v0.3.0

Highlights

Generate-and-Extract Command

This release adds a new command generate-extract that composes two operations.

• generate a natural language description
• parse the NL description using SPIRES

Cell Type Use Case

(This use case based on a conversation with @dosumis)

For example, given a cell type such as Acinar Cell Of Salivary Gland
, generate a description using GPT describing many aspects of the cell type, from it's marker genes through to its function and diseases it is implicated in.

After that use the cell-type schema (https://w3id.org/ontogpt/cell_type) to extract this into structured form. As an optional next step use linkml-owl to generate OWL TBox axioms

Iterative generate-extract

The command can be executed in iterative mode - this will traverse the extracted subtypes with each iteration, gradually building up an ontology that is entirely generated from the "latent knowledge" in the LLM

Here is a screenshot of an ontology generated entirely using OntoGPT by traversing from "Interneuron" downwards:

There are many oddities about it, currently each iteration is independent so it has no way of knowing if it is has already made a concept, but an interesting proof of principle. The ugly pct-encoded labels indicate cases where it couldn't match to an existing concept in CL or other ontology, and may represent KB gaps to be filled

More thoughts here: cell type summaries

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
• 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
• 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
• 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
• 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
• Added streamlit app for spindoctor by @cmungall in #101
• Study class as tree root in environment_sample template by @sujaypatil96 in #104
• update sections in README by @sujaypatil96 in #105
• Fixed a bug where the 'skip_annotators' option was being ignored by @daikiad in #108
• first trait commits by @cmungall in #109
• first draft of biotic interaction template by @diatomsRcool in #107
• One more fix for biotic interaction template by @caufieldjh in #113
• Adding a GPT-based reasoner, for evaluation purposes. by @cmungall in #112
• more prompt language and adding ENVTHES ontology by @realmarcin in #118
• Add general framework for specifying models by name and source by @caufieldjh in #99
• Adding a MappingEngine by @cmungall in #121
• removing importlib dependency by @cmungall in #122
• very small typo fix by @PR0CK0 in #124
• Init environmental metadata template by @caufieldjh in #117
• use latest rueaml. Avoids problems like this: monarch-initiative/talisman-paper#4 by @cmungall in #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 #127
• relaxing pinning by @cmungall in #129
• reasoner gpt changes by @cmungall in #128
• Retrieve remote models for local use and pass extract prompt to them by @caufieldjh in #123
• First pass at PhenoEngine by @cmungall in #130
• New PubMed eutil functions by @caufieldjh in #131
• Cleanup and documentation updates by @caufieldjh in #115
• Start of PR for IBD literature project by @justaddcoffee in #120
• Fixes for #139 by @caufieldjh in #142
• Add interface for HuggingFace Hub by @caufieldjh in #145
• Dependency updates by @caufieldjh in #151
• Adding generate-extract command, 158. Add cell type templates #159 by @cmungall in #162
• Removed temporary hack when generating documentation. Adding cell type to docs by @cmungall in #163
• Adding to cell/neuron template by @cmungall in #164
• Fix 157 - make webapp work, expand set of available data models by @caufieldjh in #165
• Add functionality for PubMed Central text retrieval by @caufieldjh in #156
• Improvements to iterative generate-extract. by @cmungall in #166

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
• @wdduncan made their first contribution in #53
• @sujaypatil96 made their first contribution in #104
• @daikiad made their first contribution in #108
• @diatomsRcool made their first contribution in #107
• @PR0CK0 made their first contribution in #124

Full Changelog: v0.2.0...v0.3.0