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Arnold Kuzniar edited this page May 27, 2019
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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