OntoGPT

• Playing around: adding a phenotype extractor by @matentzn in https://github.com/monarch-initiative/ontogpt/pull/14
• add unit test to makefile by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/16
• Linted and minor flake8 edits by @hrshdhgd in https://github.com/monarch-initiative/ontogpt/pull/15
• Add linter to workflow by @hrshdhgd in https://github.com/monarch-initiative/ontogpt/pull/17
• Improve dependencies, add a web optional by @vemonet in https://github.com/monarch-initiative/ontogpt/pull/21
• add recipe for test by @sierra-moxon in https://github.com/monarch-initiative/ontogpt/pull/23
• added pad krapow recipe by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/25
• Add recipe URL by @pkalita-lbl in https://github.com/monarch-initiative/ontogpt/pull/24
• Add Walforf Salad URL by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/26
• Add rajma pulao to recipe-urls.csv by @turbomam in https://github.com/monarch-initiative/ontogpt/pull/27
• Adding gene set enrichment by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/30
• enrichment by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/31
• README updates; add project.Makefile by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/32
• allow use of different models, entailing different API endpoints. extending enrichment comparison. by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/34
• Add CITATION and version updater by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/35
• Ingest and extract things from literature about inflammatory bowel disease by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/36
• eval enrich by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/37
• Create dental-restoration-material-composite-polymer-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/53
• Create dental-restoration-material-composite-resin-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/52
• Create dental-restoration-material-ceramic-composite-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/51
• Create dental-restoration-material-ceramic-composite-resin-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/50
• Create dental-restoration-material-ceramic-composite-polymer-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/49
• Create dental-restoration-material-ceramic-composite-polymer-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/48
• Create dental-restoration-material-ceramic-composite-polymer-resin-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/47
• Create dental-restoration-material-ceramic-composite-polymer-resin-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/46
• Create dental-restoration-material-composite-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/45
• Create dental-restoration-material-composite-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/44
• Create dental-restoration-material-polymer-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/42
• Create dental-restoration-material-resin-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/41
• Create dental-restoration-material-ceramic-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/39
• Create dental-restoration-material-ceramic-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/38
• Create dental-restoration-material-resin-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/40
• Create dental-restoration-material-polymer-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/43
• similarity by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/57
• Add option to provide path to input file by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/56
• Bicluster enrichment by @realmarcin in https://github.com/monarch-initiative/ontogpt/pull/62
• Added command and code for computing euclidian distances between embeddings by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/58
• Flake8 fixes + lint by @hrshdhgd in https://github.com/monarch-initiative/ontogpt/pull/63
• enrichment changes by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/65
• Missed parenthesis for random.SystemRamdom() by @hrshdhgd in https://github.com/monarch-initiative/ontogpt/pull/67
• Change citation updater in Makefile to get_version by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/68
• Raise FileNotFoundError if filepath for extract is missing by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/72
• Makefile uses all templates by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/69
• interactive-mode by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/71
• Added command to generate mock clinical notes by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/74
• Bump version of oaklib by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/73
• msigdb hallmark gene sets by @realmarcin in https://github.com/monarch-initiative/ontogpt/pull/78
• use prompts for enrichment by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/80
• fixing gene sets and updating analysis by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/81
• Adding schema for ontology issues in github. refactor enrichment by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/83
• p-value templates with edited end markers to run multiple independent… by @realmarcin in https://github.com/monarch-initiative/ontogpt/pull/82
• Add diagnostic_procedure template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/29
• Fix for web-ontogpt not working on new install by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/85
• geneweaver format by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/89
• re-ran notebook by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/90
• re-ran notebooks for enrichGPT by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/95
• Update documentation by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/92
• Autogenerate docs by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/98
• Fix for doc generation by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/100
• Added streamlit app for spindoctor by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/101
• Study class as tree root in environment_sample template by @sujaypatil96 in https://github.com/monarch-initiative/ontogpt/pull/104
• update sections in README by @sujaypatil96 in https://github.com/monarch-initiative/ontogpt/pull/105
• Fixed a bug where the 'skip_annotators' option was being ignored by @daikiad in https://github.com/monarch-initiative/ontogpt/pull/108
• first trait commits by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/109
• first draft of biotic interaction template by @diatomsRcool in https://github.com/monarch-initiative/ontogpt/pull/107
• One more fix for biotic interaction template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/113
• Adding a GPT-based reasoner, for evaluation purposes. by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/112
• more prompt language and adding ENVTHES ontology by @realmarcin in https://github.com/monarch-initiative/ontogpt/pull/118
• Add general framework for specifying models by name and source by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/99
• Adding a MappingEngine by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/121
• removing importlib dependency by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/122
• very small typo fix by @PR0CK0 in https://github.com/monarch-initiative/ontogpt/pull/124
• Init environmental metadata template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/117
• use latest rueaml. Avoids problems like this: https://github.com/monarch-initiative/enrichgpt-results/issues/4 by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/126
• Add a command 'pubmed-annotate' to retrieve PMIDs for a search term, then apply a template to all of them to extract info by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/127
• relaxing pinning by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/129
• reasoner gpt changes by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/128
• Retrieve remote models for local use and pass extract prompt to them by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/123
• First pass at PhenoEngine by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/130
• New PubMed eutil functions by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/131
• Cleanup and documentation updates by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/115
• Start of PR for IBD literature project by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/120
• Fixes for #139 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/142
• Add interface for HuggingFace Hub by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/145
• Dependency updates by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/151
• Adding generate-extract command, 158. Add cell type templates #159 by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/162
• Removed temporary hack when generating documentation. Adding cell type to docs by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/163
• Adding to cell/neuron template by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/164
• Fix 157 - make webapp work, expand set of available data models by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/165
• Add functionality for PubMed Central text retrieval by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/156
• Improvements to iterative generate-extract. by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/166

• @matentzn made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/14
• @vemonet made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/21
• @sierra-moxon made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/23
• @justaddcoffee made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/25
• @pkalita-lbl made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/24
• @turbomam made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/27
• @wdduncan made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/53
• @sujaypatil96 made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/104
• @daikiad made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/108
• @diatomsRcool made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/107
• @PR0CK0 made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/124

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.2.0...v0.3.0