biological-expression-language

There are 764 repositories under biological-expression-language topic.

pybel / pybel
🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)
bioinformatics biological-expression-language bioregistry domain-specific-language networks networks-biology pybel systems-biology
Language:Python 131
doctoral-thesis
cthoyt / doctoral-thesis
📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology
biological-expression-language knowledge-graphs knowledge-graph-embeddings data-integration curation simulation biocuration networks-biology systems-biology computational-biology
Language:TeX 29
bio2bel / bio2bel
A Python framework for integrating biological databases and structured data sources in Biological Expression Language (BEL)
data-integration biological-expression-language ontologies
Language:Python 21
PathwayMerger / PathMe
Harmonizing pathway databases using Biological Expression Language (BEL)
bioinformatics biological-expression-language pathway-analysis pathways systems-biology
Language:Python 19
bio2bel / kegg
A Bio2BEL package for integrating pathway-related information from KEGG in BEL
pathways systems-biology networks-biology proteins biological-expression-language kegg
Language:Python 13
bel2scm / bel2scm
Generate dynamic structural causal models from biological knowledge graphs encoded in the Biological Expression Language (BEL)
biological-expression-language structural-causal-model pyro systems-biology networks-biology counterfactual causal-inference
Language:Jupyter Notebook 10
bio2bel / drugbank
A Bio2BEL package for DrugBank (https://www.drugbank.ca)
cheminformatics systems-biology pharmacology biological-expression-language networks-biology drugs drugbank terminology
Language:Python 9
pybel / pybel-notebooks
Notebooks demonstrating the usage of PyBEL and PyBEL Tools
bioinformatics biological-expression-language nbviewer networks systems-biology
Language:Jupyter Notebook 9
bel-enrichment / bel-enrichment
A package for generating curation sheets for rationally enriching a BEL graph using INDRA and PyBEL
biological-expression-language indra biocuration natural-language-processing
Language:Python 7
bio2bel / hmdb
A Bio2BEL package for converting the Human Metabolite Database (HMDB) to BEL
chemistry metabolomics biological-expression-language systems-biology networks-biology cheminformatics terminology
Language:Python 5
bio2bel / pubchem
NCBI PubChem to BEL
biological-expression-language chemogenomics terminology pubchem
Language:Python 5
bio2bel / reactome
Integration of pathway-related information from Reactome in BEL
pathways system-biology networks-biology biological-expression-language reactome
Language:Python 5
pybel / hetionet-bel
A BEL export of Hetionet (https://github.com/hetio/hetionet)
biological-expression-language data-integration hetionet
Language:Python 5
pybel / pybel-tools
A PyBEL extension for analyzing BEL graphs
bioinformatics biological-expression-language networks systems-biology
Language:Jupyter Notebook 5
bel-commons / bel-commons
An environment for curating, validating, and exploring knowledge assemblies encoded in BEL
biological-expression-language systems-biology bioinformatics networks-biology
Language:HTML 4
biological-expression-language / biological-expression-language.github.io
The community homepage for the Biological Expression Language (BEL)
biological-expression-language domain-specific-language bioinformatics
Language:HTML 4
pharmacome / conib
Curation of Neurodegeneration in Biological Expression Language (CONIB)
biological-expression-language biocuration networks-biology
Language:Jupyter Notebook 4
pharmacome / curation
Guidelines and procedures for curation (manual and semi-automated)
biological-expression-language biocuration
Language:Python 4
bio2bel / doid
A Bio2BEL package for the Disease Ontology (http://www.disease-ontology.org)
biological-expression-language terminology ontology disease disease-ontology
3
bio2bel / mesh
A Bio2BEL package for the Medical Subject Headings (MeSH; https://meshb.nlm.nih.gov)
phenotypes chemistry biological-expression-language terminology mesh
Language:Python 3
bio2bel / wikipathways
Integration of pathway-related information from WikiPathways in BEL
biological-expression-language pathways systems-biology wikipathways
Language:Python 3
CoronaWhy / bel4corona
Code, notebooks, and resources for exploring and analyzing mechanistic knowledge graphs about 'rona
biological-expression-language biocuration bioinformatics knowledge-graphs
Language:Jupyter Notebook 3
hemekg / hemekg
Modeling heme pathogenicity and pathway dysregulation in the context of hemolytic disorders
heme systems-biology networks-biology pathways knowledge-modeling biological-expression-language pybel
Language:Python 3
bio2bel / bio2bel-notebooks
Notebooks demonstrating the usage of Bio2BEL packages
jupyter-notebook biological-expression-language data-integration semantics
Language:Jupyter Notebook 2
bio2bel / ctd
A Bio2BEL package for converting the Comparative Toxicogenomics Database (CTD) to BEL
cheminformatics biological-expression-language chemistry chemogenomics systems-biology chemotoxicogenomic-database
Language:Python 2
bio2bel / ddr
Disease-disease relationships from Menche et al.
biological-expression-language pathology
Language:Python 2
bio2bel / hgnc
Hugo Gene Nomenclature Consortium (HGNC) to BEL
genes biological-expression-language terminology hgnc
Language:Python 2
bio2bel / phosphosite
biological-expression-language protein-modifications post-translational-modification
Language:Python 2
cthoyt / cthoyt.github.io
My personal website, served at https://cthoyt.com
biological-expression-language machine-learning knowledge-graphs knowledge-graph-embeddings drug-discovery drug-repurposing target-prioritization target-validation biocuration ontologies bioinformatics cheminformatics toxicology wikidata obofoundry deep-learning proteochemometrics utterances drug-synergy artificial-intelligence
Language:HTML 2
pybel / pybel-jupyter
A PyBEL extension for Jupyter notebooks
biological-expression-language jupyter network-visualization
Language:Python 2
bel-curation / pybel-git
Git and continuous integration tools for PyBEL to assist in curating BEL
biological-expression-language biocuration continuous-integration pybel
Language:Python 1
bio2bel / adeptus
Convert differential gene expression signatures for diseases from ADEPTUS to BEL
differential-gene-expression biological-expression-language pathology gene-expression
Language:Python 1
bio2bel / bio2bel-manuscript
LaTeX source for "Bio2BEL: Integration of Structured Knowledge with Biological Expression Language"
semantic-web biological-expression-language systems-biology networks-biology
Language:TeX 1
bio2bel / hsdn
Convert Himmerlstein's reproduction of the Human Symptom-Disease network to BEL
biological-expression-language symptoms disease-symptom disease
Language:Python 1
pybel / bel-repository
A utility for loading data from repositories of BEL documents
biological-expression-language pybel
Language:Python 1
pybel / bel-resources
Utilities for BEL resource files.
biological-expression-language ontologies terminologies
Language:Python 1

Related Topics

bioinformatics domain-specific-language language