BioPAX/Paxtools issues and pull requests

#56 - GH-54 allow using RDF 1.1 (no need for xsd:string) and/or XML entitie…

Pull Request - State: closed - Opened by JervenBolleman 7 months ago - 2 comments

#56 - GH-54 allow using RDF 1.1 (no need for xsd:string) and/or XML entitie…

Pull Request - State: closed - Opened by JervenBolleman 7 months ago - 2 comments

#55 - GH-54 XSD Datatype should use full IRI in rdf/xml datatype attribute

Pull Request - State: closed - Opened by JervenBolleman 7 months ago - 5 comments

#55 - GH-54 XSD Datatype should use full IRI in rdf/xml datatype attribute

Pull Request - State: closed - Opened by JervenBolleman 7 months ago - 5 comments

#54 - SimpleIOHandler prints xsd datatype as an abreviated string, which is subtly off

Issue - State: closed - Opened by JervenBolleman 7 months ago - 10 comments

#54 - SimpleIOHandler prints xsd datatype as an abreviated string, which is subtly off

Issue - State: closed - Opened by JervenBolleman 7 months ago - 10 comments

#53 - Paxtools 6

Pull Request - State: closed - Opened by IgorRodchenkov about 1 year ago

#52 - #43 Updated for modern JDK; #51 removed paxtools-trove; bumped version

Pull Request - State: closed - Opened by IgorRodchenkov over 2 years ago

#51 - GNU Trove is deprecated. Remove paxtools-trove?

Issue - State: closed - Opened by MaybeJustJames almost 3 years ago - 1 comment

#50 - Remove paxtools-trove

Pull Request - State: closed - Opened by MaybeJustJames almost 3 years ago - 4 comments

#49 - Removal of paxtools-jena-io breaks psimi

Issue - State: closed - Opened by MaybeJustJames almost 3 years ago - 2 comments

#48 - Question!

Issue - State: closed - Opened by jmaggiore almost 4 years ago - 1 comment

#47 - Cannot add a new EntityReference

Issue - State: closed - Opened by metincansiper over 4 years ago - 3 comments

#45 - Problem caused by calling layout while utilizing biopax to sbgn conversion through Python

Issue - State: closed - Opened by metincansiper almost 5 years ago - 2 comments

#44 - Blank spaces in IDs in SBGN output

Issue - State: closed - Opened by ugurdogrusoz over 5 years ago - 2 comments

#43 - Does not compile with JDK9-11

Issue - State: closed - Opened by IgorRodchenkov almost 6 years ago - 3 comments

#42 - Sbgn converter improvements

Pull Request - State: closed - Opened by IgorRodchenkov almost 6 years ago - 2 comments

#41 - SBGN converter does not work for control-control and modulation cases

Issue - State: closed - Opened by IgorRodchenkov almost 6 years ago

#40 - sbgn-converter: put metadata to the SBGN-ML (using extensions feature).

Issue - State: open - Opened by IgorRodchenkov over 6 years ago

#39 - Sbgn-converter: hard-coded xml:base results in inconsistent IDs

Issue - State: closed - Opened by IgorRodchenkov over 6 years ago - 1 comment

#38 - Data property should not allow leading/tailing space characters

Issue - State: closed - Opened by IgorRodchenkov over 6 years ago - 1 comment

#37 - sbgn-converter can now convert generic physical entities (incl. complexes) defined using memberPhysicalEntity property.

Pull Request - State: closed - Opened by IgorRodchenkov over 6 years ago

#36 - Make gsea-converter optionally list IDs of small molecules and genes too.

Issue - State: open - Opened by IgorRodchenkov almost 7 years ago

#35 - Stoichiometry.physicalEntity should probably be owl:InverseFfunctionalProperty

Issue - State: closed - Opened by IgorRodchenkov almost 7 years ago - 1 comment

#34 - Control.controlled should not allow multiple values (it's a functional OWL property)

Issue - State: open - Opened by IgorRodchenkov about 7 years ago

#33 - Complex members not part of complexes in SBGN output

Issue - State: closed - Opened by ugurdogrusoz about 7 years ago - 4 comments

#32 - "Invalid BioPAX object to wrap as node" warnings

Issue - State: open - Opened by IgorRodchenkov about 7 years ago - 1 comment

#31 - Added Figure Legends to Evidence

Pull Request - State: closed - Opened by GullyAPCBurns over 7 years ago - 1 comment

#30 - sbgn-converter: include "empty" and blackbox sub-pathways.

Issue - State: open - Opened by IgorRodchenkov over 7 years ago - 2 comments

#29 - @AutoComplete in fact did not work

Issue - State: closed - Opened by IgorRodchenkov over 7 years ago

#28 - Some strings in generated sbgn cause it to be invalid xml

Issue - State: closed - Opened by d2fong over 7 years ago - 4 comments

#27 - sbgn-converter: fix the COSE layout, make optional, or remove this feature?..

Issue - State: closed - Opened by IgorRodchenkov over 7 years ago

#26 - sbgn-converter: fix compartment IDs (and labels)

Issue - State: closed - Opened by IgorRodchenkov over 7 years ago

#25 - Completer: an option (default) to avoid sub-pathways?

Issue - State: closed - Opened by IgorRodchenkov over 7 years ago - 2 comments

#24 - Cloner: bogus parameter (Model); not thread-safe (but it could be safe)

Issue - State: closed - Opened by IgorRodchenkov over 7 years ago

#23 - L3ToSBGNPDConverter.java with predefined layout

Issue - State: closed - Opened by PeterTSmith over 7 years ago - 1 comment

#22 - SBGN-ML possesses disconnected nodes

Issue - State: closed - Opened by jvwong over 7 years ago - 2 comments

#21 - Implement SIF Graph Queries

Issue - State: closed - Opened by IgorRodchenkov about 8 years ago - 2 comments
Labels: enhancement

#20 - Command 'summarize' --pathways results in some pathways are not found in the output file

Issue - State: closed - Opened by IgorRodchenkov about 8 years ago

#19 - Pattern (to SIF): performance issue or bug?

Issue - State: closed - Opened by IgorRodchenkov about 8 years ago - 1 comment

#18 - Upgrade to commons-lang3 3.4.

Pull Request - State: closed - Opened by markwoon about 8 years ago

#17 - Update to commons-lang 3

Issue - State: closed - Opened by markwoon about 8 years ago - 4 comments

#16 - Maven Dependency artifactID needs to be updated on the download website

Issue - State: closed - Opened by mehersam over 8 years ago - 1 comment

#15 - json-converter can create too many temporary files in some use cases

Issue - State: closed - Opened by IgorRodchenkov over 8 years ago - 1 comment

#14 - paxtools-core: ModelUtils.mergeEquivalentInteractions bug

Issue - State: closed - Opened by IgorRodchenkov over 8 years ago

#13 - Let's fix or remove the "Integrator"

Issue - State: open - Opened by IgorRodchenkov over 8 years ago - 1 comment

#12 - Users were confused by Xref IDs in the "nodes" section of EXTENDED SIF

Issue - State: closed - Opened by IgorRodchenkov over 8 years ago

#11 - Warning from GraphL3Undirected (paxtools-query)?

Issue - State: open - Opened by IgorRodchenkov over 8 years ago

#10 - NPE in Searcher (pattern)

Issue - State: closed - Opened by IgorRodchenkov over 8 years ago

#9 - Improve/simplify the blacklist generator in SIF/pattern module

Issue - State: closed - Opened by IgorRodchenkov almost 9 years ago

#8 - Normalizer can unnecessarily force using 'uniprot isoform' in xref.db and uri

Issue - State: closed - Opened by IgorRodchenkov almost 9 years ago

#7 - The list of optional parameters for Paxtools console's 'toSif' and 'toSifnx' commands

Issue - State: closed - Opened by IgorRodchenkov about 9 years ago - 1 comment

#6 - Add instructions for brew-based installation

Pull Request - State: closed - Opened by armish about 9 years ago - 1 comment

#5 - Tweak docs.

Pull Request - State: closed - Opened by markwoon about 9 years ago - 2 comments

#4 - One can set an incompatible EntityReference to a physical entity using the API.

Issue - State: closed - Opened by IgorRodchenkov about 9 years ago

#3 - errors in the javadoc

Issue - State: open - Opened by IgorRodchenkov about 9 years ago

#2 - another loop and overflow

Issue - State: closed - Opened by IgorRodchenkov about 9 years ago

#1 - TransitivePropertyAccessor infinite loop (and OutOfMemory)

Issue - State: closed - Opened by IgorRodchenkov over 9 years ago - 1 comment

GitHub / BioPAX/Paxtools issues and pull requests