bioconcepts2pubtatorcentral.offset.gz not available any more

[alisadeghian]

Hi,

I just wanted to bring to your attention that 'python execute.py --config config_files/pubtator_central_config.json' doesn't run because the file bioconcepts2pubtatorcentral.offset.gz hosted on the ftp is no longer available.

Also, I think the README file at step 3 of the conda installation should be moved to after the conda activate (I don't think conda always automatically switches to the newly created env)

Thank you for making this repo public!
~Ali

[danich1]

Thanks for bring this to my attention. Will ship out an update to reflect these changes soon!

[pnrobinson]

Is there a recommended way of generating the bioconcepts2pubtatorcentral.offset.gz locally?

[alexmplastow]

Looks like I'm late here, but if you are looking for the file, you can find it here:
https://ftp.ncbi.nlm.nih.gov/pub/lu/PubTatorCentral/
Not sure if I can plug that into this github