rwst

Reactome dumps are in Neo4j 4 format. To use them with Neo4j 5 the Reactome database needs to be downloaded as a dump and converted:

• Following instructions are for CLI installation of Neo4j (Linux)
• Install any 5.* version of Neo4j (tested with neo4j-community-5.15.0)
• Download Reactome database dump from https://reactome.org/download/current/reactome.graphdb.dump
• cd to installation directory, all commands below from there
• cp <PATH OF DOWNLOADED DUMP> reactome.dump (so the dump file is in the same directory, also the file is renamed because dots in the database name are not allowed)
• ./bin/neo4j-admin database migrate --force-btree-indexes-to-range reactome
• Now there should be a new directory created under data/databases
• Don't forget to add these lines in conf/neo4j.conf:

rwst

biochemistry method (Q26879200) ↑↑
|-Bradford protein assay (Q247562)
|-Serial analysis of gene expression (Q286721)
|-Förster resonance energy transfer (Q367473)
|-Bimolecular fluorescence complementation (Q863465)
|-Electrophoretic mobility shift assay (Q903596)
|-density gradient electrophoresis (Q1209472)
|-Protein Misfolding Cyclic Amplification (Q2044394)
|-perfusion culture (Q2070705)
|-submersed fermentation (Q2361902)

rwst

molecular biology technique (Q3516872) ↑
|-polymerase chain reaction (Q176996)
|-cell-free protein synthesis (Q189030)
|-Rapid amplification of cDNA ends (Q381434)
|-SuperSAGE (Q826829)
|-restriction fragment length polymorphism (Q857299)
|-Tandem affinity purification (Q893051)
|-DNA-DNA hybridization (Q900923)
|-Chromatin immunoprecipitation (Q901026)
|-Immunophenotyping (Q902926)

rwst

import csv
from sys import *

reader = csv.DictReader(open('genes-wikipedia.tab', 'r'), delimiter='\t')
gqs = {}
for item in reader:
    iturl = item.get('p')
    qit = iturl[iturl.rfind('/')+1:]
    lang = item.get('lang')
    lemma = item.get('lemma')

rwst

import csv
from anytree import Node, find, findall, PreOrderIter, RenderTree, Resolver, AsciiStyle, ChildResolverError
from sys import *

class TCNode(Node):
    q = ''
    lab = ''

print_missing_triples = False
print_qs = True

rwst

import csv
from anytree import Node, find, findall, PreOrderIter, RenderTree, Resolver, AsciiStyle, ChildResolverError
from sys import *

class ECNode(Node):
    q = ''
    lab = ''

tree = ECNode('Root')

rwst

from sys import *
import csv

reader = csv.DictReader(open('gene-diseaseassoc.tab', 'r'), delimiter='\t')
genes = {}
for item in reader:
    iturl = item.get('item')
    it = iturl[iturl.rfind('/')+1:]
    disurl = item.get('dis')
    dis = disurl[disurl.rfind('/')+1:]

rwst

from sys import *
import csv

reader = csv.DictReader(open('gene-entrezids.tab', 'r'), delimiter='\t')
genes = {}
for item in reader:
    gid = item.get('geneid')
    iturl = item.get('item')
    iturl = iturl[iturl.rfind('/')+1:]
    gitem = genes.get(gid)

rwst

#define BENCHPRESS_CONFIG_MAIN                                                    
#include <cstddef>                                                                
#include <benchpress/benchpress.hpp>
//#include "series-benchmark.h"

#include <string>
#include <iostream>
#include <tuple>
#include <type_traits>

rwst

Forcing sage-location, probably because a new package was installed.
Updating various hardcoded paths...
(Please wait at most a few minutes.)
DO NOT INTERRUPT THIS.
Done updating paths.
Found package ccache in /scratch/sage/upstream/ccache-3.1.9.spkg
Package ccache-3.1.9 is already installed.
Use 'sage -f /scratch/sage/upstream/ccache-3.1.9.spkg' to force a reinstallation.
--2014-05-04 08:27:25--  http://coates.ma.ic.ac.uk/grdb_polytopes-0.1.spkg
Resolving coates.ma.ic.ac.uk (coates.ma.ic.ac.uk)... 155.198.35.88