LOVD 3.0 News

LOVD 3.0 build 21 released Ivo Fokkema, 2018-03-14
Today, LOVD 3.0 build 21 has been released.
New features implemented, amongst others: Many improvements to the submission API (Built scheduling interface for importing files submitted through the API; Keep the JSON file for each API submission; Imports can be run manually or run automatically); The concluded variant effect is renamed to "by curator"; The Phenotype/Additional column will now be added to the Individuals data listing, if it's available; The variant effect fields for the genomic level will now only show on the data entry form, now when there is more than one transcript associated with the variant, or when there is a conflict between the variant effect on the genomic and transcript level; Rewrote communication with Mutalyzer to use a more stable method.
Bugs fixed, amongst others: Some fixes to the submission API (Fixed bug; 3'UTR variants were not accepted; Fixed bug; API submissions had their screenings set to "no variants found"); Fixed bug; The Owner field didn't always show a tooltip in data listings; Fixed bug; Fields edited through the Find & Replace feature will now actually be checked, and some other minor changes; Updated the ORCID API from v.1.2 to v.2.1; users could no longer register with their ORCID; Fixed bug; The "variants affecting transcripts" view didn't show all transcripts associated with each variant, but only each gene.
Closes #127, #149, #214, #270, #305, #307, #313, #327 and #340.

See the changelog.
Download the new build.
LOVD scripts included: LOVD2 file converter 3.0-21, Reading Frame Checker 3.0-19, RefSeqParser 3.0-19, Variant position fixer 3.0-20.
Manual version included: February 27th, 2018.

Introducing a search interface for variants in any public LOVD Ivo Fokkema, 2017-12-15
Looking for an easy way to find out whether there is an LOVD instance which has information concerning a certain variant?
Use our new search interface!
All LOVDs registered to our website are included in this search function. It currently only works for genomic locations, but we'll extend it to also include transcript locations soon. We'd love to get your feedback, let us know what you think of it!

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.

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

Last modified 2018/03/21 04:43:07 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.
©2004-2018 Leiden University Medical Center, Netherlands
Ivo F.A.C. Fokkema BSc., Prof. Johan T. den Dunnen PhD