Organization of Proteomics Data With YassDB

Allan Lind-Thomsen, Kris Laukens, Rune Matthiesen, Ole Nørregaard Jensen

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

In recent years the organization of mass spectrometry (MS) data obtained in large-scale proteomics projects became an important issue. This has catalyzed the development of a few different database schemes for storing MS data, as well as some dedicated user interfaces. However, many of these projects are still rather immature and often do not cover all needs. Because our needs were quite specific, it was necessary to build a database that accommodates all the major types of experiments generated in house and that could be easily extended by new modules made by collaborators or students. A database application named "YassDB" will be described in this chapter. The application is implemented in a "three-tier" application architecture, with a database layer, a middle layer consisting of web services and a client layer, containing the user interface. This offers high flexibility: it allows other applications, written in any language, to be written as clients to the database. The setup and use of the YassDB database application with two client programs "pProRep" and "VEMS" will be outlined.
OriginalsprogEngelsk
TidsskriftMethods in Molecular Biology
Vol/bind367
Sider (fra-til)271-87
Antal sider17
ISSN1064-3745
DOI
StatusUdgivet - 2007

Fingeraftryk

Databases
Language

Citer dette

@article{4f3324a0e03211db9628000ea68e967b,
title = "Organization of Proteomics Data With YassDB",
abstract = "In recent years the organization of mass spectrometry (MS) data obtained in large-scale proteomics projects became an important issue. This has catalyzed the development of a few different database schemes for storing MS data, as well as some dedicated user interfaces. However, many of these projects are still rather immature and often do not cover all needs. Because our needs were quite specific, it was necessary to build a database that accommodates all the major types of experiments generated in house and that could be easily extended by new modules made by collaborators or students. A database application named {"}YassDB{"} will be described in this chapter. The application is implemented in a {"}three-tier{"} application architecture, with a database layer, a middle layer consisting of web services and a client layer, containing the user interface. This offers high flexibility: it allows other applications, written in any language, to be written as clients to the database. The setup and use of the YassDB database application with two client programs {"}pProRep{"} and {"}VEMS{"} will be outlined.",
keywords = "Databases, Protein, Internet, Mass Spectrometry, Proteomics, Software, User-Computer Interface",
author = "Allan Lind-Thomsen and Kris Laukens and Rune Matthiesen and Jensen, {Ole N{\o}rregaard}",
year = "2007",
doi = "10.1385/1-59745-275-0:271",
language = "English",
volume = "367",
pages = "271--87",
journal = "Methods in Molecular Biology",
issn = "1064-3745",
publisher = "AAAI Press",

}

Organization of Proteomics Data With YassDB. / Lind-Thomsen, Allan; Laukens, Kris; Matthiesen, Rune; Jensen, Ole Nørregaard.

I: Methods in Molecular Biology, Bind 367, 2007, s. 271-87.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - Organization of Proteomics Data With YassDB

AU - Lind-Thomsen, Allan

AU - Laukens, Kris

AU - Matthiesen, Rune

AU - Jensen, Ole Nørregaard

PY - 2007

Y1 - 2007

N2 - In recent years the organization of mass spectrometry (MS) data obtained in large-scale proteomics projects became an important issue. This has catalyzed the development of a few different database schemes for storing MS data, as well as some dedicated user interfaces. However, many of these projects are still rather immature and often do not cover all needs. Because our needs were quite specific, it was necessary to build a database that accommodates all the major types of experiments generated in house and that could be easily extended by new modules made by collaborators or students. A database application named "YassDB" will be described in this chapter. The application is implemented in a "three-tier" application architecture, with a database layer, a middle layer consisting of web services and a client layer, containing the user interface. This offers high flexibility: it allows other applications, written in any language, to be written as clients to the database. The setup and use of the YassDB database application with two client programs "pProRep" and "VEMS" will be outlined.

AB - In recent years the organization of mass spectrometry (MS) data obtained in large-scale proteomics projects became an important issue. This has catalyzed the development of a few different database schemes for storing MS data, as well as some dedicated user interfaces. However, many of these projects are still rather immature and often do not cover all needs. Because our needs were quite specific, it was necessary to build a database that accommodates all the major types of experiments generated in house and that could be easily extended by new modules made by collaborators or students. A database application named "YassDB" will be described in this chapter. The application is implemented in a "three-tier" application architecture, with a database layer, a middle layer consisting of web services and a client layer, containing the user interface. This offers high flexibility: it allows other applications, written in any language, to be written as clients to the database. The setup and use of the YassDB database application with two client programs "pProRep" and "VEMS" will be outlined.

KW - Databases, Protein

KW - Internet

KW - Mass Spectrometry

KW - Proteomics

KW - Software

KW - User-Computer Interface

U2 - 10.1385/1-59745-275-0:271

DO - 10.1385/1-59745-275-0:271

M3 - Journal article

VL - 367

SP - 271

EP - 287

JO - Methods in Molecular Biology

JF - Methods in Molecular Biology

SN - 1064-3745

ER -