I’ve created many open-source projects as well as made significant contributions to others:

PyBEL Logo PyBEL GitHub logo WikiData logo
A compiler for the Biological Expression Language (BEL)
Bio2BEL Logo Bio2BEL GitHub logo
A framework for reproducible data integration in BEL and knowledge graph construction
BEL Commons Logo BEL Commons GitHub logo
A web application for the interactive exploration of networks encoded in BEL
PyKEEN Logo PyKEEN GitHub logo WikiData logo
The most expansive knowledge graph embedding framework to date
SeMRA GitHub logo
Automated assembly and inference of semantic mappings
Bioontologies GitHub logo
Access and processing of ontologies on top of ROBOT and OBO Graphs
PyOBO Logo PyOBO GitHub logo
Harmonization of biological ontologies and controlled vocabularies
curies GitHub logo
Idiomatic conversion between URIs and compact URIs (CURIEs)
GuiltyTargets Logo GuiltyTargets GitHub logo
Target prioritization framework using gene expression and network representation learning
RatVec Logo RatVec GitHub logo
Sequence-based representation learning
PS4DR Logo PS4DR GitHub logo
Drug repositioning based on bioactivity pattern matching and GWAS
SeffNet Logo SeffNet GitHub logo
Drug repositioning framework based on network representation learning
CLEP Logo CLEP GitHub logo
Patient stratification framework based on network representation learning
BEL2SCM Logo BEL2SCM GitHub logo
Generation of structural causal models (SCMs) from BEL
y0 Causal Inference Engine Logo y0 Causal Inference Engine GitHub logo
Representation and manipulating probabilistic expressions
STonKGs Logo STonKGs GitHub logo
Multimodal Transformers for biomedical text and Knowledge Graph data
ChemicalX Logo ChemicalX GitHub logo
A deep learning library for drug-drug interaction, polypharmacy side effect, and synergy prediction.
PathMe Logo PathMe GitHub logo
Web application for exploration of pathway databases
Pathway Forte Logo Pathway Forte GitHub logo
Benchmarking pathway databases in functional enrichment analysis and prediction methods
INDRA Logo INDRA GitHub logo
Automated knowledge assembly and modeling in biomedicine
INDRA CoGEx GitHub logo
A $10^8$ relation-scale knowledge graph extending on causal knowledge from INDRA
MIRA GitHub logo
Machine-assisted scientific modeling using meta-model templates and domain knowledge graphs
Gilda GitHub logo
Biomedical named entity recognition and grounding using machine-learned disambiguation


I’ve created many databases myself through curation, automated assembly, and also by coordinating others.

Bioregistry Logo Bioregistry creator, maintainer GitHub logo
An integrative meta-registry of biological databases, ontologies, and nomenclatures.
Biomappings Logo Biomappings creator, maintainer GitHub logo
Predicted and curated mappings between named biological entities
Biolookup Logo Biolookup creator, maintainer GitHub logo
Comprehensive database of identifiers, names, synonyms, cross-references, properties, and relations for biomedical entities
Bioversions Logo Bioversions creator, maintainer GitHub logo
Automated tracking of the current version for each biological database?
OBO Database Ingest creator, maintainer GitHub logo
Conversion of biomedical databases into ontologies
Chemical Roles Graph Logo Chemical Roles Graph creator, maintainer GitHub logo
Connecting roles in the ChEBI ontology to their targets
CONSO Logo CONSO creator, maintainer GitHub logo
Ontology of phenomena related to neurodegeneration
CONIB Logo CONIB creator, maintainer GitHub logo
Curated knowledge graphs describing neurodegeneration in BEL
ComPath Logo ComPath contributor GitHub logo
A data integration pipeline, manually curated dataset of mappings between pathway databases, and web application for integrative analysis of pathways