LOVD 3.0 user manual
Build 3.0-17
Ivo F.A.C. Fokkema
Daan Asscheman
Leiden University Medical Center
Last updated: August 31, 2016
LOVD has received funding from the European Community’s Seventh Framework Programme
(FP7/2007-2013) under grant agreement no 200754 - the GEN2PHEN project.
This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License.
To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/ or send a letter
to: Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
Contents
Contents 1
1 Introduction 3
2 View and search data in an LOVD installation 5
2.1 Searching and sorting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.2 Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.3 Transcripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.4 Variants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.5 Individuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.6 Diseases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.7 Screenings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3 Installing LOVD 11
3.1 Before you install . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3.2 Install process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
4 LOVD Setup 17
4.1 LOVD system settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
4.2 System logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
4.3 Announcements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
4.4 Uninstalling LOVD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
5 Authorized users 24
5.1 Registering a new account . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
5.2 Creating new user accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
5.3 Editing user accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
5.4 Locking users out of the system . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
5.5 Sharing access with other users . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
6 Gene databases 31
6.1 Creating a new gene database . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
6.2 The gene homepage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
6.3 Editing a gene database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
6.4 Deleting a gene database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
6.5 Assigning curators and collaborators . . . . . . . . . . . . . . . . . . . . . . . . 36
7 Gene transcripts 39
7.1 Which transcript(s) should I pick? . . . . . . . . . . . . . . . . . . . . . . . . . . 39
7.2 Creating new transcripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
7.3 Editing a transcript . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
7.4 Deleting a transcript . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
8 Custom columns 41
8.1 Custom column categories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
8.2 Creating a new custom column . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
8.3 Enabling custom columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
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Contents
8.4 Editing custom column settings . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
8.5 Changing the order of custom columns . . . . . . . . . . . . . . . . . . . . . . . 49
8.6 Disabling custom columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
8.7 Deleting custom columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
8.8 Downloading custom column data to text files . . . . . . . . . . . . . . . . . . . 52
8.9 Importing custom column data from text files . . . . . . . . . . . . . . . . . . . 53
9 Adding data to LOVD 54
9.1 Starting a submission by creating an individual . . . . . . . . . . . . . . . . . . 54
9.2 Continuing an unfinished submission . . . . . . . . . . . . . . . . . . . . . . . . 58
9.3 Submitting summary variant data . . . . . . . . . . . . . . . . . . . . . . . . . . 58
9.4 Adding data to already finished submissions . . . . . . . . . . . . . . . . . . . . 58
10 Downloading & importing data 60
10.1 The LOVD3 import format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
10.2 Downloading & importing data . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
10.3 Downloading & importing the complete data . . . . . . . . . . . . . . . . . . . . 71
10.4 Downloading & importing the custom column data . . . . . . . . . . . . . . . . 71
10.5 Downloading & importing own data . . . . . . . . . . . . . . . . . . . . . . . . . 72
10.6 Downloading & importing a gene’s data . . . . . . . . . . . . . . . . . . . . . . 73
11 The LOVD API 74
11.1 Terms of service and fair use policy . . . . . . . . . . . . . . . . . . . . . . . . . 74
11.2 Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
11.3 Possibilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
12 Keeping your data secure 79
12.1 Built-in security measures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
12.2 What you can do to protect your data . . . . . . . . . . . . . . . . . . . . . . . 80
13 Updating LOVD 81
14 Troubleshooting 82
2
1. Introduction
This is the manual for the Leiden Open (source) Variation Database (LOVD) version 3.0.
LOVD 3.0 is a partial rewrite of LOVD 2.0, which first stable release was completed in 2007.
Also, LOVD 3.0 has a greatly improved database model, and includes lots of new features
aimed at making LOVD useful for more research environments.
LOVD is designed to provide a flexible, freely available tool for gene-centered collection and
display of DNA variations. LOVD 3.0 extends this idea to also provide patient-centered data
storage and storage of NGS data, even of variants outside of genes.
LOVD was developed approaching the “LSDB-in-a-Box” idea for the easy creation and
maintenance of a fully web-based gene sequence variation database, that is platform-inde-
pendent and uses PHP and MySQL open source software only. The design of the database
follows the recommendations of the Human Genome Variation Society (HGVS) and focuses on
the collection and display of DNA sequence variations, but it has fully implemented methods
for storing complete clinical data as well. The open LOVD setup also facilitates functional
extensions with scripts written by the community.
The development of (then nameless) LOVD started in late 2002, while it was first officially
released in January, 2004. Before that LOVD was only in use by the Leiden Muscular Dystrophy
pages, as a not-so-modular system with lots of characteristics specific for that website only.
With the official release of LOVD in 2004 the system had become much more dynamic and
customizing LOVD was made easy mostly by editing text-files.
In 2004, LOVD became available under the open source license GPL and with the 1.1.0
release most of the text-files had been replaced by online forms so customizations can be
performed through the web interface. Early in 2005 the first LOVD article was published,
and in 2005 the development of LOVD was more targeted at improving the ease of use of the
system.
In 2006 the development of LOVD 2.0 started after the decision was made to rewrite all of
LOVD from scratch to be able to include a long list of upgrade suggestions that were hard to
implement in LOVD 1.1.0. Aimed at modularity and data redundancy, LOVD 2.0 was meant
to be a more flexible and more powerful successor of the popular 1.1.0 version and soon it
received the interest of LOVD users eager to try out the all-new version.
With more features being added and bugs fixed rapidly, LOVD 2.0 reached beta stage
in April 2007, after which more and more users started to upgrade their 1.1.0 databases to
2.0. Finally, in October 2007 LOVD 2.0 reached the stable stage, after which LOVD 2.0 was
continuously improved with monthly releases for two years, after which the releases became
less frequent. LOVD 2.0 is described in the second LOVD paper.
By 2009 it had became clear that although LOVD 2.0 was a great step forward, there were
still key improvements to be made. Since the complexity of necessary changes had become to
great to gradually upgrade LOVD 2.0 systems to include these options, it was again decided
to start from scratch writing LOVD 3.0. This allowed us to redesign the complete data model
in full freedom, although it should still be possible for existing LOVD 2.0 databases to have all
data transferred to LOVD 3.0.
LOVD 3.0 adds even more flexibility, allowing users to focus exclusively on sequence vari-
ants, whilst also allowing an exclusive focus on individuals and clinical data, and anything in
3
1. Introduction
between. It will be possible for different submitters to work together cooperatively on the same
data. Searching through the data is improved extensively, and webservices of many different
sources are used to automatically retrieve gene and transcript information. Also new in 3.0 is
full Next Generation Sequencing (NGS) support, with the ability to import VCF or SeattleSeq
formats. For VCF file imports, LOVD allows for automatic annotation of the variants. Both
formats support the automatic creation of genes and transcripts in the system, greatly reducing
the amount of work required by curators to get LOVD set up for their research data.
LOVD 3.0 reached beta stage in January 2012, and the first stable release was in December
of that year. Currently, the latest release is 3.0-17. Keep an eye on our news page for the latest
information on LOVD 3.0 development.
Wherever you see “he” or “his” written in this manual, it should read “he or she” and “his
or her” respectively.
Please note that this manual is work in progress. Since LOVD 3.0 is still under
development and the development is the focus of our efforts, many features in
LOVD 3.0 are not yet described in this manual. Also, features described in this
manual may become inaccurate or even incorrect in later versions of LOVD 3.0.
Please bear with us while we finish this manual.
4
2. View and search data in an LOVD
installation
To navigate in an LOVD installation you can use the tabs on the top of the page. Which tabs
you can see depends on whether you are logged in or not, and your user level. When you are
not logged in or you are logged in as a submitter, you see the following tabs: Genes, Tran-
scripts, Variants, Individuals, Diseases, Screenings, Submit and Documentation. Additionally,
Curator-level users and up can see the Configuration tab and only Managers and the Database
administrator can see the Users and Setup tabs.
Each tab has a dropdown menu and the tab itself has a default page to which you will go
when you click on the tab. The options of the dropdown menus depend on your user level.
2.1 Searching and sorting
All list views have search fields which can be used to search data. You can search for a complete
word or you can search for a part of a search term. For example, when you search for “AAM”
in the Symbol field of the genes listing, LOVD will not only find genes starting with “AAM”,
but also containing “AAM”, like “DAAM1” and “DAAM2”.
Figure 2.1: Results when searching for a gene symbol containing “AAM”. Note that the search is case insen-
sitive, so “aam” gives the same result.
To sort on a certain column, click on the column header or on the arrows. If that column
is already selected to sort on, the sort order will be swapped. The column currently sorted on
has a darker blue background color than the other columns. The up and down arrows next to
the column name indicate the current sorting direction. When sorting on any field other than
the default, LOVD will sort secondarily on the default sort column.
LOVD allows boolean search terms, meaning you can construct complex queries with AND,
OR and NOT logic. Typing a space between search terms is treated as AND. OR is indicated
with a pipe ’|’ with no spaces around it and NOT is indicated by an exclamation mark !’, not
followed by a space. If you enclose two or more words in double quotes, LOVD will search for
the combination of those words only exactly in the order you specify. Note that search terms
are case-insensitive and that wildcards such as * are treated as normal text!
5
2. View and search data in an LOVD installation Genes
You can use different operators to specify your search request:
Operator Example Description
space AM DA This gives results where both AM and DA are occuring.
| AM|DA This gives results where either AM or DA occurs.
="" ="AM" Returns results which exactly matches AM.
! !AM Returns results which does not contain AM.
!="" !="AM" Returns results which does not exactly match AM.
> >23 Filter for values higher than 23 (numeric and date columns).
< <23 Filter for values lower than 23 (numeric and date columns).
Some more advanced examples:
Asian Shows “Asian”, but also “Caucasian” entries.
Asian !Caucasian Shows “Asian”, but no “Caucasian” entries.
Asian|African !Caucasian Shows “Asian” or “African”, but no “Caucasian” entries.
"South Asian" Shows “South Asian”, but no “South East Asian” entries.
2.2 Genes
Figure 2.2: Gene menu.
When no gene is selected, the default page of the genes
tab shows all genes. When a gene is selected (shown
in the page header), the default page of the gene tab
is the gene homepage.
View all genes
Here you can see all the genes for this instal-
lation. When you click on a gene entry, you’re
taken to the gene homepage.
View gene homepage
Here you can see the details of a gene. For more information, see section The gene
homepage. This menu item is not available when no gene has been selected.
View graphs
This displays the statistics of the variants within a gene. This menu item is not available
when no gene has been selected.
Create a new gene entry
This menu item is only available for Managers or higher. See section Creating a new
gene database on how to add a new gene.
2.3 Transcripts
Figure 2.3: Transcript menu.
When no gene is selected, the default page of the tran-
scripts tab shows all transcripts. When a gene is se-
lected (shown in the page header), the default page of
the transcripts tab shows all transcripts of the selected
gene.
6