Software

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

PyBEL
A compiler for the Biological Expression Language (BEL)

Bio2BEL
A framework for reproducible data integration in BEL and knowledge graph construction

BEL Commons
A web application for the interactive exploration of networks encoded in BEL

PyKEEN
The most expansive knowledge graph embedding framework to date

SeMRA
Automated assembly and inference of semantic mappings

Bioontologies
Access and processing of ontologies on top of ROBOT and OBO Graphs

PyOBO
Harmonization of biological ontologies and controlled vocabularies

curies
Idiomatic conversion between URIs and compact URIs (CURIEs)

GuiltyTargets
Target prioritization framework using gene expression and network representation learning

RatVec
Sequence-based representation learning

PS4DR
Drug repositioning based on bioactivity pattern matching and GWAS

SeffNet
Drug repositioning framework based on network representation learning

CLEP
Patient stratification framework based on network representation learning

BEL2SCM
Generation of structural causal models (SCMs) from BEL

y0 Causal Inference Engine
Representation and manipulating probabilistic expressions

STonKGs
Multimodal Transformers for biomedical text and Knowledge Graph data

ChemicalX
A deep learning library for drug-drug interaction, polypharmacy side effect, and synergy prediction.

PathMe
Web application for exploration of pathway databases

Pathway Forte
Benchmarking pathway databases in functional enrichment analysis and prediction methods

INDRA
Automated knowledge assembly and modeling in biomedicine

INDRA CoGEx
A $10^8$ relation-scale knowledge graph extending on causal knowledge from INDRA

MIRA
Machine-assisted scientific modeling using meta-model templates and domain knowledge graphs

Gilda
Biomedical named entity recognition and grounding using machine-learned disambiguation

Databases

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

Bioregistry creator, maintainer
An integrative meta-registry of biological databases, ontologies, and nomenclatures.

Biomappings creator, maintainer
Predicted and curated mappings between named biological entities

Biolookup creator, maintainer
Comprehensive database of identifiers, names, synonyms, cross-references, properties, and relations for biomedical entities

Bioversions creator, maintainer
Automated tracking of the current version for each biological database?

OBO Database Ingest creator, maintainer
Conversion of biomedical databases into ontologies

Chemical Roles Graph creator, maintainer
Connecting roles in the ChEBI ontology to their targets

CONSO creator, maintainer
Ontology of phenomena related to neurodegeneration

CONIB creator, maintainer
Curated knowledge graphs describing neurodegeneration in BEL

ComPath contributor
A data integration pipeline, manually curated dataset of mappings between pathway databases, and web application for integrative analysis of pathways