Skip to content
Arnold Kuzniar edited this page May 27, 2019 · 30 revisions

Inventory of tools and data formats

This is an overview of useful data-related software that were/are used in the projects at the Netherlands eScience Center.

Software I/O formats API Description Projects Engineers
OpenRefine CSV, TSV, RDF GREL Data cleaning & munging ODEX4all, candYgene Arnold
Virtuoso Universal Server (OSE) CSV, TSV, XML, RDF, JSON PL/SQL, SPARQL Object-relational DB, RDF Quad Store ODEX4all, candYgene, HADRIANUS, EOSCpilot LOFAR, GTCG Arnold
Neo4j CSV, TSV Cypher Graph DB GTCG Arnold
SQLite CSV, TSV, GFF SQL (embedded) Relational DB candYgene, eMetabolomics, 3D-e-Chem Arnold, Stefan
Apache Solr TXT, XML Solr client APIs (RESTful) full-text search platform candYgene Arnold
SIGA.py GFF->SQLite DB->RDF Python Command-line tool to transform (semantify) genome annotations ODEX4all, candYgene Arnold
SAM/VCF/BCFtools BAM, VCF, BCF Command-line tools for genomics GTCG Arnold
PostgreSQL + PostGIS CSV Postgresql API Relational database with geopspatial extension eEcology Stefan
THREDDS data server NetCDF OpenDAP, WMS, HTTP Remote access for NetCDF files eWatercycle II Stefan
SQLAlchemy

TODO

Clone this wiki locally