LOVD 3.0 News

LOVD 3.0 build 20 patch 01 released Ivo Fokkema, 2017-10-17
We have released a patch due to a bug introduced in the latest LOVD release. Internet Explorer users could no longer operate the 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 20 released Ivo Fokkema, 2017-10-10
Today, LOVD 3.0 build 20 has been released.
New features implemented, amongst others: Improvements to the user account page; Improvements on the description of some form fields; Added a script to the scripts folder, to fix known errors in variant positions; Added new variant effect categories for variants that affect the protein function but are either not associated with the individual's disease phenotype or not associated with any known disease phenotype; Implemented some speed improvements, making a difference in larger databases or on servers with limited resources; Added a feature for the unique variant view to show only entries where a certain column has different values, useful for quickly finding variants where, for instance, different observations have different variant effects set; The LOVD2-style API can include the variant effect now, if requested.
Bugs fixed, amongst others: Fixed some problems with the LOVD2 to LOVD3 file converter; The variant mapper gets stuck when encountering variants with no position set and the mapper could get positions stored in the wrong order; When the LOVD logo was customized, the page header would sometimes overlap the page data; Importing a phenotype entry without specifiying a disease ID resulted in a fatal error; Fixed issues with newer MySQL versions being too strict; Sometimes search arguments in data listings got lost when using the browser's back button; Fixed issues sometimes showing up on Windows servers.
Closes #58, #59, #98, #107, #162, #189, #190, #191, #202, #206, #213, #237, #238, #242, #243, #245, #261, #277, #283, #291 and #292.

See the changelog.
Download the new build.
LOVD scripts included: LOVD2 file converter 3.0-20, Reading Frame Checker 3.0-19, RefSeqParser 3.0-19, Variant position fixer 3.0-20.
Manual version included: August 31st, 2016.

LOVD 3.0 build 19 released Ivo Fokkema, 2017-06-19
Today, LOVD 3.0 build 19 has been released.
New features implemented, amongst others: Added feature to show variants in a certain genomic range; Submission emails now have their Reply-To set to the curators and submitters; Added an LOVD2 to LOVD3 converter script; The public can now download gene-specific data when enabled by the curator; Added the LOVD Reading Frame Checker script.
Bugs fixed, amongst others: Fixed problems with adding transcripts to variants; Fixed problems with the new sticky page header; Fixed several problems with MySQL's new default strict mode; The "all variants affecting transcripts" view showed only one entry; Fixed problem with graphs; Single letter genes, like T, were not fully supported; The "Select all" feature was not working anymore on some variant views.
Closes #57, #78, #82, #89, #96, #106, #139, #142, #143, #155, #156, #166, #167, #173, #175, #176, #185, #192, #196, #200, #205, #207, #208, #210, #217, #219 and #233.

See the changelog.
Download the new build.
LOVD scripts included: LOVD2 file converter 3.0-19, Reading Frame Checker 3.0-19, RefSeqParser 3.0-19.
Manual version included: August 31st, 2016.

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 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.

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

Last modified 2017/10/17 16:50:29 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.

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