Unilever Centre for Molecular Informatics, Cambridge - Why does scholarly publishing give me so much technical grief? (A post from “Ignorant Chemist”) « petermr's blog

"As readers will know we are gearing up to index the whole of the scientific scholarly literature. The idea is simple. Download all the links to papers, and then read the papers [NOTE: we'll only do what we are allowed to do, and we promise not to burn out your servers]. So we’ve started with PLoSONE. AMI is reading the page http://www.plosone.org/#recent which gives the latest PLoS papers. She’s going to parse it into a XOM (http://about.validator.nu/htmlparser/ ) and then extract all the papers using Xpath. She knows how to do this . So off we go: It crashes on the parse. This does not upset AMI (who has the emotional capacity of a FORTRAN compiler) but it drives me wild. I should be able to read a modern document with modern tools. I know what I am doing. What has crashed it is the tag “”. Note that it’s not terminated by an “” tag. Moreover I can’t find it in the HTML5 vocabulary (which has a perfectly good, 22-year old tag: http://www.w3.org/html/wg/drafts/html/CR/text-level-semantics.html#the-i-element ) So I have to create a kludge. Since I have no idea what other horrors are waiting in PLoS (or any other publisher’s HTML – this is not a PLoS-specific complaint) it can throw my work of by days. It’s not fair to take USD 2900 (the highest PLoS charge) or even USD 1350 (PLoSONE) from authors and produce non-conformant output. [I criticize elsewhere the destruction of vector diagrams into JPEGs.] Nor should this non-standard HTML ever have happened. HTML is produced by the W3C, and a huge amount of effort has gone into producing HTML tools, including validation and compliance, Because the W3C cares about technical quality. So it’s possible and easy to validate. And it’s free. Is this XML? No. Is this HTML5? No. Are the contents of the tag rendered in italic font? No. Does this matter? Yes. Because I am looking for italic content since its may contain species. In fact Gorilla gorilla IS a species. You might be able to guess what genus ...Now I can guess the technical reason why PLOS got it wrong. I’ll leave you to guess.  I can also guess the social reason. It stems from the observation that scholarly publishing doesn’t care about technical quality. The look and feel of a journal is all that matters. (That’s not much use for unsighted humans and machines). I suspect there are a relatively small number of typesetters and that most of them (perhaps Kaveh excepted) don’t care about technical quality.  The technical quality of material in the arXiv preprints is pretty good. So it should be – maths and physics are high quality subjects. But when it comes out of the publishers the technical quality is often significantly worse.  But then it’s not their money that universities are spending – 15 Billion USD – it’s taxpayers and students. They don’t care about the quality of what they are paying for. And until somebody cares this will probably continue."