v0.0.0

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

New Contributors

• @hrshdhgd made their first contribution in #1
• @cmungall made their first contribution in #13
• @wdduncan made their first contribution in #18
• @caufieldjh made their first contribution in #47
• @dependabot made their first contribution in #62
• @realmarcin made their first contribution in #74

Full Changelog: https://github.com/Knowledge-Graph-Hub/kg-microbe/commits/v0.0.0