD.MPD attribute)
MY_DRUG_API (dipper.sources.MyDrug.MyDrug attribute)
MyChem (class in dipper.sources.MyChem)
MyDrug (class in dipper.sources.MyDrug)
N
namespaces (dipper.sources.Source.Source attribute)
NCBIGene (class in dipper.sources.NCBIGene)
normalise_units() (dipper.sources.MPD.MPD static method)
NotIntegerError
O
object_properties (dipper.models.assoc.Association.Assoc attribute)
(dipper.models.Environment.Environment attribute)
(dipper.models.Evidence.Evidence attribute)
(dipper.models.Family.Family attribute)
(dipper.models.GenomicFeature.Feature attribute)
(dipper.models.Genotype.Genotype attribute)
(dipper.models.Model.Model attribute)
(dipper.models.Pathway.Pathway attribute)
(dipper.models.Provenance.Provenance attribute)
OMA (class in dipper.sources.OMA)
OMIA (class in dipper.sources.OMIA)
OMIM (class in dipper.sources.OMIM)
open_and_parse_yaml() (dipper.sources.Source.Source static method)
Orphanet (class in dipper.sources.Orphanet)
ortho_rel (dipper.models.assoc.OrthologyAssoc.OrthologyAssoc attribute)
OrthologyAssoc (class in dipper.models.assoc.OrthologyAssoc)
OrthoXML (class in dipper.sources.OrthoXML)
OrthoXMLParser (class in dipper.sources.OrthoXML)
OutOfRangeError
P
Panther (class in dipper.sources.Panther)
parse() (dipper.sources.AnimalQTLdb.AnimalQTLdb method)
(dipper.sources.Bgee.Bgee method)
(dipper.sources.BioGrid.BioGrid method)
(dipper.sources.CTD.CTD method)
(dipper.sources.ClinVar.ClinVar method)
(dipper.sources.Coriell.Coriell method)
(dipper.sources.Decipher.Decipher method)
(dipper.sources.EOM.EOM method)
(dipper.sources.Ensembl.Ensembl method)
(dipper.sources.FlyBase.FlyBase method)
(dipper.sources.GWASCatalog.GWASCatalog method)
(dipper.sources.GeneOntology.GeneOntology method)
(dipper.sources.GeneReviews.GeneReviews method)
(dipper.sources.HGNC.HGNC method)
(dipper.sources.HPOAnnotations.HPOAnnotations method)
(dipper.sources.IMPC.IMPC method)
(dipper.sources.KEGG.KEGG method)
(dipper.sources.MGI.MGI method)
(dipper.sources.MGISlim.MGISlim method)
(dipper.sources.MMRRC.MMRRC method)
(dipper.sources.MPD.MPD method)
(dipper.sources.Monarch.Monarch method)
(dipper.sources.Monochrom.Monochrom method)
(dipper.sources.MyChem.MyChem method)
(dipper.sources.MyDrug.MyDrug method)
(dipper.sources.NCBIGene.NCBIGene method)
(dipper.sources.OMIA.OMIA method)
(dipper.sources.OMIM.OMIM method)
(dipper.sources.Orphanet.Orphanet method)
(dipper.sources.OrthoXML.OrthoXML method)
(dipper.sources.Panther.Panther method)
(dipper.sources.RGD.RGD method)
(dipper.sources.Reactome.Reactome method)
(dipper.sources.SGD.SGD method)
(dipper.sources.Source.Source method)
(dipper.sources.StringDB.StringDB method)
(dipper.sources.UCSCBands.UCSCBands method)
(dipper.sources.UDP.UDP method)
(dipper.sources.WormBase.WormBase method)
(dipper.sources.ZFIN.ZFIN method)
(dipper.sources.ZFINSlim.ZFINSlim method)
parse_checksum_file() (dipper.sources.IMPC.IMPC method)
parse_mapping_file() (dipper.sources.Source.Source static method)
Pathway (class in dipper.models.Pathway)
pathway_parts (dipper.models.Pathway.Pathway attribute)
PNTHDL (dipper.sources.Panther.Panther attribute)
PostgreSQLSource (class in dipper.sources.PostgreSQLSource)
prefix_exists() (dipper.utils.CurieUtil.CurieUtil method)
process_all_common_disease_files() (dipper.sources.HPOAnnotations.HPOAnnotations method)
process_allele_phenotype() (dipper.sources.WormBase.WormBase method)
process_associations() (dipper.sources.OMIA.OMIA method)
process_catalog() (dipper.sources.GWASCatalog.GWASCatalog method)
process_classes() (dipper.sources.OMIA.OMIA method)
process_common_disease_file() (dipper.sources.HPOAnnotations.HPOAnnotations method)
process_disease_association() (dipper.sources.WormBase.WormBase method)
process_entries() (dipper.sources.OMIM.OMIM method)
process_feature_loc() (dipper.sources.WormBase.WormBase method)
process_fish() (dipper.sources.ZFIN.ZFIN method)
process_fish_disease_models() (dipper.sources.ZFIN.ZFIN method)
process_gaf() (dipper.sources.GeneOntology.GeneOntology method)
process_gene_desc() (dipper.sources.WormBase.WormBase method)
process_gene_ids() (dipper.sources.WormBase.WormBase method)
process_gene_interaction() (dipper.sources.WormBase.WormBase method)
process_mgi_note_allele_view() (dipper.sources.MGI.MGI method)
process_mgi_relationship_transgene_genes() (dipper.sources.MGI.MGI method)
process_nbk_html() (dipper.sources.GeneReviews.GeneReviews method)
process_omia_phenotypes() (dipper.sources.Monarch.Monarch method)
process_orthology_evidence() (dipper.sources.ZFIN.ZFIN method)
process_pub_xrefs() (dipper.sources.WormBase.WormBase method)
process_rnai_phenotypes() (dipper.sources.WormBase.WormBase method)
process_species() (dipper.sources.OMIA.OMIA method)
process_xml_table() (dipper.sources.Source.Source method)
properties (dipper.models.assoc.Association.Assoc attribute)
(dipper.models.Environment.Environment attribute)
(dipper.models.GenomicFeature.Feature attribute)
(dipper.models.Genotype.Genotype attribute)
(dipper.models.Pathway.Pathway attribute)
Provenance (class in dipper.models.Provenance)
provenance_types (dipper.models.Provenance.Provenance attribute)
Q
querys (dipper.sources.FlyBase.FlyBase attribute)
R
RDFGraph (class in dipper.graph.RDFGraph)
Reactome (class in dipper.sources.Reactome)
REACTOME_BASE (dipper.sources.Reactome.Reactome attribute)
ref_types (dipper.models.Reference.Reference attribute)
Reference (class in dipper.models.Reference)
region_type_map (dipper.sources.Monochrom.Monochrom attribute)
remove_backslash_r() (dipper.sources.Source.Source static method)
remove_control_characters() (dipper.utils.DipperUtil.DipperUtil method)
replace() (in module dipper.utils.pysed)
resources (dipper.sources.FlyBase.FlyBase attribute)
(dipper.sources.MGI.MGI attribute)
(dipper.sources.NCBIGene.NCBIGene attribute)
return_target_list() (dipper.sources.MyChem.MyChem static method)
RGD (class in dipper.sources.RGD)
RGD_BASE (dipper.sources.RGD.RGD attribute)
rmlinematch() (in module dipper.utils.pysed)
rmlinenumber() (in module dipper.utils.pysed)
RomanError
S
SCIGRAPH_BASE (dipper.sources.NCBIGene.NCBIGene attribute)
scrub() (dipper.sources.ClinVar.ClinVar method)
(dipper.sources.HPOAnnotations.HPOAnnotations method)
(dipper.sources.OMIA.OMIA method)
(dipper.sources.ZFIN.ZFIN method)
serialize() (dipper.graph.Graph.Graph method)
(dipper.graph.StreamedGraph.StreamedGraph method)
set_association_id() (dipper.models.assoc.Association.Assoc method)
(dipper.models.assoc.Chem2DiseaseAssoc.Chem2DiseaseAssoc method)
(dipper.models.assoc.D2PAssoc.D2PAssoc method)
(dipper.models.assoc.G2PAssoc.G2PAssoc method)
set_citation() (dipper.models.Dataset.Dataset method)
set_date_issued() (dipper.models.Dataset.Dataset method)
set_description() (dipper.models.assoc.Association.Assoc method)
set_environment() (dipper.models.assoc.G2PAssoc.G2PAssoc method)
set_license() (dipper.models.Dataset.Dataset method)
set_object() (dipper.models.assoc.Association.Assoc method)
set_relationship() (dipper.models.assoc.Association.Assoc method)
set_score() (dipper.models.assoc.Association.Assoc method)
set_stage() (dipper.models.assoc.G2PAssoc.G2PAssoc method)
set_subject() (dipper.models.assoc.Association.Assoc method)
set_version_by_date() (dipper.models.Dataset.Dataset method)
set_version_by_num() (dipper.models.Dataset.Dataset method)
setAuthorList() (dipper.models.Reference.Reference method)
setFileAccessUrl() (dipper.models.Dataset.Dataset method)
setShortCitation() (dipper.models.Reference.Reference method)
settestmode() (dipper.sources.Source.Source method)
settestonly() (dipper.sources.Source.Source method)
setTitle() (dipper.models.Reference.Reference method)
setType() (dipper.models.Reference.Reference method)
setVersion() (dipper.models.Dataset.Dataset method)
setYear() (dipper.models.Reference.Reference method)
SGD (class in dipper.sources.SGD)
SGD_BASE (dipper.sources.SGD.SGD attribute)
skolemizeBlankNode() (dipper.graph.Graph.Graph method)
(dipper.graph.RDFGraph.RDFGraph method)
(dipper.graph.StreamedGraph.StreamedGraph method)
Source (class in dipper.sources.Source)
species (dipper.sources.WormBase.WormBase attribute)
static_files (dipper.sources.CTD.CTD attribute)
StreamedGraph (class in dipper.graph.StreamedGraph)
STRING_BASE (dipper.sources.StringDB.StringDB attribute)
StringDB (class in dipper.sources.StringDB)
T
tables (dipper.sources.EOM.EOM attribute)
(dipper.sources.FlyBase.FlyBase attribute)
terms (dipper.models.assoc.OrthologyAssoc.OrthologyAssoc attribute)
(dipper.sources.Coriell.Coriell attribute)
(dipper.sources.GWASCatalog.GWASCatalog attribute)
test_graph_equality() (dipper.utils.TestUtils.TestUtils method)
test_ids (dipper.sources.AnimalQTLdb.AnimalQTLdb attribute)
(dipper.sources.IMPC.IMPC attribute)
(dipper.sources.KEGG.KEGG attribute)
(dipper.sources.MMRRC.MMRRC attribute)
(dipper.sources.MPD.MPD attribute)
(dipper.sources.OMIM.OMIM attribute)
(dipper.sources.WormBase.WormBase attribute)
(dipper.sources.ZFIN.ZFIN attribute)
test_keys (dipper.sources.FlyBase.FlyBase attribute)
(dipper.sources.MGI.MGI attribute)
test_lines (dipper.sources.Coriell.Coriell attribute)
TestUtils (class in dipper.utils.TestUtils)
toRoman() (in module dipper.utils.romanplus)
types (dipper.models.GenomicFeature.Feature attribute)
(dipper.models.Model.Model attribute)
U
UCSCBands (class in dipper.sources.UCSCBands)
UDP (class in dipper.sources.UDP)
UDP_SERVER (dipper.sources.UDP.UDP attribute)
update_wsnum_in_files() (dipper.sources.WormBase.WormBase method)
V
variant_ids (dipper.sources.ClinVar.ClinVar attribute)
W
wbdev (dipper.sources.WormBase.WormBase attribute)
wbprod (dipper.sources.WormBase.WormBase attribute)
wbrel (dipper.sources.WormBase.WormBase attribute)
whoami() (dipper.sources.Source.Source method)
WormBase (class in dipper.sources.WormBase)
write() (dipper.sources.Source.Source method)
(dipper.utils.GraphUtils.GraphUtils method)
write_molgen_report() (dipper.sources.OMIA.OMIA method)
Z
ZFIN (class in dipper.sources.ZFIN)
ZFINSlim (class in dipper.sources.ZFINSlim)
zygosity (dipper.models.Genotype.Genotype attribute)
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