First of all, thank you very much for sharing this repository! It works very nicely. With your repo as a dependency, I could easily create an ImageJ/Fiji plugin that extracts a calibrated image stack from an imzml dataset for further analysis in ImageJ.
I'd like to share this plugin to the ImageJ community (and mentioning your repo and the associated paper of course), but before that I have a few questions:
Can you add a license to your project ? I did not see any license associated. IANAL but I think this means that you own it completely and thus it can be re-used - and thus I can't ship it as a plugin for ImageJ.
I do not understand completely what's happening regarding the controlled vocabulary download, but currently, a psi-ms.obo file is downloaded which contains the line:
import: http://purl.obolibrary.org/obo/stato.owl
this lines triggers the parsing of stato.owl, but unfortunately, the owl format is not recognized and this creates an error (I think this repo just assumes that stato.owl is in the obo format and thus throws errors). To build the repo I had to cheat by skipping this import. Am I correct ? If yes, how would you like to fix this bug ? Depend on an owl parser ? Skip any owl file? Maybe there's an equivalent stato.obo file somewhere that can be used instead ?
When this bug is fixed, could you upload the new version to maven central ?
Thanks again for sharing your work, it is extremely useful.
First of all, thank you very much for sharing this repository! It works very nicely. With your repo as a dependency, I could easily create an ImageJ/Fiji plugin that extracts a calibrated image stack from an imzml dataset for further analysis in ImageJ.
I'd like to share this plugin to the ImageJ community (and mentioning your repo and the associated paper of course), but before that I have a few questions:
psi-ms.obofile is downloaded which contains the line:this lines triggers the parsing of
stato.owl, but unfortunately, the owl format is not recognized and this creates an error (I think this repo just assumes that stato.owl is in the obo format and thus throws errors). To build the repo I had to cheat by skipping this import. Am I correct ? If yes, how would you like to fix this bug ? Depend on an owl parser ? Skip any owl file? Maybe there's an equivalent stato.obo file somewhere that can be used instead ?Thanks again for sharing your work, it is extremely useful.