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Recent Releases of pybiodatafuse

pybiodatafuse - v1.2.0

What's Changed

  • Added WikiPathways and STRING annotations to the example notebook by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/25
  • test by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/29
  • Add generator module to construct NetworkX graph from annotation Data… by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/30
  • DEA loader by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/31
  • Bgee annotator by @dssib in https://github.com/BioDataFuse/pyBiodatafuse/pull/24
  • add pubchem name grounder by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/28
  • Annotator template for Wikidata by @egonw in https://github.com/BioDataFuse/pyBiodatafuse/pull/19
  • MolMeDB by @DominikMartinat in https://github.com/BioDataFuse/pyBiodatafuse/pull/32
  • Add graph generation example to the workflow fix typo in generator module by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/33
  • Create export modules for cytoscape and neo4j, and add node types to the networkx graph by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/36
  • load dea table by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/37
  • Export to Neo4j by @hasanbalci in https://github.com/BioDataFuse/pyBiodatafuse/pull/38
  • add basic docs by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/26
  • add score to interactions and check for duplicates for all edges by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/41
  • docstring fix by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/47
  • collapsedatasource method fixed by @DominikMartinat in https://github.com/BioDataFuse/pyBiodatafuse/pull/44
  • bug fix by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/49
  • Add Cytoscape related functions by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/55
  • Add DEA statistics to gene node attributes by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/57
  • added Minerva Annotator by @adriaque in https://github.com/BioDataFuse/pyBiodatafuse/pull/65
  • Count for empty annotation column when generating the graph by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/66
  • Update generator.py to check for None annotation results when creating the graph by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/67
  • Add issue templates by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/70
  • Add tests for the WikiPathways and Stringdb annotators by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/74
  • New Minerva annotator version by @adriaque in https://github.com/BioDataFuse/pyBiodatafuse/pull/68
  • Molmedb anotator index fix by @DominikMartinat in https://github.com/BioDataFuse/pyBiodatafuse/pull/78
  • MolMeDB inhibitor subgraph addition by @DominikMartinat in https://github.com/BioDataFuse/pyBiodatafuse/pull/79
  • check the API by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/81
  • Add drug-disease function by @adriaque in https://github.com/BioDataFuse/pyBiodatafuse/pull/71
  • Fixed the metadata returned by @egonw in https://github.com/BioDataFuse/pyBiodatafuse/pull/82
  • FIx Minerva by @adriaque in https://github.com/BioDataFuse/pyBiodatafuse/pull/80
  • Change gene-drug edge direction by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/83
  • Bgee annotator tests and small fixes by @dssib in https://github.com/BioDataFuse/pyBiodatafuse/pull/85
  • update component name by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/86
  • Add handling or API and SPARQL endpoint exceptions by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/89
  • Graph node types fix by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/91
  • Add id to nodes in molmedb by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/93
  • Add Bgee annotation to the graph by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/92
  • DisGeNet sparql by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/97
  • Molmedb testing by @DominikMartinat in https://github.com/BioDataFuse/pyBiodatafuse/pull/88
  • Add api warning minerva by @adriaque in https://github.com/BioDataFuse/pyBiodatafuse/pull/95
  • Add test for minerva, it is not fully working yet, needs review by @adriaque in https://github.com/BioDataFuse/pyBiodatafuse/pull/94
  • minor fix minerva by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/101
  • Update generator and neo4j exporter by @adriaque in https://github.com/BioDataFuse/pyBiodatafuse/pull/96
  • Updated Bgee annotator to use predefined anatomical entities list by @dssib in https://github.com/BioDataFuse/pyBiodatafuse/pull/103
  • fix bgee linting error by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/105
  • Pubchem annotator by @DominikMartinat in https://github.com/BioDataFuse/pyBiodatafuse/pull/98
  • Generator fix by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/106
  • Updated Bgee annotator with devel stage and expression level, updated test by @dssib in https://github.com/BioDataFuse/pyBiodatafuse/pull/112
  • update annotators and tests by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/113
  • annotatorgeneratorfix by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/115
  • Annotator generator fix by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/119
  • added confidencelevelname for bgee by @dssib in https://github.com/BioDataFuse/pyBiodatafuse/pull/120
  • This new version takes ENSEMBL IDs instead of symbol by @adriaque in https://github.com/BioDataFuse/pyBiodatafuse/pull/122
  • fix annotators by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/121
  • minerva test by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/102
  • updated Bgee annotator to query for gene expression separately per ge… by @dssib in https://github.com/BioDataFuse/pyBiodatafuse/pull/124
  • Adding drugbank_id and side effects for drugs in the annotator by @adriaque in https://github.com/BioDataFuse/pyBiodatafuse/pull/123
  • converting tests to unittest format by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/118
  • Generator by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/125
  • there was a problem importing the graphml file, by @adriaque in https://github.com/BioDataFuse/pyBiodatafuse/pull/126
  • fix molmedb error by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/128
  • Example fix by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/136
  • Update genetograph_workflow.ipynb by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/138
  • Add merge_node function for nodes with same label by @ammar257ammar in https://github.com/BioDataFuse/pyBiodatafuse/pull/137
  • test fixes and annotators by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/131
  • disgenet: SPARQL to API by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/144
  • update disgenet and fix molmedb by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/147
  • downgrade numpy version by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/148
  • fix disgenet test bug by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/149
  • Fix opentargets functions and test by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/150
  • Fix empty df bug andadd codes to check intermediate_df by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/151
  • add opentargets cmpd-disease function by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/157
  • Common id annotator by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/154
  • fix pubchem issue by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/158
  • Update generator by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/156
  • harmonize all variables by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/161
  • Pcs usecase upadets by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/162
  • debug generator by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/163
  • generator bug fix by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/164
  • Update rdf branch to main by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/166
  • nan node fix by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/165
  • PCS usecase and fixing errors in the package while running the usecase by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/170
  • generator debugging by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/167
  • add literature data by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/171
  • update notebooks by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/172
  • update use case by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/173
  • Updated for the Wikidata graph split by @egonw in https://github.com/BioDataFuse/pyBiodatafuse/pull/174
  • Sample code for small analyses with networkx graph by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/87
  • Added RDF module by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/159
  • Fix usecase 1 by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/179
  • Update README.md by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/184
  • Dreamwalk algorithm by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/183
  • Bump tqdm from 4.65.0 to 4.66.3 by @dependabot in https://github.com/BioDataFuse/pyBiodatafuse/pull/178
  • Add generic annotator template and fix Bgee by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/190
  • support graphml by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/191
  • Implement BDFGraph object by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/194
  • Updates to the RDF module by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/195
  • Fix return for empty df by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/192
  • More RDF fixes by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/196
  • Small fixes: Pubchem and Bridgedb by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/197
  • Notebook and RDF code fixes and testing by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/198
  • Bump version: 0.0.4-dev → 0.0.4 by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/200
  • Release 1.0.0 by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/201
  • debug_stringdb by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/202
  • Update generator.py by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/206
  • fix Docs build by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/210
  • Recover metabolite by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/204
  • Restore PubChem output_datasource to fix bridgedb metabolite mapping by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/205
  • Release 1.1.0 by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/207
  • Automate input identifier type matching using regex by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/215
  • Sync with main by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/216
  • Addition of mouse species & KEGG annotator by @djwetstede in https://github.com/BioDataFuse/pyBiodatafuse/pull/176
  • Fix StringDB annotator for HGNC gene input by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/219
  • Use typing Literal to help with the database names by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/221
  • updated SPARQL queries by @DominikMartinat in https://github.com/BioDataFuse/pyBiodatafuse/pull/209
  • [New annotator] WikiPathways molecular interactions by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/223
  • Add neo4j schema by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/227
  • Example cleanup by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/228
  • Adding test_kegg.py by @djwetstede in https://github.com/BioDataFuse/pyBiodatafuse/pull/231
  • pubchem annotator update by @DominikMartinat in https://github.com/BioDataFuse/pyBiodatafuse/pull/235
  • [New Annotator] IntAct by @djwetstede in https://github.com/BioDataFuse/pyBiodatafuse/pull/225
  • [New annotator] AOP-Wiki RDF + Add GraphDB REST API support by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/211
  • Create newdatasourcerequest.yaml by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/239
  • Add identifier examples by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/241
  • Fix iteration over df by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/242
  • Muscle usecase by @tabbassidaloii in https://github.com/BioDataFuse/pyBiodatafuse/pull/203
  • Catch table processing exceptions by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/243
  • Kegg test script and generator fix by @djwetstede in https://github.com/BioDataFuse/pyBiodatafuse/pull/236
  • Small script fixes by @djwetstede in https://github.com/BioDataFuse/pyBiodatafuse/pull/240
  • Update ShEx diagram by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/246
  • Fix examples and neo4j by @YojanaGadiya in https://github.com/BioDataFuse/pyBiodatafuse/pull/247
  • Trigger workflow every 2 weeks by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/248
  • Refactor aop annotator by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/249
  • 1.2.0 by @jmillanacosta in https://github.com/BioDataFuse/pyBiodatafuse/pull/250

New Contributors

  • @dssib made their first contribution in https://github.com/BioDataFuse/pyBiodatafuse/pull/24
  • @DominikMartinat made their first contribution in https://github.com/BioDataFuse/pyBiodatafuse/pull/32
  • @hasanbalci made their first contribution in https://github.com/BioDataFuse/pyBiodatafuse/pull/38
  • @adriaque made their first contribution in https://github.com/BioDataFuse/pyBiodatafuse/pull/65
  • @dependabot made their first contribution in https://github.com/BioDataFuse/pyBiodatafuse/pull/178
  • @djwetstede made their first contribution in https://github.com/BioDataFuse/pyBiodatafuse/pull/176

Full Changelog: https://github.com/BioDataFuse/pyBiodatafuse/compare/v0.0.3...v1.2.0

- Python
Published by YojanaGadiya 8 months ago