Index

A

accession (FASTA property) add_attribute_to_xml() (BioMart method) add_dataset_to_xml() (BioMart method) add_filter_to_xml() (BioMart method)

Annotation() (QuickGO method) Annotation_from_goid() (QuickGO method) ArrayExpress (class in bioservices.arrayexpress) attributes() (BioMart method)

B

BiGG (class in bioservices.bigg) Biocontainers (class in bioservices.biocontainers) BioDBNet (class in bioservices.biodbnet) BioMart (class in bioservices.biomart) BioModels (class in bioservices.biomodels) bioservices.apps.fasta module bioservices.apps.peptides module bioservices.arrayexpress module bioservices.bigg module bioservices.biocontainers module bioservices.biodbnet module bioservices.biomart module bioservices.biomodels module bioservices.chebi module bioservices.chembl module bioservices.cog module bioservices.dbfetch module bioservices.ena module bioservices.ensembl module bioservices.eutils module bioservices.eva module bioservices.geo module bioservices.hgnc module bioservices.intact module bioservices.interpro module

bioservices.kegg module bioservices.muscle module bioservices.mygeneinfo module bioservices.ncbiblast module bioservices.ncbiblastapi module bioservices.omnipath module bioservices.panther module bioservices.pathwaycommons module bioservices.pdb module bioservices.pdbe module bioservices.pfam module bioservices.pride module bioservices.pubchem module bioservices.quickgo module bioservices.reactome module bioservices.rhea module bioservices.seqret module bioservices.services module bioservices.string module bioservices.unichem module bioservices.uniprot module bioservices.wikipathway module BioServicesError briteIds (KEGG property)

C

CACHING (Service property) ChEBI (class in bioservices.chebi) check_nh_format() (Ensembl method) check_sequence() (Ensembl method) ChEMBL (class in bioservices.chembl) clear_cache() (REST method) code2Tnumber() (KEGG method) COG (class in bioservices.cog) COMPOUND_PROPERTIES (in module bioservices.pubchem)

compoundIds (KEGG property) compounds2accession() (ChEMBL method) configuration() (BioMart method) content_types (REST attribute) conv() (ChEBI method) (KEGG method) create_attribute() (BioMart method) create_filter() (BioMart method) createPathway() (WikiPathways method) custom_query() (BioMart method)

D

data_warehouse() (ENA method) databases (BioMart property) (EUtils property) (KEGG property) (NCBIblast property) datasets() (BioMart method) db2db() (BioDBNet method) DBFetch (class in bioservices.dbfetch) dbFind() (BioDBNet method) dbinfo() (KEGG method) dbOrtho() (BioDBNet method) dbReport() (BioDBNet method)

dbtype (FASTA property) dbWalk() (BioDBNet method) debug_message() (REST method) default_extension (PathwayCommons property) delete_cache() (REST method) delete_one() (REST method) details() (IntactComplex method) df (FASTA property) (MultiFASTA property) displayNames (BioMart property) download() (BiGG method) drugIds (KEGG property)

E

ECitMatch() (EUtils method) EFetch() (EUtils method) EGQuery() (EUtils method) EInfo() (EUtils method) ELink() (EUtils method) email (EUtils attribute) ENA (class in bioservices.ena) Ensembl (class in bioservices.ensembl) entry (FASTA property)

entry() (KEGG method) enzymeIds (KEGG property) EPost() (EUtils method) ESearch() (EUtils method) ESpell() (EUtils method) ESummary() (EUtils method) EUtils (class in bioservices.eutils) EUtilsParser (class in bioservices.eutils) EVA (class in bioservices.eva)

F

FASTA (class in bioservices.apps.fasta) fasta (FASTA property) (MultiFASTA property) fetch() (DBFetch method) (GEO method) (HGNC method)

fetch_allinfo() (EVA method) filters() (BioMart method) find() (KEGG method) findInteractions() (WikiPathways method) findPathwaysByLiterature() (WikiPathways method) findPathwaysByText() (WikiPathways method) findPathwaysByXref() (WikiPathways method)

G

gene_name (FASTA property) gene_product_search() (QuickGO method) genes() (BiGG method) GEO (class in bioservices.geo) get() (KEGG method) (PathwayCommons method) get_about() (OmniPath method) get_accession_info() (GEO method) get_activity() (ChEMBL method) get_aids_by_cid() (PubChem method) get_alignment_by_region() (Ensembl method) get_all_cogs_definition() (COG method) get_all_database_info() (DBFetch method) get_all_models() (BioModels method) get_all_src_ids() (UniChem method) get_annotation_datasets() (Panther method) get_approved_drugs() (ChEMBL method) get_archive() (Ensembl method) get_assay() (ChEMBL method) (PubChem method) get_assay_description() (PubChem method) get_assay_summary() (PubChem method) get_assembly() (PDBe method) get_async() (REST method) get_ATC() (ChEMBL method) get_binding_site() (ChEMBL method) get_binding_sites() (PDBe method) get_biotherapeutic() (ChEMBL method) get_branched_entities() (PDBe method) get_carbohydrate_polymer() (PDBe method) get_cell_line() (ChEMBL method) get_chembl_id_lookup() (ChEMBL method) get_cids_by_aid() (PubChem method) get_cids_by_formula() (PubChem method) get_cids_by_inchi() (PubChem method) get_cids_by_inchikey() (PubChem method) get_cids_by_name() (PubChem method) get_cids_by_sid() (PubChem method) get_cids_by_smiles() (PubChem method) get_cog_definition_by_cog_id() (COG method) get_cog_definition_by_name() (COG method) get_cogs() (COG method) get_cogs_by_assembly_id() (COG method) get_cogs_by_category() (COG method) get_cogs_by_category_id() (COG method) get_cogs_by_gene() (COG method) get_cogs_by_id() (COG method) get_cogs_by_id_and_category() (COG method) get_cogs_by_id_and_organism() (COG method) get_cogs_by_organism() (COG method) get_cogs_by_protein_name() (COG method) get_cogs_by_taxon_id() (COG method) get_complex_subunits() (Reactome method) get_complexes() (Reactome method) get_compound_by_cid() (PubChem method) get_compound_by_name() (PubChem method) get_compound_by_smiles() (PubChem method) get_compound_record() (ChEMBL method) get_compound_structural_alert() (ChEMBL method) get_compounds() (UniChem method) get_connectivity() (UniChem method) get_current_ids() (PDB method) get_data() (ENA method) get_database_format_styles() (DBFetch method) get_database_formats() (DBFetch method) get_database_info() (DBFetch method) get_datasets() (BioMart method) get_description() (PubChem method) get_df() (UniProt method) get_discover() (Reactome method) get_diseases() (Reactome method) get_diseases_doid() (Reactome method) get_document() (ChEMBL method) get_document_similarity() (ChEMBL method) get_document_term() (ChEMBL method) get_drug() (ChEMBL method) get_drug_indication() (ChEMBL method) get_drugbank_annotation() (PDBe method) get_electron_density_statistics() (PDBe method) get_enrichment() (Panther method) (STRING method) get_entities() (PDBe method) get_entity_componentOf() (Reactome method) get_entity_otherForms() (Reactome method) get_entries() (InterPro method) get_entries_by_member_database() (InterPro method) get_entries_by_type() (InterPro method) get_entry() (InterPro method) get_entry_proteomes() (InterPro method) get_entry_structures() (InterPro method) get_entry_taxonomy() (InterPro method) get_event_ancestors() (Reactome method) get_eventsHierarchy() (Reactome method) get_experiment() (PDBe method) get_exporter_diagram() (Reactome method) get_exporter_fireworks() (Reactome method) get_exporter_reaction() (Reactome method) get_exporter_sbml() (Reactome method) get_family_msa() (Panther method) get_family_ortholog() (Panther method) get_fasta() (FASTA method) (UniProt method) get_fasta_sequence() (Peptides method) get_files() (ArrayExpress method) (PDBe method) get_functional_annotation() (PDBe method) (STRING method) get_genes() (MyGeneInfo method) get_genetree_by_id() (Ensembl method) get_genetree_by_member_id() (Ensembl method) get_genetree_by_member_symbol() (Ensembl method) get_geo_datasets() (GEO method) get_geo_platforms() (GEO method) get_geo_samples() (GEO method) get_geo_series() (GEO method) get_go_ancestors() (QuickGO method) get_go_chart() (QuickGO method) get_go_children() (QuickGO method) get_go_paths() (QuickGO method) get_go_slim() (ChEMBL method) get_go_terms() (QuickGO method) get_headers() (REST method) get_homolog_position() (Panther method) get_homology() (STRING method) get_homology_by_species_and_id() (Ensembl method) get_homology_by_symbol() (Ensembl method) get_id_from_name() (UniChem method) get_image() (ChEMBL method) get_images() (UniChem method) get_inchi_from_inchikey() (UniChem method) get_info() (HGNC method) (OmniPath method) get_info_analysis() (Ensembl method) get_info_assembly() (Ensembl method) get_info_assembly_by_region() (Ensembl method) get_info_biotypes() (Ensembl method) get_info_compara_by_method() (Ensembl method) get_info_compara_methods() (Ensembl method) get_info_comparas() (Ensembl method) get_info_data() (Ensembl method) get_info_external_dbs() (Ensembl method) get_info_ping() (Ensembl method) get_info_rest() (Ensembl method) get_info_software() (Ensembl method) get_info_species() (Ensembl method) get_interaction_partners() (STRING method) get_interactions() (OmniPath method) (STRING method) get_interactors_psicquic_molecule_details() (Reactome method) get_interactors_psicquic_molecule_summary() (Reactome method) get_interactors_psicquic_resources() (Reactome method) get_interactors_static_molecule_details() (Reactome method) get_interactors_static_molecule_pathways() (Reactome method) get_interactors_static_molecule_summary() (Reactome method) get_ligand_monomers() (PDBe method) get_lookup_by_id() (Ensembl method) get_lookup_by_symbol() (Ensembl method) get_map_assembly_one_to_two() (Ensembl method) get_map_cdna_to_region() (Ensembl method) get_map_cds_to_region() (Ensembl method) get_map_translation_to_region() (Ensembl method) get_mapping() (Panther method) get_mapping_identifier_pathways() (Reactome method) get_mapping_identifier_reactions() (Reactome method) get_mechanism() (ChEMBL method) get_member_database_entry() (InterPro method) get_metabolism() (ChEMBL method) get_metabolites() (Rhea method) get_metadata() (MyGeneInfo method) get_model() (BiGG method) (BioModels method) get_model_download() (BioModels method) get_model_files() (BioModels method)

get_modified_residues() (PDBe method) get_molecule() (ChEMBL method) get_molecule_form() (ChEMBL method) get_molecules() (PDBe method) get_mutated_residues() (PDBe method) get_network() (OmniPath method) (STRING method) get_observed_ranges() (PDBe method) get_observed_ranges_in_pdb_chain() (PDBe method) get_observed_residues_ratio() (PDBe method) get_one() (REST method) get_one_gene() (MyGeneInfo method) get_one_query() (MyGeneInfo method) get_ontology_ancestors_by_id() (Ensembl method) get_ontology_ancestors_chart_by_id() (Ensembl method) get_ontology_by_id() (Ensembl method) get_ontology_by_name() (Ensembl method) get_ontology_descendants_by_id() (Ensembl method) get_organism() (ChEMBL method) get_ortholog() (Panther method) get_overlap_by_id() (Ensembl method) get_overlap_by_region() (Ensembl method) get_overlap_by_translation() (Ensembl method) get_p2m_missing() (BioModels method) get_p2m_representative() (BioModels method) get_p2m_representatives() (BioModels method) get_parameter_details() (MUSCLE method) (NCBIblast method) (Seqret method) get_parameters() (MUSCLE method) (NCBIblast method) (Seqret method) get_pathway_by_gene() (KEGG method) get_pathway_containedEvents() (Reactome method) get_pathway_containedEvents_by_attribute() (Reactome method) get_pathways() (Panther method) get_pathways_low_diagram_entity() (Reactome method) get_pathways_low_diagram_entity_allForms() (Reactome method) get_pathways_low_entity() (Reactome method) get_pathways_low_entity_allForms() (Reactome method) get_pathways_top() (Reactome method) get_pdgsmm_missing() (BioModels method) get_pdgsmm_representative() (BioModels method) get_pdgsmm_representatives() (BioModels method) get_peptide_evidence() (PRIDE method) get_phosphosite_position() (Peptides method) get_ppi_enrichment() (STRING method) get_project() (PRIDE method) get_project_files() (PRIDE method) get_projects() (PRIDE method) get_projects_count() (PRIDE method) get_properties() (PubChem method) get_protein() (InterPro method) (Pfam method) get_protein_entries() (InterPro method) get_protein_evidences() (PRIDE method) get_proteins_by_entry() (InterPro method) get_proteome() (InterPro method) get_ptms() (OmniPath method) get_publications() (PDBe method) get_queries() (MyGeneInfo method) get_references() (Reactome method) get_regulatory_by_id() (Ensembl method) get_related_dataset() (PDBe method) get_related_publications() (PDBe method) get_release_status() (PDBe method) get_residue_listing() (PDBe method) get_residue_listing_in_pdb_chain() (PDBe method) get_resources() (OmniPath method) get_result() (MUSCLE method) (NCBIblast method) (NCBIBlastAPI method) (Seqret method) get_result_types() (MUSCLE method) (NCBIblast method) (Seqret method) get_secondary_structure() (PDBe method) get_sequence_by_id() (Ensembl method) get_sequence_by_region() (Ensembl method) get_set() (InterPro method) get_sids_by_aid() (PubChem method) get_sids_by_cid() (PubChem method) get_sifgraph_common_stream() (PathwayCommons method) get_sifgraph_neighborhood() (PathwayCommons method) get_sifgraph_pathsbetween() (PathwayCommons method) get_sifgraph_pathsfromto() (PathwayCommons method) get_similarity() (ChEMBL method) get_similarity_sequence() (PDB method) get_source() (ChEMBL method) get_source_info_by_id() (UniChem method) get_source_info_by_name() (UniChem method) get_sources() (UniChem method) get_sources_by_inchikey() (UniChem method) get_sources_by_inchikey_verbose() (UniChem method) get_species_all() (Reactome method) get_species_main() (Reactome method) get_stats() (PRIDE method) get_status() (ChEMBL method) (MUSCLE method) (NCBIblast method) (NCBIBlastAPI method) (Seqret method) get_status_resources() (ChEMBL method) get_string_ids() (STRING method) get_structure() (InterPro method) (UniChem method) get_study() (ArrayExpress method) get_substance_by_sid() (PubChem method) get_substructure() (ChEMBL method) get_summary() (GEO method) (PDBe method) get_supported_families() (Panther method) get_supported_genomes() (Panther method) get_sync() (REST method) get_synonyms() (PubChem method) get_target() (ChEMBL method) get_target_component() (ChEMBL method) get_target_prediction() (ChEMBL method) get_target_relation() (ChEMBL method) get_taxon() (ENA method) get_taxon_id() (Panther method) get_taxonomic_categories() (COG method) get_taxonomic_category_by_name() (COG method) get_taxonomy() (InterPro method) (MyGeneInfo method) get_taxonomy_by_id() (Ensembl method) get_taxonomy_by_name() (Ensembl method) get_taxonomy_classification_by_id() (Ensembl method) get_tissue() (ChEMBL method) get_tool() (Biocontainers method) get_tool_classes() (Biocontainers method) get_tool_version() (Biocontainers method) get_tool_versions() (Biocontainers method) get_tools() (Biocontainers method) get_tree_info() (Panther method) get_variation_by_id() (Ensembl method) get_vep_by_id() (Ensembl method) get_vep_by_region() (Ensembl method) get_version() (STRING method) get_versions_one_tool() (Biocontainers method) get_xml() (BioMart method) get_xref_source() (ChEMBL method) get_xrefs() (PubChem method) get_xrefs_by_id() (Ensembl method) get_xrefs_by_name() (Ensembl method) get_xrefs_by_symbol() (Ensembl method) getAE() (ArrayExpress method) getAllOntologyChildrenInPath() (ChEBI method) getColoredPathway() (WikiPathways method) getCompleteEntity() (ChEBI method) getCompleteEntityByList() (ChEBI method) getCurationTags() (WikiPathways method) getCurationTagsByName() (WikiPathways method) getDirectOutputsForInput() (BioDBNet method) getInputs() (BioDBNet method) getLiteEntity() (ChEBI method) getOntologyChildren() (ChEBI method) getOntologyParents() (ChEBI method) getOntologyTermsByPathway() (WikiPathways method) getOutputsForInput() (BioDBNet method) getPathway() (WikiPathways method) getPathwayHistory() (WikiPathways method) getPathwayInfo() (WikiPathways method) getPathwaysByOntologyTerm() (WikiPathways method) getPathwaysByParentOntologyTerm() (WikiPathways method) getRecentChanges() (WikiPathways method) getStructureSearch() (ChEBI method) getUpdatedPolymer() (ChEBI method) getUserAgent() (REST method) getXrefList() (WikiPathways method) glycanIds (KEGG property) go_search() (QuickGO method) graph() (PathwayCommons method)

H

header (FASTA property) help() (EUtils method) HGNC (class in bioservices.hgnc) hist_size() (MultiFASTA method) host (BioMart property)

hosts (BioMart property) http_delete() (REST method) http_get() (REST method) http_post() (REST method) HTTPResponseError (class in bioservices.services)

I

identifier (FASTA property) ids (MultiFASTA property) IntactComplex (class in bioservices.intact)

InterPro (class in bioservices.interpro) isOrganism() (KEGG method) items() (HTTPResponseError method)

K

KEGG (class in bioservices.kegg) KEGGParser (class in bioservices.kegg)

keys() (HTTPResponseError method) known_dbtypes (FASTA attribute) koIds (KEGG property)

L

link() (KEGG method) list() (KEGG method) listOrganisms() (WikiPathways method) listPathways() (WikiPathways method) load() (FASTA method)

load_fasta() (FASTA method) (MultiFASTA method) login() (WikiPathways method) lookfor() (BioMart method) lookfor_organism() (KEGG method) lookfor_pathway() (KEGG method)

M

mapping() (UniProt method) marts (BioMart property) metabolites() (BiGG method) models (BiGG property) module bioservices.apps.fasta bioservices.apps.peptides bioservices.arrayexpress bioservices.bigg bioservices.biocontainers bioservices.biodbnet bioservices.biomart bioservices.biomodels bioservices.chebi bioservices.chembl bioservices.cog bioservices.dbfetch bioservices.ena bioservices.ensembl bioservices.eutils bioservices.eva bioservices.geo bioservices.hgnc bioservices.intact bioservices.interpro bioservices.kegg bioservices.muscle bioservices.mygeneinfo bioservices.ncbiblast bioservices.ncbiblastapi bioservices.omnipath bioservices.panther bioservices.pathwaycommons bioservices.pdb bioservices.pdbe bioservices.pfam bioservices.pride bioservices.pubchem bioservices.quickgo bioservices.reactome bioservices.rhea bioservices.seqret bioservices.services bioservices.string bioservices.unichem bioservices.uniprot bioservices.wikipathway

moduleIds (KEGG property) MultiFASTA (class in bioservices.apps.fasta) MUSCLE (class in bioservices.muscle) MyGeneInfo (class in bioservices.mygeneinfo)

N

name (FASTA property) (Reactome property) names (BioMart property)

NCBIblast (class in bioservices.ncbiblast) NCBIBlastAPI (class in bioservices.ncbiblastapi) new_query() (BioMart method) nh_format_to_frmt() (Ensembl method)

O

OmniPath (class in bioservices.omnipath) on_web() (Service method) order_by() (ChEMBL method) organism (FASTA property) (KEGG property) (WikiPathways property)

organismIds (KEGG property) organisms (WikiPathways attribute) organismTnumbers (KEGG property)

P

Panther (class in bioservices.panther) parameters (MUSCLE property) (NCBIblast property) (Seqret property) parse() (KEGG method) (KEGGParser method) parse_kgml_pathway() (KEGG method) parse_xml() (EUtils method) pathway2sif() (KEGG method) PathwayCommons (class in bioservices.pathwaycommons) pathwayIds (KEGG property) PDB (class in bioservices.pdb)

PDBe (class in bioservices.pdbe) PE (FASTA property) Peptides (class in bioservices.apps.peptides) Pfam (class in bioservices.pfam) post_archive() (Ensembl method) post_lookup_by_id() (Ensembl method) post_lookup_by_symbol() (Ensembl method) post_one() (REST method) post_vep_by_id() (Ensembl method) post_vep_by_region() (Ensembl method) PRIDE (class in bioservices.pride) PubChem (class in bioservices.pubchem) pubmed() (Service method)

Q

query() (BioMart method) (Rhea method) queryAE() (ArrayExpress method)

queryExperiments() (ArrayExpress method) queryFiles() (ArrayExpress method) quick_search() (UniProt method) QuickGO (class in bioservices.quickgo)

R

reactionIds (KEGG property) reactions() (BiGG method) Reactome (class in bioservices.reactome) read_fasta() (FASTA method) (MultiFASTA method) reason (HTTPResponseError attribute) registry() (BioMart method) removeCurationTag() (WikiPathways method) response_codes (Service attribute) REST (class in bioservices.services)

retrieve() (UniProt method) retrieve_file() (ArrayExpress method) retrieveExperiment() (ArrayExpress method) retrieveFile() (ArrayExpress method) retrieveFilesFromExperiment() (ArrayExpress method) Rhea (class in bioservices.rhea) run() (MUSCLE method) (NCBIblast method) (NCBIBlastAPI method) (Seqret method)

S

save_fasta() (FASTA method) (MultiFASTA method) save_pathway() (KEGG method) save_str_to_image() (Service method) saveCurationTag() (WikiPathways method) savePathwayAs() (WikiPathways method) search() (ArrayExpress method) (BiGG method) (BioModels method) (GEO method) (HGNC method) (IntactComplex method) (PathwayCommons method) (PDB method) (Rhea method) (UniProt method) search_activity() (ChEMBL method) search_assay() (ChEMBL method) search_chembl_id_lookup() (ChEMBL method) search_document() (ChEMBL method) search_download() (BioModels method) search_entries() (InterPro method)

search_facet() (Reactome method) search_facet_query() (Reactome method) search_molecule() (ChEMBL method) search_organism() (COG method) search_parameter() (BioModels method) search_query() (Reactome method) search_spellcheck() (Reactome method) search_suggest() (Reactome method) search_target() (ChEMBL method) Seqret (class in bioservices.seqret) sequence (FASTA property) Service (class in bioservices.services) session (REST property) show() (Pfam method) show_entry() (KEGG method) show_module() (KEGG method) show_pathway() (KEGG method) showPathwayInBrowser() (WikiPathways method) snp_summary() (EUtils method) status_code (HTTPResponseError attribute) STRING (class in bioservices.string) supported_databases (DBFetch property) SV (FASTA property)

T

taxonomy_summary() (EUtils method) TIMEOUT (REST property)

Tnumber2code() (KEGG method) top_pathways() (PathwayCommons method) traverse() (PathwayCommons method)

U

UniChem (class in bioservices.unichem) UniProt (class in bioservices.uniprot) uniref() (UniProt method)

updatePathway() (WikiPathways method) url (ENA attribute) (HTTPResponseError attribute) (Service property)

V

valid_attributes (BioMart property) valid_mapping (UniProt property) values() (HTTPResponseError method)

version (BiGG property) (Reactome property) version() (BioMart method)

W

wait() (MUSCLE method) (NCBIblast method) (NCBIBlastAPI method)

WikiPathways (class in bioservices.wikipathway)

X

XREF_TYPES (in module bioservices.pubchem)