Edam ontologies for tools

[chrisbarnettster]

Labelling tools with EDAM ontologies

Galaxy Cofest inspired 🌀🎉

This PR should probably be paired with work on the docking/cheminformatics tools at chemicaltoolbox, no PR there yet. Discussion and contribs welcome! 👍

For each tool do the following (cofest doc for details):

• [ ] Check bio.tools https://bio.tools/
• [ ] Check https://ifb-elixirfr.github.io/edam-browser/
• [ ] include an annotations section in macros.xml with most core topics and operations
• [ ] expand annotations in tools and expand as needed.

List of relevant IDs

topics

• http://edamontology.org/topic_3332 computational chemistry
• ❌Rather be more specific http://edamontology.org/topic_0081 Structure analysis
  • ✔️ http://edamontology.org/topic_0176 Molecular dynamics (includes MD, QM, coarse grain)
  • ✔️ http://edamontology.org/topic_2275 Molecular mechanics (includes docking)

operations

• ❌ Rather be more specific http://edamontology.org/operation_2480 Structure analysis
  • ✔️ http://edamontology.org/operation_2476 Molecular dynamics (which includes modelling and simulations, prediction and recognition is a subcategory of structure analysis
• http://edamontology.org/operation_2409 Data handling
• for PCA analysis I found to entries one aimed at doing PCA and the other at visualisation.
  • http://edamontology.org/operation_3891 essential dynamics - this is a child of simulation analysis and a child of protein property prediction, that is a bit confining as PCA is generally applicable.
  • http://edamontology.org/operation_2939 PCA visualisation

tools by dir

For the moment a check means it has been worked on:

• [x] bio3d
• [ ] biomoldyn
• [ ] buildtools
  • [ ] ambertools
  • [ ] packmol
• [ ] free_energy
  • [ ] alchemical_analysis
  • [ ] alchemical_run
• [x] gromacs
• [x] mdanalysis
• [x] mdfileconverter
• [x] mdslicer
• [x] mdtraj
• [x] vmd
  • [x] hbonds

[chrisbarnettster]

I'll work on bio3d, mdanalysis and mdtraj so long

[simonbray]

@chrisbarnettster can I help with this?

[chrisbarnettster]

mdtraj is also the key part of mdslicer and mdfileconverter. working on these as well (for the future should probably move these tools under the mdtraj dir..)

[chrisbarnettster]

I am finishing up fastpca /moldyn and on to buildtools*