Discover cthoyt/semantic-pydantic Open Source project

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Python
License
MIT License
Created 11 months ago
Updated 5 months ago

cthoyt

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Annotate data models in Pydantic and APIs in FastAPI with the Bioregistry to make them more FAIR

class-resolver

🔍 Lookup classes and instantiate them with style

Python

chembl-downloader

Write reproducible code for getting and processing ChEMBL

Jupyter Notebook

pystow

👜 Easily pick a place to store data for your Python code.

Python

doctoral-thesis

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

TeX

drugbank_downloader

Don't worry about DrugBank licensing - write code that knows how to download it automatically

Python

cookiecutter-snekpack

🍪 A cookiecutter package for an enlightened python package

Python

autoreviewer

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

Python

umls_downloader

Don't worry about UMLS, RxNorm, SNOMED, or SemMedDB licensing - write code that knows how to download it automatically

Python

pyrdle

Play Wordle in the CLI. Write an algorithm to play Wordle for you. Ruin all of the fun you've been having.

Python

ols-client

🎡 Unified access to OLS instances like from the EBI and TIB

Python

zenodo-client

A tool for automated uploading and version management of scientific data to Zenodo

Python

onto2nx

Converts OWL ontologies and OBO to NetworkX Graphs

Python

curies4j

🐸 Idiomatic conversion between URIs and compact URIs (CURIEs)

Java

quickstatements_client

A data model and client for QuickStatements (for Wikidata)

Python

rhea-fingerprints

Automatically generate differential reaction fingerprints on reactions in Rhea

Python

pybacting

A Python wrapper around Bacting (https://github.com/egonw/bacting)

Python

more_click

Extra stuff for click I use in basically every repo

Python

geometric-graphs

Generate knowledge graphs with interesting geometries, like lattices

Python

nrl

Network Representation Learning in Python with igraph

Python

authorship

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

Python

ontoportal-client

🎡 Unified access to OntoPortal instances like BioPortal, AgroPortal, and EcoPortal

Python

cthoyt.github.io

My personal website, served at https://cthoyt.com

HTML

nsockg

"Not Scared of Chemistry" Knowledge Graph

Python

opencheck-embed

Graph-based embedding of Twitter followers in OpenCheck

Python

orcid_downloader

Get ORCID in bulk and free it from XML

Python

unittest-templates

Write less unittest boilerplate

Python

twin-identifier-analysis

How many local unique identifiers overlap between each biomedical vocabulary in the Bioregistry?

Jupyter Notebook

citation-url

Parse URLs for DOIs, PubMed identifiers, PMC identifiers, arXiv identifiers, etc.

Python

obo-community-health

🫀 Check the OBO Foundry repositories to see what's going on

Python

rorio

Convert the Research Organization Registry (ROR) into an OWL instance ontology

Python

orcidio

🐨 Make a subset of ORCID available as an OWL ontology

Python

depmap_downloader

Reproducibly download the latest version of various DepMap datasets

Python

flask-celery-docker-demo

A short demo on how to process files with Flask and Celery inside Docker

Python

embeddingdb

A database for storing and comparing entity embeddings

Python

chemrxiv-summarize

Summarize usage of ChemRxiv by using Figshare's API endpoint

Python

vsmo

Revival of the Vector Surveillance and Management Ontology

chendi

Chemical Entities of Neurodegenerative Disease Interest

schoolwork

✎ Code I've written for classes in school

Racket

translational-toys

Knowledge graphs representing geometric shapes matched to knowledge graph embedding models to learn them

Python

biocuration-diversity-search

Find biocurators that aren't from Australia, Canada, USA, or western Europe

Python

dotfiles

My dot files

Python

biomodels-metadata-analysis

Generate a summary of metadata annotations in the BioModels database

Python

more_node2vec

Python

pydeogram

Generate Ideograms using ideogram.js in Python

Python

obo-foundry-graph

Demonstrate combining all OBO Foundry ontologies via Bioregistry, Bioontologies, and ROBOT

Python

n2t-ark-resolver

Re-implement N2T's ARK resolver using curies (https://github.com/cthoyt/curies/)

Python

apicuron-client

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

Python

flask-dance-with-redirects

Extend Flask-Dance to handle URL redirects

Python

cthoyt/semantic-pydantic

cthoyt

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