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LOVD v.1.1.0 - Leiden Open Variation Database

Online gene-centered collection and display of DNA variations

Information LOVD v.2.0 is the successor of the current 1.1.0 version. We recommend that you try the 2.0 release as it is more user friendly and has more possibilities.

Quick Reference Guide

  1. Relevant directory listing
    - Config
    - Help
    - Include
    - Install
    - Refseq
    - 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

  6. LOVD Scripts
    - LOVD Reference Sequence Parser

  1. Relevant directory listing (Alphabetical listing)

    Config
    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.

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

    Include
    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.

    Install
    Installation directory.

    Refseq
    Location of reference sequences created by the LOVD Reference Sequence Parser. This directory should be made writable for the parser.

    Scripts
    Additional scripts that might be of interest for you.

    Source
    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
    You will need to rename the standard config file config.ini-lovd 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 root 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.


  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

    You can set some gene-specific settings to customize the LOVD public area a bit. For example, you can add links, remarks and OMIM disease ids. All of this is done either when creating a new gene database or when editing the specified gene database. Please note that these settings can not be changed by curators.

    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.


  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!

    System settings
    There are a few system-wide settings available in the Setup area. These are mainly settings for customizing your legend in the public area. Currently you can choose whether you want to use cookies for user authentication, input a list of phenotypes, specify an url with more information about the phenotypes mentioned, modify the list of detection techniques and specify an url for more information about the detection techniques. The mutation submission form also uses information specified here.

    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.


  6. LOVD Scripts

    If you are a programmer and you have a script that you think is of use to other LOVD users, please contact me at I.F.A.C.Fokkema@LUMC.nl. Maybe we can add it to the next LOVD releases.

    LOVD currently comes with one script that is very useful if you want to create coding DNA reference sequences for the genes in your database. For it to work, you will need to make the refseq directory writable.

    Making the refseq directory writable
    Your LOVD package comes with a directory called 'refseq'. As explained above, this directory needs to be made writable. Below we will explain how to do that on Unix/Linux systems. If your LOVD is installed on a different server (Windows, Macintosh), please contact the person responsible for that server in order to make the directory world writable.

    Using the commandline
    • Log in to the server using SSH, telnet or any non-graphical (S)FTP client.
    • Move into the directory LOVD is placed using the 'cd' command.
    • Type in 'chmod 777 refseq'.
    • Check if the Reference Sequence Parser is still generating an error. If not, you're done.

    Using a graphical (S)FTP client
    Of course, there are so many different FTP clients that I can't write a exact manual on how to change rights on a folder. This will describe a generally used method.
    • Log in to the server using your favorite (S)FTP client.
      (FTP is a protocol used to transfer files to or from the internet. If you have uploaded your LOVD files to a server, you can use the same program you used then.)
    • Move into the directory LOVD is placed (usually by double clicking on the folder names).
    • Right click on the folder 'refseq', this will bring up a menu.
    • Select 'chmod' if it is an option. Otherwise, click 'Properties' and look for the folder rights.
    • Fill in '777' as the new value.
    • Check if the Reference Sequence Parser is still generating an error. If not, you're done.

    Information For advanced users
    It is more secure to do a 'chgrp' on the folder to the user running the webserver, but you will need to do a 'ps' to find out which user that is (i.e. 'www-data').

    Input formats Reference Sequence Parser
    The Reference Sequence Parser accepts a specific input formats for each step. Step 2 requires the genomic sequence formatted to provide the positions of the upstream sequence, exons, introns, downstream sequence and the start of the translation.
    Step 3 requires the coding DNA sequence formatted to provide the positions of the exon borders and the start of the translation.
    Both formats are case-insensitive. It does not matter whether you use capital or non-capital nucleotides.

    Input format for step 2
    UPSTREAM<EXON>INTRON<EXON>INTRON<EXON>INTRON (...) <EXON>DOWNSTREAM
    Make sure you include the starting point of the translation by putting a '|' in front of the 'a' of the 'atg' starting codon.

    Example:
    cccccccc<gggggg|at>tttttttt<gggggggg>aaaaaaaa
    will parse:
    - 'cccccccc' as the upstream sequence.
    - 'ggggggat' as exon 1, with the translation starting at the 'a'.
    - 'tttttttt' as intron 1.
    - 'gggggggg' as exon 2.
    - 'aaaaaaaa' as the downstream sequence.

    Step 2 will create the upstream sequence, intronic sequences and the downstream sequence and save them in the refseq directory. It will also create the input for step 3 for you.

    Input format for step 3
    EXON;EXON;EXON; (...) ;EXON
    Make sure you include the starting point of the translation by putting a '|' in front of the 'a' of the 'atg' starting codon.

    Example:
    gggggg|at;gggggggg
    will parse:
    - 'ggggggat' as exon 1, with the translation starting at the 'a'.
    - 'gggggggg' as exon 2.

    Step 3 will create the coding DNA sequence including the translation and save it in the refseq directory.

    For examples on how these reference sequences will look like, take a look at the reference sequences www.DMD.nl, such as the CAPN3 reference sequence.
Last modified 2014/08/25 14:48:46


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