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geneontology
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pathways2GO
Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
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Molecular Events should not be entities
#119
ukemi
opened
3 years ago
8
Add promapping.txt; fix entity type default
#118
dustine32
closed
3 years ago
1
fix missing locations
#117
goodb
closed
3 years ago
0
No reacto option
#116
goodb
closed
3 years ago
0
Remove class prop labels
#115
goodb
closed
3 years ago
1
models should not assert labels for classes and properties
#114
balhoff
closed
2 years ago
2
neurotransmitter clearance
#113
cmungall
closed
3 years ago
13
Add inferred bps
#112
goodb
closed
3 years ago
0
Cleanup
#111
goodb
closed
3 years ago
0
generalize physical entity classification
#110
goodb
opened
3 years ago
0
Bump junit from 4.12 to 4.13.1 in /exchange
#109
dependabot[bot]
closed
3 years ago
0
drugs and reactions
#108
goodb
closed
3 years ago
16
Add connected reactions from neighboring pathways
#107
goodb
closed
3 years ago
0
Capture Pathway hierarchical structure
#106
goodb
closed
3 years ago
0
Adding molecular event placeholder class
#105
goodb
closed
3 years ago
0
missing causal relationships in different pathways
#104
goodb
closed
3 years ago
35
inferring enabled by from upstream
#103
goodb
closed
3 years ago
10
update transport template and rule
#102
goodb
closed
3 years ago
23
check into Entity Regulation Rule 1.
#101
goodb
closed
4 years ago
19
Adding molecular event placeholder class
#100
goodb
closed
4 years ago
0
Reconsider small molecular regulation
#99
goodb
closed
4 years ago
3
Reconsider Binding related conversion rules
#98
goodb
closed
3 years ago
31
Issue#91 active unit
#97
goodb
closed
4 years ago
1
Add tag to converted reactions and pathways to indicate original biopax type. Useful for manuscript statistics.
#96
goodb
closed
4 years ago
0
Clean up repository for public consumption.
#95
goodb
opened
4 years ago
1
Create an repository for Reactome models that would be immutable by curators
#94
ukemi
opened
4 years ago
6
remove owl import go-lego
#93
goodb
closed
4 years ago
0
Write manuscript describing the results of this project.
#92
goodb
closed
2 years ago
7
How to represent complex active unit structure
#91
goodb
closed
4 years ago
12
#88 reacto sataisfiability
#90
goodb
closed
4 years ago
0
adding taxon metadata
#89
goodb
closed
4 years ago
0
reacto unsatisfiable when all imports loaded
#88
goodb
closed
4 years ago
8
Fix entity regulates rule 1
#87
goodb
closed
4 years ago
0
classifying reactions (black box and other) by type
#86
deustp01
opened
4 years ago
2
Annotations of Rho GTPase cycle pathway members derived from Reactome
#85
cmungall
opened
4 years ago
8
filter reactions that involve a drug
#84
goodb
closed
4 years ago
21
Figure out round-trip amongst Reactome, PRO, and NEO
#83
goodb
closed
4 years ago
0
Converting binding reactions in Reactome to causal relationships
#82
huaiyumi
closed
11 months ago
11
Build table of conversion rules with stats for manuscript and general documentation
#81
goodb
closed
4 years ago
1
Specification of causal formats and their connections
#80
cmungall
closed
4 years ago
2
shift shex testing to minerva cmdline via travis
#79
goodb
closed
4 years ago
0
Document requirements for Reactome models as Templates use case
#78
goodb
opened
4 years ago
4
Revisit representation of non-catalytic regulation as binding functions
#77
goodb
closed
4 years ago
18
Implement testing framework for pathways2go
#76
goodb
closed
4 years ago
4
define and implement model for transport and dissociation processes
#75
goodb
closed
4 years ago
122
missing some conversions from causally upstream of to directly positive regulates
#74
goodb
closed
4 years ago
3
add root MF as rdf:type for transport reactions
#73
goodb
closed
4 years ago
0
remove contributes_to
#72
goodb
closed
4 years ago
1
Checklist of things for REO prior to importing into go-lego
#71
cmungall
closed
4 years ago
21
UniProt versus reactome entity id issue
#70
goodb
closed
4 years ago
5
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