cmungall

Computer Research Scientist at Berkeley Lab. Interests: AI / Ontologies / Bioinformatics. Projects: GO, Monarch, Alliance, OBOFoundry, NMDC

Lawrence Berkeley National LaboratoryBerkeley, CA

Pinned Repositories

blipkit
biological logic programming toolkit
Language:Prolog27 6 83
gosf2github
migrates tickets to GH from SF
Language:Perl37 5 1619
owljs
Javascript wrapper for the OWLAPI
Language:Web Ontology Language34 12 710
sparqlprog
logic programming with SPARQL
Language:Prolog45 9 47
biomake
GNU-Make-like utility for managing builds and complex workflows
Language:Prolog99 11 609
go-ontology
Source ontology files for the Gene Ontology
Language:Makefile214 37 19.8k39
obographs
Basic and Advanced OBO Graphs: specification and reference implementation
Language:Java62 19 7912
linkml
Linked Open Data Modeling Language
Language:Python291 14 1.2k89
ontogpt
LLM-based ontological extraction tools, including SPIRES
Language:Jupyter Notebook531 18 17266
uberon
An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
Language:Emacs Lisp129 29 2.4k28

cmungall's Repositories

cmungall/venomx
Vector Embedding Named Object Model indeX
Language:Python9 2 21
cmungall/json-flattener
Python library for denormalizing nested dicts or json objects to tables and back
Language:Python8 2 23
cmungall/linkml-phenopackets
EXPERIMENTAL rendering of phenopackets in linkml
Language:Python7 4 2
cmungall/obo-scripts
standalone perl scripts for hacking obo files
Language:Perl5 3 02
cmungall/formal-ontology-analysis
Language:Jupyter Notebook3 1 1
cmungall/bibliomancer
Performs magic on bibliographies
Language:Jupyter Notebook2 2 0
cmungall/gpt-reasoning-manuscript
Language:Jupyter Notebook2 2 0
cmungall/bioregistry
📮 An integrative registry of biological databases, ontologies, and nomenclatures.
Language:Python1 1 0
cmungall/curies
🐸 Idiomatic conversion between URIs and compact URIs (CURIEs)
Language:Python1 0 0
cmungall/gbwg
Genomic Biodiversity Interest Group
Language:Jupyter Notebook1 0 0
cmungall/go-db
TEST bulk loading of go into duckdb
Language:Python1 1 0
cmungall/obolog
Obolog specification (abandoned)
Language:HTML1 2 0
cmungall/rhea-go-llm-analysis
validate-mappings for GO-RHEA
Language:Jupyter Notebook1 1 0
cmungall/ucumvert
Python parser for UCUM (Unified Code for Units of Measure) incl. converter to pint units
Language:Python1 0 0
cmungall/Exomiser
A Tool to Annotate and Prioritize Exome Variants
Language:Java2 0
cmungall/funrun
1 0
cmungall/go-cam-analysis
Language:Jupyter Notebook1 0
cmungall/hoopla
Language:Python1 0
cmungall/hra-vccf
HRA VCCF: Human Reference Atlas - Vasculature Common Coordinate Framework
Language:TSQL
cmungall/linkml-cfde
EXPERIMENTAL rendering of Common Fund Data Ecocystem as LinkML
Language:Python1 2
cmungall/litellm
Call all LLM APIs using the OpenAI format. Use Bedrock, Azure, OpenAI, Cohere, Anthropic, Ollama, Sagemaker, HuggingFace, Replicate (100+ LLMs)
Language:Python0 0
cmungall/llm
Access large language models from the command-line
Language:Python0 0
cmungall/llm-openrouter
LLM plugin for models hosted by OpenRouter
Language:Python0 0
cmungall/mondo-refactoring
Language:Makefile1 0
cmungall/obi
The Ontology for Biomedical Investigations
Language:Makefile1 0
cmungall/PhenopacketLab
An Angular/Springboot web application for the loading, editing, saving of data that follows the Phenopacket Schema
Language:TypeScript0 0
cmungall/rdf-expressionizer
Translates named classes to equivalent class expressions
Language:Python1 0
cmungall/reusabledata
The home repository for the (Re)usable Data Project.
Language:JavaScript0 0
cmungall/simona
Semantic Similarity in Bio-Ontologies
Language:R0 0
cmungall/w3id.org
Website source code for w3id.org
Language:HTML2 0