The ContentMine project aims to provide structured text and image mining of scientific literature to everyone for free through open source software. It receives funding from the Shuttleworth Foundation and works with various scientific communities and organizations. ContentMine trains workshops to teach text and data mining skills and has created regular expressions to mine texts about Ebola. It demonstrates chemical entity recognition through the ChemicalTagger tool and phylogenetic tree extraction from bacterial literature.

1. TheContentMine: Mining for Everyone
Peter Murray-Rust
BL_Labs, London, 2014-11-27

2. The Right to Read is the Right to Mine
http://contentmine.org

3. ContentMine
• 1-2 year Shuttleworth Funding from 2014-03
• Free to everyone, Open Source, updated daily
• Structured Text, and Image/Diagram Mining
• Workshops for training and training trainers
• Bottom-up community development
– Bioscience (EuropePMC, BBSRC)
– Disease Ebola
– Astrophysics (Stray Toaster)
– Chemistry (TSB, EBI, PennState - Citeseer)
• We fight for Justice and Freedom

4. ContentMine People
• Jenny Molloy
• Ross Mounce
• Peter Murray-Rust + volunteers (Bioscience, disease)
• Richard Smith-Unna + 20 quickscrape volunteers
• Steph Unna
• Cottage Labs (Mark MacGillivray, Emanuil Tolev,
Richard Jones)
• Prof Charles Oppenheim
• Karien Bezuidenhout (Shuttleworth)
• Advisory Board RSN

5. ContentMine Workshops
(1-hour -> full day or more)
2014-May->Nov
• Budapest/Shuttleworth
• Leicester Univ
• Electronic Theses and Dissertations
• Austrian Science Fund AT
• OKFest DE
• Eur. Bioinformatics Institute
• Open Science Rio de Janeiro BR
• Sci DataCon , Delhi IN
• Univ of Chicago US
• OpenCon 2014, Wash DC. US
Upcoming
• JISC
• LIBER
• BL
• Wellcome Trust
• WHO

6. Ebola Collaborators (Atlanta)
Roxanne Further Moore, Jessie
Gunter, April Clyburne-Sherin

7. Regular Expressions
(Easier than Crosswords or Sudoku)
Ebola Ebola
Mali (not
Malicious)
MaliW (end of word)
Bat or bat [Bb]at (alternatives)
bat or bats bats? (optional letter)
Bat or Bats or bat
[Bb]ats?
or bats
Sudden onset [Ss]uddens+onset (space/s)
Panthera leo or
[A-Z][a-z]+s+[a-z]+
Gorilla gorilla
(ranges of letters)

8. Ebola regex
• <compoundRegex title="ebola">
• <regex weight="1.0" fields="ebola" case="">(Ebola)</regex>
• <regex weight="1.0" fields="marburg">(Marburg)</regex>
• <regex weight="1.0" fields="hemorrhagic_fever">([Hh]a?emorrhagics+fever)</regex>
• <regex weight="0.8" fields="sudden_onset">([Ss]uddens+onset)</regex>
• <regex weight="0.6" fields="vomiting_diarrhoea">([Vv]omitings+diarrho?ea)</regex>
• <regex weight="0.5" fields="guinea">(Guinea)</regex>
• <regex weight="0.5" fields="sierra_leone">(Sierras+Leone)</regex>
• <regex weight="0.5" fields="liberia">(Liberia)</regex>
• <regex weight="0.5" fields="mali">(Mali)W</regex>
• <regex weight="0.6" fields="contact_tracing">([Cc]ontacts+tracing)</regex>
• <regex weight="0.5" fields="bat">W([Bb]ats?W)</regex>
• <regex weight="0.5" fields="bushmeat">([Bb]ushmeat)</regex>
• <regex weight="0.5" fields="drc">(Democratic Republics*(s*of)?(s*the)?s*Congo)(DRC)</regex>
• <regex weight="0.6" fields="safe_burial">([Ss]afes+burials+practice?s)</regex>
• <regex weight="1.0" fields="etu">([Ee]bolas+treatments+units?)(ETU)</regex>
• </compoundRegex>
I
15 mins to create, 15 mins to install and test
Or run online at CottageLabs

9. Results of Regex on Ebola
• <resultsList xmlns="http://www.xml-cml.org/ami">
• <results xmlns="">
• <source xmlns="http://www.xml-cml.org/ami"
• name="/Users/pm286/workspace/ami-core/./docs/ebola/text/14Nov.txt" />
• <result>
• <regex xmlns="http://www.xml-cml.org/ami" lineNumber="7"
• lineValue=" There have been 14 413 reported Ebola cases in eight countries since the outbreak ">
• <regex xmlns="" weight="1.0" fields="[ebola]">
• <pattern>(Ebola)</pattern>
• </regex>
• <hits xmlns="">
• <hit ebola="Ebola" />
• </hits>
• </regex>
• </result>
• <result>
• <regex xmlns="http://www.xml-cml.org/ami" lineNumber="9"
• lineValue="HIGHLIGHTS Case incidence continues to increase in Sierra Leone, and transmission also remains ">
• <regex xmlns="" weight="0.5" fields="[sierra_leone]">
• <pattern>(Sierras+Leone)</pattern>
• </regex>
• <hits xmlns="">
• <hit sierra_leone="Sierra Leone" />
• </hits>
• </regex>
• </result>

10. Demo of Content Mining
ChemicalTagger (Lezan Hawizy) a shallow,
domain-specific, semantic parser for un/natural
language.

11. Bacterial WP_phylogenetic tree
Genbank ID
American Type
Culture Collection
WP: Clostridium_butyricum
Our machines have read and interpreted 4300 in an hour with > 95% accuracy
Trees From http://ijs.sgmjournals.org/ used under new UK legislation (Hargreaves)

12. RSU: Richard Smith-Unna
PMR: Peter Murray-Rust
CL: CottageLabs
Queues
Repos
Scientific
literature
Science
Plugins
Science
Volunteers
Collaboration with
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