![http://www.nytimes.com/2015/04/08/opinion/yes-we-were-warned-about-
ebola.html
[Liberian Ministry of Health] 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.
Adage in public health: “The road to inaction is paved with research
papers.”
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/neuroscience2015a-151022054611-lva1-app6892/85/ContentMining-in-Neuroscience-10-320.jpg)
![Output of scholarly publishing
[2] https://en.wikipedia.org/wiki/Mont_Blanc#/media/File:Mont_Blanc_depuis_Valmorel.jpg
586,364 Crossref DOIs 201,507 [1] per month
1.5 million (papers + supplemental data) /year [citation needed]*
each 3 mm thick
4500 m high per year [2]
* Most is not Publicly readable
[1] http://www.crossref.org/01company/crossref_indicators.html](https://image.slidesharecdn.com/neuroscience2015a-151022054611-lva1-app6892/85/ContentMining-in-Neuroscience-16-320.jpg)
![Scientific and Medical publication (STM)[+]
• World Citizens pay $450,000,000,000…
• … for research in 1,500,000 articles …
• … cost $300,000 each to create …
• … $7000 each to “publish” [*]…
• … $10,000,000,000 from academic libraries …
• … to “publishers” who forbid access to 99.9% of citizens of
the world …
• 85% of medical research is wasted (not published, badly
conceived, duplicated, …) [Lancet 2009]
[+] Figures probably +- 50 %
[*] arXiV preprint server costs $7 USD per paper](https://image.slidesharecdn.com/neuroscience2015a-151022054611-lva1-app6892/85/ContentMining-in-Neuroscience-17-320.jpg)
![Bacillus subtilis [131238]*
Bacteroides fragilis [221817]
Brevibacillus brevis
Cyclobacterium marinum
Escherichia coli [25419]
Filobacillus milosensis
Flectobacillus major [15809775]
Flexibacter flexilis [15809789]
Formosa algae
Gelidibacter algens [16982233]
Halobacillus halophilus
Lentibacillus salicampi [18345921]
Octadecabacter arcticus
Psychroflexus torquis [16988834]
Pseudomonas aeruginosa [31856]
Sagittula stellata [16992371]
Salegentibacter salegens
Sphingobacterium spiritivorum
Terrabacter tumescens
• [Identifier in Wikidata]
• Missing = not found with Wikidata API
20 commonest organisms (in > 30 papers) in trees from IJSEM*
Half do not appear to be in Wikidata
Can the Wikipedia Scientists comment?
*Int. J. Syst. Evol. Microbiol.](https://image.slidesharecdn.com/neuroscience2015a-151022054611-lva1-app6892/85/ContentMining-in-Neuroscience-51-320.jpg)
![Elsevier wants to control Open Data
[asked by Michelle Brook]](https://image.slidesharecdn.com/neuroscience2015a-151022054611-lva1-app6892/85/ContentMining-in-Neuroscience-71-320.jpg)
ContentMining in Neuroscience
- 1. Open Mining of the Bioscience Literature Peter Murray-Rust, ContentMine.org and the University of Cambridge UNAM, MX 2015-10-09 Millions of data points are hidden in the bioscience literature. ContentMine has Open technology to liberate them automatically. Using OpenNotebook approaches The major problem is politico-legal This is an exploratory talk, looking for ideas and projects The future depends on young people
- 2. Oxford 2013 Berlin 2014 Delhi 2014 Jenny Molloy with mascot AMI
- 3. Panton Authors and Fellows
- 4. Some particularly relevant Fellows/Alumni and projects: • Rufus Pollock: Open Knowledge Foundation • Mark Surman: Mozilla • Dan Whaley: Hypothes.is • Daniel Lombrana-Gonzales: PyBossa/Crowdcrafting Erin McKiernan, 2015 Flash Award ContentMine and Peter Murray-Rust are funded by:
- 5. The Right to Read is the Right to Mine http://contentmine.org
- 6. ContentMine Workshops and Hackdays Open Science Brazil, 2014-08 Easily distributed software Get started in 30 mins Build application in a morning Start simple: bagOfWords, Stemming, Regex, templates
- 8. Why do we publish science? • Communicate our results • Archival • Get feedback from peers. • Provide material that others can re-use. • Priority and esteem.
- 10. http://www.nytimes.com/2015/04/08/opinion/yes-we-were-warned-about- ebola.html [Liberian Ministry of Health] 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. Adage in public health: “The road to inaction is paved with research papers.” 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
- 11. Re-use You cannot assume how others will want to re-use your work.
- 12. PM-R’s “first real paper”, doing science by re-using the results of others in a novel way
- 13. 1974: Each point is a separate paper! Needing 1-4 hours in library – discovery,hardcopy delivery, Transcription, hand calculation.
- 14. 1976-9: PMR and WDSM developed software And protocols to search and analyze Cambridge Crystallographic DB
- 15. We need machines to read the literature
- 16. Output of scholarly publishing [2] https://en.wikipedia.org/wiki/Mont_Blanc#/media/File:Mont_Blanc_depuis_Valmorel.jpg 586,364 Crossref DOIs 201,507 [1] per month 1.5 million (papers + supplemental data) /year [citation needed]* each 3 mm thick 4500 m high per year [2] * Most is not Publicly readable [1] http://www.crossref.org/01company/crossref_indicators.html
- 17. Scientific and Medical publication (STM)[+] • World Citizens pay $450,000,000,000… • … for research in 1,500,000 articles … • … cost $300,000 each to create … • … $7000 each to “publish” [*]… • … $10,000,000,000 from academic libraries … • … to “publishers” who forbid access to 99.9% of citizens of the world … • 85% of medical research is wasted (not published, badly conceived, duplicated, …) [Lancet 2009] [+] Figures probably +- 50 % [*] arXiV preprint server costs $7 USD per paper
- 18. What is “Content”? http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.01113 03&representation=PDF CC-BY SECTIONS MAPS TABLES CHEMISTRY TEXT MATH contentmine.org tackles these
- 19. ContentMine approaches 0. Open software, Open content, Open notebooks 1. Daily liberation of facts which are easy and widely useful. – Species (Bacillus subtilis, Okapia johnstoni) – Genes (BRCA1*, APOE) – Chemicals (acetone, CH3OH) – Identifiers (RRIDs, museum specimens, ) 1. CMunities of practice with bespoke tools: – Clinical Trials – Phylogenetic trees – Systematic reviews
- 20. http://chemicaltagger.ch.cam.ac.uk/ • Typical Typical chemical synthesis
- 21. Open Content Mining of FACTs Machines can interpret chemical reactions We have done 500,000 patents. There are > 3,000,000 reactions/year. Added value > 1B Eur.
- 22. C) What’s the problem with this spectrum? Org. Lett., 2011, 13 (15), pp 4084–4087 Original thanks to ChemBark
- 23. After AMI2 processing….. … AMI2 has detected a square
- 25. catalogue getpapers query Daily Crawl EuPMC, arXiv CORE , HAL, (UNIV repos) ToC services PDF HTML DOC ePUB TeX XML PNG EPS CSV XLSURLs DOIs crawl quickscrape norma Normalizer Structurer Semantic Tagger Text Data Figures ami UNIV Repos search Lookup DAILY CONTENT MINING Chem Phylo Trials Crystal Plants COMMUNITY plugins Visualization and Analysis PloSONE, BMC, peerJ… Nature, IEEE, Elsevier… Publisher Sites scrapers queries taggers abstract methods references Captioned Figures Fig. 1 HTML tables 30, 000 pages/day Semantic ScholarlyHTML Facts
- 27. http://opentrials.net/ ContentMine will work with OpenTrials
- 28. “adult nonpregnant patients, aged ≥18 years”, “randomization sequence using a permuted block design with random block sizes stratified by study center”. “blinding of the patients and caregivers is not possible”. “Investigators performing analysis are blinded for the intervention”. “Continuous normally distributed variables … mean and standard deviation, counts (n) and percentages (%). … Student’s t-test … or the Mann–Whitney U test … Categorical … Chi-square test or Fisher's exact tests. Statistical significance is considered to be at a P value <0.05 …” Formulaic language in reporting clinical trials
- 29. Text-based plugins • Bag of words (https://en.wikipedia.org/wiki/Bag-of- words_model) • https://en.wikipedia.org/wiki/Tf%E2%80%93idf (Term-frequency, inverse document frequency) • Templates and regexes (regular expressions).
- 30. “Bag of Words” Three fulltext articles from trialsjournal.com
- 31. Regular Expressions for Systematic Reviews of Animal Tests Preceding Text Following Text Extracted term In 30 minutes 6 scientists (most were unfamiliar with regex) wrote 200 regexes for ARRIVE (NC3R guidelines)
- 32. TEMPLATES
- 33. https://en.wikipedia.org/wiki/Consolidated_Standards_of_Reporting_Trials Some communities have standard Reporting, which helps extraction
- 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
- 38. Dumb PDF CSV Semantic Spectrum 2nd Derivative Smoothing Gaussian Filter Automatic extraction
- 39. PLUTo
- 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. PMR’s Tribute Planned Memorial Meeting July 14th 2014 Cambridge OPEN NOTEBOOK SCIENCE
- 43. Traditional Research and Publication “Lab” work paper/th esis Write rewrite Re-experiment publish ??? Validation?? DATA output “belongs” to publisher
- 44. TOOLS Open Notebook Science Open engineered repository World community INSTRUMENT validate merge MODEL CODE DATA DATA knowledge calibrate Problems are solved communally; Nothing is needlessly duplicated; “publication“ is continuous ; data are SEMANTIC Machines and humans Working together
- 45. Open Notebook Content Mining • “No insider knowledge” • Anyone can become involved • All raw non-copyright material on Github • Planning and discussion on Open Discourse • All output (however imperfect) on Github CC0 • Immediate upload • Inspired by Free/Libre/Open Source, Wikipedia, Open StreetMap.
- 46. 4300 images
- 47. “Root”
- 48. 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)
- 50. Automatic Open Notebook of computations Everything is posted to Github before being analyzed
- 51. Bacillus subtilis [131238]* Bacteroides fragilis [221817] Brevibacillus brevis Cyclobacterium marinum Escherichia coli [25419] Filobacillus milosensis Flectobacillus major [15809775] Flexibacter flexilis [15809789] Formosa algae Gelidibacter algens [16982233] Halobacillus halophilus Lentibacillus salicampi [18345921] Octadecabacter arcticus Psychroflexus torquis [16988834] Pseudomonas aeruginosa [31856] Sagittula stellata [16992371] Salegentibacter salegens Sphingobacterium spiritivorum Terrabacter tumescens • [Identifier in Wikidata] • Missing = not found with Wikidata API 20 commonest organisms (in > 30 papers) in trees from IJSEM* Half do not appear to be in Wikidata Can the Wikipedia Scientists comment? *Int. J. Syst. Evol. Microbiol.
- 52. Supertree for 924 species Tree
- 53. Supertree created from 4300 papers
- 54. Minor branch
- 55. Part of major branch
- 56. Part of major branch
- 57. Ideas for Neuroscience Can we extract digital information from published electroneurophysiology traces?... …and build super-information?
- 65. Extraction into data format (CSV, Excel)
- 66. catalogue getpapers query Daily Crawl EuPMC, arXiv CORE , HAL, (UNIV repos) ToC services PDF HTML DOC ePUB TeX XML PNG EPS CSV XLSURLs DOIs crawl quickscrape norma Normalizer Structurer Semantic Tagger Text Data Figures ami UNIV Repos search Lookup CONTENT MINING Chem Phylo Trials Crystal Plants COMMUNITY plugins Visualization and Analysis PloSONE, BMC, peerJ… Nature, IEEE, Elsevier… Publisher Sites scrapers queries taggers abstract methods references Captioned Figures Fig. 1 HTML tables 30, 000 pages/day Semantic ScholarlyHTML Facts
- 67. Peter Murray-Rust BMC publisher Blue Obelisk paper (20 co-authors) Sub-network From CATalog
- 68. Phytochemistry extraction O. dayi “volatile composition of “ A.sibeiri A. judaica Displayed by CAT (CottageLabs)
- 69. The problem ©
- 70. Prof. Ian Hargreaves (2011): "David Cameron's exam question”: "Could it be true that laws designed more than three centuries ago with the express purpose of creating economic incentives for innovation by protecting creators' rights are today obstructing innovation and economic growth?” “yes. We have found that the UK's intellectual property framework, especially with regard to copyright, is falling behind what is needed.” "Digital Opportunity" by Prof Ian Hargreaves - http://www.ipo.gov.uk/ipreview.htm. Licensed under CC BY 3.0 via Wikipedia - https://en.wikipedia.org/wiki/File:Digital_Opportunity.jpg#/media/File:Digital_Opportunity.jpg
- 71. Elsevier wants to control Open Data [asked by Michelle Brook]
- 72. http://www.epip2015.org/copyright-wars-frozen-conflict/ UPDATE 20150902: Ian Hargreaves "the voices of the digital many should not be drowned out by the digital self-interested few"
Editor's Notes
- #2: Hi, I’m here to talk about AMI; a data extraction framework and tool. First, I just want highlight some of key contributors to the projects; Andy for his work on the ChemistryVisitor and Peter for the overall architecture. In this talk, I’m going to impress the importance of data in a specific format and its utility to automated machine processing. Then I’m going to demonstrate AMI’s architecture and the transformation of data as it flows through the process. I’m going to dwell a little on a core format used, Scalable Vector Graphics (SVG) before introducing the concept of visitors, which are pluggable context specific data extractors. Next, I’m going to introduce Andy’s ChemVisitor, for extracting semantic chemistry data, along with a few other visitors that can process non-chemistry specific data. Finally, I will demonstrate some uses of the ChemVisitor, within the realm of validation and metabolism.
- #23: ChemBark