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Include protein-protein interactions in covid dataset
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@Habush
Habush committed May 14, 2020
1 parent 19b7e1b commit 9920d05
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Showing 2 changed files with 44 additions and 29 deletions.
9 changes: 4 additions & 5 deletions biogrid_gene2uniprot.py
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Expand Up @@ -7,14 +7,13 @@
# Requires: uniprot to biogrid_id mapping file uniprot2biogrid.csv and
# Biogrid gene to biogrid_id mapping file gene2biogrid.csv (run biogrid_genes.py to get this file)

import pandas as pd
import sys
import math
from collections import defaultdict
import metadata
import os
from datetime import date

import pandas as pd

import metadata

script = "https://github.com/MOZI-AI/knowledge-import/biogrid_gene2uniprot.py"

def to_atomese(data):
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64 changes: 40 additions & 24 deletions coronavirus_biogrid.py
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Expand Up @@ -82,7 +82,8 @@ def import_data(data, source, version, gene_level=False, form='tab2'):
g = open('gene-level/COVID-19-biogrid_'+version+"_gene-level_"+str(date.today())+'.scm','w')

with open('dataset/COVID-19-biogrid_'+version+"_"+str(date.today())+'.scm','w') as f:
pairs = []
gene_pairs = []
protein_pairs = []
entrez = []
genes = []
covid_genes = []
Expand All @@ -102,7 +103,7 @@ def import_data(data, source, version, gene_level=False, form='tab2'):
taxonomy_id_1 = int(data.iloc[i]['Organism ID Interactor A'])
taxonomy_id_2 = int(data.iloc[i]['Organism ID Interactor B'])

if (gene1, gene2) not in pairs or (gene2, gene1) not in genes:
if (gene1, gene2) not in gene_pairs or (gene2, gene1) not in genes:
if not gene1 in entrez:
f.write(evaLink(gene1, "GeneNode", entrez1,"ConceptNode", "has_entrez_id",prefix2="entrez:"))
entrez.append(gene1)
Expand All @@ -115,42 +116,57 @@ def import_data(data, source, version, gene_level=False, form='tab2'):
if gene_level:
g.write(evaLink(gene1, "GeneNode",gene2,"GeneNode", "interacts_with", symmetric=True, stv=stv))

if taxonomy_id_1 == 2697049:
covid_genes.append(gene1)
f.write(
evaLink(gene1, "GeneNode", taxonomy_id_1, "ConceptNode", "from_organism", prefix2="ncbi:"))
f.write(evaLink(prot1, "MoleculeNode", taxonomy_id_1, "ConceptNode", "from_organism",
prefix1="Uniprot:", prefix2="ncbi:"))
if gene_level:
g.write(evaLink(gene1, "GeneNode", taxonomy_id_1, "ConceptNode", "from_organism",
prefix2="ncbi:"))
g.write(evaLink(prot1, "MoleculeNode", taxonomy_id_1, "ConceptNode", "from_organism",
prefix1="Uniprot:", prefix2="ncbi:"))
if taxonomy_id_2 == 2697049:
covid_genes.append(gene2)
f.write(
evaLink(gene2, "GeneNode", taxonomy_id_2, "ConceptNode", "from_organism", prefix2="ncbi:"))
f.write(evaLink(prot2, "MoleculeNode", taxonomy_id_2, "ConceptNode", "from_organism",
prefix1="Uniprot:", prefix2="ncbi:"))
if gene_level:
g.write(evaLink(gene2, "GeneNode", taxonomy_id_2, "ConceptNode", "from_organism",
prefix2="ncbi:"))
g.write(evaLink(prot2, "MoleculeNode", taxonomy_id_2, "ConceptNode", "from_organism",
prefix1="Uniprot:", prefix2="ncbi:"))

gene_pairs.append((gene1, gene2))

if (prot1, prot2) not in protein_pairs:

f.write(evaLink(prot1, "MoleculeNode", prot2, "MoleculeNode", "interacts_with", symmetric=True, stv=stv,
prefix1="Uniprot:", prefix2="Uniprot:"))

if not prot1 in proteins:
bio = str(data.iloc[i]['BioGRID ID Interactor A']).strip()
f.write(evaLink(gene1, "GeneNode", prot1,"MoleculeNode", "expresses", prefix2="Uniprot:"))
f.write(evaLink(gene1, "GeneNode", prot1, "MoleculeNode", "expresses", prefix2="Uniprot:"))
f.write(evaLink(gene1, "GeneNode", bio,"ConceptNode", "has_biogridID", prefix2="Bio:"))
f.write(evaLink(prot1, "MoleculeNode", bio,"ConceptNode", "has_biogridID", prefix1="Uniprot:",prefix2="Bio:"))
proteins.append(prot1)

if not prot2 in proteins:
bio = str(data.iloc[i]['BioGRID ID Interactor B']).strip()
f.write(evaLink(gene2, "GeneNode", prot2,"MoleculeNode", "expresses", prefix2="Uniprot:"))
f.write(evaLink(gene2, "GeneNode", bio,"ConceptNode", "has_biogridID", prefix2="Bio:"))
f.write(evaLink(prot2, "MoleculeNode", bio,"ConceptNode", "has_biogridID", prefix1="Uniprot:",prefix2="Bio:"))
proteins.append(prot2)

if taxonomy_id_1 == 2697049:
covid_genes.append(gene1)
f.write(evaLink(gene1, "GeneNode", taxonomy_id_1 , "ConceptNode","from_organism", prefix2="ncbi:"))
f.write(evaLink(prot1, "MoleculeNode", taxonomy_id_1, "ConceptNode","from_organism", prefix1="Uniprot:",prefix2="ncbi:"))
if gene_level:
g.write(evaLink(gene1, "GeneNode", taxonomy_id_1 , "ConceptNode","from_organism",prefix2="ncbi:"))
g.write(evaLink(prot1, "MoleculeNode", taxonomy_id_1, "ConceptNode","from_organism", prefix1="Uniprot:", prefix2="ncbi:"))
if taxonomy_id_2 == 2697049:
covid_genes.append(gene2)
f.write(evaLink(gene2, "GeneNode", taxonomy_id_2 , "ConceptNode","from_organism",prefix2="ncbi:"))
f.write(evaLink(prot2, "MoleculeNode", taxonomy_id_2, "ConceptNode","from_organism", prefix1="Uniprot:",prefix2="ncbi:"))
if gene_level:
g.write(evaLink(gene2, "GeneNode", taxonomy_id_2 , "ConceptNode", "from_organism", prefix2="ncbi:"))
g.write(evaLink(prot2, "MoleculeNode", taxonomy_id_2, "ConceptNode", "from_organism", prefix1="Uniprot:", prefix2="ncbi:"))

genes.append(gene1)
genes.append(gene2)
proteins.append(prot1)
proteins.append(prot2)
pairs.append((gene1,gene2))
protein_pairs.append((prot1, prot2))

f.write(evaLink("2697049", "ConceptNode", "SARS-CoV-2", "ConceptNode","has_name",prefix1="ncbi:"))
g.write(evaLink("2697049", "ConceptNode", "SARS-CoV-2", "ConceptNode","has_name",prefix1="ncbi:"))
pairs = set((a,b) if a<=b else (b,a) for a,b in pairs)
number_of_interactions = len(pairs)
gene_pairs = set((a,b) if a<=b else (b,a) for a,b in gene_pairs)
number_of_interactions = len(gene_pairs)
script = "https://github.com/MOZI-AI/knowledge-import/coronavirus_biogrid.py"
metadata.update_meta("Coronavirus Biogrid:"+version, source,script,genes=str(len(set(genes))),prot=len(set(proteins)), interactions=str(number_of_interactions))
print("Done, check "+'dataset/COVID-19-biogrid_'+version+"_"+str(date.today())+'.scm')
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