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Hi there 👋

I work with biological knowledge graphs, machine learning, and artificial intelligence to identify active molecules and to deconvolute their mechanisms of action.

🧰 My Projects

  • 📮 Bioregistry: an integrative registry of biological databases, ontologies, and nomenclatures.
  • 🧬 Biological Expression Language (BEL): a domain specific language for representing molecular biology
  • 🌶️ PyBEL: the computational ecosystem for compiling, querying, and analyzing knowledge graphs encoded in BEL
  • 📛 PyOBO: making ontologies and semantics accessible
  • 🤖 PyKEEN: knowledge graph embedding models for humans

⚖️ My Core Scientific Values

  • ♻️ Reproducibility: code is part of the scientific process. It should be documented and re-usable by anyone.
  • 🔓 Openness: science is best when people can build on each others' work. Sharing data, code, and ideas has benefitted everyone, and is also the responsiblity of a scientist to pay forward.
  • 🎯 Thoroughness: quality is dependent on taking great care throughout all steps

📫 My Interblag

Besides my email and blog (on the left), I'm also in the internet in the following places:

Charles Tapley Hoyt's Projects

add-trailing-comma icon add-trailing-comma

A tool (and pre-commit hook) to automatically add trailing commas to calls and literals.

adeft icon adeft

Tool for disambiguating acronyms and abbreviations in text for NLP applications

agr_schemas icon agr_schemas

A repository of JSON schemas for incorporating data into the Alliance of Genome Resources.

agro icon agro

AgrO describes agronomic practices, techniques, and variables used in agronomic experiments.

aism icon aism

This repository contains the ontology for the Anatomy of the Insect SkeletoMuscular system (AISM), which contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research.

apicuron-client icon apicuron-client

A python client for interacting with the APICURON curation metadatabase's RESTful API

archivo icon archivo

DBpedia Archivo - Augmented Ontology Archive powered by Databus

aro icon aro

The Antibiotic Resistance Ontology (ARO) organizes the information describing the ability of a microorganism to withstand the effects of an antibiotic

authorship icon authorship

🚢 Generate publication-ready authorship lists via Google Sheets and more

autoreviewer icon autoreviewer

👁️‍🗨️ Scientists often do the same bad stuff. Automate giving feedback during peer review.

b2 icon b2

Bertini 2.0: The redevelopment of Bertini in C++.

baton icon baton

Baton is a Composer dependency analytics tool which helps you keep track of the Composer dependencies in your PHP projects.

behavior-ontology icon behavior-ontology

Neuro Behaviour Ontology: an ontology for human and animal behaviour processes and behaviour phenotypes

bern2 icon bern2

BERN2: an advanced neural biomedical namedentity recognition and normalization tool

bfo icon bfo

BFO repository including source code and latest documents

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