get_organisms.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

"""
Fetch the set of currently supported organism names and ids
"""

import requests
import json
from core import config as cfg

request_url = cfg.BASE_URL + "/organisms"

# These parameters can be modified to match any search criteria following
# the rules outlined in the Wiki: https://wiki.thebiogrid.org/doku.php/biogridrest
# In this particular instance, we've chosen just the format to use in json
params = {"accesskey": cfg.ACCESS_KEY, "format": "json"}

r = requests.get(request_url, params=params)
organisms = r.json()

# Pretty print out the results
print(json.dumps(organisms, indent=4, sort_keys=True))

""" 
Expected Output as of version 4.0:
{
    "10029": "Cricetulus griseus",
    "10090": "Mus musculus",
    "10116": "Rattus norvegicus",
    "10141": "Cavia porcellus",
    "10160": "Octodon degus",
    "10181": "Heterocephalus glaber",
    "10228": "Trichoplax adhaerens",
    "10245": "Vaccinia Virus",
    "10298": "Human Herpesvirus 1",
    "10310": "Human Herpesvirus 2",
    "10335": "Human Herpesvirus 3",
    "10359": "Human Herpesvirus 5",
    "10366": "Murid Herpesvirus 1",
    "10372": "Human Herpesvirus 7",
    "10376": "Human Herpesvirus 4",
    "10589": "Human papillomavirus (41)",
    "10600": "Human papillomavirus (6b)",
    "10616": "Human papillomavirus (49)",
    "10617": "Human papillomavirus (4)",
    "10620": "Human papillomavirus (7)",
    "10621": "Human papillomavirus (9)",
    "10633": "Simian Virus 40",
    "11103": "Hepatitus C Virus",
    "1140": "Synechococcus elongatus (PCC7942)",
    "11676": "Human Immunodeficiency Virus 1",
    "11709": "Human Immunodeficiency Virus 2",
    "11723": "Simian Immunodeficiency Virus",
    "121224": "Pediculus humanus",
    "12242": "Tobacco Mosaic Virus",
    "1304279": "Mycobacterium tuberculosis (Haarlem/NITR202)",
    "1310114": "Mycobacterium tuberculosis (CAS/NITR204)",
    "1335626": "Middle-East Respiratory Syndrome-related Coronavirus",
    "13616": "Monodelphis domestica",
    "13735": "Pelodiscus sinensis",
    "15368": "Brachypodium distachyon",
    "170187": "Streptococcus pneumoniae (ATCCBAA334)",
    "171101": "Streptococcus pneumoniae (ATCCBAA255)",
    "180454": "Anopheles gambiae (PEST)",
    "185453": "Chrysochloris asiatica",
    "224308": "Bacillus subtilis (168)",
    "227321": "Emericella nidulans (FGSC A4)",
    "237561": "Candida albicans (SC5314)",
    "237631": "Ustilago maydis (521)",
    "246197": "Myxococcus xanthus (DK1622)",
    "246437": "Tupaia chinensis",
    "269084": "Synechococcus elongatus (PCC6301)",
    "2697049": "Severe acute respiratory syndrome coronavirus 2",
    "272634": "Mycoplasma pneumoniae (M129)",
    "27679": "Saimiri boliviensis",
    "28311": "Human papillomavirus (63)",
    "28377": "Anolis carolinensis",
    "284812": "Schizosaccharomyces pombe (972h)",
    "28737": "Elephantulus edwardii",
    "29073": "Ursus maritimus",
    "29760": "Vitis vinifera",
    "30538": "Vicugna pacos",
    "3055": "Chlamydomonas reinhardtii",
    "30611": "Otolemur garnettii",
    "31033": "Takifugu rubripes",
    "31234": "Caenorhabditis remanei",
    "316385": "Escherichia coli (K12/DH10B)",
    "316407": "Escherichia coli (K12/W3110)",
    "3218": "Physcomitrella patens",
    "32603": "Human Herpesvirus 6A",
    "32604": "Human Herpesvirus 6B",
    "333759": "Human papillomavirus (10)",
    "333760": "Human papillomavirus (16)",
    "333762": "Human papillomavirus (26)",
    "333763": "Human papillomavirus (32)",
    "333764": "Human papillomavirus (34)",
    "333766": "Human papillomavirus (54)",
    "333923": "Human papillomavirus (5)",
    "347515": "Leishmania major (Friedlin)",
    "34839": "Chinchilla lanigera",
    "352472": "Dictyostelium discoideum (AX4)",
    "362242": "Mycobacterium ulcerans (AGY99)",
    "36329": "Plasmodium falciparum (3D7)",
    "3641": "Theobroma cacao",
    "3659": "Cucumis sativus",
    "367110": "Neurospora crassa (OR74A)",
    "3694": "Populus trichocarpa",
    "3702": "Arabidopsis thaliana (Columbia)",
    "3711": "Bassica campestris",
    "37296": "Human Herpesvirus 8",
    "3750": "Malus domestica",
    "3760": "Prunus persica",
    "3847": "Glycine max",
    "3880": "Medicago truncatula",
    "3885": "Phaseolus vulgaris",
    "3988": "Ricinus communis",
    "39947": "Oryza sativa (Japonica)",
    "400682": "Amphimedon queenslandica",
    "403677": "Phytophthora infestans (T30-4)",
    "40538": "Human papillomavirus (48)",
    "407148": "Campylobacter jejuni (81116)",
    "4081": "Solanum lycopersicum",
    "4096": "Nicotiana sylvestris",
    "4097": "Nicotiana tabacum",
    "4098": "Nicotiana tomentosiformis",
    "4113": "Solanum tuberosum",
    "419947": "Mycobacterium tuberculosis (H37Ra)",
    "42254": "Sorex araneus",
    "43179": "Ictidomys tridecemlineatus",
    "44689": "Dictyostelium discoideum",
    "45351": "Nematostella vectensis",
    "4555": "Setaria italica",
    "4558": "Sorghum bicolor",
    "4577": "Zea mays",
    "4641": "Musa acuminata",
    "4754": "Pneumocystis carinii",
    "4787": "Phytophthora infestans",
    "482537": "Galeopterus variegatus",
    "48698": "Poecilia formosa",
    "487213": "Streptococcus pneumoniae (Taiwan19F-14)",
    "487214": "Streptococcus pneumoniae (Hungary 19A-6)",
    "488221": "Streptococcus pneumoniae (70585)",
    "488222": "Streptococcus pneumoniae (JJA)",
    "488223": "Streptococcus pneumoniae (P1031)",
    "511145": "Escherichia coli (K12/MG1655)",
    "512566": "Streptococcus pneumoniae (G54)",
    "516950": "Streptococcus pneumoniae (CGSP14)",
    "525381": "Streptococcus pneumoniae (TCH8431)",
    "559292": "Saccharomyces cerevisiae (S288c)",
    "561276": "Streptococcus pneumoniae (ATCC700669)",
    "59463": "Myotis lucifugus",
    "59538": "Pantholops hodgsonii",
    "595496": "Escherichia coli (K12/MC4100/BW2952)",
    "59729": "Taeniopygia guttata",
    "59894": "Ficedula albicollis",
    "60711": "Chlorocebus sabaeus",
    "61622": "Rhinopithecus roxellana",
    "6183": "Schistosoma mansoni",
    "61853": "Nomascus leucogenys",
    "6238": "Caenorhabditis briggsae",
    "6239": "Caenorhabditis elegans",
    "652616": "Mycobacterium tuberculosis (Erdman/35801)",
    "694009": "Severe acute respiratory syndrome coronavirus",
    "6945": "Ixodes scapularis",
    "694581": "Marseillevirus marseillevirus",
    "7029": "Acyrthosiphon pisum",
    "71139": "Eucalyptus grandis",
    "7159": "Aedes aegypti",
    "7165": "Anopheles gambiae",
    "7176": "Culex quinquefasciatus",
    "7209": "Loa loa",
    "7227": "Drosophila melanogaster",
    "7234": "Drosophila persimilis",
    "7238": "Drosophila sechellia",
    "7245": "Drosophila yakuba",
    "73337": "Ceratotherium simum",
    "7460": "Apis mellifera",
    "7668": "Strongylocentrotus purpuratus",
    "7719": "Ciona intestinalis",
    "7739": "Branchiostoma floridae",
    "7897": "Latimeria chalumnae",
    "7918": "Lepisosteus oculatus",
    "7955": "Danio rerio",
    "7994": "Astyanax mexicanus",
    "8083": "Xiphophorus maculatus",
    "8090": "Oryzias latipes",
    "8128": "Oreochromis niloticus",
    "81972": "Arabidopsis lyrata",
    "83331": "Mycobacterium tuberculosis (CDC1551)",
    "83332": "Mycobacterium tuberculosis (H37Rv)",
    "83333": "Escherichia coli (K12)",
    "8355": "Xenopus laevis",
    "88036": "Selaginella moellendorffii",
    "8839": "Anas platyrhynchos",
    "885580": "Fukomys damarensis",
    "89462": "Bubalus bubalis",
    "9031": "Gallus gallus",
    "90675": "Camelina sativa",
    "9103": "Meleagris gallopavo",
    "9258": "Ornithorhynchus anatinus",
    "9305": "Sarcophilus harrisii",
    "9361": "Dasypus novemcinctus",
    "9365": "Erinaceus europaeus",
    "9371": "Echinops telfairi",
    "9478": "Tarsius syrichta",
    "9483": "Callithrix jacchus",
    "9541": "Macaca fascicularis",
    "9544": "Macaca mulatta",
    "9555": "Papio anubis",
    "9593": "Gorilla gorilla",
    "9597": "Pan paniscus",
    "9598": "Pan troglodytes",
    "9601": "Pongo abelii",
    "9606": "Homo sapiens",
    "9615": "Canis familiaris",
    "9646": "Ailuropoda melanoleuca",
    "9669": "Mustela putorius furo",
    "9685": "Felis catus",
    "9739": "Tursiops truncatus",
    "9785": "Loxodonta africana",
    "9796": "Equus caballus",
    "9798": "Equus przewalskii",
    "9823": "Sus scrofa",
    "9913": "Bos taurus",
    "9940": "Ovis aries",
    "9978": "Ochotona princeps",
    "9986": "Oryctolagus cuniculus"
}
"""