Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / pybel/pybel issues and pull requests

#502 - hetionet does not work

Issue - State: open - Opened by chaxor over 1 year ago - 1 comment

#501 - Getting problems with examples (pybel)

Issue - State: open - Opened by flalix over 1 year ago - 1 comment

#500 - attribute error for pybel

Issue - State: closed - Opened by ahmed4899 over 2 years ago - 1 comment
Labels: OpenBabel

#499 - Unorganized data to_sif and No attribute 'to_triples_file

Issue - State: open - Opened by Ahmed-fub over 2 years ago

#498 - Cannot write the graph in any extension

Issue - State: open - Opened by Ahmed-fub over 2 years ago

#497 - Add py310

Pull Request - State: closed - Opened by cthoyt almost 3 years ago

#496 - Problem getting a BEL graph from the Fraunhofer OrientDB

Issue - State: open - Opened by mjmoron about 3 years ago - 2 comments

#495 - Update citation enrichment functions

Pull Request - State: closed - Opened by cthoyt over 3 years ago

#494 - Update dependencies

Pull Request - State: closed - Opened by cthoyt over 3 years ago

#492 - Troubles with loading .json files created with pybel 14.0.8

Issue - State: closed - Opened by leon-k-martin over 3 years ago - 4 comments

#491 - Fix out of date dependencies

Pull Request - State: closed - Opened by cthoyt over 3 years ago

#490 - Update interface for accessing transitivities

Pull Request - State: closed - Opened by cthoyt over 3 years ago

#489 - Add HTML summary for better jupyter notebook output

Issue - State: open - Opened by cthoyt over 3 years ago

#488 - How to convert files in SMILES or MOL format to MOL2 3D structure

Issue - State: closed - Opened by miracle1111111 over 3 years ago - 1 comment
Labels: OpenBabel

#487 - Add directly regulates relation

Pull Request - State: closed - Opened by cthoyt over 3 years ago

#486 - Convert .Molecule or OBMol to SMILES

Issue - State: closed - Opened by LivC193 over 3 years ago - 1 comment
Labels: OpenBabel

#485 - Add named reaction DSL object

Pull Request - State: closed - Opened by cthoyt almost 4 years ago - 2 comments

#484 - Named reactions

Issue - State: closed - Opened by cthoyt almost 4 years ago

#483 - Update EMMAA downloader

Issue - State: closed - Opened by cthoyt almost 4 years ago
Labels: bug

#482 - Fix bug nodes without concept

Pull Request - State: closed - Opened by ddomingof almost 4 years ago

#481 - Fix collapse algorithm on list abundances

Pull Request - State: open - Opened by cthoyt almost 4 years ago

#480 - collapse_nodes does not apply to members of ListAbundance

Issue - State: open - Opened by ddomingof almost 4 years ago - 3 comments
Labels: bug

#479 - Variable name typo

Issue - State: closed - Opened by ddomingof almost 4 years ago
Labels: bug

#478 - Switch to PyStow

Pull Request - State: closed - Opened by cthoyt almost 4 years ago

#477 - pybel.to_indra_statements() fails on KEGG COVID pathway BEL script

Issue - State: closed - Opened by djinnome almost 4 years ago - 2 comments

#476 - Add postgres and mysql container tests to GitHub Actions

Issue - State: open - Opened by cthoyt almost 4 years ago

#475 - Switch from Travis-CI to GitHub Actions

Issue - State: closed - Opened by cthoyt almost 4 years ago

#474 - Add GitHub actions

Pull Request - State: closed - Opened by cthoyt almost 4 years ago - 1 comment

#472 - Add enrichment for PMC citations

Pull Request - State: closed - Opened by cthoyt about 4 years ago - 1 comment

#471 - Query citation in database using chunks

Pull Request - State: closed - Opened by ddomingof about 4 years ago - 1 comment

#470 - Mock calls to eUtils

Pull Request - State: closed - Opened by cthoyt about 4 years ago

#469 - Add python39 testing to travis configuration

Pull Request - State: closed - Opened by cthoyt about 4 years ago - 1 comment

#468 - Update citations

Pull Request - State: closed - Opened by cthoyt about 4 years ago - 1 comment

#467 - Update grounding

Pull Request - State: closed - Opened by cthoyt about 4 years ago - 2 comments

#466 - Add backwards compatability for PyBEL 14

Pull Request - State: closed - Opened by cthoyt about 4 years ago - 1 comment

#465 - Fix bug in creation of DSL objects

Pull Request - State: closed - Opened by cthoyt over 4 years ago - 1 comment

#463 - Add exporter to a local MongoDB

Pull Request - State: open - Opened by amanchoudhri over 4 years ago - 2 comments

#462 - Begin neo4j update

Pull Request - State: open - Opened by cthoyt over 4 years ago - 1 comment

#461 - Update annotation storage

Pull Request - State: closed - Opened by cthoyt over 4 years ago - 1 comment

#460 - Fix parsing for ec-code and related

Pull Request - State: closed - Opened by cthoyt over 4 years ago - 1 comment

#459 - Can't parse official ec-code keyword

Issue - State: closed - Opened by cthoyt over 4 years ago
Labels: bug

#458 - Store annotations using pybel.language.Entity

Issue - State: closed - Opened by cthoyt over 4 years ago

#457 - Add default regex namespaces for all MIRIAM entries

Issue - State: open - Opened by cthoyt over 4 years ago

#456 - write kekulised molecules

Issue - State: closed - Opened by shalkya over 4 years ago - 1 comment
Labels: OpenBabel

#455 - Remove the rest of the BEL default namespace

Pull Request - State: closed - Opened by cthoyt over 4 years ago - 2 comments

#454 - Update insertions

Pull Request - State: closed - Opened by cthoyt over 4 years ago - 1 comment

#453 - Update parser and data structure

Pull Request - State: closed - Opened by cthoyt over 4 years ago - 1 comment

#452 - MongoDB Export

Issue - State: open - Opened by cthoyt over 4 years ago - 1 comment
Labels: I/O

#451 - Add new "streamable" BEL I/O format

Pull Request - State: closed - Opened by cthoyt over 4 years ago - 1 comment

#450 - Add Node and Edge Validator

Pull Request - State: closed - Opened by amanchoudhri over 4 years ago - 7 comments

#449 - Add initial graph dispatches

Pull Request - State: closed - Opened by cthoyt over 4 years ago

#448 - Example from readme does not work / should be updated

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

#447 - Streamable graphs

Issue - State: closed - Opened by cthoyt over 4 years ago
Labels: I/O

#446 - Implement RDF Exporter

Pull Request - State: open - Opened by cthoyt over 4 years ago

#445 - Add RDF export

Issue - State: open - Opened by cthoyt over 4 years ago
Labels: I/O

#444 - Improve Travis-CI configuration

Pull Request - State: closed - Opened by cthoyt over 4 years ago

#443 - Update annotation grounding

Pull Request - State: closed - Opened by cthoyt over 4 years ago - 1 comment

#442 - Added most recent NCBI Taxonomy namespace to NAMESPACE_URLS

Pull Request - State: closed - Opened by djinnome over 4 years ago - 2 comments

#441 - from_graphdati() reads jgif network format, not graphdati nanopub format

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

#440 - CellDesigner Importer

Issue - State: open - Opened by cthoyt over 4 years ago
Labels: I/O

#439 - Add SBGN-ML importer

Pull Request - State: open - Opened by cthoyt over 4 years ago - 1 comment

#438 - Automatically fix edges containing degradations

Issue - State: open - Opened by cthoyt over 4 years ago

#437 - ImportError: cannot import name 'write_namespace'

Issue - State: open - Opened by charalamm over 4 years ago - 2 comments

#435 - Update grounding and database

Pull Request - State: closed - Opened by cthoyt over 4 years ago

#434 - Reorganize parser to expose line-by-line functionality

Issue - State: closed - Opened by cthoyt over 4 years ago - 1 comment

#433 - Jupyter notebook integration via cytoscape

Issue - State: open - Opened by cthoyt over 4 years ago

#432 - Add EMMAA importer

Pull Request - State: closed - Opened by cthoyt over 4 years ago - 1 comment

#431 - Add Amazon S3 upload/download

Pull Request - State: closed - Opened by cthoyt over 4 years ago - 1 comment

#430 - Add SPIA exporter

Pull Request - State: closed - Opened by cthoyt over 4 years ago

#429 - Add importer for Fraunhofer OrientDB

Pull Request - State: closed - Opened by cthoyt over 4 years ago - 1 comment

#428 - Make PyBEL Python 3.6+

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

#427 - UnicodeDecodeError with Windows

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

#426 - Add grounding module

Pull Request - State: closed - Opened by cthoyt over 4 years ago - 1 comment

#425 - Add GraphDati/BioDati importer

Pull Request - State: closed - Opened by cthoyt over 4 years ago - 1 comment

#424 - Implement BioDati importer

Issue - State: closed - Opened by cthoyt over 4 years ago
Labels: I/O

#423 - SBGN Importer

Issue - State: open - Opened by cthoyt over 4 years ago
Labels: I/O

#422 - Update Hipathia exporter and add demo conversions

Pull Request - State: closed - Opened by cthoyt over 4 years ago - 1 comment

#420 - Implement enrich_pubmed_central_citations

Issue - State: closed - Opened by cthoyt over 4 years ago
Labels: help wanted

#418 - Add test BEL file for BEP-0005 (obo names)

Issue - State: closed - Opened by cthoyt over 4 years ago - 1 comment
Labels: bug, BEP

#415 - Update travis config

Pull Request - State: closed - Opened by cthoyt over 4 years ago - 1 comment

#405 - Implement Hetionet JSON importer

Issue - State: closed - Opened by cthoyt almost 5 years ago
Labels: I/O

#401 - Implement GraphDati importer

Issue - State: closed - Opened by cthoyt almost 5 years ago
Labels: I/O

#390 - Implement annotation patterns in database

Issue - State: closed - Opened by cthoyt about 5 years ago

#359 - WIP: Add JSON validator for PyBEL nodes

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

#296 - Create JSON Schema for PyBEL Nodes

Issue - State: closed - Opened by cthoyt over 6 years ago - 5 comments
Labels: medium, medium priority

#283 - Don't add empty elements on CX export

Issue - State: closed - Opened by cthoyt over 6 years ago - 1 comment
Labels: bug, wontfix, I/O

#260 - Document issues with NetworkX GraphML output

Issue - State: closed - Opened by cthoyt almost 7 years ago
Labels: documentation, easy, I/O

#201 - Rewrite to_csv

Issue - State: closed - Opened by maximilianh over 7 years ago - 9 comments
Labels: bug, I/O

#194 - Export of JSON Graph Interchange Format

Issue - State: closed - Opened by cthoyt over 7 years ago
Labels: enhancement, medium, low priority, I/O

#189 - Export GSEA gene list

Issue - State: closed - Opened by cthoyt over 7 years ago
Labels: I/O

#127 - JSON Export crashes if no list annotations

Issue - State: closed - Opened by cthoyt over 7 years ago
Labels: bug, I/O

#87 - Export to CX

Issue - State: closed - Opened by cebel almost 8 years ago - 4 comments
Labels: enhancement, I/O

#28 - Export to BEL

Issue - State: closed - Opened by cthoyt about 8 years ago - 1 comment
Labels: duplicate, enhancement, I/O

#20 - Export to SMBL

Issue - State: closed - Opened by cthoyt about 8 years ago - 1 comment
Labels: question, I/O

#19 - Export to BEL

Issue - State: closed - Opened by cthoyt about 8 years ago
Labels: enhancement, I/O

#5 - Implementation of Neo4j Export

Issue - State: closed - Opened by cthoyt about 8 years ago
Labels: enhancement, I/O