cmungall
Computer Research Scientist at Berkeley Lab. Interests: AI / Ontologies / Bioinformatics. Projects: GO, Monarch, Alliance, OBOFoundry, NMDC
Lawrence Berkeley National LaboratoryBerkeley, CA
Pinned Repositories
gosf2github
migrates tickets to GH from SF
owljs
Javascript wrapper for the OWLAPI
semantic-llama
A knowledge extraction tool that uses a large language model to extract semantic information from text
sparqlprog
logic programming with SPARQL
biomake
GNU-Make-like utility for managing builds and complex workflows
go-ontology
Source ontology files for the Gene Ontology
obographs
Basic and Advanced OBO Graphs: specification and reference implementation
linkml
Linked Open Data Modeling Language
ontogpt
LLM-based ontological extraction tools, including SPIRES
uberon
An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
cmungall's Repositories
cmungall/linkml-phenopackets
EXPERIMENTAL rendering of phenopackets in linkml
cmungall/gold-ontology
cmungall/awesome-semantic-web
A curated list of various semantic web and linked data resources.
cmungall/chemessence
EXPERIMENTAL extraction of essence from CHEBI
cmungall/gpt-reasoning-manuscript
cmungall/agent-tutorial
Monarch agent tutorial
cmungall/bioregistry
📮 An integrative registry of biological databases, ontologies, and nomenclatures.
cmungall/comet
cmungall/dbic_chado
Meant to be a standard DBIx::Class layer for the Chado database schema. Generated using DBIx::Class::Schema::Loader
cmungall/go-db
TEST bulk loading of go into duckdb
cmungall/amigo
AmiGO is the public interface for the Gene Ontology.
cmungall/aro
The Antibiotic Resistance Ontology (ARO) organizes the information describing the ability of a microorganism to withstand the effects of an antibiotic
cmungall/contextualizer
cmungall/conto_diff
This project is the implementation of the ContoDiff approach.
cmungall/edd-schema
cmungall/family_history_terminology
cmungall/gilda
Grounding of biomedical named entities with contextual disambiguation
cmungall/go-cam-reviews
AI generated reviews of GO-CAMs
cmungall/go-ontology
Source ontology files for the Gene Ontology
cmungall/hra-vccf
HRA VCCF: Human Reference Atlas - Vasculature Common Coordinate Framework
cmungall/llm
Access large language models from the command-line
cmungall/metabolights-enriched
cmungall/neo4j2owl
Semantics preserving mapping of OWL 2 EL and Neo4J.
cmungall/phenopacket-store
Collections of GA4GH phenopackets that represent individuals with Mendelian diseases.
cmungall/py-horned-owl
A library for Web Ontology Language in Python created using a bridge from horned-owl to python using PyO3.
cmungall/pydantic-ai
Agent Framework / shim to use Pydantic with LLMs
cmungall/pyobo
📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures
cmungall/simona
Semantic Similarity in Bio-Ontologies
cmungall/w3id.org
Website source code for w3id.org
cmungall/whelk
Whelk is an OWL EL reasoner