Frank Gibson has continued the discussion that kicked off here and has continued here [1, 2, 3, 4] and in other places [1, 2] along the way. Frank’s exposition on using FuGE as a data model is very clear in what it says and does not say and some of his questions have revealed sloppiness in the way I originally described what I was trying to do. Here I will respond to his responses and try to clarify what it is that I want, and what I want it to achieve. I still feel that we are trying to describe and achieve different things, but that this discussion is a great way of getting to the bottom of this and achieving some clarity in our description and language. Read more »

Posted: March 30th, 2008 under FuGE, data formats, data model, definitions, format, glueware, metadata, ontologies, rdf, semantics, tools, xml.
Comments: none

Frank Gibson of peanutbutter has left a long comment on my post about data models for lab notebooks which I wanted to respond to in detail. We have also had some email exchanges. This is essentially an incarnation of the heavyweight vs lightweight debate when it comes to tools and systems for description of experiments. I think this is a very important issue and that it is also subject to some misunderstandings about what we and others are trying to do. In particular I think we need to draw a distinction between recording what we are doing in the lab and reporting what we have done after the fact. Read more »

Posted: March 25th, 2008 under data formats, data model, metadata, semantics, tools.
Comments: 4

Michael Barton has a very nice little video on web tools for science and sharing up at Bioinformatics Zen.

Posted: January 24th, 2008 under open science, sharing, tools.
Comments: none

UK PubMedCentral, a UK mirror of PMC and a growing project at the British Library is soliciting responses to a survey:

Dear Colleague,

As you will know, UKPMC provides free access to an extensive repository of biomedical research literature, as well as an easy way for researchers to submit newly published work to meet the UKPMC Funders Group members’ Open Access requirements. The vision is for UKPMC to be much more than that!

As we enter the next stage of developing UKPMC into an innovative and useful resource for UK researchers we want to ensure that your needs and ideas are heard and incorporated at the outset. Please help us by completing our online questionnaire.

It should only take a few minutes and, as our way of saying thank you, all respondents will be entered into a prize draw to win an all-expenses paid weekend for two in London.

Click here to be taken straight to the survey page:

http://www.bl.uk/surveys/ukpmc/ukpmc.htm

Much of the survey asks questions about what additional tools you use for scientific search etc and what features you would like to see in UK PMC. This worries me as it seems like duplication both of effort and the creation of yet another del.icio.us/Facebook/Google/whatever for scientists. We don’t need another one, we need integration between the existing ones and improvement of user interfaces, interoperability, and useability. This wonderful video on the data portability initiative, which I saw featured on Deepak’s blog, tells the story. That’s my view anyway. Feel free to take the survey and disagree with me!

In addition the UK Biochemical Society has also commissioned some research and is looking for people to fill out another survey;

The Biochemical Society, in collaboration with other members of the Biosciences Federation (www.bsf.ac.uk), is conducting research into your experience of Open Access; I am writing to ask you to participate in this, by completing a brief questionnaire that should take no longer than 15 minutes.

The survey can be found here and the deadline is 1 February.

Posted: January 16th, 2008 under open access, tools.
Comments: none