wikipathways reactome2gpml-converter issues

wikipathways / reactome2gpml-converter

Converts Reactome pathways to GPML format

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issues

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explore Maven route

#81 egonw opened 1 year ago
0
book references on pathway get converted to an empty reference with pmid=0

#80 egonw opened 3 years ago
0
Rhea IDs iso Reactome IDs

#79 DeniseSl22 opened 3 years ago
0
Complex visualisation bottom cut-off at certain length

#78 DeniseSl22 opened 3 years ago
0
Buggy visualisation of complexes, including small datanodes at top left corner

#77 DeniseSl22 opened 3 years ago
0
Check for special characters in description of PW

#76 DeniseSl22 opened 3 years ago
3
binaries should not be in the source code repo

#75 egonw opened 4 years ago
1
Add Luc to this repo + Run MySQL on server

#74 DeniseSl22 closed 3 years ago
15
Create name of complex (in hexagon) above full complex below PW

#73 DeniseSl22 opened 4 years ago
1
check if we propagate author and curator info properly

#72 egonw opened 4 years ago
0
Update BridgeDb Jars

#71 DeniseSl22 opened 5 years ago
0
do not create empty PubMed citations

#70 egonw opened 5 years ago
0
Include not UTF-8 characters in PW title+description

#69 DeniseSl22 opened 5 years ago
0
Another weird visualisation

#68 DeniseSl22 opened 5 years ago
0
Complex visible on RCbranch, not in GPML?

#67 DeniseSl22 opened 5 years ago
0
Sets converted to complexes

#66 mkutmon opened 5 years ago
2
Dovitinib is not annotated with a structure identifier in GPML (but is in original)

#65 egonw opened 5 years ago
1
Better layout (closes #62)

#64 egonw closed 5 years ago
0
Description has a stray `</div>`

#63 egonw opened 5 years ago
0
Replace ':' with a space in pathway description

#62 egonw closed 5 years ago
0
WP2785, WP3334, WP3574, WP3339, WP2790, WP2766 not present in version 66

#61 DeniseSl22 opened 5 years ago
4
"PubChem Compound" & "NCBI Nucleotide" unknown DataSource v66 (and before)

#60 DeniseSl22 closed 5 years ago
1
Exception: class not found -> renderableChemicalDrug v66

#59 DeniseSl22 opened 5 years ago
3
Unable to trace where WP1898 went in version 64

#58 DeniseSl22 closed 3 years ago
1
Missing child PW for 166520

#57 DeniseSl22 opened 5 years ago
0
Nucleotide salvage PW not properly converted v.62 Reactome (8956321)

#56 DeniseSl22 opened 5 years ago
0
Created GPML file names

#55 DeniseSl22 opened 5 years ago
1
Fix log file

#54 DeniseSl22 opened 5 years ago
1
create a working build.xml (Ant) or pom.xml (Maven) to compile the software

#53 egonw closed 5 years ago
7
pathways have unconnected lines: caused by converter or in original Reactome version?

#52 egonw closed 5 years ago
1
Update with BridgeDb 2.2

#51 egonw opened 7 years ago
2
write documentation for command line tool

#50 egonw closed 5 years ago
1
Fix time performance, initialize BridgeDb datasources in main method

#49 JonathanMELIUS closed 8 years ago
0
WP2719 has a Reactome ID for a metabolite which has an incorrect format

#48 egonw closed 5 years ago
2
trim spaces in text labels of data nodes

#47 egonw opened 8 years ago
5
WP1903 has a complex with an ChEBI identifiers which is not an ChEBI identifier

#46 egonw closed 5 years ago
3
the build.xml has hardcoded paths

#45 egonw closed 5 years ago
1
Megapathways not converted

#44 pennatula closed 8 years ago
1
Problems with Plant Pathways

#43 pennatula closed 8 years ago
0
Change Complex colour to brown

#42 pennatula closed 9 years ago
1
Change RNA color to purple

#41 pennatula closed 9 years ago
1
Create link between complex nodes and their components

#40 pennatula closed 9 years ago
1
capitalize pathway titles

#39 pennatula closed 8 years ago
1
Error in WP2972

#38 pennatula closed 5 years ago
1
On some pathways, one or more nodes are missing.

#37 pennatula opened 9 years ago
1
Store duplicates found in complex component list

#36 pennatula closed 9 years ago
1
Add datasource as proper hyperlinks

#35 pennatula closed 9 years ago
1
Problem in WP1825

#34 pennatula opened 9 years ago
0
Link to Reactome in Plant pathways is wrong

#33 pennatula opened 9 years ago
0
hardcode some types in the convertor?

#32 egonw opened 9 years ago
1