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Adding metadata to tracks

Contents

Adding metadata to tracks
Previous metadata versions
Tagstorm metadata
Tab-separated metadata

Adding metadata to tracks

Adding metadata to your tracks about cell lines, experimental protocols, or assays can be accomplished in a number of ways, via the newly supported metaDb or metaTab trackDb fields, or via the older style metadata trackDb field. The metaDb and metaTab fields link external tagStorm or tab-separated metadata files to the data in the hub. The new formats are preferred over the older metadata field, although the metadata lines will continue to be supported for track hubs, but no new features will be added as they will for tagStorm and tab-separated files.

The following is an example of a genomes.txt file calling the tagStorm metadata file: 

genome hg38
metaDb relativePath/to/tagStorm.txt

and specifying a tab-separated metadata file:

genome hg38
metaTab relativePath/to/tabSep.txt

When using tab-separated or tagStorm metadata, a meta column or line will be needed to specify which metadata information is applied to a track. The meta value should be a unique alphanumeric string.

Previous metadata versions

Currently, in order to add metadata to your tracks, you must specify all of the metadata key-value pairs in each stanza of a track that includes metadata, like the last line of the following example: 

track experiment1
shortLabel Donor A
longLabel Donor A's Metadata Experiment
type bigWig
bigDataUrl http://genome.ucsc.edu/goldenPath/help/examples/bigWigExample.bw
parent treatmentX on
subGroups view=X
metadata differentiation="10 hour" treatment=X donor=A lab="List Meta Lab" data_set_id=ucscTest1 access=group assay=long-RNA-seq enriched_in=exon life_stage=postpartum species="Homo sapiens" ucsc_db=hg38

Each track must have a separate metadata field and its own list of key-values, which can become cumbersome when each track in a group all share a common subset of metadata. For instance, if there are 10 tracks in a composite or multiWig, where each subtrack only differs in the "differentiation" tag, it would be more convenient to have a shared set of metadata and then specify the differences for each track. This is the motivation behind the tagStorm format, described below.

You can find an example of a hub using the metadata example here and you can load the following session to view the hub, https://genome.ucsc.edu/s/PublicSessions/metadata_field.

Tagstorm metadata

The tagStorm format is a plain text file similar to a trackDb file that describes all of the tracks in a track hub, in that both are files where the first word in a line is the tag and the rest of the line is the value, and different stanza's are line delimited. TagStorm's are also similar to a spreadsheet, where a tag corresponds to a column and a stanza to an entire row. The tagStorm format is easy for computers to parse, reduce the redundancy of a tab-separated file, and they are human readable. Here is a canonical tagStorm example: 

lab tagStorm Lab
data_set_id ucscTest1
access group
assay long-RNA-seq
enriched_in exon
life_stage postpartum
species Homo sapiens
ucsc_db hg38

    treatment X
    donor A

        differentiation 10 hour
        meta ucsc1_1

        differentiation 1 day
        meta ucsc1_4

        differentiation 5 days
        meta ucsc1_7

    treatment Y

        donor B

            differentiation 10 hour
            meta ucsc1_2

            differentiation 1 day
            meta ucsc1_5

            differentiation 5 days
            meta ucsc1_8

        donor C

            differentiation 10 hour
            meta ucsc1_3

            differentiation 1 day
            meta ucsc1_6

            differentiation 5 days
            meta ucsc1_9

Each stanza, such as "donor B", inherits from any stanzas above it at the right indentation level, and is a parent to stanzas beneath. In the example above, Treatment Y applies to both "donor B" and "donor C". Treatment X only applies to "donor A" as they are at the same indentation level. There are three differentiation times that apply to each of the donors and they can be referenced in the trackDb stanza using the meta line in the tagStorm file, i.e., meta ucsc1_1.

The meta ucsc1_1 line would reference the following metadata:

lab tagStorm Lab
data_set_id ucscTest1
access group
assay long-RNA-seq
enriched_in exon
life_stage postpartum
species Homo sapiens
ucsc_db hg38
treatment X
donor A
differentiation 10 hour

A trackDb stanza using the tagStorm metadata can be seen in the following example: 

track experiment1
shortLabel Donor A
longLabel Donor A's TagStorm Experiment
type bigWig
bigDataUrl http://genome.ucsc.edu/goldenPath/help/examples/bigWigExample.bw
parent treatmentX on
subGroups view=X
meta ucsc1_1

You can find the complete example of the hub using the tagStorm metadata here and you can load the following session to view the hub, https://genome.ucssc.edu/s/PublicSessions/tagStorm_metadata. The hub uses a composite track, so if you are unfamiliar with composite tracks, the Quick Start Guide on composites can explain how the tracks are organized. The details page for the trackDb stanza example (Donor A) can be seen below.

Tab-separated metadata

Column or tab-separated metadata can be useful to store computer readable information as an array. While this format is very easy for a computer to parse, it can be bit confusing or difficult for humans to read and interpret. As you can see in the example below, many columns become redundant as they repeat the same information on each line. 

#lab	data_set_id	access	assay	enriched_in	life_stage	species	ucsc_db	treatment	donor	differentiation	meta
tabSepLab	ucscTest1	group	long-RNA-seq	exon	postpartum	Homo sapiens	hg38	X	A	10 hour	ucsc1_1
tabSepLab	ucscTest1	group	long-RNA-seq	exon	postpartum	Homo sapiens	hg38	X	A	1 day	ucsc1_4
tabSepLab	ucscTest1	group	long-RNA-seq	exon	postpartum	Homo sapiens	hg38	X	A	5 days	ucsc1_7
tabSepLab	ucscTest1	group	long-RNA-seq	exon	postpartum	Homo sapiens	hg38	Y	B	10 hour	ucsc1_2
tabSepLab	ucscTest1	group	long-RNA-seq	exon	postpartum	Homo sapiens	hg38	Y	B	1 day	ucsc1_5
tabSepLab	ucscTest1	group	long-RNA-seq	exon	postpartum	Homo sapiens	hg38	Y	B	5 days	ucsc1_8
tabSepLab	ucscTest1	group	long-RNA-seq	exon	postpartum	Homo sapiens	hg38	Y	C	10 hour	ucsc1_3
tabSepLab	ucscTest1	group	long-RNA-seq	exon	postpartum	Homo sapiens	hg38	Y	C	1 day	ucsc1_6
tabSepLab	ucscTest1	group	long-RNA-seq	exon	postpartum	Homo sapiens	hg38	Y	C	5 days	ucsc1_9

To reference a line in the TSV or CSV file in the trackDb stanza, a meta column must contain a unique alpha-numeric string. For example, ucsc1_1 would reference the following metadata in your track: 

#lab	data_set_id	access	assay	enriched_in	life_stage	species	ucsc_db	treatment	donor	differentiation	meta
tabSepLab	ucscTest1	group	long-RNA-seq	exon	postpartum	Homo sapiens	hg38	X	A	10 hour	ucsc1_1

A trackDb stanza using the tab-separated metadata can be seen in the following example: 

track experiment1
shortLabel Donor A
longLabel Donor A's Tab Separated Experiment
type bigWig
bigDataUrl http://genome.ucsc.edu/goldenPath/help/examples/bigWigExample.bw
parent treatmentX on
subGroups view=X
meta ucsc1_1

You can find the complete example of the hub using the tab-separated metadata here and you can load the following session to view the hub, https://genome.ucsc.edu/s/PublicSessions/TabSeparated_metadata. The hub uses a composite track, so if you are unfamiliar with composite tracks, the Quick Start Guide on composites can explain how the tracks are organized. The details page for the trackDb stanza example (Donor A) can be seen below.

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