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

Both Worlds

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

Both Worlds? jpg

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

Connotea is a social bookmarking tool

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

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

Searching

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

Bookmarks in a web of data

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

entrez/query.fcgi? cmd=Retrieve &db=pubmed &dopt=Abstract &list_uids= &query_hl=4 &itool=pubmedhttp:// entrez/query.fcgi? cmd=Retrieve &db=pubmed &dopt=Abstract &list_uids= &query_hl=4 &itool=pubmed_docsum

... Genetical implications of the structure of deoxyribonucleic acid WATSON J D CRICK F H...

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

Database Plug-ins Universal Application URL understand? no URLCitation GET HTML Contains auto-discovery link? GET RSS/Atom document yes! no parsecitation

Blog plug-in 2 3 1

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

Data out: RSS

Data out (and in): RIS

Remixing: Web API Write programs to post, edit, annotate, search, retrieve links RESTful RDF (DC, PRISM, FOAF)

#!/usr/bin/ruby require '../lib/www/connotea' require 'digest/md5' USER = 'username' PASSWORD = 'password' article_url = ' url_hash = Digest::MD5.hexdigest(article_url) c = WWW::Connotea.new(:user => USER, :password => PASSWORD, :base => ' :realm => 'Connotea') c.authenticateate tags = c.tags_for(:htags = 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

Future Bookmarks are just annotated URLs Connotea = Article URLs + bibliographic data schema + tagging Evolves into? Data URLs + semantic tagging = emergent schemata

More Thanks!