Releases · Knowledge-Graph-Hub/kg-microbe

What's Changed

Fierer data transform by @hrshdhgd in #1
Doc using sphinx by @hrshdhgd in #11
trait table schema by @cmungall in #13
Adding trait schema by @cmungall in #16
add notebooks for pivoting data by @wdduncan in #18
Update README.md by @cmungall in #19
Jenkins first stab by @hrshdhgd in #22
pinned biolinkml to 1.5.8 by @hrshdhgd in #23
removed extra dependencies and update linkml by @hrshdhgd in #25
Sphinx sources addition by @hrshdhgd in #29
Sphinx sources addition by @hrshdhgd in #30
Sphinx sources addition by @hrshdhgd in #31
Rename example to data source by @hrshdhgd in #32
Refresh: dependencies, Poetry, workflows, and cleanup by @caufieldjh in #47
Fixes for transforms by @caufieldjh in #49
Produce CHEBI JSON before doing TraitsTransform by @caufieldjh in #51
Fixes for TypeError in transforms when writing to file by @caufieldjh in #53
Merge file name fixes by @caufieldjh in #55
Install multi-indexer during Jenkins run by @caufieldjh in #57
Changed setup docs by @hrshdhgd in #59
Bump cryptography from 39.0.0 to 39.0.1 by @dependabot in #62
Upgrade kg-microbe to follow the cookiecutter. by @hrshdhgd in #73
nb paths, new summaries in ./scripts by @realmarcin in #74
More improvements by @hrshdhgd in #75
Remove CHEBI pruning from the KG and use entirely by @hrshdhgd in #76
BugFix: Some terms had extra spaces that prevented CHEBI match by @hrshdhgd in #78
Updated KGX to latest version by @hrshdhgd in #79
new nb with GRAPE viz by @realmarcin in #77
expanded feature set by @realmarcin in #82
NER for unmatched terms by @hrshdhgd in #83
make edits by @realmarcin in #81
Uniprot by @bsantan in #88
Feba exploration by @hrshdhgd in #84
Summaries by @realmarcin in #90
Paths&blank files fix by @bsantan in #91
lower case uniprot paths by @realmarcin in #92
aligning uniprot paths by @realmarcin in #93
Update download_utils.py by @bsantan in #95
uniprot cache fixes by @realmarcin in #98
one more line for cache by @realmarcin in #99
Uniprot empty queries patch by @bsantan in #101
Create UniProt_s3_dump.yml by @hrshdhgd in #109
Use GH workflow to populate Uniprot data into an S3 bucket by @hrshdhgd in #107
Uniprot sourcename fix by @bsantan in #108
Accommodate pagination by @hrshdhgd in #112
Add to parallel code by @hrshdhgd in #113
Fixes #117 by @hrshdhgd in #118
Update README.md by @realmarcin in #119
Update README.md by @realmarcin in #120
Update README.md by @realmarcin in #121
Update README.md by @realmarcin in #122
Update README.md by @realmarcin in #123
Update README.md by @realmarcin in #124
Prefix refactor by @hrshdhgd in #125
Summaries by @realmarcin in #127
Assays by @hrshdhgd in #128
BacDive resource files by @hrshdhgd in #130
New run by @hrshdhgd in #133
Make summary by @realmarcin in #134
deleting stray nb by @realmarcin in #135
RHEA mappings by @hrshdhgd in #136
Added keyword nodes by @hrshdhgd in #138
BactoTraits & Uniprot TrEMBL format transforms by @hrshdhgd in #139
Added labels by @hrshdhgd in #147
BactTraits ingest by @hrshdhgd in #146
Fine tuning by @hrshdhgd in #152
Added medium-type Category and re-ran transform by @hrshdhgd in #153
get latest master by @bsantan in #156
Add strain nodes by @hrshdhgd in #157
Uniprot2s3 transform new by @bsantan in #149
Normalized provided_by column by @hrshdhgd in #161
Refactor provided_by to primary_knowledge_source in edges file. by @hrshdhgd in #162
unipathways post processing transform by @bsantan in #160
Fix protein name parsing by @bsantan in #163
fix issue of getting "EC: " nodes by @bsantan in #164
Updates to Rhea and EC ingest by @bsantan in #165
Bacdive fixes by @hrshdhgd in #167
Add assay: prefix instead of API_XX by @hrshdhgd in #169
Update README.md by @realmarcin in #171
Add UPA pathway to go edges by @bsantan in #172
isolation sources for all bacdive ncbitaxon entities by @bsantan in #175
transformed and tmp files results for isolation source by @bsantan in #176
update all carbon substrate edges to use "consumes" by @bsantan in #179
Add name-taxonomy-classification information by @hrshdhgd in #178