Repositories list

• knetminer-common

  Public
  Parent POM for Knetminer projects, also containing common files.

  Shell

  •0•2•0•3•Updated Aug 6, 2025Aug 6, 2025

• knetminer-backend

  Public
  The new Knetminer backend, based on graph databases.

  Java

  •2•0•0•1•Updated Aug 5, 2025Aug 5, 2025

• knetbuilder

  Public
  KnetBuilder data integration platform for building knowledge graphs. Previously known as ondex.

  Java

  •

  MIT License

  •10•14•6•4•Updated Jul 30, 2025Jul 30, 2025

• knetminer

  Public
  KnetMiner - webapp to search and visualize genome-scale knowledge graphs

  JavaScript

  •

  MIT License

  •17•29•53•4•Updated Jul 28, 2025Jul 28, 2025

• rdf2pg

  Public
  tools to convert/load RDF into Neo4j

  Java

  •

  GNU Lesser General Public License v3.0

  •10•51•0•0•Updated Jun 19, 2025Jun 19, 2025

• agri-schemas

  Public
  Development of schemas and ontologies for the agrifood, inspired to schema.org and bioschemas.

  Python

  •1•4•0•0•Updated May 6, 2025May 6, 2025

• knetmaps.js

  Public
  KnetMaps: a BioJS component to visualize biological knowledge networks

  JavaScript

  •

  MIT License

  •6•10•9•14•Updated Apr 14, 2025Apr 14, 2025

• neo4j-server-maven-plugin

  Public
  Start and stop any version of Neo4j community server

  Java

  •

  Apache License 2.0

  •1•0•0•1•Updated Jan 7, 2025Jan 7, 2025

• graphdb-benchmarks

  Public
  Application to benchmark Neo4j+Cypher/Virtuoso+SPARQL/ArcadeDB+Gremlin querying

  neo4jsparqlgremlin+ 4arcadedbbenchmarkrdfgraph-database

  Jupyter Notebook

  •5•8•1•2•Updated Jun 23, 2024Jun 23, 2024

• knetgraphs-gene-traits

  Public
  Enrichment Analysis Use Cases. Tools to analyse plant biology knowledge graphs and find significant traits and bioprocess from gene expression sets. The project uses data from Knetminer, ENSEMBL, EBI Gene Expression Atlas and others, exported as Knowledge graphs using Agrischemas/Bioschemas annotations.

  pythonneodashbinder+ 1jupyter-notebook

  Jupyter Notebook

  •

  GNU Affero General Public License v3.0

  •1•4•0•0•Updated Nov 17, 2023Nov 17, 2023

• knetminer-testing

  Public
  Material about testing knetminer

  0•0•0•0•Updated Nov 15, 2023Nov 15, 2023

• knetminer-lodestar

  Public
  Knetminer-customised version of LODEStar

  JavaScript

  •

  Apache License 2.0

  •21•1•0•10•Updated Oct 16, 2023Oct 16, 2023

• genomaps.js

  Public
  Interactive visualization of highdensity SNP, QTL, GWAS and gene data.

  JavaScript

  •

  MIT License

  •2•10•5•2•Updated Oct 5, 2023Oct 5, 2023

• bioknet-onto

  Public
  The Bio Knowledge Network, powering knowledge graphs released by the Knetminer project

  XSLT

  •0•4•1•0•Updated May 25, 2023May 25, 2023

• easybuild-easyconfigs

  Public
  A collection of easyconfig files that describe which software to build using which build options with EasyBuild.

  Python

  •

  GNU General Public License v2.0

  •748•0•0•0•Updated Apr 25, 2023Apr 25, 2023

• ondex-old-components

  Public
  ONDEX outdated components, which are not used anynmore.

  Java

  •0•0•0•0•Updated Jan 26, 2023Jan 26, 2023

• knetminer-backend-doc

  Public
  Documentation, demos, presentations, etc for the Knetminer Data Backend.

  Jupyter Notebook

  •

  Other

  •0•0•0•0•Updated May 26, 2022May 26, 2022

• ondex-base

  Public
  Basic ONDEX components.

  Java

  •0•1•0•4•Updated Feb 1, 2022Feb 1, 2022

• ondex-doc

  Public archive
  ONDEX Documentation.

  TeX

  •0•0•0•0•Updated Jan 10, 2022Jan 10, 2022

• ondex-desktop

  Public archive
  ONDEX Desktop Applications.

  Java

  •1•1•0•2•Updated Jan 10, 2022Jan 10, 2022

• ondex-opt

  Public archive
  ONDEX Optional Components.

  Java

  •0•0•0•8•Updated Jan 10, 2022Jan 10, 2022

• ondex-full

  Public archive
  Aggregator used to download and build all about ONDEX

  data-miningnetwork-graphdata-visualization+ 1data-integration

  Shell

  •

  MIT License

  •1•0•0•3•Updated Jan 10, 2022Jan 10, 2022

• covid19-kg

  Public
  Documentation for the COVID-19 KnetGraph SPARQL and Cypher endpoints

  Python

  •

  GNU Affero General Public License v3.0

  •0•2•0•0•Updated Oct 14, 2021Oct 14, 2021

• knetminer-lightgraph

  Public archive
  Low RAM Knowledge Graphs for Knetminer

  Java

  •

  MIT License

  •0•2•0•0•Updated Sep 10, 2021Sep 10, 2021

• graphql-api

  Public
  KnetMiner Platform API BETA

  JavaScript

  •

  Apache License 2.0

  •1•1•3•0•Updated Sep 8, 2021Sep 8, 2021

• kgraph-usecases

  Public
  A test project to develop Knetminer use cases about using raw data endpoints.

  Java

  •0•0•0•0•Updated Aug 22, 2021Aug 22, 2021

• ProfileGenerator

  Public
  Experimental scripts for creating a new Bioschemas Profile

  Python

  •

  MIT License

  •3•0•0•0•Updated Apr 14, 2021Apr 14, 2021

• fculmorum-kg

  Public
  Fusarium culmorum KG ETLs for public access

  Python

  •0•0•0•0•Updated Sep 30, 2020Sep 30, 2020

• wordcloud

  Public
  Python wordcloud example for knetminer viz

  Python

  •

  MIT License

  •1•1•0•0•Updated Jul 28, 2020Jul 28, 2020

• knetminer-website

  Public
  KnetMiner website

  network-visualisationgraph-query

  HTML

  •0•0•0•0•Updated Jun 5, 2020Jun 5, 2020