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


  1. 🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

    Python 88 28

  2. 📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology

    TeX 23 2

  3. 🤖 A Python library for learning and evaluating knowledge graph embeddings

    Python 673 97

  4. 📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures

    Python 24 9

6,326 contributions in the last year

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Mon Wed Fri

Contribution activity

January 2022

Created 8 repositories

Created a pull request in OBOFoundry/ that received 18 comments

🎅 Update repo metadata

This PR makes the following updates to OBO Foundry metadata: Updates some out of date GitHub repository URLs (BCO, MP, NCRO) Adds GitHub repositor…

+78 −22 18 comments
Opened 54 other pull requests in 11 repositories
AstraZeneca/chemicalx 12 merged
OBOFoundry/ 3 open 6 merged
AstraZeneca/rexmex 2 open 7 merged
biopragmatics/bioregistry 1 open 7 merged
pykeen/pykeen 3 open 3 merged
cthoyt/pystow 2 merged 1 open
bgyori/indra_cogex 3 merged
cthoyt/geometric-graphs 1 merged
cthoyt/pyrdle 1 merged
json-ld/ 1 merged
bioclipse/bioclipse.scripting 1 open
Reviewed 41 pull requests in 11 repositories
pykeen/pykeen 19 pull requests
AstraZeneca/chemicalx 5 pull requests
OBOFoundry/ 5 pull requests
bgyori/indra_cogex 3 pull requests
biopragmatics/bioregistry 3 pull requests
cthoyt/pystow 1 pull request
indralab/gilda 1 pull request
oborel/obo-relations 1 pull request
manubot/manubot 1 pull request
AstraZeneca/rexmex 1 pull request
mapping-commons/sssom-py 1 pull request

Created an issue in OBOFoundry/ that received 8 comments

Update OPL contact information

While the Ontology for Parasite LifeCycle (OPL) has the contact person listed as Priti Parikh, I don't see any evidence of a person by that name in…

Opened 26 other issues in 17 repositories
AstraZeneca/chemicalx 4 closed 3 open
OBOFoundry/ 1 closed 3 open
ontoice/ICEO 1 open
AnimalGenome/vertebrate-trait-ontology 1 closed
aellenhicks/htn_owl 1 open
cthoyt/umls_downloader 1 open
chemkg/linkml-rhea 1 open
DeepGraphLearning/torchdrug 1 open
dmis-lab/BERN2 1 open
indralab/indra_curation 1 open
cthoyt/cookiecutter-snekpack 1 closed
AstraZeneca/rexmex 1 open
cthoyt/class-resolver 1 open
pykeen/pykeen 1 open
bgyori/indra_cogex 1 open
biopragmatics/biomappings 1 open
biopragmatics/bioregistry 1 open

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