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 CSV/TSV.
Availability and installation
Source at https://github.com/jeremyjyang/BioClients;
releases available via pypi.org:
https://pypi.org/project/BioClients/
(pip3 install BioClients).
However, current development snapshot recommended.
(First download or clone.)
$ cd BioClients
$ python3 setup.py install
Dependencies
- Python 3.6+
- Python packages:
pandas,requests,urllib,json,xml, etc.
Modules
AMP-T2D • BioGrid • BRENDA • Chem2Bio2RDF • ChEMBL • Disease Ontology • DisGeNet • DNorm • DrugCentral • EnsEMBL • FDA • Gene Ontology • GWAS Catalog • HUGO • HumanBase • iCite • IDG • JensenLab • LINCS • MaayanLab • MeSH • MONARCH • OMIM • Open Targets • Panther • PDB • PubChem • PubMed • PubTator • Reactome • RXNorm • STRINGDB • TCGA • TIN-X • UMLS • UniProt
Usage
$ python3 -m BioClients.pubchem.Client -h
Data structures and formats, XML, JSON, and CSV/TSV
BioClients is designed to be simple and practical, and XML, JSON and CSV/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. CSV/TSV represents tables of rows and columns, the relational db view, flattened as needed for many applications (e.g. ML) but related by common keys. Transforming REST JSON results to CSV/TSV, as these clients generally do, projects data structures to tables useful for many applications.
1 maintainer
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file BioClients-0.0.5.tar.gz.
File metadata
- Download URL: BioClients-0.0.5.tar.gz
- Upload date:
- Size: 137.0 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via:
twine/3.1.1 pkginfo/1.5.0.1 requests/2.23.0 setuptools/46.0.0 requests-toolbelt/0.9.1 tqdm/4.45.0 CPython/3.8.2
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
00aba902aadebbb51c71405e4bad0b55733dee0dc1a6513bcc2e307e037e497c
|
|
| MD5 |
a0a61215585a92d4170122db219a333d
|
|
| BLAKE2b-256 |
5d184ce01f85de1a43ef6bde2074b4c1ebc64adeb28ffd9f89e6e7ebdb2fd3b5
|
File details
Details for the file BioClients-0.0.5-py3-none-any.whl.
File metadata
- Download URL: BioClients-0.0.5-py3-none-any.whl
- Upload date:
- Size: 206.4 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via:
twine/3.1.1 pkginfo/1.5.0.1 requests/2.23.0 setuptools/46.0.0 requests-toolbelt/0.9.1 tqdm/4.45.0 CPython/3.8.2
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
ecc912f7057e06f36d959aa5507ed5b5fe014595427817f494b8fc50165e609c
|
|
| MD5 |
6c82910bc686139a5a31eb7b86bcdaee
|
|
| BLAKE2b-256 |
7440035a6f2c44a827131b8dda0e4df528615be9229f2bf8f222684dca1de394
|
