98 projects
bioversions
What's the current version for each biological database?
pystow
Easily pick a place to store data for your Python code
bioregistry
Integrated registry of biological databases and nomenclatures
sssom
Operations on SSSOM mapping tables
pyobo
A python package for handling and generating OBO
bioontologies
Tools for biomedical ontologies
biopragmatics
Biomedical semantics and pragmatics.
class-resolver
Lookup and instantiate classes with style.
curies
Idiomatic conversion between URIs and compact URIs (CURIEs)
pykeen
A package for training and evaluating multimodal knowledge graph embeddings
biosynonyms
Decentralized database of biomedical synonyms
quickstatements-client
A data model and client for Wikidata QuickStatements
orcid-downloader
Download and process ORCID in bulk
zenodo-client
A wrapper for the Zenodo API.
semantic-pydantic
Integration between the Bioregistry and Pydantic type annotations.
biotools-client
An API client to bio.tools
drugbank-downloader
A tool for reproducibly downloading and extracting DrugBank data
docdata
Add structured information to the end of your python docstrings.
curies-rs
Python bindings for the curies library
nonadditivity
A program to find key complex patterns in SAR data
famplex
Resources for grounding protein complexes and families from text and describing their hierarchical relationships.
pybacting
A python wrapper around Bacting
y0
Python code for causal modeling.
semra
Semantic mapping reasoner and assembler
umls-downloader
Automate downloading UMLS data.
autoreviewer
Automate scientific software review
biolexica
Generate and apply coherent biomedical lexica
chembl-downloader
Reproducibly download, open, parse, and query ChEMBL
eliater
A high level, end-to-end causal inference workflow.
biomappings
Curated and predicted mappings between biomedical identifiers in different namespaces
selventa-knowledge
Selventa Large and Small Corpora via PyBEL
ols-client
A client to the EBI Ontology Lookup Service
unittest-templates
Write less unittest boilerplate.
fairsharing-client
A client to the FAIRsharing API
more-click
More click.
debio
A community-curated, decentralized biomedical ontology.
ontoportal-client
A client to BioPortal and other OntoPortal instances.
authorship
Format author lists for academic texts and journal submissions.
biolookup
Get metadata and ontological information about all biomedical entities.
apicuron-client
A client for interacting with APICURON
pydeogram
Generate karyotype pictures using Ideogram.js.
citation-url
Parse URLs for DOIs, PubMed identifiers, PMC identifiers, arXiv identifiers, etc.
pybel
Parsing, validation, compilation, and data exchange of Biological Expression Language (BEL)
pyrdle
Play Wordle interactively in the CLI/GUI. Also contains various algorithms to defeat the game.
depmap-downloader
Reproducibly/automatically download data from the DepMap.
geometric-graphs
Generate knowledge graphs with interesting geometries, like lattices.
bio2bel
A framework for converting biological data sources to BEL
more-node2vec
Utilities for node2vec and gensim
stonkgs
Sophisticated Transformers for Biomedical Text and Knowledge Graph Data
conib
Curation of Neurodegeneration in BEL (CONIB)
y0-bio
Biological applications of y0
pybel-tools
A cool pool of tools for BEL
neurommsig-epilepsy
Mechanistic pathway knowledge on Epilepsy encoded in Biological Expression Language
hemekg
Mechanistic knowledge about heme and hemolytic disorders in Biological Expression Language with PyBEL
compath-resources
ComPath Resource Utilities
bio2bel-kegg
A package for converting KEGG gene sets into BEL
compath
A web application for exploring and comparing the overlaps across pathway resources
bio2bel-msig
A package for converting MSigDB gene sets into BEL
bel-enrichment
A package for generating curation sheets for rationally enriching a BEL graph using INDRA and PyBEL.
guiltytargets
A tool for ranking potential targets for a given disease
bel-repository
A utility for loading data from repositories of BEL documents.
bel-commons
A web application exposing core PyBEL functionalities
pybel-jupyter
A PyBEL extension for Jupyter notebooks
compath-utils
A utilities package for ComPath
biokeen
A package for training and evaluating biological knowledge graph embeddings
bio2bel-hgnc
A package for converting HGNC to BEL
pybel-git
PyBEL Git utilities
bel-resources
Utilities for BEL resource files.
pybel-cx
A PyBEL extension for interconversion with CX
bio2bel-entrez
A package for parsing and storing Entrez Gene
hbp-knowledge
Knowledge curated in BEL from full text during the Human Brain Pharmacome project
embeddingdb
A package for storing and querying knowledge graph embeddings
bio2bel-mirtarbase
A package for converting miRTarBase to BEL
bio2bel-mirbase
Convert miRBase to BEL
bio2bel-interpro
A package for converting InterPro to BEL
ratvec
Generating dense embeddings for proteins using kernel PCA
bio2bel-wikipathways
A package for converting Wikipathways to BEL
pybel-ols
A package for building BEL resource files with the EBI Ontology Lookup Service.
nrl
Network representation learning in Python
bio2bel-chebi
A package for converting ChEBI to BEL
bio2bel-reactome
A wrapper around Reactome RESTful API
neurommsig-knowledge
Knowledge curated for NeuroMMSig during the AETIONOMY project
multisplitby
Split an iterable into multiple using arbitrary predicates.
bio2bel-drugbank
A package for converting DrugBank to BEL
bio2bel-sider
Bio2BEL SIDER.
bio2bel-famplex
Downloader, parser, and BEL converter for FamPlex
bio2bel-hsdn
Converts the human symptoms-disease network produced by Zhou and Himmelstein to BEL
bio2bel-adeptus
Bio2BEL ADEPTUS.
bio2bel-expasy
A package for parsing and storing the ExPASy Enzyme Database
bio2bel-mesh
A package for converting MeSH to BEL
bio2bel-uniprot
A package for downloading, parsing, storing, and serializing UniProt
onto2nx
A package for parsing ontologies in the OWL and OBO format into NetworkX graphs
bio2bel-pfam
Bio2BEL PFAM.
bio2bel-go
A package for converting GO to BEL
bio2bel-hippie
Bio2BEL HIPPIE.
compath-hgnc
A package that wraps PyHGNC to perform mappings between different gene identifiers
pybel-artifactory
A PyBEL extension for handling BEL resources with Artifactory
bio2bel-hmdd
A package for converting the Human microRNA Disease Database (HMDD) to BEL.
