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write GenR blog post for Simon Worthington #14
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SimonW asked: 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 most effective 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 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 CC to some degree. This is searching the biomedical literature (explanation later, and you'll find it's very simple):
This uses Rik Smith-Unna's
and they're about everywhere on the planet. So if you want to find out about crops and West Africa...
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:
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 one), or data, or tackling scientific problems or combatting CC 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 ar 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) promoted by Jean_Claude Bradley. Don't think that because you aren't a "scientist" you can't understand scientific papers. Not 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 here, on Github. The technology 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. 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) at |
I need to check a few things about the software mentioned above: I want to make sure I'm getting the correct address for the software, installation manuals, and use manuals.
Thanks Simon |
Yes,
although I am creating a new repo `ami3` instead of `normami`
I want to extract the key components out of TIGR2ESS into openNoteBook
…On Wed, Sep 11, 2019 at 2:18 PM Simon Worthington ***@***.***> wrote:
I need to check a few things about the software mentioned above:
I want to make sure I'm getting the correct address for the software,
installation manuals, and use manuals.
1. getpapers - Is this the software repository and install
instructions used https://github.com/contentmine/getpapers and is this
the tutorial for use you would recommend
https://github.com/petermr/tigr2ess/blob/master/getpapers/TUTORIAL.md
2. AMI - software and installation guide -
https://github.com/ContentMine/ami - the tutorial for using AMI
https://github.com/petermr/tigr2ess/blob/master/search/TUTORIAL.md
Thanks
Simon
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That's great, I can go with these addresses for the moment. Thank you. Another question: Why use getpapers + AMI and not just search on say europepmc https://europepmc.org/search?query=climate%20change I can obviously string together a bunch of reasons groups ed around 'data science', 'having a collection, 'putting to use in another context' e.g., literature, media for a class, a citizen science project, etc.: with actions like, download all the papers, keep the papers, carry out further searches as a when you want, using the content in another context for your community - in a project with a groups There is also the post processing that is not be touched on yet. But it's better you give me the 'OK' that I'm on the right track, or you have another or a complementary vision. |
NB: I will make three info boxes:
I'll pass them by you when done and move the whole package to a collaborative doc to finish it off. |
On Wed, Sep 11, 2019 at 2:55 PM Simon Worthington ***@***.***> wrote:
That's great, I can go with these addresses for the moment. Thank you.
Another question: Why use getpapers + AMI and not just search on say
europepmc https://europepmc.org/search?query=climate%20change
It's a wrapper but a nice substantial wrapper. It builds the directory
structure (CProject) and also allows cutoffs and download of PDFs. It can
be done with "curl" but you have to work out the cursor and write a script.
I can obviously string together a bunch of reasons groups ed around 'data
science', 'having a collection, 'putting to use in another context' e.g.,
literature, media for a class, a citizen science project, etc.: with
actions like, download all the papers, keep the papers, carry out further
searches as a when you want, using the content in another context for your
community - in a project with a groups There is also the post processing
that is not be touched on yet.
But it's better you give me the 'OK' that I'm on the right track, or you
have another or a complementary vision.
You're on the right track completely. The main problem is that libraries,
including slightly EPMC , all think people want to download a few papers
and read them. There is little support for automatic mining. And there was
even less in 2015 when getpapers was written. I expect Getpapers to be
overtaken but it hasnt happened yet.
P.
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Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
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Great thank you. I'll add a line or two to the article to point out what its more than search. Info: block 1. about the eLife Sprint InstruMinetal team: eLifeSprint 2019Project: SaWaMine (working title) #eLifeSprint2019 4–5 September 2019, Cambridge UK and online. The ContentMine software was used by a sprint groups of seven (Sabine Weber, Michael Owonibi, Tiago Lubiana, Peter Murray-Rust, Sophia K. Cheng, Wambui Karuga, and Leonie Mueck) to protoytpe a UI for users to identifying scientific instuments from canidate search results made using ContenMine's software getpapers and AMI extracted from a corpus of papers about phytochemistry called CEVOpen. Goals of the Project:
NB: Content is partly based on https://github.com/caffiendFrog/elife2019 from Sophia Cheng |
Please edit the above infobox here on this pad, will be easier https://cryptpad.fr/code/#/2/code/edit/2nIMow-uTuQpNJv2RzZwdark/ |
Tomorrow...
…On Wed, Sep 11, 2019 at 4:32 PM Simon Worthington ***@***.***> wrote:
Please edit the above infobox here on this pad, will be easier
https://cryptpad.fr/code/#/2/code/edit/2nIMow-uTuQpNJv2RzZwdark/
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Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
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I've turned the 1. eLifeSprint 'infobox' around, my version yesterday was mixed up and a bit rubbish. I think i was running on empty. Much better now. I will complete the whole blog piece edit and add other infoboxes in the same doc, a bit more sane. I'm just trying to resolve the order of things. I think that my infobox 2. Content Mine software: getpapers + AMI, should really be called 'openNotebook' https://github.com/petermr/openNotebook | Am I getting this right openNotebook is the wrapper, vehicle, to put forward the toolset and method? I'll get finished up in content here |
Article is in reasonable shape now. It has an intro and three infoboxes for the end of the article. I need to give it another working over and gather together some images. I'll do this in an hours time, first I have to have a meeting with a colleague. https://cryptpad.fr/code/#/2/code/edit/2nIMow-uTuQpNJv2RzZwdark/ I will finish up the article today, recheck in the morning and post before 12 noon CEST Friday. Keep the momentum going :-) |
OK, I have the article ready to publish. There is one term I'm not sure if I'm getting it right 'species distribution and migration', its one of the subjects we said we'd cover in the openNotebook OA searches. I think I'm mixing up the term? I will shortly move the doc to Wordpress, but not before I gather pics and I'll make a note here when it moves. I can see that there is a need to explain a lot more about openNotebook, how it works, what you get out of it: stats, files, data? Good we're starting a new blog for it, there will be plenty to do :-) |
That's fine
…On Fri, Sep 13, 2019 at 10:53 AM Simon Worthington ***@***.***> wrote:
OK, I have the article ready to publish. There is one term I'm not sure if
I'm getting it right 'species distribution and migration', its one of the
subjects we said we'd cover in the openNotebook OA searches. I think I'm
mixing up the term?
I will shortly move the doc to Wordpress, but not before I gather pics and
I'll make a note here when it moves.
I can see that there is a need to explain a lot more about openNotebook,
how it works, what you get out of it: stats, files, data? Good we're
starting a new blog for it, there will be plenty to do :-)
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OK blogpost published, fiddle, fiddle, fiddle https://genr.eu/wp/open-climate-knowledge-100-oa-for-climate-change/ any mistakes please drop me a line - phew |
Many thanks - just picked it up. Very good. You've managed to get a lot
from the eLife pages.
More later.
…On Fri, Sep 13, 2019 at 12:57 PM Simon Worthington ***@***.***> wrote:
OK blogpost published, fiddle, fiddle, fiddle
https://genr.eu/wp/open-climate-knowledge-100-oa-for-climate-change/ any
mistakes please drop me a line - phew
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Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
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