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LOVD v.1.0.2 - Leiden Open Variation Database
Online gene-centered collection and display of DNA variants

Quick Reference Guide

  1. Relevant directory listing
    - Config
    - Data
    - Help
    - Include
    - Install
    - Scripts
    - Source

  2. Pre-install Setup
    - After downloading

  3. Installing LOVD
    - Uploading the files and installing
    - Creating your first gene
    - Adding variations

  4. Gene-specific Setup
    - Text-file based
    - Reference sequence

  5. System-wide Setup
    - Creating, editing, deleting users
    - Custom columns
    - Custom links
    - Uninstalling LOVD

  1. Relevant directory listing (Alphabetical listing)

    Configuration and setup interface for authorized users. Managers have access to the setup area where general settings for the LOVD database can be set; Curators have access to the variations in the database they curate through the configuration area.

    Configuration files that need to be edited manually and uploaded to the server. Contains the general config ini file and the legend settings file. Additional gene information can be put in data files also in this directory (also see configure your genes).

    These helpfiles can be found in the help directory. Contains Quick Reference Guide and FAQ.

    Custom (gene-specific) page headers and footers can be put in this directory. The presence of the headers and footers are detected automatically. They need to be named according to 'GeneSymbol_top.txt' or 'GeneSymbol_bot.txt', respectively (Gene symbols need to be in uppercase letters). For example; DMD_top.txt.

    Installation directory.

    Additional scripts that might be of interest for you.

    If you already have a lot of variation data that you would like to import into your LOVD installation, put this data in a textfile named after the gene symbol in this directory. For more information on the format, see loading data.

  2. Pre-install Setup

    After downloading
    Firstly, you will need to rename the standard config file config.ini-lovd in the data directory to config.ini and edit it in, for example, a basic text editor. This is absolutely mandatory, because you will need to enter the MySQL database name, username and password here.

    Warning! In this LOVD install, a .htaccess is put in the data directory protecting the .ini file. This will keep the .ini file from being viewed on Apache HTTP servers (if configured properly), the most commonly used webserver. If you use Apache, please check that your version and configuration support this feature. If you don't, make sure to configure your webserver to deny access to this file. LOVD will access .ini file through the filesystem.

    Secondly, you probably want to rename the legend.txt-lovd file in the data directory to legend.txt and edit it. You can create a list of phenotypes related to the genes in your database. You can also modify the list of techniques usable to detect variations. These lists will be used in the legend as well as the submission page.

  3. Installing LOVD

    Uploading the files and installing
    Now create a directory on your webserver and upload all the files in the package to the server. Then open your browser and proceed to the install directory. You will need to fill in your data here. This will install the database and make you the Database Manager.

    Information The DB manager is the absolute owner of the LOVD installation. Not only is he the only one that can uninstall the database using the uninstaller, he/she will also (depending on the settings) receive submission and registration notifications and can create or delete user accounts for the system.

    Creating your first gene
    After a successful install of the LOVD system you will be taken to the Configuration area where you can create the first gene. After filling in everything needed and creating the gene in the database, you can start adding variations, either manually or by loading data from a textfile into the database.

    Adding variations
    This can be done manually or by importing a textfile. Manually adding variations is made easy by clicking on the 'Add' button in the menu. However, if you already have a list of variations, you can import a textfile into LOVD. To do this, you need a tab-delimited (preferably data enclosed by double quotes) text-file, for example saved from a spreadsheet program such as OpenOffice Calc or MS Excel. This textfile must be named 'GeneSymbol.txt', for example DMD.txt, and put in the source directory. The number of columns needed depends on whether or not custom columns have been added to the LOVD system.

    The file should have these columns:
    Exonnumber;  DNA allele 1;  Restriction site change;  DNA allele 2;  RNA allele 1;  Protein change;  Frequency;  Phenotype;  Reference;  Detection template;  Detection technique;  DB Id;  Remarks;  (possible custom columns;)  Patient Id;  Off DB remarks;  Times reported;  Status.

    You can also directly import a file that has been downloaded from the LOVD system (provided there wasn't a change in the number of custom columns). After you have uploaded the file to the source directory, click on the 'Load Data' button in the menu.

  4. Gene-specific Setup

    Text-file based
    You can upload gene-specific settings in a text file in the data directory. This file should be named 'GeneSymbol.txt', for example 'DMD.txt'. Within this file, you can customize the LOVD public area a bit. For example, you can add links, remarks and OMIM disease ids.

    You can also add headers and footers to the public area. Name these files 'GeneSymbol_top.txt' or 'GeneSymbol_bot.txt' (for example, DMD_top.txt) and put these in the include directory. The header and footer will, if present, be viewed on the public index, variant table, search forms and search results.

    Reference sequence
    Included with the LOVD package is a script to generate cDNA reference sequences (scripts/lovd_parse_cdnarefseq.php). To create the reference sequence, you need the cDNA sequence with exons separated by '|'. This will aid in the numbering of exons and, if you select this option, it makes linking to intron sequences possible. The script has some capabilities to separate DNA sequence from protein sequence (pasting an previously created reference sequence in this script will return an good result), you are recommended to use the DNA sequence only (for example, FASTA sequence without the header).

  5. System-wide Setup

    The setup is only available for managers (DB manager or manager) and can be accessed by clicking on the 'Setup' icon in the menu.

    Creating, editing, deleting users
    Creating, editing and deleting users is only possible with users with a lower level than you. In other words, when you are a manager, you can create, edit and delete curators only. As the DB manager, you can create, edit and delete managers and curators. There is only one DB manager!

    Custom columns
    You can add custom columns to the database, columns you are missing from the initial set provided by LOVD. These columns will appear in all overviews and forms, except the submission form. You can set whether or not a column is public or not. If you 'hide' a column, it will not show up in the public area. It will still be in the forms and tables within the configuration area, though. Hidden columns have a lighter background color in overviews.

    Custom links
    Custom links are designed to allow you to type shortcuts in certain columns that stand for external resources, such as OMIM pages or PubMed articles. A few have been created for you during installation, but you can edit or delete those, or create new ones if you wish. The custom links are also mentioned on the forms in the configuration area, so that you can quickly add the shortcuts to the columns.

    Uninstalling LOVD
    If, for whatever reason, you wish to uninstall LOVD, you need the DB manager's password. Only he/she can uninstall LOVD. If you have selected the uninstall lock when installing LOVD, you will need to remove this lock manually first, by directly accessing the MySQL database.
    Once you have removed the link, access the uninstaller by clicking on the link on the setup page. You will need to fill in the DB manager's password twice to proceed.

    Warning! Once you have uninstalled LOVD, you have lost all variations. If you wish to keep them, make sure you downloaded the gene tables!

    Information Please note that the LOVD uninstaller will not remove the files itself, just the database tables that it has created during install and use.

Last modified 2014/08/25 14:47:20

When using or discussing LOVD please refer to:
Fokkema IFAC, Den Dunnen JT and Taschner PEM (2005). LOVD: easy creation of a locus-specific sequence variation database using an "LSDB-in-a-Box" approach.
Hum Mutat. 2005 Aug;26(2):63-8.

Leiden University Medical Center, Netherlands
Ing. Ivo F.A.C. Fokkema, Dr. Johan T. den Dunnen