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msidb [2012/03/02 14:28] 132.168.72.131 |
msidb [2016/08/24 15:11] (current) 132.168.73.77 |
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===== What are MSIdb ===== | ===== What are MSIdb ===== | ||
- | Mass Spectrometry Identification Database or MSI db, are database containing validated identification data. They are populated using [[start|IRMa ]] application and then can be exploited using generic database exploration software or the hEIDI ([[http://biodev.extra.cea.fr/docs/heidi/doku.php|(h) Exploitation et Intégration des Données d'Identification]]) application developed at EDyP laboratory | + | Mass Spectrometry Identification Database or MSI db, are database containing validated identification data. They are populated using [[start|IRMa ]] application and then can be exploited using generic database exploration software or the [[http://biodev.extra.cea.fr/docs/heidi/doku.php|hEIDI]] (//h// Exploitation et Intégration des Données d'Identification) application developed at EDyP laboratory |
+ | |||
+ | ===== Installing database ===== | ||
+ | |||
+ | Database supported for exporting validated identification data is Postgresql 8.x, 9.x (test done on 8.1, 8.4, 9.1). Executables can be downloaded from [[https://www.postgresql.org/download/| Postgres downloads page]] | ||
+ | |||
+ | ==== Installing Postgresql ==== | ||
+ | {{:userguide:postgres-install-msi.png?400}} | ||
+ | * Execute PostgreSQL 8.1.msi | ||
+ | * Follow instructions | ||
+ | * Note : master password needs to be set at this stage | ||
+ | |||
+ | |||
+ | === Setting up a database === | ||
+ | {{:userguide:setting-up-database.png?600}} | ||
+ | |||
+ | {{:userguide:setting-up-database-2.png?600}} | ||
+ | |||
+ | Under user « postgres » : | ||
+ | * Connect to database (dble_click) | ||
+ | * Create new user « example » with permission to login and create a database | ||
+ | * Disconnect from database (R-click) | ||
+ | * Reconnect under « example » username (cf. above) | ||
+ | |||
+ | ==== Adding a MSIdb ==== | ||
+ | |||
+ | {{:userguide:setting-up-database-3.png?500}} | ||
+ | |||
+ | {{:userguide:setting-up-database-4.png?600}} | ||
+ | * Select database Uppsala and click the button « execute arbitraty sql queries » | ||
+ | * In query window select file/open | ||
+ | * Select the file MSIDBModel (previously named ExportDBModel) included in the IRMa installation folder | ||
+ | * All the queries necessary to create the MSidb are now open | ||
+ | |||
+ | {{:userguide:setting-up-database-5.png?500}} \\ | ||
+ | {{:userguide:setting-up-database-6.png?400}} \\ | ||
+ | {{:userguide:setting-up-database-7.png?400}} \\ | ||
+ | * Execute the queries | ||
+ | * The database gets populated with all the tables IRMa needs to store identifications data | ||
+ | |||
===== MSI db model ===== | ===== MSI db model ===== | ||
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* {{:userguide:msidbmodeld.4.pdf|model version D.4}} - [[:userguide:MSIdbModelD.4-desc|model description]] | * {{:userguide:msidbmodeld.4.pdf|model version D.4}} - [[:userguide:MSIdbModelD.4-desc|model description]] | ||
* {{:userguide:msidbmodelE.1.pdf|model version E.1}} | * {{:userguide:msidbmodelE.1.pdf|model version E.1}} | ||
+ | * {{:userguide:msidbmodelE.2.pdf|model version E.2}} | ||