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A library for linking entities of biological knowledge bases.

Project description

biodblinker

A library for linking entities of biological knowledge bases.

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

Installing

pip install biodblinker

Installing from source

python setup.py

Usage

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)

Use Case - Linking uniprot proteins and mesh diseases via KEGG

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}')

Downloading mappings

When a biodblinker is initialized it verifies that all necessary mapping files are present and if not downloads the precompiled mappings

Building the mapping files

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>)

Mapping sources and licenses

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

Funding

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.

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