dominiquesydow commented 2 years ago

Description

Address manuscript issues raised in https://github.com/volkamerlab/opencadd/issues/133 and https://github.com/volkamerlab/opencadd/issues/134.

I am sorting the (very good!) raised points here in the following grouped into the corresponding sections - adding a few additional checks that came to my mind.

Check manuscript: https://whedon.theoj.org/

Todos

1. Summary section

[x] Check if this section can stay as it is after having updated the other sections. > Yes but moved the comment on OpenCADD-KLIFS being part of the larger OpenCADD package here.

2. Statement of need section

[x] Shorter and more concise! Move some of the text to Description/Key Features/System Overview/Usage section
[x] Check again if target audience is highlighted enough

3. State of the field section

[x] Check if this section is already part of the JOSS author's guide; if not, raise an issue so that it can be added > Maybe add "State of the field" section here? > Not needed; section not explicitly necessary, state of the field simply needs to be discussed somewhere.
[x] How was data accessed previously?
- via KLIFS website: manually
- via KLIFS KNIME nodes
- via KLIFS API : programmatically
- with e.g. requests
- with bravado that can turn OpenAPI in Python module
[x] How does OpenCADD-KLIFS compare to other commonly-used packages? How is it easier now?
- Less technical to set up (only a few lines of code without the need to know how to set up a bravado-generated Python module from the KLIFS OpenAPI definitions)
- Makes switching between local and remote access extremely easy (API and output the same!)
- Output is ready to work with (OpenAPI results are formatted as ABC classes; always needs additional lines of code to bring results in a format that is useful)
[x] Is this package the open-source version of proprietary software? No, the underlying infrastructure is not proprietary.
[x] Any other packages out there that offer ways to query/analyse PDB structure data in a similar way? Double-check but not to my knowledge - KLIFS is integrating and annotating different kinase resources
- Structures from the PDB annotated with the KLIFS pockets of 85 residues that are aligned across all kinase structures, including a split of PDB files by all chains/models
- KLIFS interaction fingerprint (only available at KLIFS) investigating kinase-ligand interactions seen in experimental structures
- Bioactivity data measured against kinases (fetched from ChEMBL)
- Kinase inhibitor data (fetched from PKIDB)
- All entry points (kinases, structures, ligands) have unique identifiers in KLIFS, which makes it super easy to fetch all relevant information for a query kinase, structure, or ligand!

4. Key Features section

[x] Move bullet points from Statement of need here

Typos

[x] Incomplete reference to Raschka on line 46

Documentation!

[x] Sync new Statement of need with documentation! (after approval from reviewers)

Status

[x] Ready to go

codecov-commenter commented 2 years ago

Codecov Report

Merging #135 (d5c4149) into master (d46ca3e) will not change coverage. The diff coverage is n/a.