The Content MinePeter Murray-Rust

University of Cambridge and Open Knowledge Foundation

A community of people and machines to extract 100,000,000 scientific facts from the scholarly literature

Slides: CC-BY

Images © Wikimedia CC-BY-SA

If you’re bored …THREE most important Open Access publishers?(besides BMC and PLoS) THREE most important Open Access repositories?

important

TDM* (“Text-and-Data-mining”) is the use of machines to read and understand massive amounts of documents

“The Right to Read is the Right to Mine“. PMR + OKFN“Closed Access means people die” (PM-R)“Text and Data Mining saves Lives “ (John McNaught)*PMR uses “content mining”

(Credit: Seth Rosenblatt/CNET)

Who’s this?

(Credit: Seth Rosenblatt/CNET)

http://news.cnet.com/8301-13578_3-57611642-38/call-to-action-kicks-off-second-aaron-swartz-hackathon/

Aaron SwartzDied 2012-11-08

Facing 30 years in jail forDownloading JStor

Typical papers destroy data

Numeric: astro1307.5851v4.pdf

Diagram: birds1471-2148-11-313.pdf

[at Research Data Alliance, we are entering a new “era of open science”, which will be “good for citizens, good for scientists and good for society”.She explicitly highlighted the transformative potential of open access, open data, open software and open educational resources – mentioning the EU’s policy requiring open access to all publications and data resulting from EU funded research.

http://blog.okfn.org/2013/03/21/we-are-entering-an-era-of-open-science-says-eu-vp-neelie-kroes/#sthash.3SWDXDE6.dpuf

RCUKWellcomeERCNSF …

requirefully OPEN

• Make science discoverable• Extract facts for research• Build reusable objects• Aggregate • Create new businesses• Check for errors => better science

Content Mining

• Secondary publishers create walled gardens• Publishers’ contracts ban content-mining.• Publishers cut off Universities who mine• Publishers lobby governments to require

“licences for content mining”

• UK Hargreaves legislation will override this by law. Starts 2014.

Content Mining Problems

http://blogs.ch.cam.ac.uk/pmr/2013/10/02/text-and-data-mining-fighting-for-our-digital-future-peter-murray-rust-is-the-problem/

service provider has control over applications, content, and media and restricts convenient access to non-approved applications or content.

Walled Gardens (“Free” but not “Open”)

Examples: Mendeley, Facebook, Cambridge Crystallographic Data Centre, OCLC

#animalgarden “Walled Gardens” https://vimeo.com/34323486

http://www.theguardian.com/science/2012/may/23/text-mining-research-tool-forbidden

STM Publishers Licence2012_03_15_Sample_Licence_Text_Data_Mining.pdf (Summary: PMR has NO rights)• [cannot publish to: ] “libraries, repositories, or archives”• [cannot] “Make the results of any TDM Output available on an externally facing server or

website”• “Subscriber shall pay a […] fee”

Heather Piwowar: “negotiating with publishers [made me physically ill]”

WE WALKED OUT• Brit Library• JISC• RLUK• OKFN• …• Ross Mounce• PM-R

Licences destroy Content Mining

Licensing TDM is like publishers taxing spectacles

But we can now turn PDFs into

Science

We can’t turn a hamburger into a cow

Zoom in …

UNITS

TICKS

QUANTITYSCALE

TITLES

DATA!!2000+ points

Dumb PDF

CSV

SemanticSpectrum

2nd Derivative

Gaussian Filter

Automaticextraction

Evolution of ultraviolet vision in the largest avian radiation - the passerines Anders Ödeen 1* , Olle Håstad 2,3 and Per Alström 4

PDF

HTML

Styles , superscripts

And diåcritics preserved!

AMI

PDF Turdus iliacusTaeniopygia guttataSerinus canariaLanius excubitorMelopsittacus undulatusPavo cristatusSturnus vulgarisDolichonyx oryzivorusFicedula hypoleucaVaccinium myrtillusFalco tinnunculus

TurdusPomatostomus LeothrixAmytornis AcanthisittaOrthonyx x 2MalurusCnemophilus x 4Philesturnus x 2Motacilla x 2Toxorhampus x 2

Typical phylo tree: 60 nodes, complex and miniscule annotation, vertical text, hyphenation and valuable branch lengths. AMI extracts ALL

Acanthisittidae Acanthizidae Acrocephalidae Callaeidae Campephagidae Cnemophilidae Corvidae

0.84 0.91 0.93 0.95

Acanthisitta Acrocephalus Ailuroedus Ailuroedus Amytornis Camptostoma

AMI23.1234.5437.2138.55

Posterior probability

AMI can MEASUREBranch lengths!

NexML

Genus Family

HTML

10 million spectra published /year

Review of the NMR data reported in the Supporting Information in this article evidences instances where some of the spectra were inappropriately edited to remove impurities. A coauthor and former student, Dr. Bruno Anxionnat, has shared with me formal communication in which he states “I would like to take full responsibility for this entire situation. I was in charge of making the SI of my papers and I erased some peaks without telling anybody. All my supervisors (Pr. Cossy, Dr. Gomez Pardo and Dr. Ricci) trusted me and I wasn't dependable. I am the only one who has to be blamed for all that, in any case them. I know my behavior is highly unethical. I am deeply sorry for what I have done and for hurting people….”

Crystallography Walled Garden

service provider has control over applications, content, and media and restricts convenient access to non-approved applications or content.

From Saulius Grazulis

Crystaleye• A database of 200,000 crystal structures scraped from

publications CIF supplemental information• CML molecules and name-value pairs• Re-usable as fragment base

Nick Day, Jim Downing, Sam Adams, N. W. England and Peter Murray-Rust*J.Appl.Cryst. (2012). 45 , 316–323, doi:10.1107/S0021889812006462

http://wwmm.ch.cam.ac.uk/crystaleye

“nuggets” in a scientific paper

quantity

units

Value ranges

Humans aren’t designed to mine this … chemical

project places

The Content MineA community of people and machines to extract scientific facts from the scholarly literature on a global scale.

https://vimeo.com/78353557

100,000 lines of Open code for translating PDFs to science.10 years work (PMR).

AMI works!

AMI

We have friends

• ProPublica is a NY digital-democracy newspaper• Tabula is an Open PDF-table extractor • Mozilla fights for web freedom

Boot-Camps and hacks

Open Science, Oxford 2013-11-27(sold out before announcement!)

Collaborators:I have talked with:• BMC• PLoS• British Library• Mozilla• Software Carpentry• EuropePMC• Creative Commons• OKFNI hope to talk with:• Wellcome• JISC• Ubiquity• Royal Society• Kitware• SPARC• …• …

• “The right to read is the right to mine”• Unrestricted TDM saves lives• Libraries – reject TDM restrictions• Publishers – Damascene conversion • Funders – insist on CC-BY

@petermurrayrusthttp://blogs.ch.cam.ac.uk/pmr

3 most important Open Access repositories?

• Wikimedia• Github, StackOverflow.• National libraries and museums.

3 most important Open Access publishers?

• Wikipedia• NIH+EBI+OtherBioDatabases• arXiv, CERN/SCOAP• +PLoS+BMC

300 Billion USD annually on Science+Medicine

FACTS! LOST! FACTS! LOST! FACTS! LOST! FACTS! • “we repeat about 25% of our chemistry

because we didn’t know we’d done it already”• 10,000 phylogenetic trees at 25,000 USD each;

only 4% have data (loss = 240 Million USD) • Computational chemistry – materials NO

DATA, perhaps 1,000,000,000 USDFACTS! LOST! FACTS! LOST! FACTS! LOST! FACTS!