LOVD 3.0 News

LOVD 3.0 build 29 released Ivo Fokkema, 2023-02-23
Today, LOVD 3.0 build 29 has been released.
New features implemented, amongst others: Added an visual HGVS syntax checker tool. This is an online form that takes a variant and finds out whether it seems to be described following the HGVS nomenclature. The form accepts either a single variant input, or a batch variant input, where a list of variants can be pasted into the input form. In both cases, it checks the variants' syntax and suggests a correction when possible. It also allows to validate variants using the VariantValidator service. When generating a suggested fix ourselves, we express our level of confidence that this correction is indeed as intended, in the text of the suggestion. The interface allows downloading the results to a text file so that the user can store the result of the analysis. You can find this tool in the scripts folder. Also, we upgraded the javascript libraries, improved how numeric values and selection lists are validated, and changed the default value for the "chromosome" field from "1" to empty.
Bugs fixed, amongst others: Fixed some URL parsing issues; Several fixes in and improvements to the VariantValidator library; Fixed issue with the LOVD2-style API not fully working; Fixed the connection to Mutalyzer, since they changed their URL, breaking all interactions with their services; Fixed several issues with running LOVD on PHP8.1; Updated the links to dbSNP since they changed their URLs; Added several fixes to the position fixing script.
Closes #526, #575 and #618.

See the changelog.
Download the new build.
LOVD scripts included: LOVD2 file converter 3.0-29, Reading Frame Checker 3.0-28, RefSeqParser 3.0-29, Variant position fixer 3.0-29, Variant Validation 3.0-29.
Manual version included: June 15th, 2021.

Introducing a new API that allows you to check and correct your HGVS syntax Ivo Fokkema, 2022-09-19
We have released a new API, hosting a service that allows you to check whether your variant descriptions follow the HGVS nomenclature for the description of DNA variants. While this service does not validate the variant on the sequence level like other available services such as Mutalyzer and VariantValidator, our API does provide several advantages over those services.
  • Our service validates the variant description only on a syntax level and not on the sequence level. This allows you to submit variant descriptions without reference sequences, and it enables us to support more variant types than all other available services combined. For instance, variants with uncertain positions, e.g., NC_000017.10:g.(41228632_41234420)_(41234593_41242960)dup, aren't supported in other tools as they cannot easily be validated on the sequence level. Our API does correctly interpret and validate this variant description, and checks whether the HGVS nomenclature has been applied correctly.
  • Our service focuses on providing constructive errors and warnings in case the variant description does not conform to the HGVS nomenclature guidelines. E.g., the variant mentioned above, when input in the Mutalyzer syntax checker, results in the error message "Expected "del" (at char 34), (line:1, col:35)", which doesn't provide you with relevant information - that this service does not support the given variant description.
  • Our service attempts to correct variant descriptions that do not follow the HGVS guidelines. We have analyzed hundreds of thousands of variant descriptions to learn what errors are commonly made and how we can automatically correct them. Corrections are annotated with a 3-tier confidence score, showing the certainty that the modification represents what the user intended to write.
The release of this API will allow developers to use this service and integrate it into their software. In addition, we will soon release a web page using the same service, allowing non-developers to use our new tool as well.

Give the API a try through the Swagger interface, or see the documentation on the GitHub page.

The development of this API was part of a project between LOVD developer Ivo Fokkema and Bioinformatics student Loes Werkman, who obtained her degree with her work on this project.

LOVD 3.0 build 28 released Ivo Fokkema, 2022-07-18
Today, LOVD 3.0 build 28 has been released.
New features implemented, amongst others: Allow passing the classification method to the submission API using the pathogenicity's @source value; Improved variant recognition functions; Enabled the "Your submissions" link that was defined but not enabled; Added a /diseases/[OMIMID] redirect.
Bugs fixed, amongst others: Applied several fixes to the LOVD2-style API; Several internal XSS issues were fixed, adding protection against stored XSS; Fixed warning shown when editing somebody else's data; Fixed several PHP warnings and notices throughout the code; Fixed LOVD for PHP8; Fixed multiple-selection lists display issue on Windows browsers; Fixed link to LRGs; Fixed several issues in our Variant Validator library.
Closes #548, #566, #568, #570, #571, #583, #590, #591 and #599.

See the changelog.
Download the new build.
LOVD scripts included: LOVD2 file converter 3.0-22, Reading Frame Checker 3.0-28, RefSeqParser 3.0-22, Variant position fixer 3.0-20, Variant Validation 3.0-25.
Manual version included: June 15th, 2021.

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

Last modified 2023/02/23 12:16:52 CET

When using or discussing LOVD please refer to:
Fokkema IF, Kroon M, López Hernández JA, Asscheman D, Lugtenburg I, Hoogenboom J, den Dunnen JT. The LOVD3 platform: efficient genome-wide sharing of genetic variants. Eur J Hum Genet (2021). https://doi.org/10.1038/s41431-021-00959-x.

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.
©2004-2023 Leiden University Medical Center, Netherlands
Ivo F.A.C. Fokkema BSc., Prof. Johan T. den Dunnen PhD
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