pybel/pybel

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

Language: Python - Size: 12.3 MB - Last synced at: 12 months ago - Pushed at: almost 3 years ago - Stars: 130 - Forks: 30

cthoyt/doctoral-thesis

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

Language: TeX - Size: 68.6 MB - Last synced at: about 1 month ago - Pushed at: over 5 years ago - Stars: 29 - Forks: 2

bio2bel/bio2bel

A Python framework for integrating biological databases and structured data sources in Biological Expression Language (BEL)

Language: Python - Size: 417 KB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 20 - Forks: 5

PathwayMerger/PathMe

Harmonizing pathway databases using Biological Expression Language (BEL)

Language: Python - Size: 698 KB - Last synced at: 22 days ago - Pushed at: 10 months ago - Stars: 19 - Forks: 2

bio2bel/kegg

A Bio2BEL package for integrating pathway-related information from KEGG in BEL

Language: Python - Size: 297 KB - Last synced at: 14 days ago - Pushed at: about 3 years ago - Stars: 13 - Forks: 4

bel2scm/bel2scm

Generate dynamic structural causal models from biological knowledge graphs encoded in the Biological Expression Language (BEL)

Language: Jupyter Notebook - Size: 13 MB - Last synced at: 9 months ago - Pushed at: over 4 years ago - Stars: 10 - Forks: 4

bio2bel/drugbank

A Bio2BEL package for DrugBank (https://www.drugbank.ca)

Language: Python - Size: 150 KB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 9 - Forks: 4

pybel/pybel-notebooks

Notebooks demonstrating the usage of PyBEL and PyBEL Tools

Language: Jupyter Notebook - Size: 16.6 MB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 4

bel-enrichment/bel-enrichment

A package for generating curation sheets for rationally enriching a BEL graph using INDRA and PyBEL

Language: Python - Size: 92.8 KB - Last synced at: 3 days ago - Pushed at: almost 5 years ago - Stars: 7 - Forks: 0

pybel/hetionet-bel

A BEL export of Hetionet (https://github.com/hetio/hetionet)

Language: Python - Size: 39.1 KB - Last synced at: 9 months ago - Pushed at: almost 5 years ago - Stars: 6 - Forks: 2

pybel/pybel-tools

A PyBEL extension for analyzing BEL graphs

Language: Jupyter Notebook - Size: 3.25 MB - Last synced at: 2 days ago - Pushed at: about 4 years ago - Stars: 5 - Forks: 5

bio2bel/reactome

Integration of pathway-related information from Reactome in BEL

Language: Python - Size: 1.21 MB - Last synced at: 9 months ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 1

bio2bel/pubchem

NCBI PubChem to BEL

Language: Python - Size: 22.5 KB - Last synced at: 9 months ago - Pushed at: almost 6 years ago - Stars: 5 - Forks: 0

bio2bel/hmdb

A Bio2BEL package for converting the Human Metabolite Database (HMDB) to BEL

Language: Python - Size: 206 KB - Last synced at: 9 months ago - Pushed at: almost 6 years ago - Stars: 5 - Forks: 1

bel-commons/bel-commons

An environment for curating, validating, and exploring knowledge assemblies encoded in BEL

Language: HTML - Size: 8.89 MB - Last synced at: 17 days ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 0

pharmacome/conib

Curation of Neurodegeneration in Biological Expression Language (CONIB)

Language: Jupyter Notebook - Size: 38.2 MB - Last synced at: about 1 month ago - Pushed at: almost 4 years ago - Stars: 4 - Forks: 7

biological-expression-language/biological-expression-language.github.io

The community homepage for the Biological Expression Language (BEL)

Language: HTML - Size: 549 KB - Last synced at: 9 months ago - Pushed at: almost 5 years ago - Stars: 4 - Forks: 0

pharmacome/curation

Guidelines and procedures for curation (manual and semi-automated)

Language: Python - Size: 85 KB - Last synced at: 9 months ago - Pushed at: over 5 years ago - Stars: 4 - Forks: 2

hemekg/hemekg

Modeling heme pathogenicity and pathway dysregulation in the context of hemolytic disorders

Language: Python - Size: 2.32 MB - Last synced at: 7 days ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 3

bio2bel/wikipathways

Integration of pathway-related information from WikiPathways in BEL

Language: Python - Size: 126 KB - Last synced at: 7 days ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 1

CoronaWhy/bel4corona

Code, notebooks, and resources for exploring and analyzing mechanistic knowledge graphs about 'rona

Language: Jupyter Notebook - Size: 37.9 MB - Last synced at: 9 months ago - Pushed at: almost 5 years ago - Stars: 3 - Forks: 1

bio2bel/mesh

A Bio2BEL package for the Medical Subject Headings (MeSH; https://meshb.nlm.nih.gov)

Language: Python - Size: 74.2 KB - Last synced at: 14 days ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 0

bio2bel/doid

A Bio2BEL package for the Disease Ontology (http://www.disease-ontology.org)

Size: 1.95 KB - Last synced at: 9 months ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 0

cthoyt/cthoyt.github.io

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

Language: HTML - Size: 40.7 MB - Last synced at: 8 days ago - Pushed at: 9 days ago - Stars: 2 - Forks: 4

pybel/pybel-jupyter 📦

A PyBEL extension for Jupyter notebooks

Language: Python - Size: 36.1 KB - Last synced at: about 2 months ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 0

bio2bel/hgnc

Hugo Gene Nomenclature Consortium (HGNC) to BEL

Language: Python - Size: 188 KB - Last synced at: 16 days ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 0

bio2bel/bio2bel-notebooks

Notebooks demonstrating the usage of Bio2BEL packages

Language: Jupyter Notebook - Size: 80.8 MB - Last synced at: 9 months ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 2

bio2bel/ddr

Disease-disease relationships from Menche et al.

Language: Python - Size: 9.77 KB - Last synced at: 9 months ago - Pushed at: about 6 years ago - Stars: 2 - Forks: 0

bio2bel/ctd

A Bio2BEL package for converting the Comparative Toxicogenomics Database (CTD) to BEL

Language: Python - Size: 47.9 KB - Last synced at: 9 months ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 0

pybel/bel-repository

A utility for loading data from repositories of BEL documents

Language: Python - Size: 86.9 KB - Last synced at: 21 days ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

bel-curation/pybel-git

Git and continuous integration tools for PyBEL to assist in curating BEL

Language: Python - Size: 29.3 KB - Last synced at: 25 days ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 1

bio2bel/go

A Bio2BEL package for converting the Gene Ontology (GO) to BEL

Language: Python - Size: 65.4 KB - Last synced at: 17 days ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

pybel/bel-resources

Utilities for BEL resource files.

Language: Python - Size: 41 KB - Last synced at: 12 months ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

bio2bel/hsdn

Convert Himmerlstein's reproduction of the Human Symptom-Disease network to BEL

Language: Python - Size: 16.6 KB - Last synced at: 3 months ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

bio2bel/phosphosite

Language: Python - Size: 33.2 KB - Last synced at: 9 months ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

bio2bel/chebi

A Bio2BEL package for converting Chemical Entities of Biological Interest (ChEBI) to BEL

Language: Python - Size: 108 KB - Last synced at: about 13 hours ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

bio2bel/sider

A Bio2BEL package for the Side Effect Resource (SIDER; http://sideeffects.embl.de/)

Language: Jupyter Notebook - Size: 48.8 KB - Last synced at: about 11 hours ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 1

bio2bel/bio2bel-manuscript

LaTeX source for "Bio2BEL: Integration of Structured Knowledge with Biological Expression Language"

Language: TeX - Size: 946 KB - Last synced at: 9 months ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

bio2bel/adeptus

Convert differential gene expression signatures for diseases from ADEPTUS to BEL

Language: Python - Size: 21.5 KB - Last synced at: 16 days ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

pybel/pybel-resources 📦

Curated and automatically generated BEL resources

Size: 15.6 MB - Last synced at: 9 months ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

bio2bel/mir2disease

A Bio2BEL package for mir2disease (http://www.mir2disease.org)

Language: Python - Size: 28.3 KB - Last synced at: 6 months ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 0

neurommsig-epilepsy/neurommsig-epilepsy

Mechanistic pathway knowledge on Epilepsy encoded in Biological Expression Language

Language: Python - Size: 6.5 MB - Last synced at: about 2 months ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

neurommsig/neurommsig-knowledge

Knowledge curated for NeuroMMSig during the AETIONOMY project

Language: Python - Size: 5.86 MB - Last synced at: 14 days ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 1

cthoyt/masters-thesis

LaTeX source for my master's thesis

Language: TeX - Size: 16.5 MB - Last synced at: about 1 month ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

bio2bel/mirtarbase

Serializes text-mined miRNA-target interactions to BEL

Language: Python - Size: 141 KB - Last synced at: 16 days ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

bio2bel/mirbase

A Bio2BEL package for miRBase (http://www.mirbase.org)

Language: Python - Size: 58.6 KB - Last synced at: 11 days ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

bio2bel/entrez

A Bio2BEL package for converting Entrez and HomoloGene to BEL

Language: Python - Size: 111 KB - Last synced at: about 1 month ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

bio2bel/flybase

A Bio2BEL package for the terminology from FlyBase (http://flybase.org/)

Language: Python - Size: 23.4 KB - Last synced at: 9 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

bio2bel/pfam

A Bio2BEL package for PFAM (https://pfam.xfam.org/)

Language: Python - Size: 19.5 KB - Last synced at: 16 days ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

bio2bel/mgi

A Bio2BEL package for converting the Mouse Genome Informatics Database (MGI) to BEL

Language: Python - Size: 22.5 KB - Last synced at: 9 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

pybel/pybel-cx

A PyBEL extension for interconversion with CX

Language: Python - Size: 55.7 KB - Last synced at: 9 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

bio2bel/rgd

Rat Genome Database to BEL

Language: Python - Size: 1.02 MB - Last synced at: 9 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

bio2bel/hippie

Convert PPIs in HIPPIE to BEL

Language: Python - Size: 55.7 KB - Last synced at: 5 days ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

bio2bel/uniprot

UniProt Knowledge Base to BEL

Language: Python - Size: 43.9 KB - Last synced at: 18 days ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 1

bio2bel/expasy

A Bio2BEL package for converting ExPASy to BEL

Language: Python - Size: 204 KB - Last synced at: 25 days ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

bio2bel/famplex

Convert FamPlex to BEL

Language: Python - Size: 30.3 KB - Last synced at: about 2 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

pharmacome/semi-automated-curation

Results from semi-automated curation with INDRA/PyBEL

Language: Python - Size: 12 MB - Last synced at: 9 months ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

bio2bel/excape

Convert curated assays from ExCAPE-DB to BEL

Language: Jupyter Notebook - Size: 42 KB - Last synced at: 9 months ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

bio2bel/complexportal

Nomenclature and definitions of protein complexes in BEL

Language: Python - Size: 22.5 KB - Last synced at: 9 months ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

bio2bel/interpro

A Bio2BEL package for converting InterPro to BEL

Language: Python - Size: 129 KB - Last synced at: 18 days ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

bio2bel/hp

A Bio2BEL package for converting the Human Phenotype Ontology (HP) to BEL

Language: Python - Size: 22.5 KB - Last synced at: 9 months ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

bio2bel/antibodyregistry

Language: Python - Size: 13.7 KB - Last synced at: 9 months ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

neurommsig/neurommsig-terminology

Terminologies used in NeuroMMSig and AETIONOMY

Size: 107 KB - Last synced at: 9 months ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

bio2bel/hmdd

A Bio2BEL package for converting the Human microRNA Disease Database (HMDD) to BEL

Language: Jupyter Notebook - Size: 35.2 KB - Last synced at: about 1 month ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

pybel/pybel-application-note

LaTeX source for "PyBEL: a computational framework for Biological Expression Language"

Language: TeX - Size: 683 KB - Last synced at: 9 months ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

bel2abm/bel2abm-application-note

LaTeX source for "BEL2ABM: agent-based simulation of static models in Biological Expression Language"

Language: TeX - Size: 738 KB - Last synced at: 9 months ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

bio2bel/scai-mirna-corpra

SCAI miRNA text mining corpra to BEL

Language: Python - Size: 17.6 KB - Last synced at: 9 months ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0

bio2bel/bkms

A Bio2BEL package for converting BMKS-react to BEL

Language: Python - Size: 20.5 KB - Last synced at: 9 months ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

bio2bel/chembl

A Bio2BEL package for converting biochemical inhibition and binding information in ChEMBL to BEL

Language: Python - Size: 1.3 MB - Last synced at: 9 months ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0