Pinned Repositories
Applied-Bioinformatics
Student course material for the Applied Bioinformatics course at Scripps Research
DrugMechDB
A database of paths that represent the mechanism of action from a drug to a disease in an indication.
mark2cure
Mark2Cure allows anyone that can read English, regardless of background, to help in the process of biomedical discovery.
mygene.info
MyGene.info: A BioThings API for gene annotations
myvariant.info
MyVariant.info: A BioThings API for human variant annotations
scheduled-bots
GeneWiki Scheduled Bots
sparql_to_pandas
Example for accessing SPARQL endpoints in Python with Pandas
WikidataIntegrator
A Wikidata Python module integrating the MediaWiki API and the Wikidata SPARQL endpoint
WikiGenomesBase
A configurable codebase for launching organism specific WikiGenomes spinoff applications (e.g. ChlamBase.org) This is a web application framework for creating a model organism database leveraging the taxonomic, genetic and functional data that has been loaded to Wikidata.org by the Gene Wiki Project.
YPet
Javascript library to rapidly annotate paragraphs of text on websites with the goal of making the annotation process as fast and simple as possible.
Su Lab's Repositories
SuLab/WikidataIntegrator
A Wikidata Python module integrating the MediaWiki API and the Wikidata SPARQL endpoint
SuLab/DrugMechDB
A database of paths that represent the mechanism of action from a drug to a disease in an indication.
SuLab/Applied-Bioinformatics
Student course material for the Applied Bioinformatics course at Scripps Research
SuLab/mark2cure
Mark2Cure allows anyone that can read English, regardless of background, to help in the process of biomedical discovery.
SuLab/sparql_to_pandas
Example for accessing SPARQL endpoints in Python with Pandas
SuLab/scheduled-bots
GeneWiki Scheduled Bots
SuLab/genewikiworld
Generate a network of all items we care about, and some we don't....
SuLab/GeneWikiCentral
GeneWiki Organization
SuLab/MechRepoNet
SuLab/TSRI-CBB
This is the Github repository for The Scripps Research Institute Computational Biology and Bioinformatics (CBB) community and affiliated core track for graduate students.
SuLab/bioshovel
Biological text mining tool.
SuLab/Wikidata-phenomizer
Incorporate wikidata statements into phenomizer
SuLab/garbanzo
Wikidata Semantic Query API
SuLab/KnowledgeGraphEmbedding
SuLab/Krusty
neo4j <-> wikibase import/export tool
SuLab/sulab.org
SuLab/biogps_core
SuLab/biogps_dataset
BioGPS.org dataset & dataset loading code repository
SuLab/CBRonMRN
SuLab/data-science-resources
A list of some of our favorite data science resources
SuLab/dataset-repository-selector
A tool to help biologists make their datasets more findable, accessible, and schema.org-compliant
SuLab/DMDB_Analysis
SuLab/DrugMechDB-1
A database of paths that represent the mechanism of action from a drug to a disease in an indication.
SuLab/Lit2Hybrid
SuLab/mercator_shiny
A web application for visualization, exploration, and analysis of public bulk RNA-seq data.
SuLab/MRN_AD
Use MechRepoNet to examine possible treatments for Alzheimer's Disease
SuLab/niaid-data-portal
NIAID Dataset Portal
SuLab/path_plots
A simple repo to quickly plot paths in a newtorkx graph
SuLab/wikidata-translate
SuLab/Wikidata_Biomedical-Subgraph
This is a follow-up effort from work done within Waagmeester et al 2020 eLife and Mayers et al 2022 Bioinformatics