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get_interactions_by_pubmed.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Fetch interactions for a specific set of publications
"""
import requests
import json
from core import config as cfg
request_url = cfg.BASE_URL + "/interactions"
# Two pubmed IDs to search for
pubmedList = ["20489023", "24142105"] # Breitkreutz A (2010), Parua PK (2014)
# These parameters can be modified to match any search criteria following
# the rules outlined in the Wiki: https://wiki.thebiogrid.org/doku.php/biogridrest
params = {
"accesskey": cfg.ACCESS_KEY,
"format": "json", # Return results in JSON format
"pubmedList": "|".join(pubmedList), # Must be | separated
"excludePubmeds": "false", # Set to true to EXCLUDE the pubmeds in the pubmedList
}
# Additional options to try, you can uncomment them as necessary
# See "get_interactions_by_gene.py" or https://wiki.thebiogrid.org/doku.php/biogridrest for a list of additional parameter options
r = requests.get(request_url, params=params)
interactions = r.json()
# Pretty print out the results
print(json.dumps(interactions, indent=4, sort_keys=True))
"""
Output as of version 4.0:
{
"1115074": {
"BIOGRID_ID_A": 36930,
"BIOGRID_ID_B": 32269,
"BIOGRID_INTERACTION_ID": 1115074,
"ENTREZ_GENE_A": "856924",
"ENTREZ_GENE_B": "851802",
"EXPERIMENTAL_SYSTEM": "Reconstituted Complex",
"EXPERIMENTAL_SYSTEM_TYPE": "physical",
"MODIFICATION": "-",
"OFFICIAL_SYMBOL_A": "BMH1",
"OFFICIAL_SYMBOL_B": "ADR1",
"ONTOLOGY_TERMS": {},
"ORGANISM_A": 559292,
"ORGANISM_B": 559292,
"PUBMED_AUTHOR": "Parua PK (2014)",
"PUBMED_ID": 24142105,
"QUALIFICATIONS": "Figure 1",
"QUANTITATION": "-",
"SOURCEDB": "BIOGRID",
"SYNONYMS_A": "APR6|14-3-3 family protein BMH1|L000000185",
"SYNONYMS_B": "DNA-binding transcription factor ADR1|L000000050",
"SYSTEMATIC_NAME_A": "YER177W",
"SYSTEMATIC_NAME_B": "YDR216W",
"TAGS": "-",
"THROUGHPUT": "Low Throughput"
},
"1115075": {
"BIOGRID_ID_A": 36930,
"BIOGRID_ID_B": 32078,
"BIOGRID_INTERACTION_ID": 1115075,
"ENTREZ_GENE_A": "856924",
"ENTREZ_GENE_B": "851592",
"EXPERIMENTAL_SYSTEM": "Reconstituted Complex",
"EXPERIMENTAL_SYSTEM_TYPE": "physical",
"MODIFICATION": "-",
"OFFICIAL_SYMBOL_A": "BMH1",
"OFFICIAL_SYMBOL_B": "REG1",
"ONTOLOGY_TERMS": {},
"ORGANISM_A": 559292,
"ORGANISM_B": 559292,
"PUBMED_AUTHOR": "Parua PK (2014)",
"PUBMED_ID": 24142105,
"QUALIFICATIONS": "Figure 4",
"QUANTITATION": "-",
"SOURCEDB": "BIOGRID",
"SYNONYMS_A": "APR6|14-3-3 family protein BMH1|L000000185",
"SYNONYMS_B": "HEX2|PZF240|SPP43|SRN1|protein phosphatase regulator REG1|L000001609",
"SYSTEMATIC_NAME_A": "YER177W",
"SYSTEMATIC_NAME_B": "YDR028C",
"TAGS": "-",
"THROUGHPUT": "Low Throughput"
},
...
"441725": {
"BIOGRID_ID_A": 35747,
"BIOGRID_ID_B": 35200,
"BIOGRID_INTERACTION_ID": 441725,
"ENTREZ_GENE_A": "855648",
"ENTREZ_GENE_B": "855043",
"EXPERIMENTAL_SYSTEM": "Synthetic Rescue",
"EXPERIMENTAL_SYSTEM_TYPE": "genetic",
"MODIFICATION": "-",
"OFFICIAL_SYMBOL_A": "MKS1",
"OFFICIAL_SYMBOL_B": "TAP42",
"ONTOLOGY_TERMS": {
"92941": {
"DESC": "The proportion of cells in a sample that are viable, i.e. able to form colonies. Often measured by spotting aliquots of a dilution series on a plate.",
"FLAG": "P",
"ID": 112,
"NAME": "viability",
"ONTOLOGY_CATEGORY": "phenotype",
"ONTOLOGY_TERM_ID": "APO:0000111",
"QUALIFIERS": {},
"TYPE_ID": 4,
"TYPE_NAME": "Unspecified"
}
},
"ORGANISM_A": 559292,
"ORGANISM_B": 559292,
"PUBMED_AUTHOR": "Breitkreutz A (2010)",
"PUBMED_ID": 20489023,
"QUALIFICATIONS": "GAL-MKS1",
"QUANTITATION": "-",
"SOURCEDB": "BIOGRID",
"SYNONYMS_A": "LYS80|L000001119",
"SYNONYMS_B": "L000002599",
"SYSTEMATIC_NAME_A": "YNL076W",
"SYSTEMATIC_NAME_B": "YMR028W",
"TAGS": "-",
"THROUGHPUT": "Low Throughput"
},
"441727": {
"BIOGRID_ID_A": 35747,
"BIOGRID_ID_B": 33823,
"BIOGRID_INTERACTION_ID": 441727,
"ENTREZ_GENE_A": "855648",
"ENTREZ_GENE_B": "853529",
"EXPERIMENTAL_SYSTEM": "Synthetic Growth Defect",
"EXPERIMENTAL_SYSTEM_TYPE": "genetic",
"MODIFICATION": "-",
"OFFICIAL_SYMBOL_A": "MKS1",
"OFFICIAL_SYMBOL_B": "TOR1",
"ONTOLOGY_TERMS": {
"125708": {
"DESC": "Growth under standard culture conditions (liquid or solid media).",
"FLAG": "P",
"ID": 107,
"NAME": "vegetative growth",
"ONTOLOGY_CATEGORY": "phenotype",
"ONTOLOGY_TERM_ID": "APO:0000106",
"QUALIFIERS": {},
"TYPE_ID": 4,
"TYPE_NAME": "Unspecified"
}
},
"ORGANISM_A": 559292,
"ORGANISM_B": 559292,
"PUBMED_AUTHOR": "Breitkreutz A (2010)",
"PUBMED_ID": 20489023,
"QUALIFICATIONS": "GAL-MKS1",
"QUANTITATION": "-",
"SOURCEDB": "BIOGRID",
"SYNONYMS_A": "LYS80|L000001119",
"SYNONYMS_B": "DRR1|phosphatidylinositol kinase-related protein kinase TOR1|L000002322",
"SYSTEMATIC_NAME_A": "YNL076W",
"SYSTEMATIC_NAME_B": "YJR066W",
"TAGS": "-",
"THROUGHPUT": "Low Throughput"
}
"""