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BioClients.emblebi

EMBL-EBI

Tools for obtaining and processing data from EMBL-EBI resources. Some EMBL-EBI resources have separate BioClients modules.

Identifiers

Examples:

$ python3 -m BioClients.emblebi.identifiers.Client -h
usage: Client.py [-h] [--i IFILE] [--o OFILE] [--ids IDS] [--query QUERY]
                 [--resolver_api_host RESOLVER_API_HOST]
                 [--resolver_api_base_path RESOLVER_API_BASE_PATH]
                 [--registry_api_host REGISTRY_API_HOST]
                 [--registry_api_base_path REGISTRY_API_BASE_PATH]
                 [--search_logic {containing,exact}] [-v]
                 {resolve,list_namespaces,list_resources,list_institutions,search_namespaces,search_institutions,search_resources}

EMBL-EBI Identifiers.org client

positional arguments:
  {resolve,list_namespaces,list_resources,list_institutions,search_namespaces,search_institutions,search_resources}
                        OPERATION

optional arguments:
  -h, --help            show this help message and exit
  --i IFILE             Input IDs
  --o OFILE             Output (TSV)
  --ids IDS             Input IDs (comma-separated)
  --query QUERY         Search query.
  --resolver_api_host RESOLVER_API_HOST
  --resolver_api_base_path RESOLVER_API_BASE_PATH
  --registry_api_host REGISTRY_API_HOST
  --registry_api_base_path REGISTRY_API_BASE_PATH
  --search_logic {containing,exact}
  -v, --verbose

Example IDs: taxonomy:9606

Unichem

$ python3 -m BioClients.emblebi.unichem.Client -h
usage: Client.py [-h] [--i IFILE] [--o OFILE] [--ids IDS] [--src_id_in SRC_ID_IN]
                 [--src_id_out SRC_ID_OUT] [--api_host API_HOST]
                 [--api_base_path API_BASE_PATH] [-v]
                 {getFromSourceId,listSources,getFromInchi,getFromInchikey}

EMBL-EBI Unichem client

positional arguments:
  {getFromSourceId,listSources,getFromInchi,getFromInchikey}
                        OPERATION

optional arguments:
  -h, --help            show this help message and exit
  --i IFILE             Input IDs
  --o OFILE             Output (TSV)
  --ids IDS             Input IDs (comma-separated)
  --src_id_in SRC_ID_IN
  --src_id_out SRC_ID_OUT
  --api_host API_HOST
  --api_base_path API_BASE_PATH
  -v, --verbose

Sources on May 3, 2022:

src_id name name_label name_long
1 chembl ChEMBL ChEMBL
2 drugbank DrugBank DrugBank
3 pdb PDBe PDBe (Protein Data Bank Europe)
4 gtopdb Guide to Pharmacology Guide to Pharmacology
5 pubchem_dotf PubChem: Drugs of the Future PubChem ('Drugs of the Future' subset)
6 kegg_ligand KEGG Ligand KEGG (Kyoto Encyclopedia of Genes and Genomes) Ligand
7 chebi ChEBI ChEBI (Chemical Entities of Biological Interest).
8 nih_ncc NIH Clinical Collection NIH Clinical Collection
9 zinc ZINC ZINC
10 emolecules eMolecules eMolecules
12 atlas Atlas Gene Expression Atlas
14 fdasrs FDA SRS FDA/USP Substance Registration System (SRS)
15 surechembl SureChEMBL SureChEMBL
16 euos EU-OPENSCREEN EU-OPENSCREEN
17 pharmgkb PharmGKB PharmGKB
18 hmdb Human Metabolome Database Human Metabolome Database (HMDB)
19 wdi WDI WDI
20 selleck Selleck Selleck
21 pubchem_tpharma PubChem: Thomson Pharma PubChem ('Thomson Pharma' subset)
22 pubchem PubChem PubChem Compounds
23 mcule Mcule Mcule
24 nmrshiftdb2 NMRShiftDB NMRShiftDB
25 lincs LINCS Library of Integrated Network-based Cellular Signatures
26 actor ACToR ACToR
27 recon Recon Recon
28 molport MolPort MolPort
29 nikkaji Nikkaji Nikkaji
30 ncc NCC NCC
31 bindingdb BindingDB BindingDB
32 comptox EPA CompTox Dashboard EPA (Environmental Protection Agency) CompTox Dashboard
33 lipidmaps LipidMaps LipidMaps
34 drugcentral DrugCentral DrugCentral
35 carotenoiddb CarotenoidDB Carotenoid Database
36 metabolights Metabolights Metabolights
37 brenda Brenda Brenda
38 rhea Rhea Rhea
39 chemicalbook ChemicalBook ChemicalBook
40 dailymed_old DailyMed DailyMed
41 swisslipids SwissLipids SwissLipids
43 gsrs GSRS Global Substance Registration System
45 dailymed DailyMed DailyMed
46 clinicaltrials clinicaltrials clinicaltrials
47 rxnorm rxnorm rxnorm
48 MedChemExpress MedChemExpress MedChemExpress
81 jochem_id Jochem_ID Jochem_ID
82 jochem_cas Jochem_CAS Jochem_CAS
83 jochem_name Jochem_Name Jochem_Name