A library for linking entities of biological knowledge bases.
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
pip install biodblinker
python setup.py
from biodblinker import UniprotLinker
uniprot_linker = UniprotLinker()
# Get list of all included uniprot accessions
uniprot_accessions = uniprot_linker.uniprot_ids
select_accessions = ['P31946', 'P62258', 'Q04917']
# Get the list of names for each accession in select_accessions
select_names = uniprot_linker.convert_uniprot_to_names(select_accessions)
# Get the list of kegg gene ids for each accession in select_accessions
select_genes = uniprot_linker.convert_uniprot_to_kegg(select_accessions)import requests
from biodblinker import KEGGLinker
linker = KEGGLinker()
unique_pairs = set()
url = 'http://rest.kegg.jp/link/hsa/disease'
resp = requests.get(url)
if resp.ok:
for line in resp.iter_lines(decode_unicode=True):
kegg_disease, kegg_gene = line.strip().split('\t')
# strip the prefix from the disease
kegg_disease = kegg_disease.split(':')[1]
# prefix is retained for genes as the ids are numeric
uniprot_protein = linker.convert_geneid_to_uniprot([kegg_gene])
mesh_disease = linker.convert_disease_to_mesh([kegg_disease])
if len(uniprot_protein[0]) == 0:
continue
if len(mesh_disease[0]) == 0:
continue
for protein in uniprot_protein[0]:
for disease in mesh_disease[0]:
unique_pairs.add((protein, disease))
for protein, disease in unique_pairs:
print(f'{protein}\tRELATED_DISEASE\t{disease}')When a biodblinker is initialized it verifies that all necessary mapping files are present and if not downloads the precompiled mappings
It is also possible to generate the mappings from their sources
- Note this process will take several hours and requires a large ammount of disk space due to the size of the source files. The source files are removed once the mappings are generated
import biodblinker
gen = biodblinker.MappingGenerator()
gen.generate_mappings(<drugbank_username>, <drugbank_password>)BioDBLinker uses multiple sources to generate the mappings. BioDBLinker must be used in compliance with these licenses and citation policies where applicable
| Source Database | License Type | URL |
|---|---|---|
| UniProt | CC BY 4.0 | https://www.uniprot.org/help/license |
| Drugbank | CC BY NC 4.0 | https://www.drugbank.ca/legal/terms_of_use |
| KEGG | Custom | https://www.kegg.jp/kegg/legal.html |
| Sider | CC BY-NC-SA | http://sideeffects.embl.de/about/ |
| Stitch | CC BY 4.0 | http://stitch.embl.de/cgi/download.pl |
| HPA | CC BY SA 3.0 | https://www.proteinatlas.org/about/licence |
| Cellosaurus | CC BY 4.0 | https://web.expasy.org/cgi-bin/cellosaurus/faq#Q22 |
The development of this module has been fully supported by the CLARIFY project that has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 875160.