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Social Bookmarking For Scientists - The Best of Both Worlds

Social Bookmarking For Scientists - The Best of Both Worlds. Ben Lund Nature Publishing Group 28th June 2006 Data Webs, Imperial College, London. Overview. Both Worlds? Social Bookmarking... ...For Scientists Bookmarks in a web of data. http://www.connotea.org /. Both Worlds.

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Social Bookmarking For Scientists - The Best of Both Worlds

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  1. Social BookmarkingFor Scientists- The Best of Both Worlds • Ben Lund • Nature Publishing Group28th June 2006 • Data Webs, Imperial College, London

  2. Overview • Both Worlds? • Social Bookmarking... • ...For Scientists • Bookmarks in a web of data http://www.connotea.org/

  3. Both Worlds http://www.flickr.com/photo_zoom.gne?id=62381076&size=o http://www.w3.org/2000/Talks/1206-xml2k-tbl/sweb-stack.gif

  4. Web 2.0 Concepts • Social • Shared, open collections , browsable, linkable • Participative • Massively multi-user , Web-based applications • Emergent properties • Tagging • Organise /categorise with keywords • Flat, non-hierarchical, uncontrolled vocabulary

  5. Both Worlds? http://www.thehindu.com/thehindu/mp/2005/01/31/images/2005013100010402.jpg http://www.flickr.com/photo_zoom.gne?id=86643036&size=l

  6. There is no conflict • Different approaches for different problems • Who has an ontology for their documents and folders?

  7. Connotea is a social bookmarking tool

  8. Why for scientists? • Concentrate commonality of interest=> Enhance discovery benefits • Hook into academic publishing technologies=> Additional features

  9. Article Identification Genetical Implications of the Structure of Deoxyribonucleic AcidWatson, J. D., and Crick, F. H. C.Nature, 171, 964–967 (1953).

  10. 2 1 3 2 2

  11. Searching

  12. Linking DOI link to publisher’s copy OpenURL link to library holdings

  13. Bookmarks in a web of data

  14. Application Plug-ins Nature understand? URL no Fetch information from Web Highwire understand? no PubMed understand? yes! citation Database URL Citation

  15. http://www.ncbi.nlm.nih.gov/ entrez/query.fcgi? cmd=Retrieve &db=pubmed &dopt=Abstract &list_uids=13063483 &query_hl=4 &itool=pubmed_docsum

  16. ... <ArticleTitle>Genetical implications of the structure of deoxyribonucleic acid.</ArticleTitle> <Pagination> <MedlinePgn>964-7</MedlinePgn> </Pagination> <AuthorList CompleteYN="Y"> <Author ValidYN="Y"> <LastName>WATSON</LastName> <ForeName>J D</ForeName> <Initials>JD</Initials> </Author> <Author ValidYN="Y"> <LastName>CRICK</LastName> <ForeName>F H</ForeName> <Initials>FH</Initials> </Author> </AuthorList> ...

  17. Data in: Autodiscovery • Currently: Dedicated plugins for online archives and publisher websites • Variety of formats and protocols • Ad-hoc, case by case, reverse-engineered • Future: Needs to scale better • Autodiscovery of metadata

  18. Application Plug-ins Universal understand? URL GET HTML Containsauto-discovery link? no no yes! GET RSS/Atom document citation parse Database URL Citation

  19. Blog plug-in 2 1 3

  20. Autodiscovery (2) • Web feeds - RSS, Atom • Dedicated metadata files - RIS, OTMI • Embedded RDF - XML, eRDF, RDF/A • Citation microformat

  21. Data out: RSS

  22. Data out (and in): RIS

  23. Remixing: Web API • Write programs to post, edit, annotate, search, retrieve links • RESTful • RDF (DC, PRISM, FOAF) • http://www.connotea.org/wiki/WebAPI

  24. #!/usr/bin/ruby require '../lib/www/connotea' require 'digest/md5' USER = 'username' PASSWORD = 'password' article_url = 'http://www.medicalnewstoday.com/healthnews.php?newsid=39046'; url_hash = Digest::MD5.hexdigest(article_url) c = WWW::Connotea.new(:user => USER, :password => PASSWORD, :base => 'http://www.connotea.org/', :realm => 'Connotea') c.authenticate tags = c.tags_for(:hash => url_hash).map! { |t| t.label } raise "No tags" unless tags.size > 0 candidates = c.bookmarks_for(:num => 100, :tag => tags.join('/')) raise "No candidate related articles\n" unless candidates.size > 0 scores = Hash.new candidates.each do |candidate| next if candidate.link == article_url score = 0; candidate.tags.each do |t| score += 1 if tags.include?(t) end scores[candidate.link] = {:tag_score => score, :popularity => candidate.posted_by_count, :title => candidate.title} end scores.keys.sort{ |a,b| scores[b][:tag_score] <=> scores[a][:tag_score] || scores[b][:popularity] <=> scores[a][:popularity] }[0..9].each do |link| puts scores[link][:title] puts link + ' (' + scores[link][:tag_score].to_s + ' | '+ scores[link][:popularity].to_s + ')' puts '' end

  25. Future • Bookmarks are just annotated URLs • Connotea = Article URLs + bibliographic data schema + tagging • Evolves into? Data URLs + semantic tagging = emergent schemata http://www.connotea.org/user/robertm

  26. More • http://www.connotea.org/ • b.lund@nature.com • http://blogs.nature.com/wp/nascent/ Thanks!

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