-
Notifications
You must be signed in to change notification settings - Fork 3
Home
Arnold Kuzniar edited this page Apr 1, 2021
·
30 revisions
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, RDF | GREL | Data cleaning & munging | ODEX4all, candYgene, EOSCpilot-LOFAR | Arnold, Valentina |
| Virtuoso Universal Server (OSE) | CSV, XML, JSON, RDF(S), OWL | PL/SQL, SPARQL | Object-relational DB, RDF Quad Store | ODEX4all, candYgene, HADRIANUS, EOSCpilot-LOFAR, GTCG | Arnold |
| RDF4J Server | RDF(S), OWL | JAVA API, REST API, SPARQL | RDF store | LINNAE | Arnold |
| Neo4j | CSV | Cypher | Graph DB | GTCG | Arnold |
| SQLite | CSV, 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 | |
| grlc | SPARQL | Python | Generates Web API from SPARQL queries | DIVE+, candYgene | Carlos, 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 |
| era5cli | NetCDF, GRIB | Python | Command-line interface to Copernicus Data Store | eWatercycle II | Team Beta |
| SQLAlchemy |
TODO