GO_Human
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN//goa_human.gaf.gz
Last-Modified: Thu, 04 Sep 2025 13:32:13 GMT
========
GO_OBO_FILE
http://current.geneontology.org/ontology/go.obo
Last-Modified: Fri, 25 Jul 2025 22:47:32 GMT
========
https://brg-files.ai.sri.com/subscription/dist/flatfiles-52983746/tier1-tier2-biopax.tar.gz
Human_phenotype_OBO_FILE
https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo
========
Human_Phenotype
https://github.com/obophenotype/human-phenotype-ontology/releases/latest/download/genes_to_phenotype.txt
========
IOB
IOB pathways were recieved from IOB in July 2011, validated and autofixed using the biopax validator.
=====================
KEGG
Kegg was downloaded from the previously public ftp site on July 1, 2011
==========================
MSigdb hallmark version 2023.1 -  Hallmark gene sets summarize and represent specific well-defined biological 
	states or processes and display coherent expression. These gene sets were generated by a 
	computational methodology based on identifying gene set overlaps and retaining genes that 
	display coordinate expression.
Human MSigDB v2023.1.Hs updated March 2023 
===============
MSigdb version 2023.1 - March 2023
Msigdb -c3 - mirs
=============
MSigdb c2 version v2023.1 - canonical pathway set (cp) from pid and biocarta
Human MSigDB v2023.1.Hs updated March 2023
==============
MSigdb version 2023.1 - March 2023
msigdb c3 - transcription factors 
===============
Panther
ftp://ftp.pantherdb.org/pathway/current_release//BioPAX.tar.gz
Last-Modified: Thu, 20 Jun 2024 17:45:57 GMT
========
PFOCR
https://data.wikipathways.org/pfocr/current//pfocr-20250701-gmt-Homo_sapiens.gmt
========
Reactome
https://www.reactome.org/download/current//biopax.zip
========
Loading GMT File...
cytoscape.CytoscapeInit[INFO]: CytoscapeInit static initialization
converting 19096 ids in total
200
{"jobId":"ac3Ty7DObW"}
ac3Ty7DObW
200
{"jobId":"jF5gcrDuFk"}
jF5gcrDuFk
200
{"jobId":"5aGo4w2svm"}
5aGo4w2svm
200
{"jobId":"tLGNm9w1lq"}
tLGNm9w1lq
200
{"jobId":"wIZlZj1MW3"}
wIZlZj1MW3
200
{"jobId":"isTKEwU1Z6"}
isTKEwU1Z6
200
{"jobId":"vd6qwXacvm"}
vd6qwXacvm
200
{"jobId":"zh2Yfpx1DT"}
zh2Yfpx1DT
200
{"jobId":"8IgIXvs87s"}
8IgIXvs87s
200
{"jobId":"cSMpo4e6Qq"}
cSMpo4e6Qq
200
{"jobId":"2i98V5Dvv4"}
2i98V5Dvv4
200
{"jobId":"buPqd6zrZV"}
buPqd6zrZV
200
{"jobId":"obT5cGdkoW"}
obT5cGdkoW
200
{"jobId":"fcxCnDLYgo"}
fcxCnDLYgo
200
{"jobId":"zYwCwC0xy1"}
zYwCwC0xy1
200
{"jobId":"A6BHxGIFKN"}
A6BHxGIFKN
200
{"jobId":"kPxRmTEVRo"}
kPxRmTEVRo
200
{"jobId":"9NlnYBGrGS"}
9NlnYBGrGS
200
{"jobId":"ozJyXI0crB"}
ozJyXI0crB
200
{"jobId":"nL9642hbYZ"}
nL9642hbYZ
 There are 3425 that are still not found
converting 15633 ids in total
200
{"jobId":"rNbhjtQtKX"}
rNbhjtQtKX
200
{"jobId":"rQfoYWYiHL"}
rQfoYWYiHL
200
{"jobId":"5SQqNNSzt4"}
5SQqNNSzt4
200
{"jobId":"4wAflG3XUe"}
4wAflG3XUe
200
{"jobId":"97m1MEey2P"}
97m1MEey2P
200
{"jobId":"xkVyrJhmxM"}
xkVyrJhmxM
200
{"jobId":"bJ7ORy8SxX"}
bJ7ORy8SxX
200
{"jobId":"tkXbcnfyqr"}
tkXbcnfyqr
200
{"jobId":"59LLXzjHjl"}
59LLXzjHjl
200
{"jobId":"uVAMhUGraX"}
uVAMhUGraX
200
{"jobId":"bNELVkf1wV"}
bNELVkf1wV
200
{"jobId":"xCdhnGhhYA"}
xCdhnGhhYA
200
{"jobId":"5bgvwJqkH6"}
5bgvwJqkH6
200
{"jobId":"nJmtF6k4YM"}
nJmtF6k4YM
200
{"jobId":"cgfRbezvFi"}
cgfRbezvFi
200
{"jobId":"d0n8jMJlcp"}
d0n8jMJlcp
There are multiple ids in line:SBP 1b(we were trying to convert Q769H0)
There are multiple ids in line:SLC14A1 JK(we were trying to convert G0W2N5)
 There are 1919 that are still not found
Loading GMT File...
cytoscape.CytoscapeInit[INFO]: CytoscapeInit static initialization
converting 19096 ids in total
200
{"jobId":"ac3Ty7DObW"}
ac3Ty7DObW
200
{"jobId":"jF5gcrDuFk"}
jF5gcrDuFk
200
{"jobId":"5aGo4w2svm"}
5aGo4w2svm
200
{"jobId":"tLGNm9w1lq"}
tLGNm9w1lq
200
{"jobId":"wIZlZj1MW3"}
wIZlZj1MW3
200
{"jobId":"isTKEwU1Z6"}
isTKEwU1Z6
200
{"jobId":"vd6qwXacvm"}
vd6qwXacvm
200
{"jobId":"zh2Yfpx1DT"}
zh2Yfpx1DT
200
{"jobId":"8IgIXvs87s"}
8IgIXvs87s
200
{"jobId":"cSMpo4e6Qq"}
cSMpo4e6Qq
200
{"jobId":"2i98V5Dvv4"}
2i98V5Dvv4
200
{"jobId":"buPqd6zrZV"}
buPqd6zrZV
200
{"jobId":"obT5cGdkoW"}
obT5cGdkoW
200
{"jobId":"fcxCnDLYgo"}
fcxCnDLYgo
200
{"jobId":"zYwCwC0xy1"}
zYwCwC0xy1
200
{"jobId":"A6BHxGIFKN"}
A6BHxGIFKN
200
{"jobId":"kPxRmTEVRo"}
kPxRmTEVRo
200
{"jobId":"9NlnYBGrGS"}
9NlnYBGrGS
200
{"jobId":"ozJyXI0crB"}
ozJyXI0crB
200
{"jobId":"nL9642hbYZ"}
nL9642hbYZ
 There are 3425 that are still not found
converting 15633 ids in total
200
{"jobId":"gQgc0uYGOX"}
gQgc0uYGOX
200
{"jobId":"r5GwnE7SLC"}
r5GwnE7SLC
200
{"jobId":"rJJh8EJFnD"}
rJJh8EJFnD
200
{"jobId":"cqpJPS89eT"}
cqpJPS89eT
200
{"jobId":"eyxtKSKSeJ"}
eyxtKSKSeJ
200
{"jobId":"nOtINAA4zO"}
nOtINAA4zO
200
{"jobId":"7L9bie4V20"}
7L9bie4V20
200
{"jobId":"N2ZgZIt4tI"}
N2ZgZIt4tI
200
{"jobId":"aWs3zss179"}
aWs3zss179
200
{"jobId":"ujCo3UKo3Y"}
ujCo3UKo3Y
200
{"jobId":"jQIMBIRI4C"}
jQIMBIRI4C
200
{"jobId":"gwes1rfrYl"}
gwes1rfrYl
200
{"jobId":"m8nKGX5I9X"}
m8nKGX5I9X
200
{"jobId":"7Xbqq2jLIN"}
7Xbqq2jLIN
200
{"jobId":"zl2ZrjzIhm"}
zl2ZrjzIhm
200
{"jobId":"hPf9V6N11V"}
hPf9V6N11V
 There are 16 that are still not found
Loading GMT File...
cytoscape.CytoscapeInit[INFO]: CytoscapeInit static initialization
converting 19096 ids in total
200
{"jobId":"ac3Ty7DObW"}
ac3Ty7DObW
200
{"jobId":"jF5gcrDuFk"}
jF5gcrDuFk
200
{"jobId":"5aGo4w2svm"}
5aGo4w2svm
200
{"jobId":"tLGNm9w1lq"}
tLGNm9w1lq
200
{"jobId":"wIZlZj1MW3"}
wIZlZj1MW3
200
{"jobId":"isTKEwU1Z6"}
isTKEwU1Z6
200
{"jobId":"vd6qwXacvm"}
vd6qwXacvm
200
{"jobId":"zh2Yfpx1DT"}
zh2Yfpx1DT
200
{"jobId":"8IgIXvs87s"}
8IgIXvs87s
200
{"jobId":"cSMpo4e6Qq"}
cSMpo4e6Qq
200
{"jobId":"2i98V5Dvv4"}
2i98V5Dvv4
200
{"jobId":"buPqd6zrZV"}
buPqd6zrZV
200
{"jobId":"obT5cGdkoW"}
obT5cGdkoW
200
{"jobId":"fcxCnDLYgo"}
fcxCnDLYgo
200
{"jobId":"zYwCwC0xy1"}
zYwCwC0xy1
200
{"jobId":"A6BHxGIFKN"}
A6BHxGIFKN
200
{"jobId":"kPxRmTEVRo"}
kPxRWikiPathways
https://data.wikipathways.org/current/gmt//wikipathways-20250910-gmt-Homo_sapiens.gmt
========