====== Mass Spectrometry Identification Database ======

===== 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 [[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 =====

  * [[:userguide:msimodel18]]
  * {{:userguide:msimodel_d1.pdf|model version D.1}}
  * {{:userguide:msimodel_d2.pdf|model version D.2}}
  * {{:userguide:MSIdbModelD.3.pdf|model version D.3}} - [[:userguide:MSIdbModelD.3-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.2.pdf|model version E.2}}