Releases · monarch-initiative/ontogpt · GitHub

12 May 21:37

What's Changed

Add diagnostic_procedure template by @caufieldjh in #29
Fix for web-ontogpt not working on new install by @caufieldjh in #85
geneweaver format by @cmungall in #89
re-ran notebook by @cmungall in #90
re-ran notebooks for enrichGPT by @cmungall in #95
Update documentation by @caufieldjh in #92
Autogenerate docs by @caufieldjh in #98
Fix for doc generation by @caufieldjh in #100

Full Changelog: v0.2.4...v0.2.5

Contributors

cmungall and caufieldjh

Assets 2

04 May 00:12

What's Changed

Adding schema for ontology issues in github. refactor enrichment by @cmungall in #83
p-value templates with edited end markers to run multiple independent… by @realmarcin in #82

Full Changelog: v0.2.3...v0.2.4

Contributors

cmungall and realmarcin

Assets 2

02 May 00:10

What's Changed

Added command to generate mock clinical notes by @justaddcoffee in #74
Bump version of oaklib by @cmungall in #73
msigdb hallmark gene sets by @realmarcin in #78
use prompts for enrichment by @cmungall in #80
fixing gene sets and updating analysis by @cmungall in #81

Full Changelog: v0.2.2...v0.2.3

Contributors

cmungall, justaddcoffee, and realmarcin

Assets 2

21 Apr 22:18

What's Changed

Adding gene set enrichment by @cmungall in #30
enrichment by @cmungall in #31
README updates; add project.Makefile by @caufieldjh in #32
allow use of different models, entailing different API endpoints. extending enrichment comparison. by @cmungall in #34
Add CITATION and version updater by @caufieldjh in #35
Ingest and extract things from literature about inflammatory bowel disease by @justaddcoffee in #36
eval enrich by @cmungall in #37
Create dental-restoration-material-composite-polymer-1.txt by @wdduncan in #53
Create dental-restoration-material-composite-resin-1.txt by @wdduncan in #52
Create dental-restoration-material-ceramic-composite-1.txt by @wdduncan in #51
Create dental-restoration-material-ceramic-composite-resin-1.txt by @wdduncan in #50
Create dental-restoration-material-ceramic-composite-polymer-2.txt by @wdduncan in #49
Create dental-restoration-material-ceramic-composite-polymer-1.txt by @wdduncan in #48
Create dental-restoration-material-ceramic-composite-polymer-resin-2.txt by @wdduncan in #47
Create dental-restoration-material-ceramic-composite-polymer-resin-1.txt by @wdduncan in #46
Create dental-restoration-material-composite-2.txt by @wdduncan in #45
Create dental-restoration-material-composite-1.txt by @wdduncan in #44
Create dental-restoration-material-polymer-1.txt by @wdduncan in #42
Create dental-restoration-material-resin-2.txt by @wdduncan in #41
Create dental-restoration-material-ceramic-2.txt by @wdduncan in #39
Create dental-restoration-material-ceramic-1.txt by @wdduncan in #38
Create dental-restoration-material-resin-1.txt by @wdduncan in #40
Create dental-restoration-material-polymer-2.txt by @wdduncan in #43
similarity by @cmungall in #57
Add option to provide path to input file by @caufieldjh in #56
Bicluster enrichment by @realmarcin in #62
Added command and code for computing euclidian distances between embeddings by @justaddcoffee in #58
Flake8 fixes + lint by @hrshdhgd in #63
enrichment changes by @cmungall in #65
Missed parenthesis for random.SystemRamdom() by @hrshdhgd in #67
Change citation updater in Makefile to get_version by @caufieldjh in #68
Raise FileNotFoundError if filepath for extract is missing by @caufieldjh in #72
Makefile uses all templates by @caufieldjh in #69
interactive-mode by @cmungall in #71

New Contributors

@wdduncan made their first contribution in #53

Full Changelog: v0.2.1...v0.2.2

Contributors

cmungall, justaddcoffee, and 4 other contributors

Assets 2

06 Apr 15:20

What's Changed

Playing around: adding a phenotype extractor by @matentzn in #14
add unit test to makefile by @cmungall in #16
Linted and minor flake8 edits by @hrshdhgd in #15
Add linter to workflow by @hrshdhgd in #17
Improve dependencies, add a web optional by @vemonet in #21
add recipe for test by @sierra-moxon in #23
added pad krapow recipe by @justaddcoffee in #25
Add recipe URL by @pkalita-lbl in #24
Add Walforf Salad URL by @caufieldjh in #26
Add rajma pulao to recipe-urls.csv by @turbomam in #27

New Contributors

@matentzn made their first contribution in #14
@vemonet made their first contribution in #21
@sierra-moxon made their first contribution in #23
@justaddcoffee made their first contribution in #25
@pkalita-lbl made their first contribution in #24
@turbomam made their first contribution in #27

Full Changelog: v0.2.0...v0.2.1

Contributors

cmungall, justaddcoffee, and 7 other contributors

Assets 2

23 Mar 01:14

What's Changed

If output is YAML, codecs not needed by @hrshdhgd in #1
Readme updates and other doc copyedits by @caufieldjh in #2
owl generation by @cmungall in #7
three cases for 'environmental_sample' by @realmarcin in #8
Env study test cases by @realmarcin in #10
refactor tests by @cmungall in #12

New Contributors

@hrshdhgd made their first contribution in #1
@caufieldjh made their first contribution in #2
@cmungall made their first contribution in #7
@realmarcin made their first contribution in #8

Full Changelog: v0.1.0...v0.2.0

Contributors

cmungall, realmarcin, and 2 other contributors

Assets 2

05 Jan 22:42

Full Changelog: https://github.com/monarch-initiative/ontogpt/commits/v0.1.1

Assets 2

05 Jan 20:09

Full Changelog: https://github.com/monarch-initiative/ontogpt/commits/v0.1.0

Assets 2