wiki:TrackRelabelling

Track labels for genome browser

Each track should have a label with five components: data type, method, track details, strand (optional) and citation.

We should get enough details via the submission form (http://www.pombase.org/submit-data/data-submission-form) to generate a label for each track; email submitters if necessary. Include the labels in the Jira ticket for the submission.

componentmore infoexample
AData typethe biological datatype; also indicate whether the track is an average/consensus/combination of replicatestranscripts
BMethodthe experimental technique usedtiling microarray
CTrack detailsthe experimental features that distinguish each track from others in the same experimentmitosis, 972h-, haploid
DStrandforward or reverse (or leave blank if not relevant)reverse strand
ECitationFirst author (year)Soriano(2013)

Note: a number of specific track labels were stored here temporarily. Most have been deleted (but can be seen in the page history); a few have been retained as illustrative examples.

Examples

Nucleosome positioning - selected tracks from Soriano (2013) PMID:24256300

ABCDE
nucleosome positioning NGSmitosis, pat1.114, diploid- Soriano (2013)
nucleosome positioning NGSmeiosis 0h, pat1.114, diploid - Soriano (2013)

Transcripts - selected tracks from Soriano (2013) PMID:24256300

ABCDE
transcripts tiling microarray mitosis, 972h-, haploid forward strand Soriano (2013)
transcripts tiling microarray mitosis, pat1.114, diploid reverse strand Soriano (2013)

poly(A) sites - tracks from Schlackow (2013) PMID: 24152550

ABCDE
poly(A) sites RNA-Seq all strand-specific data reverse strand Schlackow (2013)
poly(A) sites RNA-Seq cycling, non-strand-specific, 972 h- forward strand Schlackow (2013)

Chromatin binding - selected tracks from Woolcock (2013) PMID:21151114

ABCDE
chromatin binding DamID / tiling arraySwi6 binding sites, unfused Dam used as experimental control, repeat 1 - Woolcock (2011)
chromatin binding DamID / tiling arraySwi6 binding sites, unfused Dam used as experimental control, repeat 2 - Woolcock (2011)
chromatin binding DamID / tiling arrayDcr1 binding sites, repeat 1 - Woolcock (2011)
chromatin binding DamID / tiling arrayDcr1 binding sites, repeat 2 - Woolcock (2011)

Lists of track component content used to date (last updated 2014-10-20):

Biological data types

  • chromatin binding
  • nucleosome positioning
  • poly(A) sites
  • replication origins
  • transcripts
  • intron branch point

Methods

  • DamID / tiling array
  • HT sequencing
  • mRNA end sequencing
  • NGS
  • RNA-seq
  • tiling microarray

Historical record of additional global changes requested and implemented

  1. "Configure this page" dialog
    • Descriptions for track selection should be replaced by columns E,B,C,D
    • e.g. Soriano 2013 MN_atf1D will become "Soriano 2013, tiling microarray, mitosis, pcr1(delta)"
  1. Mouseover
    • The text visible upon mousing over the (i) icon (e.g. "Data served from a BigWig file: Nucleosome_Seq: Diploid pat1.114 Mitosis pat1.114 as described by Soriano et al 2013") isn't necessary or useful. Most of this information is provided in the track label, and the rest is superfluous for our users (or is inherently excess verbiage).
    • Instead, change this to provide only 2 things:
      • A link to this data set in the public repositories (e.g. GEO, ArrayExpress)
      • A link to the publication

Last modified 6 years ago Last modified on Oct 22, 2014, 3:08:11 PM