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

More

•http://www.connotea.org/

•b.lund@nature.com

•http://blogs.nature.com/wp/nascent/

Thanks!