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PathwayCommons
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cpath2
Biological pathway data integration and access platform (Pathway Commons)
http://www.pathwaycommons.org/pc2/
MIT License
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Some non-blackbox pathways result in empty SBGN model
#271
IgorRodchenkov
closed
7 years ago
3
Integrate TRANSFAC or a similar/better dataset (not using MSigDB)
#270
IgorRodchenkov
closed
5 years ago
1
A search query fails (beta PC9)
#269
IgorRodchenkov
closed
7 years ago
2
ability to download psimi mitab file
#268
risserlin
closed
5 years ago
2
Examples of large pathways
#267
d2fong
closed
7 years ago
8
A CV.term contains several names and identifiers
#266
IgorRodchenkov
closed
7 years ago
2
Wikipathways filtering id is inconsistent
#265
mj3cheun
closed
7 years ago
3
HumanCyc pathway names contain HTML markup
#264
IgorRodchenkov
closed
7 years ago
0
SMPDB data issues
#263
IgorRodchenkov
closed
5 years ago
6
Improve KEGG Cleaner impl.
#262
IgorRodchenkov
closed
7 years ago
0
Return PC2 version in query results
#261
IgorRodchenkov
closed
7 years ago
0
StackOverFlow error during index()
#260
IgorRodchenkov
closed
7 years ago
0
ChEBI IDs do not work for 'get' (and perhaps 'graph') queries
#259
IgorRodchenkov
closed
7 years ago
0
Pathway Missing to from pathways.txt
#258
cannin
closed
7 years ago
3
A query returns error "500"
#257
IgorRodchenkov
closed
7 years ago
6
PC2 '/search': cannot (often?) find a pathway by ID
#256
IgorRodchenkov
closed
7 years ago
1
Add the Google Analytics script and code to all PC2 views
#255
IgorRodchenkov
closed
8 years ago
0
extend web api: add 'user' parameter for logging/tracing
#254
IgorRodchenkov
closed
7 years ago
0
Servlet.service() - IllegalStateException: getOutputStream() has already been called...
#253
IgorRodchenkov
closed
3 months ago
2
large many temporary files can fill up the disk storage in several weeks...
#252
IgorRodchenkov
closed
8 years ago
0
Merge pc2v8 branch into the (much refactored) master
#251
IgorRodchenkov
closed
8 years ago
0
MI merged correctly?
#250
IgorRodchenkov
closed
5 years ago
1
Wrong HTTP response code: 500 is returned instead expected 452, 460
#249
IgorRodchenkov
closed
6 years ago
1
PANTHER: DnaRegionReference.memberEntityReference range violation (DnaReference - wrong)
#248
IgorRodchenkov
closed
8 years ago
0
v8: remove web Admin, security, login, conf., etc., pages and dependencies
#247
IgorRodchenkov
closed
8 years ago
1
Queries should return BioPAX using new official vnd.biopax.rdf+xml media type
#246
IgorRodchenkov
closed
8 years ago
1
local ip:port instead of the hostname in the examples on the home page
#245
IgorRodchenkov
closed
8 years ago
0
Users want an easy way to know child/parent pathways
#244
IgorRodchenkov
closed
8 years ago
1
SMPDB: duplicate or dummy sub-pathways
#243
IgorRodchenkov
closed
6 years ago
4
No bootstrap styling in views on first load
#242
jvwong
closed
8 years ago
2
Make the downloads page simple
#241
IgorRodchenkov
closed
8 years ago
0
Initial page may look broken when first accessed via a browser
#240
IgorRodchenkov
closed
8 years ago
0
Incorrect Pubmed IDs in Extended SIF
#239
cannin
closed
8 years ago
1
too many parent pathways in extended SIF (esp. in KEGG's)
#238
IgorRodchenkov
closed
8 years ago
2
Unwanted specific full-text search result
#237
IgorRodchenkov
closed
8 years ago
1
Login is disabled at purl.org (unable to manage our PURLs)
#236
IgorRodchenkov
closed
8 years ago
1
extend web api: add interaction type filter in get/graph queries if SIF format is requested
#235
IgorRodchenkov
closed
7 years ago
1
Allow comma-separated values for query parameters: source, target, uri
#234
IgorRodchenkov
closed
8 years ago
0
ELK to store and analyze PC2 web service logs
#233
IgorRodchenkov
closed
7 years ago
2
Wrong PR merging due to id-mapping using only xref/id without db
#232
IgorRodchenkov
closed
8 years ago
0
A graph query is too slow when *SIF format is requested.
#231
IgorRodchenkov
closed
8 years ago
4
access log (/log web view and related)
#230
IgorRodchenkov
closed
8 years ago
0
Add UniProtKB/Trembl to the Warehouse
#229
IgorRodchenkov
closed
5 years ago
1
Remove unwanted EntityReferences (e.g., INOH)
#228
IgorRodchenkov
closed
8 years ago
0
Simplify, generalize, improve the id-mapping
#227
IgorRodchenkov
closed
8 years ago
1
Could improve use of ambiguous id-mapping and get more UniProt, HGNC, ChEBI Xrefs on not-merged ERs
#226
IgorRodchenkov
closed
7 years ago
1
SMR warehouse lacks some IDs (e.g. ADP, CHEBI:16761) due to the ChEBI OBO records are inconsistent
#225
IgorRodchenkov
closed
8 years ago
1
Wrong xrefs in ProteinReference
#224
ozgunbabur
closed
8 years ago
3
Truncated entity names in extended SIF (mostly KEGG pathways)
#223
cannin
closed
8 years ago
13
Wikipathways data revealed a bug in the Merger
#222
IgorRodchenkov
closed
8 years ago
1
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