Dipper
master
Installation
Getting started with Dipper
Notebooks
Downloads
Ingest status
Applications
Working with graphs
Working with the model API
Writing ingests with the source API
Testing ingests
Configuring dipper with keys and passwords
Schemas
API Docs
Source APIs
Dipper
Docs
»
Index
Edit on GitHub
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
|
Y
|
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_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_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)
Allele (class in dipper.models.ClinVarRecord)
allele_to_triples() (in module dipper.sources.ClinVar)
AnimalQTLdb (class in dipper.sources.AnimalQTLdb)
ARGV (dipper.sources.Source.Source attribute)
Assoc (class in dipper.models.assoc.Association)
B
Bgee (class in dipper.sources.Bgee)
bind_all_namespaces() (dipper.graph.RDFGraph.RDFGraph method)
BioGrid (class in dipper.sources.BioGrid)
biogrid_ids (dipper.sources.BioGrid.BioGrid attribute)
BioLinkVocabulary (class in dipper.models.BiolinkVocabulary)
bl_file_with_path (dipper.models.BiolinkVocabulary.BioLinkVocabulary attribute)
bl_vocab (dipper.models.BiolinkVocabulary.BioLinkVocabulary attribute)
build_measurement_description() (dipper.sources.MPD.MPD static method)
C
check_fileheader() (dipper.sources.Source.Source static method)
check_if_remote_is_newer() (dipper.sources.Bgee.Bgee method)
(dipper.sources.MyDrug.MyDrug method)
(dipper.sources.Source.Source method)
check_uniprot() (dipper.sources.MyChem.MyChem static method)
Chem2DiseaseAssoc (class in dipper.models.assoc.Chem2DiseaseAssoc)
chunks() (dipper.sources.MyChem.MyChem static method)
ClinVarRecord (class in dipper.models.ClinVarRecord)
column_labels (dipper.sources.Coriell.Coriell attribute)
columns (dipper.sources.Ensembl.Ensembl attribute)
command_args() (dipper.sources.Source.Source method)
compare_checksums() (dipper.sources.IMPC.IMPC method)
compare_graph_predicates() (dipper.utils.GraphUtils.GraphUtils static method)
compare_local_remote_bytes() (dipper.sources.Source.Source method)
Condition (class in dipper.models.ClinVarRecord)
conf (in module dipper.config)
Coriell (class in dipper.sources.Coriell)
count_predicates() (dipper.utils.GraphUtils.GraphUtils static method)
CTD (class in dipper.sources.CTD)
curie_map (dipper.graph.RDFGraph.RDFGraph attribute)
(dipper.graph.StreamedGraph.StreamedGraph attribute)
curie_regexp (dipper.graph.Graph.Graph attribute)
curie_util (dipper.graph.RDFGraph.RDFGraph attribute)
(dipper.graph.StreamedGraph.StreamedGraph attribute)
CurieUtil (class in dipper.utils.CurieUtil)
CURREL (dipper.sources.FlyBase.FlyBase attribute)
cytobandideo_columns (dipper.sources.UCSCBands.UCSCBands attribute)
D
D2PAssoc (class in dipper.models.assoc.D2PAssoc)
Dataset (class in dipper.models.Dataset)
default_species (dipper.sources.Bgee.Bgee attribute)
digest_id() (dipper.utils.GraphUtils.GraphUtils static method)
(in module dipper.sources.ClinVar)
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.G2PAssoc (module)
dipper.models.assoc.InteractionAssoc (module)
dipper.models.assoc.OrthologyAssoc (module)
dipper.models.BiolinkVocabulary (module)
dipper.models.ClinVarRecord (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.EBIGene2Phen (module)
dipper.sources.Ensembl (module)
dipper.sources.EOM (module)
dipper.sources.FlyBase (module)
dipper.sources.GeneOntology (module)
dipper.sources.GWASCatalog (module)
dipper.sources.HPOAnnotations (module)
dipper.sources.IMPC (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.Orphanet (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.Xenbase (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.rdf2dot (module)
dipper.utils.romanplus (module)
dipper.utils.TestUtils (module)
DIPPERCACHE (dipper.sources.Source.Source attribute)
DipperUtil (class in dipper.utils.DipperUtil)
E
EBI_BASE (dipper.sources.EBIGene2Phen.EBIGene2Phen attribute)
EBIGene2Phen (class in dipper.sources.EBIGene2Phen)
Ensembl (class in dipper.sources.Ensembl)
Environment (class in dipper.models.Environment)
EOM (class in dipper.sources.EOM)
Evidence (class in dipper.models.Evidence)
execute_query() (dipper.sources.MyChem.MyChem static method)
expand_curie() (in module dipper.sources.ClinVar)
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.Coriell.Coriell method)
(dipper.sources.EBIGene2Phen.EBIGene2Phen 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.HPOAnnotations.HPOAnnotations method)
(dipper.sources.IMPC.IMPC 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.Orphanet.Orphanet method)
(dipper.sources.Panther.Panther method)
(dipper.sources.PostgreSQLSource.PostgreSQLSource 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.Xenbase.Xenbase 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_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)
fhandle (dipper.graph.RDFGraph.RDFGraph attribute)
(dipper.graph.StreamedGraph.StreamedGraph attribute)
(dipper.sources.ZFIN.ZFIN attribute)
file_len() (dipper.sources.Source.Source static method)
files (dipper.sources.AnimalQTLdb.AnimalQTLdb attribute)
(dipper.sources.Bgee.Bgee attribute)
(dipper.sources.BioGrid.BioGrid attribute)
(dipper.sources.CTD.CTD attribute)
(dipper.sources.Coriell.Coriell attribute)
(dipper.sources.EBIGene2Phen.EBIGene2Phen 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.HPOAnnotations.HPOAnnotations attribute)
(dipper.sources.IMPC.IMPC attribute)
(dipper.sources.MMRRC.MMRRC attribute)
(dipper.sources.MPD.MPD attribute)
(dipper.sources.Monarch.Monarch attribute)
(dipper.sources.Monochrom.Monochrom attribute)
(dipper.sources.MyDrug.MyDrug attribute)
(dipper.sources.Orphanet.Orphanet attribute)
(dipper.sources.Panther.Panther attribute)
(dipper.sources.PostgreSQLSource.PostgreSQLSource 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.Xenbase.Xenbase attribute)
(dipper.sources.ZFIN.ZFIN attribute)
(dipper.sources.ZFINSlim.ZFINSlim attribute)
FlyBase (class in dipper.sources.FlyBase)
FLYFTP (dipper.sources.FlyBase.FlyBase attribute)
format_actions() (dipper.sources.MyChem.MyChem static method)
fromRoman() (in module dipper.utils.romanplus)
G
G2PAssoc (class in dipper.models.assoc.G2PAssoc)
gaf_columns (dipper.sources.GeneOntology.GeneOntology attribute)
Gene (class in dipper.models.ClinVarRecord)
gene_info_columns (dipper.sources.AnimalQTLdb.AnimalQTLdb attribute)
GENEINFO (dipper.sources.AnimalQTLdb.AnimalQTLdb attribute)
GeneOntology (class in dipper.sources.GeneOntology)
Genotype (class in dipper.models.ClinVarRecord)
(class in dipper.models.Genotype)
Genovar (class in dipper.models.ClinVarRecord)
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_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_drug_record() (dipper.sources.MyChem.MyChem static method)
get_file_md5() (dipper.sources.Source.Source static method)
get_files() (dipper.sources.Source.Source method)
get_graph() (dipper.models.Dataset.Dataset method)
get_hgnc_id_from_symbol() (dipper.utils.DipperUtil.DipperUtil static 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 static method)
get_ncbi_taxon_num_by_label() (dipper.utils.DipperUtil.DipperUtil static method)
get_orthology_evidence_code() (dipper.sources.ZFIN.ZFIN static method)
get_orthology_sources_from_zebrafishmine() (dipper.sources.ZFIN.ZFIN method)
get_properties_from_graph() (dipper.utils.GraphUtils.GraphUtils static method)
get_remote_content_len() (dipper.sources.Source.Source method)
get_uniprot_entrez_id_map() (dipper.sources.GeneOntology.GeneOntology method)
get_uri() (dipper.utils.CurieUtil.CurieUtil method)
getChrPartTypeByNotation() (in module dipper.sources.Monochrom)
getTestSuite() (dipper.sources.AnimalQTLdb.AnimalQTLdb method)
(dipper.sources.BioGrid.BioGrid method)
(dipper.sources.CTD.CTD method)
(dipper.sources.Coriell.Coriell method)
(dipper.sources.EOM.EOM method)
(dipper.sources.Ensembl.Ensembl method)
(dipper.sources.GeneOntology.GeneOntology method)
(dipper.sources.HPOAnnotations.HPOAnnotations method)
(dipper.sources.IMPC.IMPC method)
(dipper.sources.MMRRC.MMRRC method)
(dipper.sources.MPD.MPD method)
(dipper.sources.Monochrom.Monochrom method)
(dipper.sources.Panther.Panther method)
(dipper.sources.Source.Source method)
(dipper.sources.UCSCBands.UCSCBands method)
gff_columns (dipper.sources.AnimalQTLdb.AnimalQTLdb attribute)
GHRAW (dipper.sources.EOM.EOM attribute)
GITDIP (dipper.sources.AnimalQTLdb.AnimalQTLdb attribute)
globaltcid (dipper.graph.RDFGraph.RDFGraph attribute)
(dipper.graph.StreamedGraph.StreamedGraph attribute)
globaltt (dipper.graph.RDFGraph.RDFGraph attribute)
(dipper.graph.StreamedGraph.StreamedGraph attribute)
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.models.Dataset.Dataset static method)
(dipper.sources.Source.Source static method)
HGGP (dipper.sources.UCSCBands.UCSCBands attribute)
HPOAnnotations (class in dipper.sources.HPOAnnotations)
I
IMPC (class in dipper.sources.IMPC)
InteractionAssoc (class in dipper.models.assoc.InteractionAssoc)
is_id_in_mondo() (dipper.utils.DipperUtil.DipperUtil static method)
is_literal() (in module dipper.sources.ClinVar)
K
key (dipper.models.BiolinkVocabulary.BioLinkVocabulary attribute)
L
load_local_translationtable() (dipper.sources.Source.Source method)
M
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_biolink_category_triple() (in module dipper.sources.ClinVar)
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.models.Dataset.Dataset static method)
(dipper.sources.Source.Source static method)
make_parent_bands() (dipper.sources.Monochrom.Monochrom method)
make_reagent_targeted_gene_id() (dipper.sources.WormBase.WormBase static method)
make_spo() (in module dipper.sources.ClinVar)
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 static 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 static method)
makeLeader() (dipper.models.Model.Model method)
map_files (dipper.sources.EBIGene2Phen.EBIGene2Phen attribute)
(dipper.sources.UDP.UDP attribute)
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)
O
open_and_parse_yaml() (dipper.sources.Source.Source static method)
Orphanet (class in dipper.sources.Orphanet)
OrthologyAssoc (class in dipper.models.assoc.OrthologyAssoc)
P
Panther (class in dipper.sources.Panther)
panther_format (dipper.sources.Panther.Panther attribute)
parse() (dipper.sources.AnimalQTLdb.AnimalQTLdb method)
(dipper.sources.Bgee.Bgee method)
(dipper.sources.BioGrid.BioGrid method)
(dipper.sources.CTD.CTD method)
(dipper.sources.Coriell.Coriell method)
(dipper.sources.EBIGene2Phen.EBIGene2Phen 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.HPOAnnotations.HPOAnnotations method)
(dipper.sources.IMPC.IMPC 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.Orphanet.Orphanet method)
(dipper.sources.Panther.Panther method)
(dipper.sources.PostgreSQLSource.PostgreSQLSource 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.Xenbase.Xenbase method)
(dipper.sources.ZFIN.ZFIN method)
(dipper.sources.ZFINSlim.ZFINSlim method)
(in module dipper.sources.ClinVar)
parse_checksum_file() (dipper.sources.IMPC.IMPC method)
parse_mapping_file() (dipper.sources.Source.Source static method)
Pathway (class in dipper.models.Pathway)
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_catalog() (dipper.sources.GWASCatalog.GWASCatalog method)
process_common_disease_file() (dipper.sources.HPOAnnotations.HPOAnnotations method)
process_disease_association() (dipper.sources.WormBase.WormBase 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_measure_set() (in module dipper.sources.ClinVar)
process_mgi_note_allele_view() (dipper.sources.MGI.MGI method)
process_mgi_relationship_transgene_genes() (dipper.sources.MGI.MGI 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_xml_table() (dipper.sources.Source.Source method)
Provenance (class in dipper.models.Provenance)
Q
qtl_columns (dipper.sources.AnimalQTLdb.AnimalQTLdb attribute)
queries (dipper.sources.FlyBase.FlyBase attribute)
R
rdf2dot() (in module dipper.utils.rdf2dot)
RDFGraph (class in dipper.graph.RDFGraph)
Reactome (class in dipper.sources.Reactome)
REACTOME_BASE (dipper.sources.Reactome.Reactome attribute)
record_to_triples() (in module dipper.sources.ClinVar)
Reference (class in dipper.models.Reference)
remove_backslash_r() (dipper.sources.Source.Source static method)
remove_control_characters() (dipper.utils.DipperUtil.DipperUtil static method)
remove_ontology_axioms() (dipper.utils.TestUtils.TestUtils static method)
resolve() (dipper.sources.Source.Source method)
(in module dipper.sources.ClinVar)
resources (dipper.sources.EOM.EOM attribute)
(dipper.sources.MGI.MGI attribute)
return_target_list() (dipper.sources.MyChem.MyChem static method)
RGD (class in dipper.sources.RGD)
RGD_BASE (dipper.sources.RGD.RGD attribute)
S
scv_link() (in module dipper.sources.ClinVar)
serialize() (dipper.graph.Graph.Graph method)
(dipper.graph.RDFGraph.RDFGraph 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_description() (dipper.models.assoc.Association.Assoc method)
set_environment() (dipper.models.assoc.G2PAssoc.G2PAssoc method)
set_ingest_source() (dipper.models.Dataset.Dataset method)
set_ingest_source_file_version_date() (dipper.models.Dataset.Dataset method)
set_ingest_source_file_version_num() (dipper.models.Dataset.Dataset method)
set_ingest_source_file_version_retrieved_on() (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)
setAuthorList() (dipper.models.Reference.Reference 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)
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)
small_files (dipper.sources.HPOAnnotations.HPOAnnotations attribute)
Source (class in dipper.sources.Source)
species (dipper.sources.WormBase.WormBase attribute)
StreamedGraph (class in dipper.graph.StreamedGraph)
StringDB (class in dipper.sources.StringDB)
T
tables (dipper.sources.EOM.EOM attribute)
(dipper.sources.MGI.MGI attribute)
terms (dipper.models.BiolinkVocabulary.BioLinkVocabulary attribute)
test_graph_equality() (dipper.utils.TestUtils.TestUtils static method)
test_ids (dipper.sources.AnimalQTLdb.AnimalQTLdb attribute)
(dipper.sources.MMRRC.MMRRC attribute)
(dipper.sources.MPD.MPD attribute)
(dipper.sources.ZFIN.ZFIN attribute)
test_lines (dipper.sources.Coriell.Coriell attribute)
TestUtils (class in dipper.utils.TestUtils)
toRoman() (in module dipper.utils.romanplus)
trait_mapping_columns (dipper.sources.AnimalQTLdb.AnimalQTLdb attribute)
U
UCSCBands (class in dipper.sources.UCSCBands)
UDP (class in dipper.sources.UDP)
UDP_SERVER (dipper.sources.UDP.UDP attribute)
unknown_taxa (dipper.sources.MGI.MGI attribute)
update_wsnum_in_files() (dipper.sources.WormBase.WormBase method)
V
Variant (class in dipper.models.ClinVarRecord)
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)
wont_prefix (dipper.sources.GeneOntology.GeneOntology attribute)
WormBase (class in dipper.sources.WormBase)
write() (dipper.sources.Source.Source method)
(dipper.utils.GraphUtils.GraphUtils static method)
write_review_status_scores() (in module dipper.sources.ClinVar)
write_spo() (in module dipper.sources.ClinVar)
X
Xenbase (class in dipper.sources.Xenbase)
Y
yaml_file (dipper.models.BiolinkVocabulary.BioLinkVocabulary attribute)
Z
ZFIN (class in dipper.sources.ZFIN)
ZFINSlim (class in dipper.sources.ZFINSlim)
Read the Docs
v: master
Versions
master
latest
autodoc
Downloads
pdf
html
epub
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.