Releases · BioDataFuse/pyBiodatafuse

What's Changed

Fix compound mapping issue by @jmillanacosta in #252
KEGG compounds fix by @djwetstede in #255
Fix AOP queries and update notebooks by @jmillanacosta in #258
Compound support and metadata fix for KEGG by @djwetstede in #257
fix json format by @tabbassidaloii in #254
cytoscape_format_fix by @tabbassidaloii in #260
add function back to cytoscape.py by @tabbassidaloii in #261
debug cytoscape load by @tabbassidaloii in #262
debug metadata for molmedb by @tabbassidaloii in #263
update intact codes (from #259 ) by @tabbassidaloii in #264
Compound support for generator by @djwetstede in #233
Directly use Bioregistry for updating datasources.csv by @cthoyt in #266
MolMeDB RDF query update for new schema by @DominikMartinat in #267
Revert graph label attribute to "labels" by @jmillanacosta in #238
Add CompoundWiki support by @djwetstede in #265
Patch aopwiki + ruff lint fixes by @jmillanacosta in #268
example notebook cleanup by @YojanaGadiya in #271
Fixes before release 1.3.0 by @jmillanacosta in #270

New Contributors

@cthoyt made their first contribution in #266

Full Changelog: v1.2.0...v1.3.0

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 http...