LOVD v.2.0 - Leiden Open Variation Database
Online gene-centered collection and display of DNA variants
||For all details about LOVD, see our LOVD flyer! (last updated June 6th, 2013)|
By the way, did you already know LOVD 3.0 is out?
If your question is not in the list, please send your question to Ing. Ivo F.A.C. Fokkema at I.F.A.C.Fokkema@LUMC.nl. Also see the importing variants quick reference guide, the LOVD local install CD FAQ and the required software list.
How should I cite LOVD?
When using or discussing LOVD please refer to:
Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT (2011). LOVD v.2.0: the next generation in gene variant databases. Hum Mutat. 2011 May;32(5):557-63.
What has changed in LOVD v.2.0?
Please go through the LOVD proposal document to see the changes between 1.1.0 and 2.0. The most important changes are mentioned there.
For an in-depth list of changes since the very first 2.0 releases, see the Changelog.
Will the software requirements change for LOVD v.2.0?
Yes, you now need PHP 4.2.0 and up (1.1.0 required 4.0.3). Also, we plan to drop support for the MySQL server versions older than MySQL 4.0 in a later release. MySQL Server 4.0 has been available for general release since 2003, so we predict no problems with this change. If you feel differently, please let us know.
See the software requirements.
Where can I find the data? Where can I download all the data?
LOVD is software, not a data set. The software is used by experts on genetic variation to store and share information on genetic variants, phenotypes, genes and diseases. The software is open source and free of charge, as well as access to the contents. However, specific installations of LOVD may have different rules on what you are allowed to do with the data in the database. Whether or not the LOVD software allows the download of the variant data, depends on the curator who collects and verifies the variants. We are still working on a more transparant way of sharing variant data using a fixed set of data licenses through LOVD.
If you are looking for a specific gene database, please check the list of gene variant databases in the list of registered LOVD installations or in our list of LSDBs.
Is there a webservice/API I can use to retrieve data from LOVD?
All LOVD installations starting from version 2.0-22, released October 5th 2009, have a built-in API. It enables simple queries or listing of gene and variant data (not patient data). More information on this API can be found in the LOVD3 manual.
There are plans for a more extensive API on LOVD3 installations only, allowing full data access depending on the license given to the data by the data owners. We hope to release this API in 2016.
Also, all LOVD installations that have indicated to be included in the global LOVD listing are included in the overall LOVD querying service, which is based on the API of these LOVD installations. Please see the LOVD3 manual for more information.
Will you implement ..., too?
If you have a feature request, please add it to our bug tracking system.
Can I upgrade from my 1.1.0 installation?
Implementing such an upgrade script was not a priority at first, although it was planned for a long time. However, since many of the remaining 1.1.0 installations are already manually transferred to 2.0, the need for it has decreased. We do have a script that can copy and convert all submitters from a 1.1.0 installation to a 2.0 install. If you would like to have a copy of this script, please contact us.
How much hard drive space does LOVD require?
A LOVD installation itself takes very little space on the hard drive. Only 2.0 MB for the application files, and our biggest database (32 genes, 21.000 variants) takes only 4 MB of MySQL (MyISAM) table space.
The LOVD Local install CD that we have available for Windows, requires 200 MB of free space on your C: drive, but also installs all software required by LOVD.
How do I upgrade my 2.0 installation to a new build?
Upgrading your 2.0 installation to a new build is as simple as downloading the new build, unpacking the downloaded file and overwriting all old files. Logging in to LOVD will then finish the upgrade automatically.
I get the error "Error 500 - Internal Server Error"
Apache found the .htaccess file, that should hide the config.ini and set a PHP option. Apache is currently set to disallow either Limit or Options for the AllowOverride directive. Make sure AllowOverride has at least "Limit" and "Options" set.
I get the error "Can't find config.ini"
Please rename the config.ini-lovd file to config.ini and edit its contents. For more information, please see the installation instructions contained in the INSTALL file, included in the package.
I get the error "Can't read config.ini" or "Can't open config.ini"
Please check the permissions of the config.ini file. LOVD cannot read it or open its contents.
I get the error "Your configuration file is NOT protected!"
Please see the installation instructions contained in the INSTALL file, included in the package. In short: you will need to configure your webserver to block access to the config.ini file, preferably using the .htaccess file included in the LOVD package. Make sure you have the .htaccess file into your LOVD directory, on Unix and Linux systems it's a hidden file so it can be missed easily. When using Apache, make sure to have "Limit" and "Options" enabled in Apache's "AllowOverride" setting.
I get the error "Error while creating table" during installation.
LOVD couldn't create one of the tables that are necessary for storing data in the database. Please check the error message that LOVD prints after "I got:".
You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'TYPE=InnoDB' - ('InnoDB' could also be 'MyISAM'). This happens when you try to install LOVD 2.0 build 32 or lower on MySQL 5.5 or higher. Please download the latest version of LOVD 2.0, this problem has been solved in LOVD 2.0 build 33.
Any other error given? Please file a bug report in our bug tracking system and include the given error in the bug report.
I get a blue error table which says "Error: Init"
LOVD made a serious hiccup while communicating with the MySQL database. This is most likely a problem in your config.ini file.
Error connecting to database - Check the "username" and "password" fields of your config.ini.
Error selecting database - Check the "database" field of your config.ini.
I get a blue error table which says "Error: Query"
LOVD made a serious hiccup while communicating with the MySQL database. This is most likely a bug in LOVD, but it may be prevented by changing a setting in MySQL. There are a lot of possible errors, so the list below is not complete.
Error : Column count doesn't match value count at row X - This is a bug in LOVD. File a bug report in our bug tracking system.
Error : Incorrect integer value: X for column Y at row Z - This is a problem with the strict setting in MySQL that LOVD currently does not apply to. You can fix it by editing your MySQL settings. There's a setting in your my.ini or my.cnf file, that's called "sql-mode". It has an option enabled called "STRICT_TRANS_TABLES" or "STRICT_ALL_TABLES". You need to remove those from the list, and restart the MySQL server.
Error : You have an error in your SQL syntax - This is a bug in LOVD. File a bug report in our bug tracking system.
My connection to the UCSC genome browser doesn't work. UCSC gives me the error "Expected 200 (url of the LOVD installation): 404 Not Found".
First, make sure that your LOVD installation can be reached from the outside; the UCSC needs to be able to download a so-called BED file from your installation. Another possibility for getting this error, in case you are running LOVD on Linux or Macintosh, is that you're using a softlink (symbolic link) somewhere in the path to LOVD installation.
My connection to the Ensembl genome browser doesn't work.
This is true currently for all LOVD 2.0 installations. Ensembl have changed something about the way they want to receive variant location data. Ensembl is investigating how LOVD will be able to use this feature again.
How do I get my LOVD installation included in the genome browser tracks?
Major genome browsers have implemented an LOVD track, showing variants found in LOVDs worldwide. In order to be included in this track, make sure your LOVD installation applies to the following:
If it still doesn't work, please contact us.
- Your LOVD installation must be reachable from the internet, so should not be located on a internal network only.
- You keep your LOVD updated.
- You have enabled the settings Send signature, Send statistics and Include in the global LOVD listing in the LOVD system settings.
- You describe variants using the HGVS nomenclature
- Your gene(s) have reference sequences configured, both genomic and for the gene's transcript.
- You have not disabled your LOVD's API.
When I submit a form with a file upload, I suddenly am logged out.
You're logged out because you're not using cookies to work in LOVD, and the size of the file you've tried to upload was too big. Please enable cookies in your browser to make sure you're not logged out when this happens. If you're working on your own LOVD installation, you can increase the maximum size of files to upload. Please check the PHP setting post_max_size and if needed, increase the number there. You might also want to check the upload_max_filesize setting.
I'm having trouble importing files, LOVD tells me the input is incorrectly formatted or I see that my spreadsheet program is messing up my data. What can I do?
Please check our FAQ on importing data for some suggestions on preventing problems when importing data into LOVD.
|Last modified 2016/10/04 17:18:47 CEST
When using or discussing LOVD please refer to:
Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT (2011). LOVD v.2.0: the next generation in gene variant databases
Hum Mutat. 2011 May;32(5):557-63