Cameron Neylon

Frank Gibson of [peanutbutter](http://peanutbutter.wordpress.com) has
left a long comment on my [post about data models for lab
notebooks](http://blog.openwetware.org/scienceintheopen/2008/03/23/proposing-a-data-model-for-open-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.

You can see the [full comment
here](http://blog.openwetware.org/scienceintheopen/2008/03/08/what-to-use-as-a-the-primary-key-for-chemicals/#comment-1351),
I will reply to a couple of the specifics.

> â€œâ€¦My arguement is that we need to be able to use all of these
> vocabs, or none, to describe experiments to a practical level of
> detailâ€¦.â€?
>
> I agree, FuGE will allow you to do this.

We may need to agree to disagree on this. Looking at what we are doing
and what I can understand of the FuGE model I am not sure we can capture
the experiments that we do in practise (but see below as to why this may
be more because we are at cross purposes than anythinge else)

> With all these things, especially modelling, there are lots of ways to
> reach the end goal. With respect to vocabularies, often these are just
> recommend strings (which are valuable in themselves). However
> ontologies, specifically OBI are an effort to assign meaning and
> machine interpretability to terms as a community wide consensus, to
> avoid the issues you mention.

One problem is then when you try to re-use these things slightly outside
the setting where they were defined. I have found it difficult to see
how to apply for e.g. OBO to the work we do in protein engineering.
Bio-ontologies tend to be focussed on the biology whereas my work in
using biological systems as tools is not well described. For instance,
while I love the look of GoPubMed it doesn't actually perform any better
than the old PubMed when I search for the use of something (usually in
itself a heavily modified protein) as a tool. Nonetheless all these
things are very valuable in helping us to agree what it is we are
talking about.

> Tools: tools are a big issue and often a stumbling block, ideally as
> you suggest the information or datafiles should be automatically
> exported from instrumentation. This is currently not the case and
> therefore there is a high cost involved, for some this is an
> unacceptable cast, to the â€œhumble experimenterâ€?, often the
> benefits of annotation and sharing are not obvious to the person that
> generated the data, but I am preaching to the converted :)

Absolutely. Proper export of data from instruments is critical. Making
my proposal useful relies on good metadata being associated with the
datafiles. Here FuGE or other agreed descriptions will be immensely
valuable. We need to make the case that metadata is worth the effort,
loud and strong. It does take effort; there is no way all of it can be
automated; but it can be an enormous help. This is clearer for people
who work in collaborations or who are involved in large scale projects
but our experience is that it also makes a huge different in a small
scale operation.

Another point about the necessity of tools is that the descriptions of
frameworks and ontologies are basically incomprehensible. I tried to
read the paper you reference below, I really did. The text even made
sense but I couldn't for the life of me figure out what the diagrams
meant. As a user the paper doesn't help me figure out how to apply this
to what I do. We need nice comprehensible tools that help us work
through this.

> In regards to the data model. FuGE is the data model \[PMID:
> 17921998\]. It is a heavy weight solution, although it is designed to
> represent the common aspects of a scientific experiment. The GelML
> case is an extension of the FuGE data model to be more specific in the
> representation of a gel electrophoresis experiment.

Having thought about this, I think we are at cross purposes. What we are
doing is trying to implement systems that will capture activity in the
laboratory, an smart, electronic version of the traditional laboratory
notebook. FuGE is a system for *reporting* experiments. This is a
crucial distinction and I don't think it is ones that is thought about
very often.

What we do in the lab is very hard to record. This is what I meant when
I said '*No data model survives contact with reality*'. If I write down
a protocol of what I am going to do in the lab then 50% of the time that
will change. Not the parameters, not the details, but a fundamental
change to what I planned to do. This is even more the case in synthetic
chemistry which is often 'mix and see what happens; then make a decision
about what to do next'. Now this *could* be captured in a FuGE framework
but only in a very artificial or almost meaningless way. This is why I
lean towards lightweight approaches and very free form capture.

***But*** this is very different when it comes to *reporting* the
experiment *after* the fact. Most of these initiatives have been driven
by the need to describe experiments in the published literature. Here we
can place the results and what we did into a sensible framework *because
we know what the result was*. Here we should work to towards structuring
things as much as possible. What we should be asking is how to structure
our data and procedure *capture* processes so that we already have as
much of the relevant metadata as possible. And then how do we convert
what we have generated into a more structured data model. Fundamentally
*capture* is separate to *reporting*. The two can only really be the
same for a completely automated process (such as running an instrument)

> Its feasible that text from wikis or blogs could be extracted, by text
> mining or rdf queries and then placed in a model like this, However
> this is close to the data integration paradigm that currently exists
> in bioinformatics. Its alot of wasted effort. I would argue it is
> better to structure an annotate the data at the source on day one,
> than trying to extract information later. I have this problem with my
> current project, in that semantic extraction involves picking up the
> phone and asking the experimenter what you did and what does it all
> mean. I can see similar parallels here, the only difference is that
> the lab book is electronic and not paper, its still unstructured
> information.

Our lab book is not quite unstructured, it does have metadata and it
does define different aspects of the process. We are also very in favour
of the use of templates for repeated processes which can be used to
structure specific aspects of the capture process. Don't get too
focussed on the notion that a wiki or blog is free text. It is just like
FuGE. It can be completely free or it can be a highly structured XML
document. It depends on how you are interacting with it and what layers
are between you and the underlying database.

The key to our blog system is that the structure is *arbitrary*; the
system itself is semantically unaware. How you choose to process the
information is up to you. New keys and key values can be added at any
time. We have found this crucial and it is this which makes me sceptical
about any semantically structure data model in this context.

> Like I say, there are many ways to achieve the same end. A common data
> model for scientific experiments exists, which has undergone a long,
> cross community and public consultation process. It does need tool
> support. However, just hypothesising, even an xslt representation
> maybe able to be â€œpluggedâ€? into a blog or a wiki to provide the
> structure.

I think this is similar to what I mean when I think of a template as a
widget. I want to run a gel, and someone has helpfully written a little
widget which pops up, asks me the relevant questions, and then goes away
and generates the appropriate GelML file, probably mostly based on
default values. But I'm not going to wait around until someone writes me
one of these for everything we do. Ideally there would be widget that
could go to the appropriate data standard and parse that to generate the
interface that asks the right questions. If it can't find the right
thing then you revert to free text and tables.

> I am afraid I am in the data model, structured and semantic data camp.
> Electronic notebooks and open data are a step in the right direction
> -- a massive step. However I still believe that unless the data comes
> structured with semantics, either data models RDF or whatever the
> Zeitgeist technology, we are still not maximising the potential form
> this information.

I can't disagree with this. However I don't beleive that we can
*capture* what *actually happens* in the lab within any sophisticated
data model except for extremely specific cases. Reporting it is very
different and is subject to different requirements including community
and publishing standards. What we need are systems that help us capture
what a happened (which is much more than the data) and then help us to
report it in a coherent way.


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
<em>
 vs
</em>
lightweight debate when it comes to tools and systems for description of experiments.

The heavyweights roll in…distinguishing recording the experiment from reporting it

[Michael Barton](http://www.michaelbarton.me.uk/) has a very nice little
[video on web tools for science and
sharing](http://www.bioinformaticszen.com/2008/01/three-stories-about-science-and-the-web-the-movie/)
up at [Bioinformatics Zen](http://www.bioinformaticszen.com/).


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

Gotta love the tinfoil

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 membersâ€™ 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](http://www.vimeo.com/610179), which [I saw featured on
Deepak's blog](http://feeds.feedburner.com/~r/mndoci/~3/217338108/),
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](http://www.surveymonkey.com/s.aspx?sm=O8NxxhwFB2DQwDUvW183nw_3d_3d)
and the deadline is 1 February.


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

Messaggi di Rogue Scholar

The heavyweights roll in…distinguishing recording the experiment from reporting it

Gotta love the tinfoil

Some surveys you may wish to fill out