`bioclients`

Python package for access to online biomedical resources, usually via REST APIs. Modules generally include Client.py for command-line use and Utils.py for integration into other code. With the advent of HTTP web services, first SOAP/XML and then mostly REST/JSON, many online APIs require very similar methods for data search, requests and transforms into usable formats, often TSV.

Modules

Allen • AMP-T2D • Badapple • BindingDb • BioGrid • BiomarkerKB • Bioregistry • BRENDA • CAS • CDC • CFDE • Chem2Bio2RDF • ChEBI • ChEMBL • ChemIdPlus • ClinicalTrials.gov • Disease Ontology • DisGeNet • DNorm • DrugCentral • EMBL-EBI • EnsEMBL • Entrez • FDA • Gene Ontology • GTEx • GWAS Catalog • HUGO • HumanBase • iCite • IDG • JensenLab • LINCS • MaayanLab • Medline • MeSH • MONARCH • MyGene • NCBO • NCATS • OMIM • OncoTree • Open Targets • Panther • PDB • PubChem • PubMed • PubTator • Reactome • RXNorm • STRINGDB • TCGA • TINX • UBKG • UMLS • UniProt • Wikidata • WikiPathways

Miscellaneous utilities: UTIL

Dependencies

Python 3.10+
Python packages: pandas, requests, yaml, psycopg2, tqdm, sqlalchemy, pyquery, mygene, click, PyMuPDF, py2neo, etc.

Availability and installation

Installing from PyPI

Releases at https://pypi.org/project/bioclients/.

pip install bioclients

Venv environment

It may not be necessary or advantageous to configure an environment for all of bioclients functionality. Specific modules may be supported with venv environments with required dependencies. Module documentation should indicate needed package dependencies. The following steps should create an environment for much of the functionality of bioclients.

mkdir venv
python3 -m venv venv
source venv/bin/activate
pip install -r pip_requirements.txt
pip install --upgrade bioclients

Installing from source

Source at https://github.com/jeremyjyang/bioclients

git clone https://github.com/jeremyjyang/bioclients.git
cd bioclients
python3 -m pip install --upgrade build
python3 -m build

Usage Example

python3 -m bioclients.pubchem.Client -h

Design pattern

Generally each module includes command-line app Client.py which calls functions in a corresponding Utils.py, providing all capabilities by import of the module. Command-line apps not API clients are generally named App.py. Functions can write to an output file or return a Pandas dataframe (if output file unspecified).

Data structures and formats, XML, JSON, and TSV

bioclients is designed to be simple and practical, and XML, JSON and TSV are likewise simple in many respects, yet a great deal of conceptual and technological progress is reflected. XML and JSON can represent arbitrarily complex data objects, comprised of nested lists, dictionaries, and trees of primary types. TSV represents tables of rows and columns, related by common keys, reflecting the development of SQL and relational databases. Transforming JSON to TSV, as these clients generally do, projects data objects to tables useful for many applications (e.g. machine learning).

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