search

soybase / jekyll-soybase

SoyBase site, forked from jekyll-legumeinfo mid-2022; built with Jekyll and served on GitHub Pages
Apache License 2.0
2 stars 0 forks source link

add Wang_Duan_2024 transcription tracks to JBrowse #142

Closed weihuang12 closed 2 months ago

StevenCannon-USDA commented 2 months ago

Can you make a link in the popup window that goes to either the paper (DOI) or the paper record in the mine?

It looks like the available options for this are:

  1. put the DOI in the config.description, which is seen when you click on the three dots to the left of the track, then "About track"; or
  2. put the DOI (or other parts of the citation) into a column-9 attribute for each feature.

I really dislike option 2, as it would be super-redundant and would set a bad precedent relative to other GFFs. So, that leaves option 1 - unless there are other approaches that @nathanweeks or @weihuang12 know of.

Here is the preprint citation:

Widespread transcription initiation within coding sequences marks tissue identity and accessible chromatin
Xutong Wang, Jingbo Duan, Chancelor B. Clark, Wanjie Feng, Jianxin Ma
bioRxiv 2024.03.27.587116; doi: https://doi.org/10.1101/2024.03.27.587116
maxglycine commented 2 months ago

I would vote for #1 also. Keeping in mind that there is also the option to link to the GlycineMine report for Wang_Duan_2024. Which ever is easier to execute will be fine.

weihuang12 commented 2 months ago

@nathanweeks , can we add DOI link of the paper in the description part of the MANIFEST*.yml, since the jbrowse-tracks.sh script parses the description from this yaml file?

nathanweeks commented 2 months ago

Would a link to the README (or directory containing the README) work (e.g., more info: <URL> appended to the track description)?

StevenCannon-USDA commented 2 months ago

Would a link to the README (or directory containing the README) work (e.g., more info: <URL> appended to the track description)?

That sounds like a good idea to me. It would allow people to find the underlying data, and the README will be most reliably updated -- for example, when the main paper is published and replaces the preprint.

nathanweeks commented 2 months ago

Done. Alternatively, the README could be embedded in the File Info section (as is done with with the Reference sequence tracks), though it would replace any existing track metadata (e.g., GFF or VCF headers).