Public Hub Guidelines
The Genome Browser provides links to a collection of public hubs that have been registered
with UCSC and are available to view on the Public Hubs page.
Here are guidelines for those who are trying to make a hub a UCSC public hub. If you have created a
hub that meets the requirements and is of general interest to the research community, please
contact us at
genome-www@soe.ucsc.edu
to have it added to the list.
As a reference for interpreting trackDb.txt settings, use the Hub Track Database Definition glossary. For information on using the Track
Hub features, refer to the Genome Browser Track Hub User Guide.
See also the Basic Hub Quick Start Guide, Quick Start Guide to Organizing Track Hubs into
Groupings, Track hub settings blog post, Quick Start Guide to Assembly Hubs and Quick Start Guide to Searchable Track Hubs.
Contents
Required Guidelines
The following guidelines must be met before your hub will be added to our public list:
Required for both track and assembly hubs:
- You MUST have a description page for every configuration page (composite, superTrack or stand
alone track). Note that multiple tracks and/or composites can use the same description page
with the "html" setting. You can
find more information on creating track description pages in the
recommendations section below.
- All of your description pages MUST have a contact email address prominently displayed.
- At least one track should have a visibility set to display (in full, pack,
squish, or dense), and try to have no more than 10 tracks enabled by default upon first
connecting your hub.
- Have a descriptionUrl html page specified in your hub.txt. This should be a URL to a description
page for your entire hub, often public hubs will link to a full-text paper or to their
laboratory webpage that describes the research presented in the hub. These links are presented
on the Public Hubs page as a hyperlink on the longLabel presented in the hub.txt, while the
shortLabel is a hyperlink to the hub.txt location.
Required for only assembly hubs:
- Add a gateway page for each assembly by having a htmlPath line for each genome not already
hosted by UCSC in the genomes.txt.
- The following settings should properly be set in your genomes.txt (The last 3 settings will make
it easier to find assembly hub species in hgGateway by UI search):
- defaultPos
- scientificName
- organism
- description
Recommended Guidelines
These guidelines in the following sections are recommended to improve user experience, but are
not required to be implemented before the hub is added to our list of Public Hubs.
Track organization recommendations
Related tracks can be grouped in a few different ways, namely superTracks, multiWigs, and composites. If your hub includes a large number of tracks, the grouping of
tracks may be necessary. This will prevent your hub's track group from being an overwhelming mess
of individual tracks and can make user configuration of your tracks easier.
Composite tracks
Related tracks of the same data type (e.g. a set of related bigBed tracks) should be combined into
composites where
appropriate.
- Have multi-view only when there is
more than one view. Views ideally give alternate access to the same data (e.g. signals and
called peaks). Keep in mind that the value of views is that they allow for more than one
data/configuration type (e.g. bigBed and bigWig) in a single composite. All subtracks of a
view must have the same data type. Likewise, all subtracks of a non-multi-view composite must
be the same type.
- Recommendations for using dimensions with your composite tracks:
- There should be no
dimensions with a single entry (do not have only one cell line represented in dimX=cell),
unless data growth is expected to fill in additional entries.
- Using only one dimension: preferably use dimX (e.g. dimensions dimX=cell). This saves vertical
User Interface space, but is not always the best choice.
- Using two dimensions: use dimX and dimY (e.g. dimensions dimX=cell dimY=mark)
- Using more than two: use dimX, dimY on the most important dimensions. Then use dimA,B,C as
needed on lesser dimensions. (e.g. dimensions dimX=cell dimY=mark dimA=donor_id)
- The A,B,C dimensions should probably use filterComposite (e.g. filterComposite dimA)
- Each dimension and views should be represented in sortOrder, ideally in order of dimX, dimY,
dimA,B,C, view (e.g. sortOrder cell_type=+ mark=+ donor_id=+ view=+).
- Tags of subGroup/dimension should be short and sweet with no special chars. Also labels can
have HTML codes embedded (e.g. NOT CPG_methylation_%=CPG_methylation_% RATHER
mpct=CPG_methylation_&_#37)
- Never represent the same subgroup in both view and as a dimension (e.g. NOT dimensions
dimX=view). A subgroup should never be in two dimensions (e.g. NOT dimensions
dimX=cell dimY=mark dimA=cell). The composite will appear to function but multiple ways of
selecting the same thing will create a confusing and inconsistent user interface.
Super tracks
Extremely large hubs may use superTracks as well to achieve a meaningful hierarchy. Super tracks
can be used to group together any type of related tracks; for example, you could combine a multiWig,
a composite, and a bigBed track together into a single superTrack.
Track display recommendations
- Avoid setting a composite track and all of its subtracks to the same visibility. When you have
composite tracks that are hidden by default, it is best to still designate some subtracks to
display when the composite track is turned on (visibility dense, versus the default of hide).
This provides an example of your track data to users who turn on your composite track. If no
subtracks are turned on by default, a user who changes your composite track visibility to
"show" won't see anything.
- The shortLabel text should be under 20 characters, or meaningful information may be cut off
from display when tracks are set to "dense" visibility.
Track description page recommendations
- The description page should preferably contain UCSC's standard track description, Display
Conventions and Configuration, Methods, Credits, and References. More information can be
found on the template page.
- Your track description pages should provide meaningful documentation for your tracks.
- If you are creating a hub based on a paper, use the paper's abstract as a starting point for
your track's description section
- The Methods section expand upon the overview of the Description section and provide more
details about how the data for the track was produced
- You should assume a broad audience of students and researchers will use your hubs. You should
spell out common acronyms for those who may be new to genomics. For example, you might write
out a term and its acronym as follows "Fluorescent in situ hybridization (FISH)" which spells
it out and then provides the acronym that you can use throughout the rest of your description
page.
- It might be a good idea to include a "Data Access" section on your track description page
which describes how to access the data in your hub and where to download the raw data for the
tracks in your hub.
Public Hub Examples
Many of the public hubs in
the Genome Browser provide excellent examples or templates for creating your own hub. As a
reference for interpreting trackDb.txt lines used in these example hubs, please refer to the Hub
Track Database Definition glossary.
Some Hub Track Database Definition settings like filters have additional help documentation. Also note that if
you are only displaying one genome you can use the useOneFile on setting.
Example Track Hubs
Example 1
The Principal Splice Isoforms APPRIS hub provides a good example of basic hub that
includes a few different annotation tracks. Each track includes its own description page and is
colored in such a way that distinguishes it from the other tracks in the hub and native track in
the UCSC Genome Browser.
Here are some links to their configuration files and some description pages:
Example 2
The Roadmap Epigenomics Integrative Analysis Hub provides a great example of how
you might use organize your hub if you have thousands of different tracks. The hub uses composites
with dimensions to organize thousands of different tracks across a number of cell lines and uses
supertracks to group these tracks even further.
Here are some links to their configuration files and some description pages:
Example Assembly Hub
The C elegans isolates hub provides an excellent example of what your assembly hub could
look like. The hub creators provide a detailed description page for each assembly, many different annotations
tracks each with their own description page, and clearly defined track groups with those related
tracks grouped together.
Here are some links to their configuration files and some description pages: