| 4 | | ||Browse source: || || |
| 5 | | ||Demo: || || |
| | 4 | ||Browse source: ||http://gbic.target.rug.nl/svn/molgenis/molgenis_projects/magetab/ || |
| | 5 | ||Demo: ||http://gbic.target.rug.nl:8080/magetab4molgenis/molgenis.do || |
| | 6 | |
| | 7 | MAGE-TAB MOLGENIS is primary a web environment for microarray experiment data management although through the definition of MAGE-TAB it can manage a large variety of high throughput biomedical experiments. The basic notion is the “Investigation” which handles all the meta-data such as investigator’s contact details, bibliographic references and free-text descriptions. The “Investigation” also contains links to various experiments that were conducted. Each experiment is a directed acyclic graph where each node is a material used such as samples, extracts, scans and normalizations. The edges of the graph are references to the protocols used through the production of a material. Whenever an array is used is linked as meta-data of a protocol. The array is a distinct entity that contains the array’s design. That is the location of the sequences on the array and what the annotations of these sequences are. Finally raw and processed data files that contain arbitrary textual or binary data can be referred as meta-data. |
| | 8 | Apart from the provided web environment we also offer a JAVA and R API for third party data management. The JAVA API has been used to write a MAGE-TAB parser for data input. This parser was used to import the complete MAGE-TAB corpus available in ArrayExpress. Thus, an alternative use of the environment is as a browser of available microarray experiments or a database in-a-box system. Finally we offer SOAP and REST web service implementations of methods for data access as well as semantic interfaces to RDF and SPARQL. |
