The document discusses the challenges of accessing scientific literature related to climate change and COVID-19, emphasizing the need for open access knowledge. It presents ContentMine's initiative to automatically extract and analyze data from scientific articles to aid in research. Various tools and frameworks for scraping, cleaning, and annotating open-source data are mentioned, highlighting the importance of collaboration and community engagement in overcoming data access barriers.

1. Trinity College Dublin , IE,
”virtual” , 2020-07-01
openBattery
Materials Knowledge for citizens in the time of climate change
Peter Murray-Rust
Dept of Chemistry University of Cambridge and contentmine.org
Images from ContentMine CC BY and Wikimedia CC BY-SA
pm286@cam.ac.uk
peter@contentmine.org
Automatic extraction of materials and properties reported in the scientific literature.
Are you interested in having machines automatically search and retrieve data? Free?

2. ContentMine is OpenLocked Non-Profit http://contentmine.org
The Right to Read is the Right to Mine
openVirus collaborators
Remko Popma,
Lezan Hawizy, Tim Voronov,
Andy Jackson,
Clyde Davies,
Thomas Shafee,
Priya JK , Kareena Singh,
Simon Worthington,
Open-battery
Matthew Dunstan

3. The world’s existential problems need
knowledge
2019* “Open Climate Knowledge” (OCK)
to mine scientific articles about climate change.
50-90% of all published science is PAYWALLED. The rest is very hard to
find…
*Simon Worthington and PMR
BUT COVID-19 hit …

4. Ebola in West Africa
was forecast
35 years ago …
… was COVID-19
Also forecast?
… or its mitigation
suggested?

6. Delhi, IN
Priya and Kareena are 3rd year interns on openVirus
PMR
Gitanjali Yadav

7. Mining!
• build scrapers for Openly readable sources.
• Users queries for scraping
• download raw content
• clean and semantify
• annotate with dictionaries.
• analyze, display.
Scrape -> Clean-> Annotate -> Display
Open sources publish
|
v
|
v
|
v

8. Sources
https://ethos.bl.uk/Home.dohttps://www.redalyc.org/
100,000 Theses
4,700,000 abstracts
50,000 preprints
https://doaj.org https://biorxiv.org
https://medrxiv.org
Mexico, Latin America
https://europepmc.org
And your archive?

9. “(virus OR viral) AND
epidemic”
45 hits
DOAJ
Directory of Open Access Journals100,000
abstracts
Only 4.6 million
more to go 0.05%
20 GB total
Clyde Davies
Complete repo would yield
> 2000 articles
The power is with the READER

10. framework: ami + CProject data
scrapers: getpapers, Ferret, curl, scrapy
cleaners: PDFBox, Tidy/Jsoup, etc. Grobid
transformers: xml2html, ami ocr, KNIME
dictionaries: ami dictionary
indexing and annotation: Solr, ami
Analysis and display: R, KNIME
openVirus Tools
scrape clean annotate display

11. Dictionaries
materials.xml
country.xml
Generous support from
<entry term="anode" wikipedia="anode" wikidata="Q181232" name="anode" description="el
<entry term="castep" wikidata="Q5008880" name="CASTEP" description="density functional
<entry term="cathode" wikipedia="cathode" wikidata="Q175233" name="cathode" descriptio

12. getpapers -q "lithium-ion battery" -n
info: Searching using eupmc API
info: Found 3305 open access results

14. Wikipedia
Wikidata
UniqueID
We need Wikimedia!

15. Dashboard of 200 articles searched with 5 dictionaries

16. Co-occurrence of words

17. Extraction of data from diagrams

18. Extraction of data from diagrams

19. ami-image
ami-pixel
Extraction of data from diagrams

20. Publishers are a major problem

21. • http://github.com/petermr/openVirus
• pm286@cam.ac.uk
• https://github.com/the-grey-group/open-battery/
• Thanks to Matthew Dunstan
• These slides are on slideshare and the event is recorded on YouTube – address to
follow.