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Repository Details
β Code I've written for classes in school
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π Lookup classes and instantiate them with stylePython
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Write reproducible code for getting and processing ChEMBLJupyter Notebook
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π Easily pick a place to store data for your Python code.Python
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drugbank_downloader
Don't worry about DrugBank licensing - write code that knows how to download it automaticallyPython
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5
cookiecutter-snekpack
πͺ A cookiecutter package for an enlightened python packagePython
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autoreviewer
ποΈβπ¨οΈ Scientists often do the same bad stuff. Automate giving feedback during peer review.Python
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umls_downloader
Don't worry about UMLS, RxNorm, SNOMED, or SemMedDB licensing - write code that knows how to download it automaticallyPython
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8
pyrdle
Play Wordle in the CLI. Write an algorithm to play Wordle for you. Ruin all of the fun you've been having.Python
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9
zenodo-client
A tool for automated uploading and version management of scientific data to ZenodoPython
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10
onto2nx
Converts OWL ontologies and OBO to NetworkX GraphsPython
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curies4j
πΈ Idiomatic conversion between URIs and compact URIs (CURIEs)Java
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12
ols-client
π‘ Unified access to OLS instances like from the EBI and TIBPython
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13
rhea-fingerprints
Automatically generate differential reaction fingerprints on reactions in RheaPython
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14
pybacting
A Python wrapper around Bacting (https://github.com/egonw/bacting)Python
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15
quickstatements_client
A data model and client for QuickStatements (for Wikidata)Python
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16
more_click
Extra stuff for click I use in basically every repoPython
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17
geometric-graphs
Generate knowledge graphs with interesting geometries, like latticesPython
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18
nrl
Network Representation Learning in Python with igraphPython
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19
authorship
π’ Generate publication-ready authorship lists via Google Sheets and morePython
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20
semantic-pydantic
Annotate data models in Pydantic and APIs in FastAPI with the Bioregistry to make them more FAIRPython
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21
ontoportal-client
π‘ Unified access to OntoPortal instances like BioPortal, AgroPortal, and EcoPortalPython
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22
cthoyt.github.io
My personal website, served at https://cthoyt.comHTML
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nsockg
"Not Scared of Chemistry" Knowledge GraphPython
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opencheck-embed
Graph-based embedding of Twitter followers in OpenCheckPython
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25
unittest-templates
Write less unittest boilerplatePython
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26
citation-url
Parse URLs for DOIs, PubMed identifiers, PMC identifiers, arXiv identifiers, etc.Python
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27
twin-identifier-analysis
How many local unique identifiers overlap between each biomedical vocabulary in the Bioregistry?Jupyter Notebook
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28
obo-community-health
π« Check the OBO Foundry repositories to see what's going onPython
2
29
rorio
Convert the Research Organization Registry (ROR) into an OWL instance ontologyPython
2
30
orcidio
π¨ Make a subset of ORCID available as an OWL ontologyPython
2
31
depmap_downloader
Reproducibly download the latest version of various DepMap datasetsPython
2
32
flask-celery-docker-demo
A short demo on how to process files with Flask and Celery inside DockerPython
2
33
embeddingdb
A database for storing and comparing entity embeddingsPython
1
34
chemrxiv-summarize
Summarize usage of ChemRxiv by using Figshare's API endpointPython
1
35
vsmo
Revival of the Vector Surveillance and Management Ontology
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36
chendi
Chemical Entities of Neurodegenerative Disease Interest
1
37
translational-toys
Knowledge graphs representing geometric shapes matched to knowledge graph embedding models to learn themPython
1
38
biocuration-diversity-search
Find biocurators that aren't from Australia, Canada, USA, or western EuropePython
1
39
dotfiles
My dot filesPython
1
40
biomodels-metadata-analysis
Generate a summary of metadata annotations in the BioModels databasePython
1
41
orcid_downloader
Get ORCID in bulk and free it from XMLJupyter Notebook
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42
more_node2vec
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43
pydeogram
Generate Ideograms using ideogram.js in PythonPython
1
44
obo-foundry-graph
Demonstrate combining all OBO Foundry ontologies via Bioregistry, Bioontologies, and ROBOTPython
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45
n2t-ark-resolver
Re-implement N2T's ARK resolver using curies (https://github.com/cthoyt/curies/)Python
1
46
apicuron-client
A python client for interacting with the APICURON curation metadatabase's RESTful APIPython
1