![http://www.budapestopenaccessinitiative.org/read
… an unprecedented public good. …
… completely free and unrestricted access to [peer-
reviewed literature] by all scientists, scholars, teachers,
students, and other curious minds. …
…Removing access barriers to this literature will
accelerate research, enrich education, share the
learning of the rich with the poor and the poor with
the rich, make this literature as useful as it can be, and
lay the foundation for uniting humanity in a common
intellectual conversation and quest for knowledge.
(Budapest Open Access Initiative, 2003)](https://image.slidesharecdn.com/openpub2020-201010173212/85/OpenVirus-at-OpenPublishingFest-21-320.jpg)
OpenVirus at OpenPublishingFest
- 1. Virtual Open Publishing Fest, 2020-05-28 openVirus Knowledge for citizens in the time of COVID-19 Peter Murray-Rust TheContentMine and collaborators citizens knowledgebase Images from ContentMine CC BY and Wikimedia CC BY-SA pm286@cam.ac.uk peter@contentmine.org https://www.slideshare.net/petermurrayrust/openvirus-tools-for-discovering-literature-on-viruses
- 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,
- 3. ContentMine Workshops on Mining Chris Kittel, CM, atMozfest 2015 Stefan Kasberger, CM
- 4. 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 …
- 5. … knowledge can prevent viral epidemics … The Ebola outbreak in Liberia was predicted in 1984 … … and forgotten. https://www.nytimes.com/2015/04/08/opinion/yes-we-were-warned-about-ebola.html 11,310 dead in West Africa 2014
- 7. All: 426,613 Open: 21,919 5% is Open to citizens Is this article relevant to policy makers? openVirus will give YOU tools to test how much vital info is PAYWALLED
- 8. PREPRINTS!! Crossref EuropePMC Wikidata getpapers AMI We can change all that! We can do everything ourselves!
- 9. Delhi, IN Priya and Kareena are 3rd year interns on openVirus PMR Gitanjali Yadav
- 10. 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
- 11. 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?
- 12. “(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
- 13. UK Theses (EThOS) A full-text search API to find relevant theses. data from the EThOS service and the tools of the UK Web Archive -> full-text search API to find relevant theses. 1: Searching eTheses for the openVirus project 2: Bringing Metadata & Full-text Together This notebook illustrates how to use the API Andy Jackson
- 14. 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
- 17. Cooccurrence
- 18. bioRxiv in Citizen Health Search (CHS) A proposal to Wellcome Trust ( Open Research in Health call) with ContentMine, Cochrane and UCL-EPPI (CCU) CHS puts semantic search on the desktop of the searcher. We index all the visible Medical literature, normalize, section and index against a bank of user-chosen dictionaries. CHS takes input from EPMC, bioRxiv and emerging community sources such as Crossref, unpaywall and outputs to Zenodo, Wikidata and CM-Science Source. Citizen Dashboard
- 19. 5 million Open Scientific articles ( 0.5 TB), indexed by ContentMine . Disk 30 GBP Raspberry Pi3. 50 GBP CC BY, PeterMR Disk Raspberry PI Power CONTAINERISATION!
- 20. TESTERS!! GRAPHICS DOCUMENTING QUERIES SCRAPERS SOFTWARE Contentmine.org. Join us! We need… http://github.com/petermr/openVirus
- 21. http://www.budapestopenaccessinitiative.org/read … an unprecedented public good. … … completely free and unrestricted access to [peer- reviewed literature] by all scientists, scholars, teachers, students, and other curious minds. … …Removing access barriers to this literature will accelerate research, enrich education, share the learning of the rich with the poor and the poor with the rich, make this literature as useful as it can be, and lay the foundation for uniting humanity in a common intellectual conversation and quest for knowledge. (Budapest Open Access Initiative, 2003)