Another problem with “online methods supplements”:
I just went looking for the online supplement for a paper. The first copy I found was the online open access version from PubMed. All NIH-sponsored research is required to be made available there, now, 6 months after first publication, which is very, very good.
However, PubMed didn’t have the supplement, or a link to the supplement, or any information that there was a supplement. Very bad.
The paper (from 2005) was in Nature, and it’s not a problem to get the supplements, although I don’t know how you’d find them if you didn’t have a subscription. The way I look at it, it’s a loophole in the open access rule if important elements of the papers are excluded from PubMed.