Computational Cultural Publishing: Climate Emergency Sprint

Computational Cultural Publishing: Climate Emergency Sprint

FYI: These are workshop notes from the 21-13 May run as part of a cultural event in Linz, Austria. https://gateway.radical-openness.org/ - they cover some successful install notes and use of getpapers and ami. The notes will be written up in full and a follow on workshop will take place based in Malta on climate and migration as part of a summer school. The notes are from Open Climate Knowledge which is using the ContentMine software. https://github.com/OCKProject/climate

Overview

Slides https://docs.google.com/presentation/d/1tqnTvhSn4wOOudxaJhTnrinZB1WhgGAOCIlUmjy6GZQ/edit?usp=sharing

Open Climate Knowledge repo - https://github.com/OCKProject/climate

Open Climate Knowledge GitHub project - https://github.com/OCKProject

How to install / kind of - See below

Workshop BigBlueRoom address - https://bbb.radical-openness.org/b/amr-2n6-nez

Day 1 Thursday - 16:00-17:30 (what we'll cover)

• Introductions
• Overview
• Build up our 'climate questions'
  • Simon Worthington
    • Runaway Climate Change
    • % Climate research open access
  • Participant (or suggested topics we can work on together)
    • Terms
  • Participant - Adnan
    • Climate migration
    • What are the global effects of climate change on MENA migration
      • Desertifcation
      • Global Warming
      • Rise of Sea Level
      • Sea Temperature
      • Carbon Oxide
      • Conflict
      • Centreal Mediterrean Sea
      • North Africa
      • Sahara
      • Malta
      • Italy
      • Lampedusa
    • relationship between forced migration and climate emergency?
    • data mine climate explorer https://climexp.knmi.nl/start.cgi
  • Participant - Laura
    • Tipping points
• get-papers (see if we can install and run) - https://github.com/ContentMine/getpapers
  • Using get-papers
    • Make repo (optional) directory
    • Make dictionary
• Build dictionaries from questions -
  • Look at existing one - runaway climate change https://github.com/OCKProject/climate/blob/master/dictionary/runaway.xml
  • How to build one - https://github.com/OCKProject/climate/blob/master/docs/methods.md
  • Using Wiki data - https://www.wikidata.org/

Friday and earlier Saturday online help to get full system running

In bigblueroom

Day 2 Saturday - 16:00-17:30

• Overview:
  • Review some Open Science resources
  • X-Sketchbook
  • recap getpapers
  • Run AMI and live demo creation of a dictionary (migration and climate change)
  • Look at Jupyter Notebook / Books
  • Computational Publishing
    • Research compendium - https://research-compendium.science/
    • o2r - https://o2r.info/
    • Popper - https://falsifiable.us/
  • Intro Wikiversity - preprints - https://en.wikiversity.org/wiki/WikiJournal_Preprints/Cultural_Computational_Publishing:_A_Sprint
• Open Science - arts and humanities - Open Science / Open Scholarship / Open Research
  • LIBER Open Science skills - https://zenodo.org/record/3702401 https://twitter.com/LIBEReurope/status/1262719265217675266?s=20
  • DTU Digital History & Hermeneutics - https://twitter.com/dtu_dhh/status/1262685963433754626?s=20
  • Dariah EU - https://www.dariah.eu/
  • Open Methods / Dariah - https://openmethods.dariah.eu/
  • Tennant, Jon. “Open Science Is Just Science Done Right – Blockchain for Science.pptx”. figshare, November 5, 2018. https://doi.org/10.6084/m9.figshare.7296650.v1. Youtube https://youtu.be/DuOvwORp88U

“…this contradiction in the academic project into sharp relief—universalist in principle and unequal in practice. Shadow Libraries is a study of that tension in the digital era.”

Introduction, Shadow Libraries, Joe Karaganis, Open Access, MIT 2018. https://mitpress.mit.edu/books/shadow-libraries (see Open Access tab for download)

• XSketchbook
  • This is a concept put together with my Open Science Lab Ina Blümel to make a digital sketchbook like the sketchbook used in a architects studio practice, by a designer, or an artist.
    • Be able to past in any type of digital objects and make then citable
      • Social media
      • Media
      • Open Science
  • This workshop is a pre-pre-alpha of the XSketchbook - following on from workshop I will make a Jupyter Notebook and Wikiversity preprint
• run ami - install and run (way to complicated, will get help) See instructions below.
  • Europe Pub Med Central - https://europepmc.org/
  • Demo
  • Live demo dictionary
• run a Jupyter Notebook
  • Add results of our questions into the Notebook
    • Very complex example Notebook - https://openclimatedata.net/
    • About Juypter Notebooks - https://docs.google.com/presentation/d/14rvBuo-4Wzn_EqS7QmrQXdYg9cRcUT6Rz_CFFfM4PmE/edit
    • Jupyter Books - https://jupyterbook.org/intro.html and emerging Eexecutalble Book https://executablebooks.org/en/latest/
• Computational publishing - https://research-compendium.science/
• Fill in the start of a Wikiversity preprint - https://en.wikiversity.org/wiki/WikiJournal_Preprints/Cultural_Computational_Publishing:_A_Sprint

Links

OpenSay

Open energy Modelling

Other notes

Installation and running

For installation:

• Setup a directory (e.g., on Desktop) called ContentMine
  • Add: dictionaries - make down cloning http://github.com/ContentMine/dictionaries into ContentMine
  • Add: software (make directory) clone https://github.com/petermr/ami-jars2 into software
  • Add: myprojectfolder (e.g., xsketchbook) mkdir xsketchbook
  • Add example project: clone http://github.com/petermr/tigr2ess in ContentMine

General - ContentMine - getpapers and AMI

• For all OS https://github.com/petermr/tigr2ess/blob/master/installation/INSTALLATION.md
• Unix/Linux https://github.com/petermr/tigr2ess/blob/master/installation/unix/INSTALLATION.md tested and works SW 21.5.2020

How to run the software:

get papers

• Inside myprojectfolder run getpapers --help for options
• Create a dictionary: note file name needs to stay the same as title

<?xml version="1.0" encoding="UTF-8"?>
<dictionary title="runaway">
	<desc>created from iterative word clouds in "runaway222" corpus </desc>
	<entry url="/wiki/Tipping_points_in_the_climate_system" name="Tipping point" term="tipping" wikidata="Q7808933" term.de="Kippelement"/>
	<entry url="/wiki/Greenhouse_effect" name="greenhouse effect" term="greenhouse" wikidata="Q41560" term.de="Treibhauseffekt"/>
	<entry url="/wiki/Runaway_greenhouse_effect" name="runaway" term="runaway" wikidata="Q4357041" term.de="Galoppierender Treibhauseffekt"/>
    <entry term="acceleration" name="acceleration"/>
    <entry term="anthropogenic " name="anthropogenic " wikidata="Q29169263" term.de="anthropogen"/>
    <entry term="feedback" name="feedback"/>
    <entry term="forcing" name="forcing"/>
    <entry term="model" name="model"/>
    <entry term="sea ice" name="sea ice"/>
    <entry term="atmospheric" name="atmospheric"/>
    <entry term="insolation" name="insolation"/>
    <entry term="agricultural" name="agricultural"/>
    <entry term="anthropocene" name="anthropocene"/>
    <entry term="ipcc" name="ipcc" wikidata="Q171183"/>
    <entry term="carbon cycle" name="carbon cycle"/>
    <entry term="arctic" name="arctic"/>
    <entry term="antarctic" name="antarctic"/>
</dictionary>

• run getpapers: $ getpapers --query 'runaway' --xml --outdir test5 --limit 10
  • NB: script will generate directory if not existing
  • This will download papers from PMC as XML full test at a quality of 10

AMI

Inside myprojectfolder run $ ami -p test1 search --dictionary country runaway.xml NB: dictionary title needs to be same as file name.

This will generate the table with your dictionary in it:

articles	bibliography	dic:country	dic:runaway	word:frequencies
PMC6968565 local	titl: Comparison of the performance ... date: jour: abst: Objective: Autoantibodies to t ...	China x 2		anti-GBM x 67 nephritis x 33 ELISA x 34 patients x 23 Crescentic x 32
PMC7160642 local	titl: Virus cripples China refinery ... date: jour: abst: null	China x 2
PMC7185022 local	titl: Liquidity Backstops and Dynami ... date: jour: abst: Liquidity backstops can mitiga ...	Canada	model x 40	markets x 29 < x 28 ARS x 126 market x 63 creditors x 41
PMC7188949 local	titl: Fatigue Induced Changes in Mus ... date: jour: abst: Purpose:To investigate changes ...	Canada United States Greenland	model x 5	variability x 32 MICR. x 30 time x 22 post x 29 MDC x 40
PMC7189230 local	titl: Simultaneous human intracerebr ... date: jour: abst: Precisely localizing the sourc ...		model x 6	. mA x 47 sub- x 68 . ms x 62 run- x 61 stimulation x 41
PMC7198792 local	titl: Perspectives on Using Online P ... date: jour: abst: null	Hungary Brazil Thailand		running x 22 online x 23 virtual x 62 physical x 25 (). x 25
PMC7200005 local	titl: A simple method to assess and ... date: jour: abst: Data saturation is the most co ...	Kenya x 3 United States x 2 New Zealand South Africa South Africa.	model x 3	unique x 22 method x 27 research x 25 saturation x 111 interviews x 93
PMC7200705 local	titl: Quantifying biodiversity trade ... date: jour: abst: The challenge of balancing bio ...	United States, Canada United States. United States	greenhouse x 6 anthropogenic x 2 model	electricity x 35 conservation x 84 gas x 60 spatial x 27 energy x 124
PMC7200977 local	titl: A Non-invasive Method to Diagn ... date: jour: abst: Purpose: To find out the CT ra ...	New Zealand Canada United States	model x 18	cancer x 22 Lung x 21 lung x 52 set x 37 Adc x 21
PMC7235041 local	titl: Using the force: STEM knowledg ... date: jour: abst: How does STEM knowledge learne ...	United States.	model x 26 feedback x 2	model x 26 surface x 21 fMRI x 36 engineering x 61 neural x 56