HUPO-PSI/mzQC

Improved browsing of qc-cv.obo

Closed this issue · 8 comments

sneumann commented

Related to #107, I suggest to have a better browsing of qc-cv,
which would also help #115 . I vaguely recall that the OpenMS team
had some tools in OpenMS to create static HTML from OBO files.
Resulting HTML could be hosted on github pages then.
Yours, Steffen

nilshoffmann commented

Please see #122

nilshoffmann commented

Documentation is now in my repositories CI, deployed to https://nilshoffmann.github.io/obo-adoc/qc-cv.adoc.html

sneumann commented

The formatting looks good, but is lacking the navigationability.
I found what I remembered:
http://htmlpreview.github.io/?https://github.com/nmrML/nmrML/blob/master/docs/mapping_and_cv.html
which is created by the OpenMS CVinspector in https://github.com/nmrML/nmrML/blob/master/Makefile#L127, unfortunately it requires a mapping file to work. A dummy mapping that allows the root term would work for the output. Yours, Steffen

nilshoffmann commented

@sneumann @mwalzer

So, should we keep

  1. The generated html for the complete CV using my script
  2. The generated mapped html for the CV using the mapping file using the OpenMS tools?

Or should we just use the OpenMS tool for both?

bittremieux commented

This might also be a relevant tool: http://vowl.visualdataweb.org/webvowl.html

We'd need to convert the OBO to OWL format, but those are mostly interchangeable. And the resulting interactive view looks pretty decent.

Ideally we should set something up with GitHub Actions to automatically generate an interactive webpage on all CV updates.

mwalzer commented

would #122 also work after #141? PSI-MS-CV might appreciate a browse-friendly CV, too

nilshoffmann commented

PSI-MS obo was one of my first use-cases for this, so yes, it should work. You just need to replace (or add) a line with the url for the psi-ms obo file. Here is a version from some time ago: https://nilshoffmann.github.io/obo-adoc/psi-ms.adoc.html

bittremieux commented

As we are merging into PSI-MS-CV, it will be possible to easily navigate the QC terms in their own branch using OLS (and other tools that already index the PSI-MS-CV).