v1.2.0

What's Changed

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

New Contributors

• @dssib made their first contribution in #24
• @DominikMartinat made their first contribution in #32
• @hasanbalci made their first contribution in #38
• @adriaque made their first contribution in #65
• @dependabot made their first contribution in #178
• @djwetstede made their first contribution in #176

Full Changelog: v0.0.3...v1.2.0