Metadata-Version: 2.1
Name: BioClients
Version: 0.0.3
Summary: For access to online biomedical resources, usually via REST APIs.
Home-page: https://github.com/jeremyjyang/BioClients
Author: Jeremy Yang
Author-email: jeremyjyang@gmail.com
License: UNKNOWN
Description: # 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.
        
        ## Dependencies
        
        * Python3
        
        ## Modules
        
        `biogrid`, `brenda`, `chembl`, `diseaseontology`, `disgenet`, `dnorm`, `ensembl`, `fda`, `geneontology`, `gwascatalog`, `hugo`, `humanbase`, `icite`, `lincs`, `mesh`, `omim`, `opentargets`, `pdb`, `pubchem`, `pubmed`, `pubtator`, `reactome`, `rxnorm`, `stringdb`, `umls`, `uniprot`
        
        ## Usage
        
        ```
        $ python3 -m BioClients.stringdb.Client -h
        
        usage: Client.py [-h] [--id ID] [--ids IDS] [--idfile IDFILE] [--o OFILE]
                         [--species SPECIES] [--minscore MINSCORE]
                         [--netflavor {evidence,confidence,actions}]
                         [--imgfmt {image,highres_image,svg}] [--api_host API_HOST]
                         [--api_base_path API_BASE_PATH] [-v]
                         {getIds,getInteractionPartners,getNetwork,getNetworkImage,getEnrichment,getPPIEnrichment,getInteractors,getActions,getAbstracts}
        
        STRING-DB REST API client utility
        
        positional arguments:
          {getIds,getInteractionPartners,getNetwork,getNetworkImage,getEnrichment,getPPIEnrichment,getInteractors,getActions,getAbstracts}
                                operation
        
        optional arguments:
          -h, --help            show this help message and exit
          --id ID               protein ID (ex:DRD1_HUMAN)
          --ids IDS             protein IDs, comma-separated
          --idfile IDFILE       input file, protein IDs
          --o OFILE             output file
          --species SPECIES     taxon code, ex: 9606 (human)
          --minscore MINSCORE   signifcance threshold 0-1000
          --netflavor {evidence,confidence,actions}
                                network flavor
          --imgfmt {image,highres_image,svg}
                                image format
          --api_host API_HOST
          --api_base_path API_BASE_PATH
          -v, --verbose
        
        Example protein IDs: DRD1 DRD1_HUMAN DRD2 DRD2_HUMAN ; Example species: 9606 (human, via taxon identifiers, http://www.uniprot.org/taxonomy) ; Image formats: PNG PNG_highres SVG ; MAY BE DEPRECATED: getInteractors, getActions, getAbstracts
        ```
        
        ##  UMLS
        
        From the NIH National Library of Medicine (NLM).
        
        * Registration is required for both browser and API access.  See
        <https://www.nlm.nih.gov/research/umls/>. To use
        [BioClients.umls.Client](BioClients/umls/Client.py), create `~/.umls.yaml` with
        format:
        
        ```
        API_KEY: "===REPLACE-WITH-KEY-HERE==="
        ```
        
        ##  RxNorm
        
        From the NIH National Library of Medicine (NLM).
        
        * <https://www.nlm.nih.gov/research/umls/rxnorm/>
        
        ### Usage examples
        
        ```
        python3 -m BioClients.rxnorm.Client -h
        python3 -m BioClients.rxnorm.Client list_sourcetypes
        python3 -m BioClients.rxnorm.Client list_relationtypes
        python3 -m BioClients.rxnorm.Client list_termtypes
        python3 -m BioClients.rxnorm.Client list_propnames
        python3 -m BioClients.rxnorm.Client list_propcategories
        python3 -m BioClients.rxnorm.Client list_idtypes
        python3 -m BioClients.rxnorm.Client list_class_types
        python3 -m BioClients.rxnorm.Client list_classes
        python3 -m BioClients.rxnorm.Client list_classes --class_types 'MESHPA,ATC1-4'
        ```
        
        Requiring names:
        
        ```
        python3 -m BioClients.rxnorm.Client get_name --ids "prozac,tamiflu"
        python3 -m BioClients.rxnorm.Client get_name2rxcui --ids "prozac,tamiflu"
        ```
        
        Requiring external IDs:
        ```
        python3 -m BioClients.rxnorm.Client get_id2rxcui --ids "C2709711" --idtype UMLSCUI
        ```
        
        Requiring RxCUI IDs:
        ```
        python3 -m BioClients.rxnorm.Client get_rxcui_status --ids "131725,213269"
        python3 -m BioClients.rxnorm.Client get_rxcui_properties --ids "131725,213269"
        python3 -m BioClients.rxnorm.Client get_rxcui_ndcs --ids "131725,213269"
        python3 -m BioClients.rxnorm.Client get_rxcui_allrelated --ids "131725,213269"
        ```
        
        ##  MeSH
        
        From the NIH National Library of Medicine (NLM).
        Currently XML processing tools only.
        
        * <https://meshb.nlm.nih.gov/>
        
        ## PubChem
        
        Tools for obtaining and processing PubChem data (REST, SOAP, FTP).
        
        ```
        python3 -m BioClients.pubchem.Client --name remdesivir name2sid
        python3 -m BioClients.pubchem.Client --name remdesivir name2cid
        ```
        
        ## ChEMBL
        
        Tools for obtaining and processing ChEMBL data.
        
        * https://www.ebi.ac.uk/chembl/
        * https://chembl.gitbook.io/chembl-interface-documentation/web-services
        * https://chembl.gitbook.io/chembl-interface-documentation/downloads
        
        # PubMed, PubTator, iCite
        
        PubMed and related NIH literature resources.
        
        * (PubMed)[https://pubmed.ncbi.nlm.nih.gov/]
        * (iCite)[https://icite.od.nih.gov/]
        * (PubTator)[https://www.ncbi.nlm.nih.gov/research/pubtator/]
        
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
