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LOVD 3.0 News

LOVD proposing to share variant effect through APIs Ivo Fokkema, 2017-01-20
The following message has been sent last week to all LOVD curators known to us. So far, we only got positive replies! If you have any comments on our proposed update on sharing variant effect in LOVDs, please let us know!

Dear LOVD Curators,

Times are changing, also for LOVD. In this mail, sent to all registered curators we have on record, we would like to mention some of the latest developments and, IMPORTANT TO NOTE FOR YOU, to ask for your permission to proceed with these plans. We will repeat this request in 2-3 weeks and when you then do not reply within 2 weeks we will assume you have no objection. Important to note that also after this date you, as owner of the data you have submitted, can still change your mind and grant or withdraw permission.

While initially genes were studied one at a time, the standard now quickly develops towards gene panel, whole exome and whole genome sequencing. As a consequence, while our databases were initially used to check existing knowledge on one or a few variants per gene, users now want to check hundreds to thousands of variants. Although we built an automated tool for this, LOVD's API, this tool currently only answers the question "is this variant known in an LOVD database". Helpful, but the essential information missing is the reported classification of the variant; does the variant affect the function of the gene/protein and is it associated with a phenotype? This information is not shared because we did not yet ask your permission to do so. With this mail we now ask your permission.

      LOVD will start to share variant classification

When you do not agree with this policy, please let us know as soon as possible. Please note that the classification is already publicly available using the LOVD website. What will change, is that we will start to share this automatically using LOVD's API. This allows people to annotate variants automatically without having to go to the website and look. You can imagine that this will greatly facilitate data analysis for all our users, including yourself.

LOVD's API has a "fair use policy". Our servers have a limited capacity and will not be able to cope with the demand of many users that would all like to annotate variants from whole exome or even full genome sequencing. We have been approached by several parties with the request to share, on a regular basis, a copy of the data that is available in the API. There are two reasons for this; 1) the fair use policy, 2) privacy issues. LOVD has started to share this information but charges a fee for the service provided. We will use these fees to keep LOVD alive and further extend the possibilities offered. We are in the process of establishing an oversight committee (in collaboration with the Human Variome Project) that will annually review our work and the way we spend any income from these services.

When you see any problems with these developments, please let us know.

Best regards,
Johan den Dunnen
Ivo Fokkema
LOVD-team

LOVD 3.0 build 18 released Ivo Fokkema, 2016-12-23
Today, LOVD 3.0 build 18 has been released. New features implemented, amongst others: The LOVD header now will stick to the top of the browser's viewport, such that the links in the header are always visible; LOVD now includes a submission API, that can take VarioML formatted JSON data and convert this into an LOVD3 import file (not yet documented); When a Database administrator creates a new user, the level now selected by default will be Submitter instead of Manager; When variants are imported without position fields or variant type filled in, LOVD will now predict them.
Bugs fixed, amongst others: The "Manage transcripts for this variant" feature didn't allow the removal of a transcript anymore; When a user needed to change the password, the force option didn't work properly, and could be circumvented; The variant effect fields didn't have a default value when importing; Variants that were imported with empty intron positions, didn't group together with variants that had a 0 filled in; LOVD3 is now compatible with the ONLY_FULL_GROUP_BY MySQL setting.
Closes #140 and #144.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-12
Manual version included: August 31st, 2016.

LOVD 3.0 build 17 patch 02 released Ivo Fokkema, 2016-09-27
We have released a patch due to two bugs introduced in the latest LOVD release. Custom columns could no longer be edited, and some data views had entries that couldn't be clicked.
To apply this patch, either:
  1. If you hadn't updated your LOVD installation yet, just download the latest build, which includes this fix, and update your installation. See the manual on how to update your LOVD installation.
  2. Otherwise, if you already updated your LOVD installation to the latest build before the publication of this new item, then either redownload the latest build, or download the patch (GZIPped TARball or ZIP archive) and extract the files in your LOVD folder.
  3. If you've downloaded the latest version after publication of this news item, then you already have this patch included in that download.
We apologize for the inconvenience.

LOVD 3.0 build 17 patch 01 released Ivo Fokkema, 2016-09-22
We have released a patch due to a bug introduced in the latest LOVD release. Custom links no longer functioned in most columns in custom data listings.
To apply this patch, either:
  1. If you hadn't updated your LOVD installation yet, just download the latest build, which includes this fix, and update your installation. See the manual on how to update your LOVD installation.
  2. Otherwise, if you already updated your LOVD installation to the latest build before the publication of this new item, then either redownload the latest build, or download the patch (GZIPped TARball or ZIP archive) and extract the files in your LOVD folder.
  3. If you've downloaded the latest version after publication of this news item, then you already have this patch included in that download.
We apologize for the inconvenience.

LOVD 3.0 build 17 released Ivo Fokkema, 2016-09-21
Today, LOVD 3.0 build 17 has been released. New features implemented, amongst others: Added a remarks field for transcripts, and tissues, features and remarks fields to diseases; Added the option to block submitter registrations; Added the option to create announcements within LOVD; Described these two new features in the manual, and added a new chapter "Updating LOVD"; The Find & Replace feature from LOVD2 has been improved and incorporated into LOVD3 (still in Beta, only on selected data listings, see the data listing's menu).
Bugs fixed, amongst others: Solved various problems with the new access sharing feature; Solved two problems with the update import feature; The proxy server settings were often ignored by LOVD, and proxy servers could not be used when using HTTPS, such as with Mutalyzer resources; For curators, editing a disease could result in a fatal error in some conditions; Fixed issue with creating genes with some database settings.
Closes #53, #61, #65, #67, #72, #77, #80, #87, #88, #101, #105, #109, #112, #121 and #124.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-12
Manual version included: August 31st, 2016.

LOVD 3.0 build 16 released Ivo Fokkema, 2016-06-24
Today, LOVD 3.0 build 16 has been released. New features implemented, amongst others: Clarified the IP address allow list feature and added more warnings about the risks of this feature; Added possibility for sharing access to one's data with others - one can make another user a 'colleague' and let them view (and optionally edit) their submissions.
Bugs fixed, amongst others: RNA prediction of a variant affecting splicing was incorrect; Fixed problem with the DBID generation; Fixed problem with the update import overwriting the Owned By field under certain conditions and with it throwing errors about fields that were not defined; Fixed problem with Mutalyzer providing unstable transcript IDs, which resulted in incorrect protein descriptions or false errors on the DNA variants.
Closes #51, #53, #66, #69 and #76.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-12
Manual version included: February 5th, 2016.

Loading large numbers of genes, transcripts and diseases into LOVD3 Ivo Fokkema, 2016-05-09
We would like to draw your attention to the LOVD3 Gene Loader, a tool developed to load large numbers of genes, transcripts and optionally diseases into an LOVD3 installation.
For more information, see the LOVD3 Gene Loader GitHub page. This tool downloads gene data from the HGNC automatically, discovers transcripts for the selected genes, and when data from OMIM has been obtained, it can insert diseases and links to the genes as well. It can optionally be restricted to a certain set of genes and/or transcripts.
For questions about the script, check the LOVD3 Gene Loader GitHub page or contact us if you can't find the answer to your question.

LOVD 3.0 build 15 released Ivo Fokkema, 2016-05-02
Today, LOVD 3.0 build 15 has been released. New features implemented, amongst others: Mitochondrial genes are now supported; The view 'Individuals screened for gene X' has been replaced by the view 'Individuals with variants in gene X'; LOVD now allows more transcripts to be stored; up to 16 million; The geneswitcher in the header is now an autocomplete field for large databases; Updated the manual; On data entry forms, the "Owner of this data" field now has the user's ID visible as well, to distinguish between two users with the same name; For each shared custom column, the list of genes or diseases that this column is active for, is now shown on the column's detailed view; Automatic filling of certain password fields in forms is now blocked, and the automatically filled in username will no longer cause issues; When assigning or changing the curators for a certain gene, the LOVD logs now contain information on the exact changes; Implemented a speed optimization in LOVD when showing data listings, which should speed up any data listing.
Bugs fixed, amongst others: When a new transcript was created, variants from other chromosomes were selected to be remapped as well; Lowered spam score of emails sent out by LOVD; Fixed several issues with the importer; Variant counts on the gene homepage were counted using the gene's first transcript only; Fixed some missing and incorrect links in the tab dropdown menus.
Closes #6, #7, #9, #17, #25, #26, #27, #29, #39, #42, #43, #52 and #54.

See the changelog.
Download the new build.
LOVD scripts included: RefSeqParser 3.0-12
Manual version included: February 5th, 2016.

Moved to GitHub Ivo Fokkema, 2016-01-26
Our code respository has been moved from our own SVN server to the GitHub service, to make it easier for others to collaborate on improving LOVD as well as to increase our visibility to the open source community in general. We will also be using GitHub as our major bug tracker.

News older than 12 months can be found in the archive.

Last modified 2017/01/20 17:55:33 CET

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.

A recommended system of the Human Variome Project LOVD has received funding from the European Community's Seventh Framework Programme
(FP7/2007-2013) under grant agreement nº 200754 - the GEN2PHEN project.
©2004-2017 Leiden University Medical Center, Netherlands
Ivo F.A.C. Fokkema BSc., Prof. Johan T. den Dunnen PhD