Metadata-Version: 2.1
Name: BioClients
Version: 0.1.3
Summary: Clients to online biomedical resources, usually REST APIs.
Home-page: https://github.com/jeremyjyang/BioClients
Author: Jeremy Yang
Author-email: jeremyjyang@gmail.com
License: UNKNOWN
Description: # `BioClients` <img align="right" src="/doc/images/BioClients_logo.png" height="120" alt="BioClients logo">
        
        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.
        
        ## 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`, `yaml`, `psycopg2`,  `tqdm`, etc.
        
        ## Modules
        
         [__Allen__](doc/allen.md) &#8226; [__AMP-T2D__](doc/amp__t2d.md) &#8226; [__BindingDb__](doc/bindingdb.md) &#8226; [__BioGrid__](doc/biogrid.md) &#8226; [__BRENDA__](doc/brenda.md) &#8226; [__CDC__](doc/cdc.md) &#8226;  [__Chem2Bio2RDF__](doc/chem2bio2rdf.md) &#8226;  [__ChEMBL__](doc/chembl.md) &#8226; [__Disease Ontology__](doc/diseaseontology.md) &#8226;  [__DisGeNet__](doc/disgenet.md) &#8226;  [__DNorm__](doc/dnorm.md) &#8226;  [__DrugCentral__](doc/drugcentral.md) &#8226;  [__EnsEMBL__](doc/ensembl.md) &#8226;  [__FDA__](doc/fda.md) &#8226;  [__Gene Ontology__](doc/geneontology.md) &#8226;  [__GWAS Catalog__](doc/gwascatalog.md) &#8226;  [__HUGO__](doc/hugo.md) &#8226;  [__HumanBase__](doc/humanbase.md) &#8226;  [__iCite__](doc/icite.md) &#8226;  [__IDG__](doc/idg.md) &#8226; [__JensenLab__](doc/jensenlab.md) &#8226; [__LINCS__](doc/lincs.md) &#8226; [__MaayanLab__](doc/maayanlab.md) &#8226; [__MeSH__](doc/mesh.md) &#8226; [__MONARCH__](doc/monarch.md)  &#8226; [__MyGene__](doc/mygene.md) &#8226;  [__OMIM__](doc/omim.md) &#8226;  [__Open Targets__](doc/opentargets.md) &#8226;  [__Panther__](doc/panther.md) &#8226;  [__PDB__](doc/pdb.md) &#8226;  [__PubChem__](doc/pubchem.md) &#8226;  [__PubMed__](doc/pubmed.md) &#8226;  [__PubTator__](doc/pubtator.md) &#8226;  [__Reactome__](doc/reactome.md) &#8226;  [__RXNorm__](doc/rxnorm.md) &#8226;  [__STRINGDB__](doc/stringdb.md) &#8226; [__TCGA__](doc/tcga.md) &#8226; &#8226; [__UMLS__](doc/umls.md) &#8226; [__UniProt__](doc/uniprot.md) &#8226; [__Wikidata__](doc/wikidata.md) &#8226; [__WikiPathways__](doc/wikipathways.md) 
        
        Miscellaneous utilities: [__UTIL__](doc/util.md) 
        
        ## 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.  Functions can write to an output file
        or return a Pandas dataframe.
        
        ## 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).
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
