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The distinction between recording and presenting – and what it means for an online lab notebook

18 September 2008 16 views 2 Comments

Something that has been bothering me for quite some time fell into place for me in the last few weeks. I had always been slightly confused by my reaction to the fact that on UsefulChem Jean-Claude actively works to improve and polish the description of the experiments on the wiki. Indeed this is one of the reasons he uses a wiki as the process of making modifications to posts on blogs is generally less convenient and in most cases there isn’t a robust record of the different versions. I have always felt uncomfortable about this because to me a lab book is about the record of what happened – including any mistakes in recording you make along the way. There is some more nebulous object (probably called a report) which aggregates and polishes the description of the experiments together.

Now this is fine, but point is that the full history of a UsefulChem page is immediately available from the history. So the full record is very clearly there – it is just not what is displayed. In our system we tend to capture a warts and all view of what was recorded at the time and only correct typos or append comments or observations to a post. This tends not be very human readable in most cases – to understand the point of what is going on you have to step above this to a higher level – one which we are arguably not very good at describing at the moment.

I had thought for a long time that this was a difference between our respective fields. The synthetic chemistry of UsefulChem lends itself to a slightly higher level description where the process of a chemical reaction is described in a fairly well defined, community accepted, style. Our biochemistry is more a set of multistep processes where each of those steps is quite stereotyped. In fact for us it is difficult to define where the ‘experiment’ begins and end. This is at least partly true, but actually if you delve a little deeper and also have a look at Jean-Claude’s recent efforts to use a controlled vocabulary to describe the synthetic procedures a different view arises. Each line of one these ‘machine readable’ descriptions actually maps very well onto each of our posts in the LaBLog. Something that maps on even better is the log that appears near the bottom of each UsefulChem page. What we are actually recording is rather similar. It is simply that Jean-Claude is presenting it at a different level of abstraction.

And that I think is the key. It is true that synthetic chemistry lends itself to a slightly different level of abstraction than biochemistry and molecular biology, but the key difference actually comes in motivation. Jean-Claude’s motivation from the beginning has been to make the research record fully available to other scientists; to present that information to potential users. My focus has always been on recording the process that occurs in the lab and particular to capture the connections between objects and data files. Hence we have adopted a fine grained approach that provides a good record, but does not necessarily make it easy for someone to follow the process through. On UsefulChem the ideal final product contains a clear description of how to repeat the experiment. On the LaBLog this will require tracking through several posts to pick up the thread.

This also plays into the discussion I had some months ago with Frank Gibson about the use of data models. There is a lot to be said for using a data model to present the description of an experiment. It provides all sorts of added value to have an agreed model of what these descriptions look like. However it is less clear to me that it provides a useful way of recording or capturing the research process as it happen, at least in a general case. Stream of consciousness recording of what has happened, rather than stopping halfway through to figure out how what you are doing fits into the data model, is what is required at the recording stage. One of the reasons people feel uncomfortable with electronic lab notebooks is that they feel they will lose the ability to scribble such ‘free form’ notes – the lack of any presuppositions about what the page should loook like is one of the strengths of pen and paper.

However, once the record, or records, have been made then it is appropriate to pull these together and make sense of them – to present the description of an experiment in a structured and sensible fashion. This can of course be linked back to the primary records and specific data files but it provides a comprehensible and fine grained descriptionof the rationale for and conduct of the experiment as well as placing the results in context. This ‘presentation layer’ is something that is missing from our LaBLog but could relatively easily be pulled together by writing up the methodology section for a report. This would be good for us and good for people coming into the system looking for specific information.

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  • http://usefulchem.blogspot.com/ Jean-Claude Bradley

    Cameron,
    As we discussed many times, we are after the same outcome ultimately – both human and machine readability. I am very grateful for the arrangements you made to have me visit you lab and look at your workflows. I have a much better appreciation for how you do things.
    I think that the maturation of Open Notebook Science depends upon diversity and honest appraisal of what works and what doesn’t in specific situations.
    I can’t wait to see how it plays out !

  • http://usefulchem.blogspot.com Jean-Claude Bradley

    Cameron,
    As we discussed many times, we are after the same outcome ultimately – both human and machine readability. I am very grateful for the arrangements you made to have me visit you lab and look at your workflows. I have a much better appreciation for how you do things.
    I think that the maturation of Open Notebook Science depends upon diversity and honest appraisal of what works and what doesn’t in specific situations.
    I can’t wait to see how it plays out !