Semantic Web in Physical Science
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Transcript of Semantic Web in Physical Science
The Semantic Web in Physical Science/Engineering
Peter Murray-RustUniversity of Cambridge
Open Knowledge Foundation
Culham Laboratory, 2013-09-11, UK
Themes
To make the complete scientific literature accessible to machines and humans
• The Semantic Web.• The power and need for Open• Building Communities• Multidisciplinarity
Funding includes JISC, Unilever, EPSRC.
The Semantic Web
"The Semantic Web is an extension of the current web in which information is given well-defined meaning, better enabling computers and people to work in cooperation."
Tim Berners-Lee, James Hendler, Ora Lassila, The Semantic Web, Scientific American, May 2001
The scientist’s amanuensis• "The bane of my life is doing things I know computers could do for
me" (Dan Connolly, W3C)
Example: A semantic amanuensis could• Give me a daily digest of zeolite papers• Extract all the crystal structures from them• Compute physical properties with GULP and NWChem• Compare the results statistically• Preserve and distribute the complete operation• Prepare the results for publication
The semantic web is having a personal amanuensis
Linked Open Data – the world’s knowledge
very little physical science http://upload.wikimedia.org/wikipedia/commons/3/34/LOD_Cloud_Diagram_as_of_September_2011.png
DBPedia
BIO
Comp
Lib
PDB
Ontologies
GOV
GOV.uk
Music,ArtLiterature
Social
Knowledgebases
RDF triples
“Which Rivers flow into the Rhine and are longer than 50 kilometers?” or “Which Skyscrapers in China have more than 50 floors and have been constructed before the year 2000?”
Open Crystallography?“Which countries where tropical diseases are endemic have published structures of chiral natural products?”
Linked Open data from Wikipedia
CC-BY-SA from Wikipedia
Semantics: (Things Take Time)*
• 1994 1st WWW Conference• 1994 , Chemical MIME , Chemical Markup
Language (Henry Rzepa, PMR)• 2001 UK eScience programme, eMinerals• 2005 Materials Grid (Martin Dove group)• 2006 Blue Obelisk (Open Source chemistry)• 2011 PNNL (US) meetings and visit• 2012 Semantic Physical Science (Cambridge)
*TTT: Piet Hein
Componentised approach liberates
Individual, manual, unreusable, flaky
Commodity, standard, reliable, re-usable
Representing Semantics
Interoperating approaches: Markup Languages (“hardcoded objects”) MathML, G(eo)ML, CellML, S(ys)B(io)ML, • CML (Chemistry and numeric science):
1. Molecules (atoms, bonds, coordinates, 2. Reactions, 3. Spectra, 4. Solid state, 5. Computation
RDF (relationships, annotations, linking).Ontologies (Dictionaries)
Humans and machines use different languages
Scalable Vector Graphics (SVG)
<?xml version="1.0" encoding="UTF-8"?><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="1280" height="640" viewBox="0 0 30240 15120"><defs id="defs6"><polygon points="0,-9 1.735535,-3.6038755 7.0364833,-5.6114082 3.8997116,-0.89008374 8.7743512,2.0026884 3.1273259,2.4939592 3.9049537,8.1087198 0,4 -3.9049537,8.1087198 -3.1273259,2.4939592 -8.7743512,2.0026884 -3.8997116,-0.89008374 -7.0364833,-5.6114082 -1.735535,-3.6038755 0,-9 " id="Star7"/></defs><path d="M 0,0 L 30240,0 L 30240,15120 L 0,15120 L 0,0 z" style="fill:#00008b"/><use transform="matrix(252,0,0,252,7560,11340)" id="Commonwealth_Star" style="fill:#fff" xlink:href="#Star7"/><use transform="matrix(120,0,0,120,22680,12600)" id="Star_Alpha_Crucis" style="fill:#fff" xlink:href="#Star7"/><!– snipped 217,2520 L 10080,2520 L 15120,0 z" id="Red_Diagonals" style="fill:red"/><use transform="matrix(-1,0,0,-1,15120,7560)" id="Red_Diagonals_Rotated" style="fill:red" xlink:href="#Red_Diagonals"/></svg>
Human-friendly
Machine-friendly
Automatic!
Mathematics Markup LanguageEnergy of c.c.p lattice of argon
4 pages clippedHuman-friendly
Machine-friendly
Many editors and tools existWe used MathWeaver
Automatic!
MathML
CML (Chemical Markup Language)
Human-friendly Machine-friendly
Automatic!
Non-semantic data
Data extraction difficult and incomplete
Human readers
Current scientific information flow … is broken for data-rich science
PDFLineprinter output
Text files
Human input
Semantic network closes the loop
Data mined from document
Data available for e-science and re-use
ComputationMeasurement
SemanticAuthoring
Community
Analysis
The network grows autonomously
Machine-machine
Machine-human
Human-machine
Human-human
• Example: Materials 2012, 5, 27-46; doi:10.3390/ma5010027
CHEMICAL STRUCTURES
REACTIONS
ABBREVIATIONS
“… electron donor (ED), such as an electron rich, metal-based light absorber (LA), and electron acceptor (EA) sites.”
SPECTRA
TABLES
PROPERTIES (NAME-VALUE-UNITS)
Name Value UnitsNV U
NV U
N V
U
N
V
V V U
Note CML supports value ranges and errors
Mathematics
CML is being integrated with computable (content) MathML
Materials Search Challenge
• What would you like a “Google for materials” to find for you in the scientific literature?
TimBerners-Lee’s Open data http://5stardata.info
★ make your stuff available on the Web (whatever format) under an OPEN license
★★ make it available as structured data (i.e. NOT PDF)
★★★ use non-proprietary formats (e.g., CSV)
★★★★
use URIs to denote things, so that people can point at your stuff
★★★★★ link your data to other data to provide context
CIFDICACSIUCr
CRYSTALEYE
• http://upload.wikimedia.org/wikipedia/commons/3/34/LOD_Cloud_Diagram_as_of_September_2011.png
COD
CIFDIC
Creating semantic content
1. Authoring tools for humans2. Program output 3. Chemical databases 4. Content mining and Natural
Language Processing (Text) (NLP)5. Community
Semantic authoring IUCr• http://blogs.ch.cam.ac.uk/pmr/2012/01/23/brian-mcmahon-publishin
g-semantic-crystallography-every-science-data-publisher-should-watch-this-all-the-way-through/
• 1:08 CIF • 3:36 CIF Syntax and dataTypes • 4:30 Publishing with CIF • 6:41 Demonstration: CheckCIF • 12:02 Interactive Chemical validation • 14:42 Linking data to journal article and search for novelty of data • 15:08 Jmol display applet • 21:03 Supplementary data • 21:47 PublCIF a tool to merge data and text and annotate them
Semanticizing Logfiles: JumboConverters
LOGFILE
QUIXOTE: Semantic KnowledgeBase for Computational Chemistry
http://wwmm.ch.cam.ac.uk/chemicaltagger
Typical chemical synthesis
Content Mining of Chemistry
Automatic semantic markup of chemistry
Could be used for analytical, crystallization, etc.
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.
Machines can interpret phylogenetic treesOpen Content Mining of FACTS
>100,000 diagrams in literature; cost 1,000,000,000 hours
Unusable FACT
Re-usable FACT
Crowdcrafting and Hackathons
Crowdcrafting for Aegis/CERN• Does antimatter fall down or up?• Help the AEgIS experiment at CERN to work out how antimatter is affected by
gravity. Just join the dots!• Antimatter• The observable universe is composed almost entirely of matter but we can produce
stuff called antimatter in the lab. Antimatter is material composed of antiparticles.• Antiparticles have the same mass as normal matter particles but the opposite
charge. When an antiparticle collides with an ordinary matter particle they both annihilate - producing a burst of other particles and radiation.
• Antiparticles should interact gravitationally just like particles of ordinary matter because Einstein's weak equivalence principle states that gravity doesn't depend on composition. But if they don't then gravity is much more complicated than our current understanding indicates.
• http://crowdcrafting.org http://crowdcrafting.org/antimatter
Crowdcrafting for CERN/Aegis
[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
Open Definition• “A piece of data or content is open if anyone
is free to use, reuse, and redistribute it — subject only, at most, to the requirement to attribute and/or share-alike.”
OPEN NOT OPEN
PDBCOD,Crystaleye
CCDC, ICSD
RSC/ACS/IUCr CIFs Elsevier/Wiley/Springer CIFs
Acta Cryst E Acta Cryst ABCD (default)
CIF dictionaries
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
ACS
IUCr
RSC
Supplemental Information (CIFs) harvested from Publications
ELS
As-Cl Bond lengths
LongShort
Long
Short
Link to Journal
COD Letter to Editors 2012[We] have become aware of growing concerns regarding the publication, preservation and quality maintenance of crystallographic data. …However, we believe that completely open deposition of data and multiple checks can ensure the quality and wide availability of scientific data
[Please] recommend to your authors that, they also deposit their supplementary crystallographic data into the COD when they submit scientific papers to your journals.
Being open by its design, the COD enables the creation of multiple mirrors and backup copies. It provides, thus, archival storage of scientific data with adequate reliability. … services for reviewers and editors to facilitate the peer-review. …since our database follows the Open Access model, all material deposited into the COD is available to other databases. The COD team actually encourages the use of our data collection for any possible scientific or industrial application by putting the database into the public domain
Recommendations for Open Crystallography
• Require Open Crystal Data for all publications• Deposition of Open Data in COD• Integrate CIF dictionaries as RDF into Linked
Open Data• Integrate COD into Linked Open Data Cloud• CCDC/ICSD to publish RAW author CIFs Openly
Most “Open Access” is not re-usable
PRICE per article USD0 6000
CC-BY / Reusable
Restricted by licence or lack of clarity
Nothing/unclear
CC-ND
CC-NC
Ross Mounce Panton Fellow2012
Panton Principles for Open Data in Science
Why? Wanted to avoid the mess in OA• Peter Murray-Rust, Cameron
Neylon, Rufus Pollock, John Wilbanks
2008-> 2010 (launch) atPanton ArmsPanton Fellowships (2012)
JennyMolloy
JordanHatcher
RufusPollock
JohnWilbanks
CameronNeylon
PeterMurray-Rust
Launch 2010
“Licence STM Data as CC0”
Panton Fellows
Ross Mounce & Sophie Kershaw(Support from Open Society Foundations)
* Data should be open• Make your wishes clear• Use an appropriate licence
Open Mining Manifesto
1. Define ‘open content mining’ in a broad and useful manner‘Open Content Mining’ means the unrestricted right of subscribers to extract, process and republish content manually or by machine in whatever form (without prior specific permissions and subject only to community norms of responsible behaviour in the electronic age.Text Numbers Tables Diagrams Graphical representations of relationships between variablesImages and video and audio when it is the means of expressing a fact.Semantics (XML, RDF)
2. Urge publishers and institutional repositories to adhere to the following principles:
Principle 1: Right of Legitimate Accessors to MineWe assert that there is no legal, ethical or moral reason to refuse to allow legitimate accessors of research content (OA or otherwise) to use machines to analyse the published output of the research community. Researchers expect to access and process the full content of the research literature with their computer programs and should be able to use
their machines as they use their eyes. The right to read is the right to mine
Principle 2: Lightweight Processing Terms and ConditionsMining by legitimate subscribers should not be prohibited by contractual or other legal barriers. Publishers should add clarifying language in subscription agreements that content is available for information mining by download or by remote access. Where access is
through researcher-provided tools, no further cost should be required. Users and providers should encourage machine processing
Principle 3: UseResearchers can and will publish facts and excerpts which they discover by reading and processing documents. They expect to disseminate and aggregate statistical results as facts and context text as fair use excerpts, openly and with no restrictions other than attribution. Publisher efforts to claim rights in the results of mining further retard the advancement of science by making those results less available to the research community; Such claims should
be prohibited. Facts don’t belong to anyone.
3. Strategies
Assert the above rights by:Educating researchers and librarians about the potential of content mining and the current impediments to doing so, including alerting librarians to the need not to cede any of the above rights when signing contracts with publishers
Compiling a list of publishers and indicating what rights they currently permit, in order to highlight the gap between the rights here being asserted and what is currently possible
Urging governments and funders to promote and aid the enjoyment of the above rights.
Take-away messages
• Lost/unused STM* data costs 30-100Billion /yr [1]• Licence: DATA as CCZero and TEXT as CC-BY• Content Mining for DATA is a RIGHT• Apathy is our worst enemy• Trust and empower young people
“A piece of content or data is open if anyone is free to use, reuse, and redistribute it — subject only, at most, to the requirement to attribute and/or share-alike.”Une donnée est ouverte, si chacun est libre de l'utiliser, de la réutiliser et de la redistribuer
*Scientific Technical Medical [1] PMR: submission to UK Hargreaves process
To make the complete scientific literature accessible to machines and humans