Jan Stanstrup

Nope, I am working on pubchem so that would be great.

_From @wilsontom on October 20, 2017 15:54_ Hi Jan, I parsed HMDB into a [package](https://github.com/wilsontom/hmdbR) a while ago if it's any help. And a colleague did something similar for [PubChem](https://github.com/jasenfinch/pubchemPIP)....

@wilsontom Thanks! But you don't supply functions to actually generate the HMDB table? I'd like that have that in the package too so it is easy to update. I basically...

_From @jotsetung on October 20, 2017 17:3_ hmdb parsing is also on its way - I've just updated to use the `xml2` package instead of the `XML` package.

I have been trying to write something feasible to handle pubchem using sqlite intermediates. The problem is that it is enormous. 130 million structures supposedly. Holding the final table in...

_From @jotsetung on October 23, 2017 3:50_ The HMDB is added (see https://github.com/stanstrup/PeakABro/pull/10).

_From @jotsetung on October 23, 2017 3:59_ Re PubChem: for these large files using a tibble-based approach is not feasible. SQL might do it - or on the fly access?...

Thanks for HMDB. Re Pubchem: PubChem does have an API: https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST_Tutorial.html#_Toc458584424 But it will be way to slow for this purpose to me. It will be thousands of compounds if...

_From @jotsetung on October 25, 2017 14:22_ Re `CompoundDb` and cached - no, I don't think it's possible to cache anything in the package folder. I would keep the annotation...

That sounds very reasonable. It is a bit a learning curve for me with the S4 objects so I hope you have patients with me while I try to wrap...