HTML articles are only useful if they contain larger versions of graphics (or colour versions in some cases). PDFs are easier to read due to format (although the Biochemical Society's HTML format looks good). The project Prospect stuff is nice but what would be nicer would be a chemistry publishing industry-wide standard for this sort of thing with all publications neatly cross referenced and linked.

How about using an idea similar to Tag Clouds instead of/in conjunction with Keywords (there is a good bit of debate about this in the Geology blogosphere this week, places like Highly Allochthonous and Lounge of the Lab Lemming). That is, generating a list of terms to describe each article by the most frequent occurrence within the document, rather than author generated lists. Obviously common words are excluded.

Big graphics are nice but space restraints in print will always limit that. Perhaps larger versions of figures could be available online. Similarly, access to spectral data in its orginal format might be useful. Hyperlinks to abstracts of references are pretty useful (and standard).

A moderated comments facility would be interesting.

Hi Neil, I replied in my blog:

http://chem-bla-ics.blogspot.com/2008/05/re-what-should-nature-chemistry-paper.html

Oh, and please have your spam detection system recognize a 'Preview' as not being a 'Post'. Now, I could not post the comment after having reviewed the 'Preview' :( And had to wait...

I enjoy the HTML and PDF because usually if I am looking for something specific, i.e. a method or reference I can go open up the HTML and find it quick, whereas the PDF is great format for general reading.

Small graphics can be setup to be enlarged with a simple click. This makes loading quicker and HTML more convient.

Links to the structure's PDB or other 3D reference in the HTML would be nice or even a built in Jmol figure.

The Biochemical Society's HTML format is very awkward. It is an interesting idea for sure but doesn't seem to be implemented in a way that is friendly. What if I want to search for keywords in the document, I can't. In normal HTML ctrl-F and then search is oh so nice.

Hi Egon - thanks for your excellent comments!

Just to clarify for everyone as I used a somewhat odd term, by 'forward linking' I meant a service that finds citing articles - in other words, you click on a link and it brings up the papers that cite the one you're reading. For instance, the RSC offers 'Search for citing articles' (here) and Science Direct has a 'Cited by' button, as well as the RSS 'citation feed', in a box like this. I think they're the only ones who offer RSS feeds for citations - to be honest, I'm surprised Google Scholar doesn't offer alerts like other Google-brand services.

Neil

I think Nature could make a real splash by being the first journal to link to the chemical blogosphere. For example, using Chemical Blogspace's API to find comments on a particular paper. See my greasemonkey script for examples of this (http://baoilleach.blogspot.com/2008/01/enhancing-web-for-scientists.html).

Forward linking would be fantastic. RSS feeds...as an author, I would like them. I don't know if I would track an RSS for citations to papers I was just interested in.

See the BMC Central/Chem Central approach for HTML layout. I think they have it all worked out. I would never print out the HTML version.

Comments boxes are overmoderated and overhyped, or possibly just poorly advertised. Are the comments even emailed to the author? You never see on the front page of a journal, "latest comments by Joe Bloggs", etc.

Project Prospect is the way to go. You could even share some code and reduce the work.

Neil, I've got some responses here:

http://depth-first.com/articles/2008/05/08/building-a-unique-chemistry-journal-responses-to-questions-from-nature-chemistry

petermr has allowed me to post comments on his blog:
http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1087

Regarding HTML vs PDF, I never look at the HTML. If I am skimming a paper, I look first at the schemes--on the ACS HTML pages, the schemes are so small that one cannot typically read them, so there is really no point to using that format. If I am looking for something specific in the paper, it is almost always a compound in a scheme, so again, there is no point looking at the HTML page. If I want to read a paper in detail, I print out the PDF. Even if the HTML pages had legible schemes, I would still probably read the PDF because of the nicer formatting. The ACS style thumbnail schemes just seem like a waste--they make people go out of their way to see the most important parts of the paper, and they break up the flow of the article. When you enlarge them it opens a new page, so you cannot refer to both the text and the scheme at the same time. I really like the way the ACS webpage handles everything else, but their HTML articles are worthless.

Advantages of the HTML page could be that it is easier to search for text (although this can be done in PDF as well), and the references can be hyperlinked to the papers they are referencing (I think this can be done in PDF's but I don't often see it).

I like forward linking, and I find it to be quite useful sometimes, but I have only ever used it in SciFinder (find citing articles). Does it work as well from the actual journal pages? For example, does a RSC paper bring up cites from the whole of the chemical literature, or only from other RSC journals?

Hi Neil,

HTML: easy to view (if you have access to net), can do fancy stuff (video clips of reactions, 3D structures that you can move around), easy to tell people where you found the article (give them a link)

PFD: Pics on PDF should be small so that it is easy to download and also doesn't use up too much ink when printing. Also easy to store on your PC. Plus you can read it on train, air plane etc even if you do not have access to the net.

Therefore, I like them both! (not really a helpful comment...)

It would be interesting to have a voting system where people vote "Good" or "Bad". This is useful(or fun) when you are just browsing and wants to find out what people thought was a good paper.

Finally on Biochemical Society... well not my cup of tea...It contains too much information in too many places and it may be difficult to see with small screen... but may be good once my eyes get used to it...