Neil wondered\n“what a Nature Chemistry paper should look like”, and asked the following questions.\nBelow are my answers.
\n\n1. HTML vs PDF: does anyone read the HTML articles? Do you read the PDF on-screen or print it out?
\nI typically read the HTML to scan if a paper is interesting for me. But because electronic paper is still too\nexpensive, I typically make a print of the PDF. I would love to print the HTML instead, if only it was not clouded\nwith advertisement, link menu’s etc. Many websites have a ‘Print View’ with just the content. Nicely layed out,\nbut without the menus/etc. NC should adopt this feature (or did I miss that option?).
2. Big vs little graphics: what does everyone else think about the tiny size of the graphics in ACS html articles?
\nI hate the small figures, because they make scanning the HTML more difficult.
3a. Tagging/’semantic web’: what do you think about the toys on the RSC’s Project Prospect?
\nI love tagging and semantic work up. Just browse my blog. I blogged a bit about Project Prospect \nin the past, and also about using RDFa for semantic markup of chemistry. \nI must also mention the nice semantic work by the Beilstein Journal. Check the HTML\nsource for all the semantics and the link to the papers RDF version. I discussed some of that work\nearlier .
3b. What kind of things would you like to see tagged/linked to other content in Nature Chemistry?
\nI’d really like to see that Nature would pick up social tagging. For example, Euan/Ian/etc\ncan tell you now tags from blogs/etc, can be used to find relevant other literature. Show\nConnotea tags for NC papers on the NC website. Show related literature based on tag matching.\nI also recommend taking advantage of Postgenomic.com and Chemical blogspace\nto complement papers with user comments, or at least link to them (just like linking to F1000).\nRegarding domain knowledge: link to whatever open database present, and encourage authors to provide links to public databases,\ne.g. by providing InChIs for molecules the describe, PDB identifiers, etc, etc.
4. 3D molecular structures: do these help your understanding of a paper?
\nAbsolutely! Henry Rzepa and Christopher Braddock recently showed how one can take advantage of\nJmol to explain what is going on (doi:10.1021/np0705918),\nbut the ACS forgot to make it part of the main text :) A brilliant recent use of Jmol in explaining chemistry, is\nProtopediA that uses Jmol scripts to visualize statements\nin the textual description in the wiki.
5. How useful to you are InChIs and SMILES?
\nWhile there is an OpenSMILES project (part of the Blue Obelisk movement)\nto standardize SMILES, I’d go for InChI, and InChIKey if you mind the length of the InChI itself.
6. Forward linking: do you use it? Would you use an RSS feed that alerted you to new citations of a particular paper.
\nI am not sure what forward linking is, so cannot comment on that. However, I would use RSS feeds to alert me of new citations of\na particular paper. Right now, I am relying on Web-of-Science to do this for me,\nbut RSS are an excellent alternative. BTW, I was not aware of such feeds yet, and could use some advertisement!
7. Would you actually comment on papers if there was a comments box at the end?
\nNo, I would rather comment in my blog instead. That would place the comments in some perspective. See also my comment\non question 3b.
8. We really like the Biochemical Society’s HTML article style – do you?
\nNo, please do not inherit that layout. The use of frames should be discouraged anyway. It seems to be used to easily add\ninteractivity, but I am positive that Ajax/etc can be used to do all this inline.