114 projects
sssom_pydantic
Pydantic models for SSSOM
bioregistry
Integrated registry of biological databases and nomenclatures
dalia_dif
Tools for DALIA's data model for open educational resources
tess_downloader
Download and structure learning materials from TeSS
pystow
Easily pick a place to store data for your Python code
jskos
A data model for JSKOS
curies_processing
Pre- and post-processing configuration for prefixes, CURIEs, and URIs
ssslm
A simple standard for sharing literal mappings
sssom_curator
Tools for predicting and curating semantic mappings
curies
Idiomatic conversion between URIs and compact URIs (CURIEs)
ontoportal_client
A client to BioPortal and other OntoPortal instances
unittest_templates
Write less unittest boilerplate
pyobo
A python package for handling and generating OBO
bioontologies
Tools for biomedical ontologies
fairsharing-client
A client to the FAIRsharing API
more-click
Implementations of common CLI patterns on top of Click
pydantic-metamodel
A lightweight metamodel implemented with Pydantic
gilda-slim
Grounding for biomedical entities with contextual disambiguation
oerbservatory
Harmonization of open educational resource data models, schemata, and data
sphinx-unpack
Automatically document variadic keyword arguments annotated with typed dicts via Unpack
wikidata-client
Interact with Wikidata programmatically
sssom
Operations on SSSOM mapping tables
biomappings
Curated and predicted mappings between biomedical identifiers in different namespaces
semfarm
Greener pastures for prefixes, CURIEs, and URIs
chembl-downloader
Reproducibly download, open, parse, and query ChEMBL
pubmed-downloader
Automate downloading and processing PubMed
class-resolver
Lookup and instantiate classes with style.
pybacting
A python wrapper around Bacting
bioliterature
Access and analyze biomedical literature
ols-client
A client to the EBI Ontology Lookup Service
orcid-downloader
Download and process ORCID in bulk
qualo
NLP tools for qualifications and distinctions
obographs
A python data model for OBO Graphs
oquat
Assess the quality of biomedical ontologies
nonadditivity
A program to find key complex patterns in SAR data
pykeen
A package for training and evaluating multimodal knowledge graph embeddings
depmap-downloader
Reproducibly download the latest version of DepMap datasets
docdata
Add structured information to the end of your python docstrings.
metaregistry
A meta-registry for ontologies, controlled vocabularies, and semantic spaces
nih-reporter-downloader
Automatically download data from NIH RePORTER
clinicaltrials-downloader
Download and process ClinicalTrials.gov
semantic-pydantic
Integration between the Bioregistry and Pydantic type annotations.
evr
An open, community-driven venue of conference and event venues
zenodo-client
A wrapper for the Zenodo API.
quickstatements-client
A data model and client for Wikidata QuickStatements
biotools-client
An API client to bio.tools
drugbank-downloader
A tool for reproducibly downloading and extracting DrugBank data
curies-rs
Python bindings for the curies library
famplex
Resources for grounding protein complexes and families from text and describing their hierarchical relationships.
y0
Python code for causal modeling.
umls-downloader
Automate downloading UMLS data.
autoreviewer
Automate scientific software review
eliater
A high level, end-to-end causal inference workflow.
selventa-knowledge
Selventa Large and Small Corpora via PyBEL
debio
A community-curated, decentralized biomedical ontology.
authorship
Format author lists for academic texts and journal submissions.
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.
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.
