Releases: Knowledge-Graph-Hub/kg-microbe
Releases · Knowledge-Graph-Hub/kg-microbe
v0.0.1
Test
release
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
toprimary_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 ofAPI_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