The literature on materials science (batteries, etc.) contains huge amounts of scientific facts, but not in easily accessible form. our AMI program has been developed to automatically: scrape , clean, annotate and display/publish data for re-use in science. Examples will be given from electrochemistry, magnetism and other fields . The general principles and (open) tech are applicable to many other disciplines.

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.