An online sprint / workshop to place as part of 'AMRO 20 – Of Whirlpools and Tornadoes' based in the city of Linz, Austria. 20-23 May 2020 - Art Meets Radical Openness https://www.radical-openness.org/en
Questions DM @mrchristian | Chat on Matix #OCKProject
You're invited to ask questions about what the open scientific literature knows about climate change using Open Climate Knowledge (OCKProject) data mining software.
The sprint will involve documenting the questions and responses using Jupyter Books. We use OCKProject data mining software to turn your questions into dictionaries, which can in turn then be used to search the world's open literature.
- We can create responses, visualisations on the questions, and
- Comment and make demands for better access to the scientific community
'Cultural computational publishing’ and ‘sprints or book sprints'?
- ‘Cultural Computational Publishing' is a mixture of Jupyter Book, like The Turing Way which include live code and a reproducible computing environment as in the Research Compendium.
- The sprint is an arbitrary time constraint to get people together to author on a topic. It is important to acknowledge that many expert parts of publishing are left out of book sprints — often the feminized labor (less valued) parts of doing the behind the scenes finishing.
We’ll also publish a Wikiversity collaborative preprint.
OCKProject is an open research project hosted by TIB and organised as a working group of FORCE11. There is an open invitation to joining the working group.
Outputs from 'migration' AMI searches - https://github.com/OCKProject/CCP/tree/master/xsketchbook
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
- 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
- Simon Worthington
- get-papers (see if we can install and run) - https://github.com/ContentMine/getpapers
- Using get-papers
- Make repo (optional) directory
- Make dictionary
- Using get-papers
- 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/
In bigblueroom
- 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
- Be able to past in any type of digital objects and make then citable
- This workshop is a pre-pre-alpha of the XSketchbook - following on from workshop I will make a Jupyter Notebook and Wikiversity preprint
- 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.
- 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/
- Add results of our questions into the Notebook
- 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
OpenSay - https://forum.opensay.org/
Open energy Modelling - https://openmod-initiative.org/
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
-
ongoing documentation is here on openVirus as that is where active development and documentation is happening: https://github.com/petermr/openVirus/wiki
How to run the software:
- Inside myprojectfolder run
getpapers --helpfor 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
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
|
||
| 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 ... |
model x 40
|
||
| PMC7188949 local |
titl: Fatigue Induced Changes in Mus ...
date: jour: abst: Purpose:To investigate changes ... |
model x 5
|
||
| PMC7189230 local |
titl: Simultaneous human intracerebr ...
date: jour: abst: Precisely localizing the sourc ... |
model x 6
|
||
| PMC7198792 local |
titl: Perspectives on Using Online P ...
date: jour: abst: null |
|||
| PMC7200005 local |
titl: A simple method to assess and ...
date: jour: abst: Data saturation is the most co ... |
model x 3
|
||
| PMC7200705 local |
titl: Quantifying biodiversity trade ...
date: jour: abst: The challenge of balancing bio ... |
|||
| PMC7200977 local |
titl: A Non-invasive Method to Diagn ...
date: jour: abst: Purpose: To find out the CT ra ... |
model x 18
|
||
| PMC7235041 local |
titl: Using the force: STEM knowledg ...
date: jour: abst: How does STEM knowledge learne ... |