Batch upload data

Ivo Fokkema / Johan den Dunnen

For large data sets the “Global Variome shared LOVD” offers a batch upload service.
The file actually used for uploads is quite complicated, when interested you can obtain it
by using the option “Download all my data” (from the “Your account” page (after login,
top right)). We made a simplified version of this file (GVsharedLOVD_upload.xlsx).

Data in LOVD3
In LOVD3 powered databases data are collected and stored separately for the Individual,
the Phenotype, the Screening and the Variant (based on a genomic position and
optionally linked to one or more Transcripts). LOVD3 allows for one Individual to link
several different Phenotype and/or Screening entries. In addition one Screening can have
many different Variants. As a consequence, data can not be added in a file containing all
data on one line/row. We generated a simplified upload file to allow data entry where
possible per line/row. The file can be completed and mailed to
LOVD@JohanDenDunnen.nl where the LOVD-team will perform a last reformat and
take care of the actual batch upload.

Simplified upload file

The simplified upload file provided (GVsharedLOVD_upload.xlsx) should be opened in
a spread sheet program. The file contains an example data set (which should be removed)
and an explanation of specific formats used in the “Global Variome shared LOVD”.
Please make sure you complete all mandatory fields (marked in red) and use only options
from the selection list provided in the red and yellow marked fields.

NOTES
1. LOVD allows reporting data per Family as well as per Individual (our preference
is per Individual). Since most submissions contain data on isolated cases or
summary data per family, we explain such submissions only. When you want to
report several cases per family, please contact us for further details.
2. to find the {{diseaseid}} go to https://databases.lovd.nl/shared/diseases and find
the ID (general) of the Disease of the Individual reported. Select the Disease as
originally diagnosed, not of the ultimate diagnosis after a DNA analysis. For
complex cases use “00198” (unclassified / mixed). For controls use “00000”
(Healthy/Control). In {{Phenotype/Diagnosis/Initial}} give the initial general
diagnosis in words. In {{Phenotype/Diagnosis/Definite}} give the final diagnosis
as confirmed by DNA analysis (select abbreviation from https://databases.lovd.nl/
shared/diseases).
3. when more than one variant has been identified in one Individual you do not need
to repeat all information on Individual, Phenotype and Screening but only
complete details on the Variant on additional rows. When the additional Variants
were detected using another screening method, please make sure to add an
additional entry for the Screening.