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Social BookmarkingFor Scientists
- The Best of Both Worlds
Ben LundNature Publishing Group
28th June 2006Data Webs, Imperial College, London
Overview
•Both Worlds?
•Social Bookmarking...
•...For Scientists
•Bookmarks in a web of data
http://www.connotea.org/
Both Worldshttp://www.flickr.com/photo_zoom.gne?id=62381076&size=o
http://www.w3.org/2000/Talks/1206-xml2k-tbl/sweb-stack.gif
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?
http://www.flickr.com/photo_zoom.gne?id=86643036&size=lhttp://www.thehindu.com/thehindu/mp/2005/01/31/images/2005013100010402.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).
2
3
22
1
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
URLunderstand?
no
understand?
no
understand?
yes!
Fetch information from Web
citation
URL Citation
http://www.ncbi.nlm.nih.gov/
entrez/query.fcgi?
cmd=Retrieve
&db=pubmed
&dopt=Abstract
&list_uids=13063483
&query_hl=4
&itool=pubmed_docsum
...<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>...
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
URLunderstand?
no
URL Citation
GET HTML
Containsauto-discovery link?
GET RSS/Atom document
yes!
no
parsecitation
Blog plug-in2
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)
•http://www.connotea.org/wiki/WebAPI
#!/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.newcandidates.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
http://www.connotea.org/user/robertm
