Category Archives: xtech2007

Wellcome gets tough on Open Access depositions

When one is active in an area (in this case Open Access) it's often difficult to see how important it is from outside. So I was delighted to get an internal email to all staff making it clear that it was MANDATORY for Wellcome grantees to publish their papers as Open Access. Here's excerpts from the mail:

As you may be aware, the Wellcome Trust's award terms and conditions require that all research papers arising from Wellcome Trust funded research must be made available on the PubMed Central website ( within six months of publication.

The Wellcome Trust have been monitoring compliance rates, and have been disappointed to find that these are currently very low.  As a result of this, they intend to more actively monitor compliance, and in future will be contacting researchers who have not had articles published as Open Access papers.

The University of Cambridge has been given a grant to cover costs associated with Open Access publishing.  If your journal charges for making your article available on PubMed Central, please refer to this website: for how to claim these costs back from my office.

Further information on the Wellcome Trust's Open Access policy can be found here:, or at the Wellcome Trust's website here:

and the claims site announces:

Claiming Open Access Charges

This page describes how to claim back costs charged by publishers for placing papers on the UK PubMed Central website. Initially, you will have to pay the publisher’s Open Access charges. You can then claim these costs back as follows:

  1. Fill out a form (Open Access request form) with the requested information.
  2. Please return the form and an internal invoice ...
  3. Once we have this, the monies you have paid for Open Access charges will be re-imbursed to your account.

I have the privilege of being on the UKPMC advisory board and we've been thinking about how to make the policies and practices more widely known. UKPMC is doing roadshows (the first in Oxford last month) and I am sure they would welcome enquiries from institutions or individuals wanting more info.

We have to realise that Open Access will take hard work. It's not just building deposition systems and expecting them to get filled. It needs a commitment from the grant holder. It's simple:

  • If you receive a grant you have to publish the results as Open Access.

If you don't want to, no-one is forcing you to apply for grants.

(Well, yes they probably are, so you had better get used to the practice of publishing Open Access)

Avoiding Mass Extinction with OpenData

A very impressive talk yesterday by Gavin Starks about the challenge of Climate Change. If you ever have the chance to hear or meet him, do. The talk has been blogged by the indefatigable Talis/Nodalities (Paull Miller and (in this case) Rob Styles) as

Climate Change isn't about saving the planet

Gavin's message was simple - a necessary condition for saving the planet (and ourselves) is to have a consistent approach to using the available data. That means Open Data and Open Standards for using it.

As simple as that. How will future generations (if there are any) judge those people or organisations who did not share data?

Explore Gavin's Avoiding Mass Extinction Engine ...

"AMEE" is a technical service that features;

:: Measurement

Access to standardised co2 data and calculations (including the official UK Government figures)

:: Profiling

Store and retrieve personal footprints

:: Sharing and Transparency

Help develop, extend, share and collaborate on the measurement of energy consumption.

Our mission: enable and encourage engagment to address a truly global issue


Alf Eaton and Gavin Bell (Nature) out together a lively BOF this evening on scientific publishing. They presented many of the key components - XML, persistent identifiers, ontologies, etc. Nice to see credit being given to PLoS for its pioneering use of these things (e.g. IDs for supplemental data).

A strong feeling from all that PDF must be supplemented of replaced by greater structure. "XML" is a useful mantra - although XML by itself is sometimes too constraining - and we need RDF. Maybe XMLRDF is a better mantra - it needs the XML to emphasis the difference from PDF and the RDF to point towards the future.

An anecdote of how the bite gets bitten - a publisher had acquired a chunk of content from another source (? merger/acquisition) and found that the PDFs were read-only - the hamburgers had been encrypted and the password lost. So they could be viewed but not re-used . Time for a change!

[ADDED IN PROOF] A much fuller post from Paul Miller

XTech2007 - XForms - do I need them?

Now in XTech2007 - arrived in time for the afternoon session of XForms by Steve Pemberton. XForms allow you to pass XML into/out of forms rather than relying on HTML. In includes things like validation - if you tell it something is a date, then you can check in makes sense as a date. And there's stuff about credit cards, etc. So it makes sense to adapt them for - say - chemistry so that we can check data and molecules on submission.
I hadn't looked at them for ca 3-4 years as I hadn't seen any implementations. In fact, according to Steve, XForms has been the MOST implemented W3C spec ever. The reason I have missed them is that they tend to be used in mobiles as well as browsers and there is also a lot of star-centered business - a company whose customers all use XForms and there is central control. Nothing wrong with that, but it won't be obvious to non-customers. Also the insurance industry has gone for them in a big way.

But most of the implementations come from the actual communities rather than being based on libraries (which is what we need). There is XSmiles which might help us - I think it's now mature. But the scale seems a bit daunting "we used to have 30 programmers working on UIs for 5 years, now we solved the problem in 1 year with only 10 programmers". Sic.

But there do seem to be plugins for Firefox (or they are in the pipeline). Using, I think, XBL and some with SVG. So maybe there is still hope for the browser in this area.

But whether we can move quickly towards a validating chemical data entry tool ... I will continue to hack with broken tools for a little while

(In the original version of this post I used the erroneous "XMLForms")

XTech2007 and Open Data

I had got lazy about tagging my posts until Brian Kelly gently reporoached me for not adding "WWW2007" as a tag. The point is that Technorati and other engines index the tags and you can search on them. (What, you didn't know THAT? Well, not really). So now I do. And if you look at and search for "www2007" in "tags" you'll find many posts (and many photographs).

So I'm now going to add "xtech2007" to my tags. Is this the right tag? Don't know - but the community will converge on something. and:

shows that there are already 14 posts and that Paul Miller - who ran our Open Data session - will also be there. (Well I knew that, but there are others I don't).

So there is the Open data track - quite diverse - and I get the impression this will be as exciting ast WWW2007. The world is changing as we look at it.