Thursday, May 08, 2008

Re: What should a Nature Chemistry paper look like?

Neil wondered "what a Nature Chemistry paper should look like", and asked the following questions. Below are my answers.

1. HTML vs PDF: does anyone read the HTML articles? Do you read the PDF on-screen or print it out?
I typically read the HTML to scan if a paper is interesting for me. But because electronic paper is still too expensive, I typically make a print of the PDF. I would love to print the HTML instead, if only it was not clouded with advertisement, link menu's etc. Many websites have a 'Print View' with just the content. Nicely layed out, but 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?
I 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?
I love tagging and semantic work up. Just browse my blog. I blogged a bit about Project Prospect in the past, and also about using RDFa for semantic markup of chemistry. I must also mention the nice semantic work by the Beilstein Journal. Check the HTML source for all the semantics and the link to the papers RDF version. I discussed some of that work earlier.

3b. What kind of things would you like to see tagged/linked to other content in Nature Chemistry?
I'd really like to see that Nature would pick up social tagging. For example, Euan/Ian/etc can tell you now tags from blogs/etc, can be used to find relevant other literature. Show Connotea tags for NC papers on the NC website. Show related literature based on tag matching. I also recommend taking advantage of and Chemical blogspace to complement papers with user comments, or at least link to them (just like linking to F1000). Regarding domain knowledge: link to whatever open database present, and encourage authors to provide links to public databases, e.g. by providing InChIs for molecules the describe, PDB identifiers, etc, etc.

4. 3D molecular structures: do these help your understanding of a paper?
Absolutely! Henry Rzepa and Christopher Braddock recently showed how one can take advantage of Jmol to explain what is going on (doi:10.1021/np0705918), but the ACS forgot to make it part of the main text :) A brilliant recent use of Jmol in explaining chemistry, is ProtopediA that uses Jmol scripts to visualize statements in the textual description in the wiki.

5. How useful to you are InChIs and SMILES?
While there is an OpenSMILES project (part of the Blue Obelisk movement) to 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.
I 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 a particular paper. Right now, I am relying on Web-of-Science to do this for me, but 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?
No, I would rather comment in my blog instead. That would place the comments in some perspective. See also my comment on question 3b.

8. We really like the Biochemical Society’s HTML article style – do you?
No, please do not inherit that layout. The use of frames should be discouraged anyway. It seems to be used to easily add interactivity, but I am positive that Ajax/etc can be used to do all this inline.


  1. Nice!

    Yeah, forward linking in this case is papers that cite the paper you're currently looking at.

    re: the Postgenomic / Chemical Blogspace tracking and commenting on your own blog rather than on the paper - we're rolling this out Nature-wide. Eventually. ;)

  2. Some publishers push HTML viewing over PDF viewing in the hope that they can somehow enhance the experience of viewing the article. They do this by making use of the fact that they have the metadata for the article as well as the PDF so they can render HTML from XML via an XSLT transform to give added features. One such feature is to show a table of contents for the figures where each figure can be expanded like a popup, without having to leave the main page of the article.