Flash Forward Workshop - petermr/CEVOpen GitHub Wiki

Scientific Publications and Global Challenges

We are hosting a Flash Forward Workshop (https://ffwd.flashgrants.org/calendar.html). It is going to be a hands-on session for people to try out our software and give us feedback. We are also going to discuss briefly about our current projects, its motives, and so on. more info will be added

When?

25th Feb. 2021

Time: 12 GMT/ 17:30 IST

Timetable

PMR (Introduction) 5 min

  • global challenges (1 min) . Epidemics, climate
  • scientific publication (scale 2 million/year) - answers in the literature
  • Ebola prediction
  • automation and re-use
  • tech applicable to "all" scientific disciplines

? current project EO, past projects climate and epidemics ? demo is specific topic of invasive species ? theme invasive species ? introductions ?

[St Edmunds Game - Gita. Present science to non-scientists. Fun! Involved. May 2021]

Ambreen & Shweata - 10 min (Overview of the project)

Shweata (5 min.)

Introduction

Let us look at a possible scenario. You want to find out which organizations are actively involved in viral epidemics research. What do you do? You’ll have to go through a subset of >1 Million “open” access papers, index them for what you want and analyse them. That to me sounds impossible for a human to do.

That’s where we step in. We, as a community, are building tools to ‘get’ papers to be downloaded onto your machine, index them with a set of terms related to the question of interest and make preliminary inferences to help us get a flavour for what the plausible answers to our questions might be.

Workflow

Technically speaking, we have 3 major components.

  • getpapers
  • dictionary
  • ami (pyamisearch)

(Brief explanation)

CEVOpen: Background

We have used these technologies in our projects like open virus and openclimateknowledge and we continue to work on it, now with CEVOpen. CEVOpen was born out of TIGR2ESS and focuses on extracting plant knowledge from literature.

The Team!

Our team consists of young Indians from a varied background. Some with laptops, and some with just phones. But together we all are doing quality science. We also believe in open notebook philosophy and all of what we do is available on our GitHub page including our outreach events.

Ambreen: (5-6 min)

Why I love being a part of OpenVirus

  • how it can harness the power of Science to build a better world.
  • how it connects young minds, the world over, for a vibrant inflow of ideas
  • how it employs open-source technology for building tools that are much needed.

Please suggest:

  • Should I add a demo of our Machine Learning endeavors?
  • Jupyter Notebook YES - maybe available beforehand or Powerpoint?

Ayush - 5 min (pygetpapers)

Refactoring for portability. (e.g. in Jupyter Notebook). Google Collab.

CEVOpen Interns - 2*4=8 min (2 min. an overview of their mini-projects)

(Not in order) 2 min demo of Wikidata (preprepared as REST) - explain query and then run. (not many hits) (country and invasive species) NOTE: lack of items in WD for invasive. How to amend this- item for discussion

Use Notebooks where possible.

Kanishka ?? absent [Invasive species] recording ; IUCN list

Radhu - Wikidata demo for I.S. => dictionary of invasive species - (not enough!)

Talha - Megapublisher search (Taylor Francis) tandfonline.com

Vasant - Jupyter Notebook demo - data display (histograms, cooccurrence)

Dheeraj(multilingual dictionaries) 5 min => create presentation explaining the value of multilingual dictionaries and Wikidata.

Feedback and discussion - 30 min

Resources

  • Etherpad. we will use https://pad.riseup.net/
  • getpapers (classic)
  • pygetpapers
  • pyamisearch
  • test corpus (e.g. 100 papers)
  • jupyter notebook

Hands-on

  • manual search EPMC
  • manual search T+F to show paywalls
  • pygetpapers (maybe previously installed)
  • wikidata search
  • pyamisearch

Discussion issues

  • issues with access to science articles
  • value of scientific articles and global issues
  • barriers
    • Global North
    • academia

pyami tools (probably not ready in time)

  • search FOR files
  • search within file content

Edited Timetable (2021-02-24)

Introduction

  • PMR - 3 min.

openVirus

  • Shweata (Textmining software and community - Introduction) - 5 min.
  • Ambreen (Her experience, initial results and machine learning 101 - 5 min.

CEVOpen - Invasive species theme

  • Kanishka - Intro to Invasive species project - 2 min. recorded video
  • Talha - Megapublishers and Manual search of scientific literature - 2 min.
  • Ayush - pygetpapers demonstration - 5 min.
  • Radhu - Intro to Wikidata, Invasive species dictionary creation demo - 2 min.
  • Vasant - pyamisearch results - 2 min