Tuesday 29 January 2008

Citation format checker for ACS journals

Don't you love checking that every reference has its full-stops, commas and semicolons in the right place? I wrote a Javascript format checker some time ago for JCIM format references, but it turns out that this format is shared by several if not all of the ACS journals. Recently, I was reminded just how useful it is when submitting to an ACS journal and it found I had left out an author's initials.

All you need to do is cut and paste the references from the end of your paper into the textbox in the format checker. Then click Check. (Note: make sure you don't have any blank lines) It will find common errors in formatting such as leaving out an author's initials or the final full-stop on a line. Note that it does not check whether the references themselves are correct, although that would be possible with current APIs.

When your eyes are hurting from looking at one too many "et al."s, try the format checker - it's a cite for sore eyes.

Friday 11 January 2008

DOI or DOH? Proposal for a RESTful unique identifier for papers

Update (18/Jan/07): This proposal has been implemented by Andrew Perry

When DOIs first became widespread for papers, I was a big fan. Just by adding "http://dx.doi.org/" to the start of the DOI I could ensure that a link would always lead the reader to the correct web page of the publisher. As a unique identifier, the DOI could be used to connect disparate resources relating to papers; e.g. comments on papers in blog posts and Table of Contents pages of journals.

But...do we really need DOIs? At least in their current form? Let's consider the following paper (discussed in a previous blog post):
EL Willighagen, NM O'Boyle, H Gopalakrishnan, D Jiao, R Guha, C Steinbeck and D J Wild Userscripts for the Life Sciences BMC Bioinformatics 2007, 8, 487.

What unique identifiers could we use? Well, there's the DOI:
Then there's the PubMed ID:
PMID 18154664
Instead of these, I propose OpenRef:
openref://BMC Bioinformatics/2007/8/487
Spot the difference. Neither the DOI nor the PMID can be derived from the paper itself. Similarly, it's not possible to figure out from the DOI or the PMID what the paper is (without access to the web, at least). Furthermore, the openref is available for all papers published, whether or not the publishers have assigned them a DOI (in associated with CrossRef). Needless to say, not all papers are in PubMed and so don't have PMIDs.

So, is it too late for OpenRef? Certainly not. Any publisher could implement it on their own server with an hour or two's work. Similarly, CrossRef could do it (though it would only work for those papers which have DOIs). Other Web 2.0 sites that manipulate information on publications could use it also; e.g. CiteULike and Connotea.

This would mean that you could instantly access information on a particular paper using a web browser and going to
http://dx.openref.org/BMC Bioinformatics/2007/8/487
http://www.biomedcentral/openref/BMC Bioinformatics/2007/8/487
instead of having to know the DOI or search on a publisher's web site.

(1) For journals that don't use volumes, the openref would be of the form openref://Journal Name/Year/Page
(2) There are certain parallels for chemists between DOIs vs. openref and CAS numbers vs. InChI.
(3) The term RESTful is used in the sense of "RESTful web services" (an excellent book).

Thursday 10 January 2008

Contrast this with colour blindness

This is a bit off-topic, but I was reading a description of some projects at the 2008 BT Young Scientist and Technology Exhibition [1], and came across this:
...Similar clever thinking was evident in the project prepared by Adam Keilthy (14) and Conor Scully (13) second years from Sutton Park School in Dublin. They developed a web browser that first scans and then changes screen colours to improve the view for those with red-green colour blindness.

"We built a web browser that would automatically adjust so you can see it better," explained Adam. Those with this common genetic disorder find it difficult or impossible to differentiate between green and red. Many web pages make ample use of these colours, making it difficult for the colour blind to read them. Adam wrote software that scans pixel by pixel, changing green to turquoise and red to purple.

"You can get yellow-blue colour blindness and total colour blindness, but these two conditions are very rare so we didn't programme for them," added Conor.

They also conducted a survey of classmates finding that 8 per cent of the boys had red-green colour blindness and one girl out of 90 female classmates.

Apart from the fact that this is amazing work by a 13 and 14 year old, I didn't realise so many people are colour-blind, and it seems that it's sex-linked so that men have the worst of it (about 10% have some form, source: Wikipedia).

I can't find out any additional details on the web about the work by these guys, but I did find some good resources relating to web-accessibility and colour-blindness. The first is an existing Firefox extension called ColorBlindExt which runs the standard colour-blindness tests, and then adjusts web page colours depending on the results. The second is for those developing web pages, and lists tools to check colour constrast.

[1] This is the premier science fair for secondary school students in Ireland, and the winner is often a finalist in the equivalent European competition.

Monday 7 January 2008

Enhancing the web for scientists

Egon Willighagen, myself, Harini Gopalakrishnan, Dazhi Jiao, Rajarshi Guha, Christoph Steinbeck and David Wild have just published a paper describing userscripts we have written to enhace and extend web sites for scientists:
Userscripts for the Life Sciences BMC Bioinformatics 2007,8, 487. (Open Access)

Userscripts are Javascript programs that are triggered to run in your web browser when you go to certain web pages. They can alter the content of the web page on-the-fly. For example, one of the userscripts described in the paper looks up all PDB IDs on a web page and adds a link to a webpage showing the structure. For userscripts to work, your browser (e.g. Firefox) needs a special extension (e.g. Greasemonkey).

Our userscripts are divided into two broad categories:
  • Interacting with the scientific literature
    • OSCAR3 running on HTML
    • Add quotes from Chemical blogspace and Postgenomic to DOIs
    • Add to Connotea
  • Linking to chemical and biological data sources
    • Enhancement of PubChem with 3D structures
    • PDB-Jmol userscript
    • Sechemtic
    • Add quotes from Chemical blogspace to molecules
All of these userscripts are available from the Blue Obelisk web site. For other relevant userscripts, search Userscripts.org (the official repository for all userscripts) for userscripts with the tags "Chemistry" or "Biology".

Image credit: Spiders web by Lida Rose (CC BY-ND 2.0)

Socialized science

I suggest we ditch the term "socialized science", and use "Pubmeds under the bed" instead. :-)

(For background, see PMR's post.)