![http://www.nytimes.com/2015/04/08/opinion/yes-we-were-warned-about-
ebola.html
We were stunned recently when we stumbled across an article by European
researchers in Annals of Virology [1982]: “The results seem to indicate that
Liberia has to be included in the Ebola virus endemic zone.” In the future,
the authors asserted, “medical personnel in Liberian health centers should be
aware of the possibility that they may come across active cases and thus be
prepared to avoid nosocomial epidemics,” referring to hospital-acquired
infection.
Bernice Dahn (chief medical officer of Liberia’s Ministry of Health)
Vera Mussah (director of county health services)
Cameron Nutt (Ebola response adviser to Partners in Health)
A System Failure of Scholarly Publishing](https://image.slidesharecdn.com/mphil2020-201111183656/85/Can-machines-understand-the-scientific-literature-6-320.jpg)
![Scholarly publishing is “Big Data”
[2] https://en.wikipedia.org/wiki/Mont_Blanc#/media/File:Mont_Blanc_depuis_Valmorel.jpg
• $500 Billion public research => 2.5 million articles /year ,
7000 /day
• Most is not Publicly readable and much is unused
• ContentMining (TDM) can liberate knowledge
• Many mega-publishers fight ContentMining
[1] http://www.crossref.org/01company/crossref_indicators.html
1 year’s scholarly output!](https://image.slidesharecdn.com/mphil2020-201111183656/85/Can-machines-understand-the-scientific-literature-7-320.jpg)
![[1] The Military-Industrial-Academic complex (1961)
(Dwight D Eisenhower, US President)
Publishers Academia
Glory+?
$$, MS
review
Taxpayer
Student
Researcher
$$ $$
in-kind
The Publisher-Academic complex[1]
Infrastructure
“The scholarly poor”](https://image.slidesharecdn.com/mphil2020-201111183656/85/Can-machines-understand-the-scientific-literature-52-320.jpg)
Can machines understand the scientific literature?
- 1. MPhil Computational Biology, 2020, Cambridge, UK, 2020-11-11 Can machines understand the scientific literature? Peter Murray-Rust Dept of Chemistry, Univ of Cambridge Shweata N Hegde and Ambreen Hamadani Nat. Inst. For Plant Genome Res. (IN) Images from ContentMine CC BY and Wikimedia CC BY-SA [email protected] [email protected]
- 2. Semantic ContentMining • Knowledge generation for Global Challenges (PMR) • Semantic structure of a scientific paper (PMR) • Wikidata (PMR) • Building a textmining community and our tools (SH) • What we found (AH, Jupyter Notebook) • Image mining (PMR) • Ethical and political (PMR)
- 3. Global Crises: UN Sustainable Development Goals Health Climate https://sdgs.un.org/goals Hunger
- 4. Antti Lipponen (@anttilip) of the Finnish Meteorological Institute based on GISTEMP data (CC BY 2.0). https://www.youtube.com/watch?v= - yIHxOui9nQ&ab_channel=CarbonB rief https://twitter.com/dwallacewells/stat us/1312121745927598080/photo/1 Data that cannot be ignored Click this, it’s terrifying => climate
- 6. http://www.nytimes.com/2015/04/08/opinion/yes-we-were-warned-about- ebola.html We were stunned recently when we stumbled across an article by European researchers in Annals of Virology [1982]: “The results seem to indicate that Liberia has to be included in the Ebola virus endemic zone.” In the future, the authors asserted, “medical personnel in Liberian health centers should be aware of the possibility that they may come across active cases and thus be prepared to avoid nosocomial epidemics,” referring to hospital-acquired infection. Bernice Dahn (chief medical officer of Liberia’s Ministry of Health) Vera Mussah (director of county health services) Cameron Nutt (Ebola response adviser to Partners in Health) A System Failure of Scholarly Publishing
- 7. Scholarly publishing is “Big Data” [2] https://en.wikipedia.org/wiki/Mont_Blanc#/media/File:Mont_Blanc_depuis_Valmorel.jpg • $500 Billion public research => 2.5 million articles /year , 7000 /day • Most is not Publicly readable and much is unused • ContentMining (TDM) can liberate knowledge • Many mega-publishers fight ContentMining [1] http://www.crossref.org/01company/crossref_indicators.html 1 year’s scholarly output!
- 8. (our) software can filter this in a few minutes Ellie: “there were 10,000 abstracts and due to time pressures, we split this between 6 researchers. It took about 2-3 days of work (working only on this) to get through ~1,600 papers each. So, at a minimum this equates to 12 days of full-time work (and would normally be done over several weeks under normal time pressures).” Systematic Reviews Inst Public Health, University of Cambridge
- 9. Delhi 2014 Gita Yadav + colleagues PMR “met” Gita Yadav for a virtual mini-workshop on text-mining for science… … starting a 5-year collaboration on Plant Sciences, at NIPGR (Nat. Inst. For Plant Genome Research). Gita was then appointed Cambridge-India Lecturer in Plant Sciences… Jenny Molloy
- 10. TIGR2ESS Workshop 2019 Delhi We built dictionaries for: • Rice • Millets • Maize • And searched EuropePMC https://tigr2ess.globalfood.cam.ac.uk/events/ workshop-r-genomics-and-data-mining ContentMining for Food Securityhunger
- 11. Hypothes.is markup of article Annotated Articles Symbiont of machines and humans Can machines understand the scientific literature? amanuens.is
- 12. #DontLeaveItToGoogle Peter Kraker An Open Infrastructure is essential Or… ...Mendeley …WebOfScience …Scopus … Elsevier …Springer-Nature https://elephantinthelab.org/google-and-research-data/ Repositories: BASE , EuropePMC Free articles: Unpaywall Preprints: arXiv, bioRxiv, medRxiv Indexing: Crossref Scraping: getpapers, quickscrape Text analysis: OpenKnowledgeMaps, ami OpenKnowledgeMaps Unsupervised Learning
- 13. Peter Kraker and team http://openknowledgemaps.org Let’s ask for “childhood obesity prevention” Unsupervised learningUnsupervised Learning
- 15. metadata
- 16. Entities in text I want to ask: “which countries have SARSC and which have MERS”? virus Nucleic acid reference disease genus date country data role symptom Med. procedure organ
- 17. Tables NO structure in PDF
- 18. Maps I want to ask: “which countries have SARS and which have MERS”?
- 20. Plots
- 21. http://chemicaltagger.ch.cam.ac.uk/ • Typical Typical chemical synthesis
- 22. Automatic semantic markup of chemistry Could be used for analytical, crystallization, etc.
- 23. Document structure Automatically extracted from JATS-XML by ami-section
- 24. https://en.wikipedia.org/wiki/Linked_data#Linked_open_data things and relations named as http://....… pointing to useful resources Tim Berners-Lee (2009) Linked Open Data http://wikidata.org/Q42 http://wikidata.org/P31 http://wikidata.org/Q...
- 25. https://en.wikipedia.org/wiki/L inked_data#/media/File:Lod- cloud_2020-08-20.svg Wikidata Linked Open Data (LOD)
- 26. https://elifesciences.org/articles/5261 4 … Wikidata knowledge graph is based on the automated imports of large structured databases via Wikidata bots, … community-editing model, it harnesses the distributed efforts of a worldwide community of contributors,
- 27. https://elifesciences.org/articles/52614 Andra Waagmeester + 25 et al therapeutic pharmaceutical disease pharmacology taxon gene pathway protein anatomy medication compound family Wikidata biomedical entities and relations
- 28. https://www.wikidata.org/wiki/Wikidata:WikiFactMine ContentMine thanks the WikimediaFoundation for support 7 million articles, over 200 dictionaries
- 29. Shweata Hegde and Ambreen Hamadani present the #openVirus project
- 30. Images Extraction of features Extraction of data
- 35. Ln Bacterial load per fly 11.5 11.0 10.5 10.0 9.5 9.0 6.5 6.0 Days post—infection 0 1 2 3 4 5 Bitmap Image and Tesseract OCR
- 37. Dumb PDF CSV Semantic Spectrum 2nd Derivative Smoothing Gaussian Filter Automatic extraction
- 38. Posterisation Extracted since unique posterized colour
- 40. Note Jaggy and broken pixels NEW Bacteria must have a phylogenetic tree Length _________Weight Binomial Name Culture/Strain GENBANK ID Evolution Rate
- 41. https://blogs.ch.cam.ac.uk/pmr/2014/06/25/content-mining-we-can-now- mine-images-of-phylogenetic-trees-and-more/ for story of extraction Thinning Topology Serialization Newick
- 42. OCR (Tesseract) Norma (imageanalysis) (((((Pyramidobacter_piscolens:195,Jonquetella_anthropi:135):86,Synergistes_jonesii:301):131,Thermotoga _maritime:357):12,(Mycobacterium_tuberculosis:223,Bifidobacterium_longum:333):158):10,((Optiutus_te rrae:441,(((Borrelia_burgdorferi:…202):91):22):32,(Proprinogenum_modestus:124,Fusobacterium_nucleat um:167):217):11):9); Semantic re-usable/computable output (ca 4 secs/image)
- 44. Supertree for 924 species Tree
- 45. Supertree created from 4300 papers
- 47. C) What’s the problem with this spectrum? Org. Lett., 2011, 13 (15), pp 4084–4087 Original thanks to ChemBark
- 48. After AMI2 processing….. … AMI2 has detected a square
- 51. @Senficon (Julia Reda) :Text & Data mining in times of #copyright maximalism: "Elsevier stopped me doing my research" http://onsnetwork.org/chartgerink/2015/11/16/elsevi er-stopped-me-doing-my-research/ … #opencon #TDM Elsevier stopped me doing my research Chris Hartgerink
- 52. [1] The Military-Industrial-Academic complex (1961) (Dwight D Eisenhower, US President) Publishers Academia Glory+? $$, MS review Taxpayer Student Researcher $$ $$ in-kind The Publisher-Academic complex[1] Infrastructure “The scholarly poor”
- 54. BENEFITS OF CONTENT MINING Hague Declaration 2015 • Addressing grand challenges such as climate change and global epidemics • Improving population health, wealth and development • Creating new jobs and employment • Exponentially increasing the speed and progress of science through new insights and greater efficiency of research • Increasing transparency of governments and their actions • Fostering innovation and collaboration and boosting the impact of open science • Creating tools for education and research • Providing new and richer cultural insights • Speeding economic and social development in all parts of the globe
- 55. thanks Ambreen Hamadani Anugrah S. R. Charles Zeyang Li Kareena Singh Lakshmi Devi Priya Pruthiv Rajan Karunakaran Shweata N. Hegde Sana Saifi Vaishali Arora Vanisha Arora Dheeraj Kumar Jitu Ram Bhargav Om Prakash Mehra Pooja Pareek Simranleen Singh Urja Biswas Aishwarya Dharan Ayush Garg Mukul Bhambri Padmini Rai Ebhoimen Israel Gitanjali Yadav (Delhi/Cambridge) Wikimedia (Brazil) Redalyc (Mexico) India interns
- 56. BENEFITS OF CONTENT MINING Hague Declaration 2015 • Addressing grand challenges such as climate change and global epidemics • Improving population health, wealth and development • Creating new jobs and employment • Exponentially increasing the speed and progress of science through new insights and greater efficiency of research • Increasing transparency of governments and their actions • Fostering innovation and collaboration and boosting the impact of open science • Creating tools for education and research • Providing new and richer cultural insights • Speeding economic and social development in all parts of the globe
Editor's Notes
- #48: ChemBark