TheContentMine: Mining for Everyone

TheContentMine: Mining for Everyone

• 1.
  TheContentMine: Mining forEveryone Peter Murray-Rust BL_Labs, London, 2014-11-27
• 2.
  The Right toRead is the Right to Mine http://contentmine.org
• 3.
  ContentMine • 1-2 yearShuttleworth 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 • JennyMolloy • 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) RoxanneFurther Moore, Jessie Gunter, April Clyburne-Sherin
• 7.
  Regular Expressions (Easier thanCrosswords 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 or bats [Bb]ats? Sudden onset [Ss]uddens+onset (space/s) Panthera leoor Gorilla gorilla [A-Z][a-z]+s+[a-z]+ (ranges of letters)
• 8.
  Ebola regex • <compoundRegextitle="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 Regexon 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 ContentMining ChemicalTagger (Lezan Hawizy) a shallow, domain-specific, semantic parser for un/natural language.
• 11.
  Bacterial WP_phylogenetic tree Ourmachines have read and interpreted 4300 in an hour with > 95% accuracy Trees From http://ijs.sgmjournals.org/ used under new UK legislation (Hargreaves) WP: Clostridium_butyricum Genbank ID American Type Culture Collection
• 12.
  RSU: Richard Smith-Unna PMR:Peter Murray-Rust CL: CottageLabs Queues Repos Scientific literature Science Plugins Science Volunteers Collaboration with Open Access Button