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\begin{document}

\title{Open Notebook Science Means Better Science}



\author[1]{Peter Murray-Rust}%
\affil[1]{Affiliation not available}%


\vspace{-1em}



  
  \date{May 25, 2024}


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\subsection*{\texorpdfstring{\emph{This Blog post is in gratitude to the
visionary \href{https://en.wikipedia.org/wiki/Jean-Claude_Bradley}{Jean
Claude
Bradley}}}{This Blog post is in gratitude to the visionary Jean Claude Bradley}}

{\label{527478}}\par\null

\section*{Why do I do Open?}

{\label{860622}}

I do Open because I care about science belonging to everyone. I'm and
academic and I think the emphasis that Open is to benefit academics
(more citations, greater visibility, etc.) misses the main point, which
is that we are funded by the world to do science that the world directly
benefits from.

There have been three great open initiatives in the last century that I
have followed:

\begin{itemize}
\tightlist
\item
  Free and Open Source. Stallman and Torvalds
\item
  The World Wide Web. Berners-Lee and the immense contribution of the
  IETF
\item
  The human genome project. Sulston and Collins
\end{itemize}

All of these have massively influenced my approach to Open and act as
the ideal for collaborative communal action. I have contributed Open
Source over 20 years and have both benefitted and benefitted others.
It's a gift economy that works well, that companies have signed up to
and that funders support. If any of these three had been closed the
world would have been immeasurably poorer, often leading to control by
commercial organisations~

The benefits are many - the main ones are:

\begin{itemize}
\tightlist
\item
  building on the work of others and being built on.
\item
  permanent archiving immediate discovery of resources
\item
  permanent archival and high-quality searching
\item
  immediate validation and correction of my work (Continuous
  Integration, etc.)
\end{itemize}

\section*{~Open Access today}

{\label{541883}}

I had hoped that ``Open Access'' as visioned in the BOAI would parallel
Open Code and Open Bioscience. In practice, for me, current Open Access
has not delivered its promise and is not likely to in the next decade -
there is too much fragmentation, open-washing, timidity, and restrictive
practices. 15 years after BOAI I cannot go to a single point -of-contact
and ask to download all Open Access papers (which is what I wish to do).

I~\emph{can} download some subsets - most notably EuropePMC - and my
non-profit organization Contentmine.org does this every day. We've
worked with Wikimedia (Wikidata) to
create~\href{https://www.wikidata.org/wiki/Wikidata:WikiFactMine}{WikiFactmine}
which aims to index all publica science against Wikidata (a collection
of nearly 40 million facts). 15\% of Wikidata is now the WikifactMine
list of Open Access papers. A partial success for Open Access, making
the science effectively available to the whole world, not just
academics.

But vast swathes of chemistry, materials, engineering are effectively
closed. So yes, WikiFactMine is a partial success for Open Access and is
only~

\section*{\texorpdfstring{\href{https://en.wikipedia.org/wiki/Open_notebook_science}{Open
Notebook Science}}{Open Notebook Science}}

{\label{700919}}

F/OSS Software is developed in public view - warts and all. Why not
science thought one visionary chemist, Jean Claude Bradley, whom I knew
well and collaborated with. J-C's vision was that scientists should do
all their work in public view and post their results as soon as they got
them. His motto ``No insider knowledge'' requires that any reader should
know as much about the experiment as as the scientists who did this. It
is Open \textbf{by design} .

J-C developed this with young chemists, often undergraduates, measuring
solubilities and publishing them immediately. The Open approach has an
immediate effect on quality. People are often happy to expose their
work, but they are not happy to expose palpably sloppy science. I
contend that

\begin{quote}
\textbf{Open Notebook Science mean Better Science}
\end{quote}

and this is the primary benefit. I've been through this myself and I
feel the pressure always to be better, more organized, more thorough -
to show work I am proud of.

This doesn't mean that you have to get it right first time. For 30 years
F/OSS has accepted that buggy code is fine and that it will be gradually
improved. Similarly for science - experiments often go wrong and need
repeating, and we should glory in this, not pretend that it's private
until it's ``publishable''. There are an increasing number of Open
Notebook practitioners and I'll just highlight one - Mat Todd and
colleagues in Sydney who run \href{http://opensourcemalaria.org/}{Open
Source Malaria}. :

\begin{quote}
Guided by open source principles, everything is open and anyone can
contribute.
\end{quote}

\par\null

\href{https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/549}{Here's
today's experiment} and note that the data is all on Github.

\section*{My own OpenNotebookScience}

{\label{316053}}

I've tried to practice what I preach. Here are two examples where
everything appeared in public as soon as it was created.

\begin{itemize}
\tightlist
\item
  \href{https://riojournal.com/article/13589/}{A machine-compiled
  microbial supertree from figure-mining thousands of papers}
  {[}RIOJournal{]} (Mounce, Wills,
  PMR).~\href{https://riojournal.com/article/13589/instance/3608586/}{Methodology}.~\href{http://discuss.contentmine.org/t/error-analysis-in-ami-phylo/116/46}{Daily
  notebooks} on public Discuss
  and~\href{https://github.com/ContentMine/ijsem}{data on Github}.
  Without ONS the work would probably have been lost when Ross
  moved.~\href{https://riojournal.com/article/13589/instance/3608671/}{Results!}
\end{itemize}

\par\null\selectlanguage{english}
\begin{figure}[h!]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/singlefig-128767/singlefig-128767}
\caption{{Supertree from 924 articles
{\label{693103}}%
}}
\end{center}
\end{figure}

\begin{itemize}
\tightlist
\item
  \href{https://arxiv.org/abs/1709.02261}{Extracting data from vector
  figures in scholarly articles} {[}arXiv{]} (Hartgerink, PMR).
  \href{http://discuss.contentmine.org/t/extracting-data-from-tilburg-funnel-plot-diagrams/386/33}{Daily
  notebook}.
\end{itemize}

\par\null

\textbf{So, simply, Open Notebook Science is better, faster, more
inclusive science.}

\par\null

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