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On sabbatical - unable to respond until Fall 2024.
On sabbatical - unable to respond until Fall 2024.
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Hi there ๐Ÿ‘‹

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

๐Ÿงฐ My Projects

  • ๐Ÿ“ฎ Bioregistry: an integrative registry of biological databases, ontologies, and nomenclatures.
  • ๐Ÿงฌ Biological Expression Language (BEL): a domain specific language for representing molecular biology
  • ๐ŸŒถ๏ธ PyBEL: the computational ecosystem for compiling, querying, and analyzing knowledge graphs encoded in BEL
  • ๐Ÿ“› PyOBO: making ontologies and semantics accessible
  • ๐Ÿค– PyKEEN: knowledge graph embedding models for humans

โš–๏ธ My Core Scientific Values

  • โ™ป๏ธ Reproducibility: code is part of the scientific process. It should be documented and re-usable by anyone.
  • ๐Ÿ”“ 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.
  • ๐ŸŽฏ Thoroughness: quality is dependent on taking great care throughout all steps

๐Ÿ“ซ My Interblag

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

Pinned Loading

  1. pybel/pybel pybel/pybel Public

    ๐ŸŒถ๏ธ An ecosystem in Python for working with the Biological Expression Language (BEL)

    Python 131 31

  2. pykeen/pykeen pykeen/pykeen Public

    ๐Ÿค– A Python library for learning and evaluating knowledge graph embeddings

    Python 1.6k 183

  3. biopragmatics/pyobo biopragmatics/pyobo Public

    ๐Ÿ“› A Python package for using ontologies, terminologies, and biomedical nomenclatures

    Python 59 13

  4. biopragmatics/bioregistry biopragmatics/bioregistry Public

    ๐Ÿ“ฎ An integrative registry of biological databases, ontologies, and nomenclatures.

    Python 108 48