Peter Murray-Rust launched the openNotebook resource at last week’s #eLifeSprint2019*. openNotebook is a framework for data mining, searching, and reusing research publications. Below he walks through the steps of how to use the framework in the context of climate change and opening up research to the public. Peter Murray-Rust, GenR and the Open Science Lab at TIB have initiated an open research collaboration Open Climate Knowledge to address the question of how to improve on the low rates of open access publishing related to climate change. Together we want to change this. Firstly by establishing better stats on OA rates and secondly, by coming up with a plan and recommendations for an accelerated transition to 100% OA for climate change.

Image: NOAA | From Earth System Models https://www.gfdl.noaa.gov/earth-system-model/

* See Infobox: ‘eLifeSprint 2019’ at end of article

Greetings to GenR!

I’m Peter Murray-Rust, a retired chemistry academic from Cambridge University, and I feel that the most important thing in our lives now is climate change.

But what can I do that’s the most effective response for me and the world?

However we solve climate change one thing seems certain — we need global collaboration based on facts. Emotions will keep us going, but facts will decide what we do?

I don’t know all the facts that I should. If I lectured on climate change to a first year university course I couldn’t give an accurate picture of the facts and what actions they dictate. So I’m going to try to learn what is common knowledge. But my special contribution comes from a technology and philosophy that allows us to get huge numbers of facts from reliable sources — the scientific literature.

There are literally hundreds of thousands of articles (papers) that are about climate change to some degree. This is an example of searching the biomedical literature (explanation later, and you’ll find it’s very simple.):

getpapers -q "climate change" -n -a
info: Searching using eupmc API
info: Running in no-execute mode, so nothing will be downloaded
info: Found 135931 results

This uses Rik Smith-Unna’s getpapers software to search EuropePubMedCentral for papers with “climate change” in the text. From a total of 135,931 papers about half of them (65,516) are “open access” and can be downloaded (but this figure is likely to be lower for non-biomedical).

The papers are about everything:

• species extinction
• sea level rise
• spread of parasite vectors
• weather changes
• engineering responses
• response by society,

and they’re about everywhere on the planet.

So if you want to find out about crops and West Africa…

getpapers -q "((climate change) AND (west africa) AND (crops))" -n -a
info: Found 1628 results

1,628, that’s a lot of papers! But if you have enough disk space and a reasonably good connection you can download them in 5 minutes.

Are they useful? That’s where our AMI comes in. AMI searches these papers on your disk, within a minute or two, for things you might be interested in:

• species
• vectors
• tropical diseases
• chemicals
• countries
• funders
• international organizations,

and lots more.

The great thing is that anyone who can run a program can do this! Lars, in the Netherlands, 15 years old, learn how to do this and developed more software. If you love computers (and have access to one), or data, or tackling scientific problems, or combatting climate change that’s all you need.

This makes a great citizen science project. Anyone anywhere with a Net connection can do it. The software, data and dictionaries are all open (no restrictions on use, no fee, and you can change them without permission). We’ll share the data we find (probably on GitHub) as soon as we capture it. This is “OpenNoteBook Science”, (no insider knowledge) as promoted by Jean Claude Bradley.

Don’t think that because you aren’t a “scientist” you can’t understand scientific papers. Of course your not going to understand all of them (I can’t either) or some parts of them, but there are many you can understand the key bits of. If you like maps, graphs, and similar data then you’ll feel right at home.

We’ve set up a project called Open Climate Knowledge (OCK) on GitHub. The technology is packaged as openNotebooks and is used in several projects (most notably plants and their medicinal products) so that means that bugs get reported and hopefully fixed. No matter what your interests and skills you’re welcome.

See Infobox: ‘OCK‘ at end of article

See Infobox: ‘openNotebook’ at end article, including installation and user instructions

There’s a lot of useful stuff on the sister project, essential oils. Also the data we extract is open and well organized so we can use a wide range of other software to analyse it.

If you are a techie, there’s a tutorial (rather XML-heavy!) I’m giving next week at XMLSummerSchool (Oxford) — you’ll have to download it. We’re also starting a communal article for Beilsten J. Organic Chem at https://github.com/petermr/CEVOpen/blob/master/BJOC

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