bioservices
main
1. Quick Start
2. Tutorials
3. Combining BioServices with external tools
4. Developer Guide
5. Gallery
6. NoteBooks
7. Utilities
8. Services
9. Applications and extra tools
10. References to BioServices on the Web
11. FAQS
12. Contributors
bioservices
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Index
A
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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
A
accession (FASTA property)
activeDBs (PSICQUIC 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)
attributes() (BioMart method)
B
BiGG (class in bioservices.bigg)
Biocontainers (class in bioservices.biocontainers)
BioDBNet (class in bioservices.biodbnet)
BioGRID (class in bioservices.biogrid)
BioMart (class in bioservices.biomart)
BioModels (class in bioservices.biomodels)
bioservices.apps.fasta
module
bioservices.apps.peptides
module
bioservices.bigg
module
bioservices.biocontainers
module
bioservices.biodbnet
module
bioservices.biogrid
module
bioservices.biomart
module
bioservices.biomodels
module
bioservices.chebi
module
bioservices.chembl
module
bioservices.cog
module
bioservices.dbfetch
module
bioservices.ena
module
bioservices.eutils
module
bioservices.hgnc
module
bioservices.intact
module
bioservices.kegg
module
bioservices.muscle
module
bioservices.mygeneinfo
module
bioservices.ncbiblast
module
bioservices.omnipath
module
bioservices.panther
module
bioservices.pathwaycommons
module
bioservices.pdb
module
bioservices.pdbe
module
bioservices.pride
module
bioservices.psicquic
module
bioservices.quickgo
module
bioservices.reactome
module
bioservices.rhea
module
bioservices.seqret
module
bioservices.services
module
bioservices.unichem
module
bioservices.uniprot
module
bioservices.wikipathway
module
bioservices.xmltools
module
BioServicesError
briteIds (KEGG property)
C
CACHING (Service property)
ChEBI (class in bioservices.chebi)
ChEMBL (class in bioservices.chembl)
clear_cache() (REST method)
code2Tnumber() (KEGG method)
COG (class in bioservices.cog)
compoundIds (KEGG property)
compounds2accession() (ChEMBL method)
configuration() (BioMart method)
content_types (REST attribute)
conv() (ChEBI method)
(KEGG method)
convert() (PSICQUIC method)
convertAll() (PSICQUIC 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
easyXML (class in bioservices.xmltools)
easyXML() (Service method)
easyXMLConversion (Service property)
ECitMatch() (EUtils method)
EFetch() (EUtils method)
EGQuery() (EUtils method)
EInfo() (EUtils method)
ELink() (EUtils method)
email (EUtils attribute)
ENA (class in bioservices.ena)
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)
F
FASTA (class in bioservices.apps.fasta)
fasta (FASTA property)
(MultiFASTA property)
fetch() (DBFetch method)
(HGNC method)
filters() (BioMart method)
find() (KEGG method)
findInteractions() (WikiPathways method)
findPathwaysByLiterature() (WikiPathways method)
findPathwaysByText() (WikiPathways method)
findPathwaysByXref() (WikiPathways method)
formats (PSICQUIC property)
G
gene_name (FASTA property)
gene_product_search() (QuickGO method)
genes() (BiGG method)
get() (KEGG method)
(PathwayCommons method)
get_about() (OmniPath method)
get_activity() (ChEMBL 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_assay() (ChEMBL 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_cell_line() (ChEMBL method)
get_chembl_id_lookup() (ChEMBL 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_() (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_orgnanism() (COG method)
get_cogs_by_taxon_id() (COG method)
get_complex_subunits() (Reactome method)
get_complexes() (Reactome 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_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)
get_entity_componentOf() (Reactome method)
get_entity_otherForms() (Reactome 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() (PDBe method)
get_functional_annotation() (PDBe method)
get_genes() (MyGeneInfo 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_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_interactions() (OmniPath 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_mapping() (Panther method)
get_mapping_identifier_pathways() (Reactome method)
get_mapping_identifier_reactions() (Reactome method)
get_mechanism() (ChEMBL method)
get_metabolism() (ChEMBL method)
get_metabolites() (Rhea method)
get_metadata() (MyGeneInfo method)
get_model() (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)
get_nmr_resources() (PDBe 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_organism() (ChEMBL method)
get_ortholog() (Panther 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_project() (PRIDE method)
get_project_files() (PRIDE method)
get_projects() (PRIDE method)
get_projects_count() (PRIDE method)
get_protein_class() (ChEMBL method)
get_protein_evidences() (PRIDE method)
get_ptms() (OmniPath method)
get_queries() (MyGeneInfo method)
get_references() (Reactome 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)
(Seqret method)
get_result_types() (MUSCLE method)
(NCBIblast method)
(Seqret method)
get_secondary_structure() (PDBe 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() (Biocontainers method)
(PRIDE method)
get_status() (ChEMBL method)
(MUSCLE method)
(NCBIblast method)
(Seqret method)
get_status_resources() (ChEMBL method)
get_structure() (UniChem method)
get_substructure() (ChEMBL method)
get_summary() (PDBe method)
get_supported_families() (Panther method)
get_supported_genomes() (Panther method)
get_sync() (REST 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() (MyGeneInfo method)
get_tissue() (ChEMBL method)
get_tools() (Biocontainers method)
get_tree_info() (Panther method)
get_versions_one_tool() (Biocontainers method)
get_xml() (BioMart method)
get_xref_source() (ChEMBL method)
getAllOntologyChildrenInPath() (ChEBI method)
getchildren() (easyXML method)
getColoredPathway() (WikiPathways method)
getCompleteEntity() (ChEBI method)
getCompleteEntityByList() (ChEBI method)
getCurationTags() (WikiPathways method)
getCurationTagsByName() (WikiPathways method)
getDirectOutputsForInput() (BioDBNet method)
getInputs() (BioDBNet method)
getInteractionCounter() (PSICQUIC method)
getLiteEntity() (ChEBI method)
getName() (PSICQUIC method)
getOntologyChildren() (ChEBI method)
getOntologyParents() (ChEBI method)
getOntologyTermsByPathway() (WikiPathways method)
getOutputsForInput() (BioDBNet method)
getPathway() (WikiPathways method)
getPathwayAs() (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)
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)
I
identifier (FASTA property)
ids (MultiFASTA property)
IntactComplex (class in bioservices.intact)
isOrganism() (KEGG method)
K
KEGG (class in bioservices.kegg)
KEGGParser (class in bioservices.kegg)
known_dbtypes (FASTA attribute)
knownName() (PSICQUIC method)
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)
mappingOneDB() (PSICQUIC method)
marts (BioMart property)
metabolites() (BiGG method)
models (BiGG property)
module
bioservices.apps.fasta
bioservices.apps.peptides
bioservices.bigg
bioservices.biocontainers
bioservices.biodbnet
bioservices.biogrid
bioservices.biomart
bioservices.biomodels
bioservices.chebi
bioservices.chembl
bioservices.cog
bioservices.dbfetch
bioservices.ena
bioservices.eutils
bioservices.hgnc
bioservices.intact
bioservices.kegg
bioservices.muscle
bioservices.mygeneinfo
bioservices.ncbiblast
bioservices.omnipath
bioservices.panther
bioservices.pathwaycommons
bioservices.pdb
bioservices.pdbe
bioservices.pride
bioservices.psicquic
bioservices.quickgo
bioservices.reactome
bioservices.rhea
bioservices.seqret
bioservices.services
bioservices.unichem
bioservices.uniprot
bioservices.wikipathway
bioservices.xmltools
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)
new_query() (BioMart 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)
post_one() (REST method)
postCleaning() (PSICQUIC method)
postCleaningAll() (PSICQUIC method)
preCleaning() (PSICQUIC method)
PRIDE (class in bioservices.pride)
print_status() (PSICQUIC method)
PSICQUIC (class in bioservices.psicquic)
pubmed() (Service method)
Q
query() (BioMart method)
(PSICQUIC method)
(Rhea method)
queryAll() (PSICQUIC 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)
read_registry() (PSICQUIC method)
readXML (class in bioservices.xmltools)
registry (PSICQUIC property)
registry() (BioMart method)
registry_actives (PSICQUIC property)
registry_counts (PSICQUIC property)
registry_names (PSICQUIC property)
registry_restexamples (PSICQUIC property)
registry_restricted (PSICQUIC property)
registry_resturls (PSICQUIC property)
registry_soapurls (PSICQUIC property)
registry_versions (PSICQUIC property)
removeCurationTag() (WikiPathways method)
response_codes (Service attribute)
REST (class in bioservices.services)
retrieve() (UniProt method)
Rhea (class in bioservices.rhea)
run() (MUSCLE method)
(NCBIblast 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() (BiGG method)
(BioModels 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_facet() (Reactome method)
search_facet_query() (Reactome method)
search_molecule() (ChEMBL method)
search_parameter() (BioModels method)
search_protein_class() (ChEMBL 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_entry() (KEGG method)
show_module() (KEGG method)
show_pathway() (KEGG method)
showPathwayInBrowser() (WikiPathways method)
snp_summary() (EUtils method)
soup (easyXML property)
supported_databases (DBFetch property)
SV (FASTA property)
T
taxonomy_summary() (EUtils method)
TIMEOUT (REST property)
(WSDLService 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)
(Service property)
V
valid_attributes (BioMart property)
valid_mapping (UniProt property)
version (BiGG property)
(Reactome property)
version() (BioMart method)
W
wait() (MUSCLE method)
(NCBIblast method)
WikiPathways (class in bioservices.wikipathway)
wsdl_create_factory() (WSDLService method)
wsdl_methods (WSDLService property)
wsdl_methods_info() (WSDLService method)
WSDLService (class in bioservices.services)
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