LOVD 3.0 - Frequently Asked Questions (FAQ)

• How should I cite LOVD?
• What is new in LOVD v.3.0?
• Where can I find the data? Where can I download all the data?
• Is there a webservice/API I can use to retrieve data from LOVD?

• I can not log in / my account is locked. Please help!
• I get "Your registration has been blocked based on suspicion of spamming" while registering.
• How do I submit data to LOVD?
• How do I get my LOVD installation included in the genome browser tracks?
• Will you implement ..., too?

• Did the software requirements change since LOVD v.2.0?
• Can I upgrade from my 2.0 installation?
• How do I upgrade my 3.0 installation to a new build?
• Can I run LOVD while offline, for instance on my laptop when it's not connected to the internet?

• Will LOVD 3.0 also work with database servers other than MySQL?
• I get the error "Error 500 - Internal Server Error"
• I get the error "Can't find config.ini.php"
• I get the error "Can't read config.ini.php" or "Can't open config.ini.php"
• I get a blue error table which says "Error: Init"
• I get a blue error table which says "Error: Query"
• I get the error "Class 'SoapClient' not found"

General

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.

There are two main fields where LOVD 3.0 is superior to LOVD 2.0; more flexibility in the data storage, and an improved user interface to help you do your job faster than ever.
In short:

• We have added more data objects; like LOVD 2.0 has Gene, Patient (Individual) and Variant, LOVD 3.0 will have additionally Disease, Phenotype and Screening. This solves one of the biggest LOVD 2.0 hurdles, where in databases with many different genes the list of patient/individual columns can grow enormously and submitters have to fill out long forms containing many fields on many different, and unrelated, diseases. Also:
  • LOVD 3.0 can also store variants outside of genes, and of variants within genes LOVD will now always store both genomic information as well as the effects of the variant on one or more transcripts.
  • In LOVD 3.0 curators are able to configure which phenotypical information to store on the individuals in the database, and no longer need managers for that.
  • Phenotype information can be added many times for each individual, allowing storage of changing values like blood pressure.
  • Individuals can be added to the system also without variant information attached.
  • Mutation screening information can be added, also if no variants have been identified.
  • Each entry will have a history, allowing users to look back in time for each entry separately (still under development).
• New techniques improve LOVD speed.
• All data overviews allow sorting and searching, and will allow column hiding.
• New HTML and Javascript techniques allow you to do more in less clicks.

LOVD is software that 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. LOVD3 supports data licensing, allowing submitters to indicate the data licenses that apply to each submission they make. This can make data reusability a bit complex. Collaborating with participating LOVD3 instances and submitters in these databases, we have developed downloads containing full case-level data in a JSON format. These are available for a commercial license, with which you will be supporting the LOVD project. Contact us for more information.

How to obtain data from LOVD for free, depends on the curator who collects and verifies the variants. If you want a download of a certain gene database, or you would like to otherwise obtain a copy of the data, look for the "Download all data" link on the gene home page. If you don't see that option, then the curator has not enabled it, and you'll need to contact the curator of that gene database to request permission, and they can send you a data file if agreed.
LOVD installations do have an API, but the data returned is rather limited. 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.

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 also commercial licenses available for full case-level data in a JSON format. Contact us for more details.

Finally, 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.

Support

LOVD is freely downloadable software. As such, we might not have any control over the installation you are trying to log into. Also, different LOVD installations do not share their user's credentials with each other, as this has security implications, so an account created in one LOVD installation, is not valid in another LOVD installation. So first check if you're trying to log into the LOVD installation that you also registered to!
Then, many LOVD installations have the option to unlock your account directly, and receive a new password through email. Did you try this option yet? You'll need your username, which you can find in your registration confirmation sent to you when you registered.

Otherwise, our team will only be able to help you, if the LOVD installation you are trying to login to is located on one of the following servers:
databases.lovd.nl, www.dmd.nl, chromium.lovd.nl, or grenada.lumc.nl.
If so, please contact us, and mention the LOVD database that you're trying to log in to.

For all other servers, please contact a curator of that LOVD installation.

LOVD installations use two anti-spam features to prevent automatic registration of false accounts to LOVDs. First is the CAPTCHA, the feature that requires you to enter words or numbers that you read in a picture, to check if you're an actual human being or a machine. However, spammers sometimes bypass these kind of features, and try to register anyway. Therefore, as a second line of defense, LOVD checks the given username, email address and the IP address of the user against a database of known spam attacks. When you see the error "Your registration has been blocked based on suspicion of spamming. If you feel this is an error, please contact us.", then based on the information received from the spam database, LOVD blocked your registration. You can check yourself if your IP address, email address or preferred username is listed. It is usually the latter. If so, try to register using a different username. If it still doesn't work, we can possibly create the account for you, if the LOVD installation you are trying to register for is located on one of the following servers:
databases.lovd.nl, www.dmd.nl, chromium.lovd.nl, or grenada.lumc.nl.
If so, please contact us, and mention the LOVD database that you're trying to register for.

For all other servers, please contact a curator of that LOVD installation.

As LOVD is freely downloadable software, there are many LOVD installations world-wide. The database most people use to submit data is the central "Global Variome shared LOVD". This database also implemented a system facilitating automated data sharing (for details see the LOVD3 manual, section "Data submission API"). Before you can submit you have to register at the LOVD installation; click the "Submit" tab, and follow the steps described. After submission, the curator of the gene database you submitted to will process your submission.

Another way to find an LOVD instance for your gene of interest is the LOVD.nl/GENE URL, such as LOVD.nl/DMD.
To help you find your gene of interest in any other gene variant database (LSDB), we have constructed a list of locus-specific databases, containing all databases we know (including all registered LOVD installations). Note that not all databases accept submissions. To be sure, check the "Database name" field. The "Software" column shows if the mentioned URL is an LOVD installation.

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:

• 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 statistics? and Include in the global LOVD listing? in the LOVD system settings.
• You describe variants using the HGVS nomenclature, and you map your variants to genes.
• You have not disabled your LOVD's API.
• If you have an LOVD 2.0 installation, also check LOVD 2.0's FAQ on the subject.

If it still doesn't work, please contact us.

If you have a feature request, please add it to our bug tracking system.

Hosting LOVD

Yes, you now need PHP 5.3.0 and up (LOVD 2.0 required 4.2.0) and MySQL 4.1.2 (LOVD 2.0 required 3.23.33) to be able to run LOVD on your server. Very few LOVD 2.0 installations do not already run on PHP >= 5.3.0, which has been released in 2009, and MySQL Server 4.1 has been available for general release since 2004. Especially newer MySQL versions support a wide variety of new techniques to speed up LOVD.
See the software requirements.

Since the file and database structure of LOVD 3.0 is very different from the 2.0 installations, you can not upgrade LOVD 2.0 to 3.0 by just overwriting your files, like you normally update your LOVD 2.0 installation.

However, we have developed a conversion script that will take an LOVD 2.0 export file and create an LOVD 3.0 import file. This conversion script is located in the scripts folder of the LOVD 3.0 installation. The created import file needs to be read into the same LOVD 3.0 database that it was created in. A manager or the database administrator will need to perform this import.
This conversion script is available from LOVD 3.0-19.

Upgrading your current 3.0 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.

In principle, yes. There are, however, a few features which don't work when you're offline. In general, when setting up LOVD and adding data, it is very much recommended to have a connection with the internet. The following features do no work when LOVD can not connect to the internet.

• The HGNC can not be contacted, so you cannot create new genes.
• Mutalyzer can not be reached, so transcripts can not be created, variants can not be mapped and the protein change prediction does not work.
• The LOVD's API can not be reached from the internet, and therefore the genome browser links will not show the LOVD's variant track.
• The feature that checks for a variant existence in public LOVDs does not work.
• When new users register, they can not use their ORCID ID to register.
• LOVD can not fetch the frequencies of variants in large NGS datasets.
• LOVD's Reference Sequence Parser script can't retrieve the raw reference sequence file, and therefore does not work.
• LOVD can not check for new updates, and can not be listed on the list of public LOVD installations.

Technical support

No... but then again, maybe yes. LOVD 3.0, in contrast to LOVD 2.0, makes use of the PHP PDO class to communicate with the database. In principle, this will allow you to run LOVD on any database server that has a PHP PDO module, such as PostgreSQL, MS SQL, Oracle or SQLite. However, PDO does not translate SQL and that's how we like it (lightweight). Therefore, there might be SQL used in LOVD that is not compatible with databases other than MySQL. We've played around a bit with LOVD3 on SQLite, and had just a few problems. But we're not testing with other databases, and provide no support for it. But if you really want to, changing the database backend might not be that much work for you.

Apache found the .htaccess file, that should hide the config.ini.php file and set a few PHP options. Apache is currently set to disallow either Limit or Options for the AllowOverride directive. Make sure AllowOverride has at least "Limit" and "Options" set.

Please rename the config.ini.php-lovd file to config.ini.php and edit its contents. For more information, please see the installation instructions contained in the INSTALL.txt file, included in the package.

Please check the permissions of the config.ini.php file. LOVD cannot read it or open its contents.

LOVD made a serious hiccup while communicating with the MySQL database. This is most likely a problem in your config.ini.php file.

Error connecting to database - Check the "username" and "password" fields of your config.ini.php.
Error selecting database - Check the "database" field of your config.ini.php.

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 : You have an error in your SQL syntax - This is a bug in LOVD. File a bug report in our bug tracking system.

LOVD uses the SoapClient class to communicate with Mutalyzer. Although LOVD indicated during installation that the class was not available, it does let you install LOVD without it. When LOVD then tries to contact Mutalyzer, LOVD fails with this error.
To enable the SoapClient class, follow the following instructions.

1. Locate your PHP.ini file. When you're using XAMPP, you will find it in XAMPP's "php" directory.
2. Find the line like ";extension=php_soap.dll", and remove the ";" at the beginning of the line.
3. Save the file, and restart Apache.