Getting more out of
social bookmarking sites
for science
Ian Mulvany, Web Publishing, Nature Publishing Group. i.mulvany@nature.com

The first bookmarking site was delicious
now there are a few oerings for science, key feature is ability
to import citation metadata.
Connotea was inspired by this,
some design decision, such as using the uri as the main key in the db, were influenced by this
has led to some problems
buggotea
inability to import citations without uri,
but we are working on these fixes
citeulike has about the same beginnings
bibsonomy is from bielefield in germany and is a research project
elsevier has just joined in for fun with 2collab

The first bookmarking site was delicious
now there are a few oerings for science, key feature is ability
to import citation metadata.
Connotea was inspired by this,
some design decision, such as using the uri as the main key in the db, were influenced by this
has led to some problems
buggotea
inability to import citations without uri,
but we are working on these fixes
citeulike has about the same beginnings
bibsonomy is from bielefield in germany and is a research project
elsevier has just joined in for fun with 2collab

The first bookmarking site was delicious
now there are a few oerings for science, key feature is ability
to import citation metadata.
Connotea was inspired by this,
some design decision, such as using the uri as the main key in the db, were influenced by this
has led to some problems
buggotea
inability to import citations without uri,
but we are working on these fixes
citeulike has about the same beginnings
bibsonomy is from bielefield in germany and is a research project
elsevier has just joined in for fun with 2collab

The first bookmarking site was delicious
now there are a few oerings for science, key feature is ability
to import citation metadata.
Connotea was inspired by this,
some design decision, such as using the uri as the main key in the db, were influenced by this
has led to some problems
buggotea
inability to import citations without uri,
but we are working on these fixes
citeulike has about the same beginnings
bibsonomy is from bielefield in germany and is a research project
elsevier has just joined in for fun with 2collab

The first bookmarking site was delicious
now there are a few oerings for science, key feature is ability
to import citation metadata.
Connotea was inspired by this,
some design decision, such as using the uri as the main key in the db, were influenced by this
has led to some problems
buggotea
inability to import citations without uri,
but we are working on these fixes
citeulike has about the same beginnings
bibsonomy is from bielefield in germany and is a research project
elsevier has just joined in for fun with 2collab

The first bookmarking site was delicious
now there are a few oerings for science, key feature is ability
to import citation metadata.
Connotea was inspired by this,
some design decision, such as using the uri as the main key in the db, were influenced by this
has led to some problems
buggotea
inability to import citations without uri,
but we are working on these fixes
citeulike has about the same beginnings
bibsonomy is from bielefield in germany and is a research project
elsevier has just joined in for fun with 2collab

Connotea front page, blog, community pages.

user home page,
toolbox, on right
user tags
related tags
related users, groups

Getting data into Connotea
There is a bookmarklet for any browser which is javascript
On a page from pubmed authors and pmid highlighted are captured by connotea, and
added by the connotea bookmarklet

Getting data in, part 2
The meta-data from the paper has been captured
When you begin to add tags suggested tags are presented based on
tags you have already used
paper by Huberman et all shows that displaying all tags drives tag-onomies to stable state (Polya-
Renyi urn model)
You need to display the full community tags, which we don’t do ... yet.

Getitng data out
Open Data, important
Export only gets out the citation data, and not extra meta data that the user
has added such as comments or tags.
Formats: txt, rdf, BibTex,RIS,EndNote an api??

RDF HTML
RSS XML
More generally there are 4 types of interglue at work
We provide an API
1 rss: nature clinical practice articles via rss -> connotea
2 rdf: e.g. Entity Describer
3 plain html: add to connotea script and other greasemonkey scripts
4 xml: MultiGuise

http://www.connotea.org/user/IanMulvany
http://www.connotea.org/users/tag/scifoo
http://www.connotea.org/user/IanMulvany/tag/scifoo
http://www.connotea.org/user/IanMulvany/tag/science
http://www.connotea.org/user/IanMulvany/tag/
science2.0+citation
Example of calls to query the data, html output

http://www.connotea.org/data/user/IanMulvany
http://www.connotea.org/data/users/tag/scifoo
http://www.connotea.org/data/user/IanMulvany/tag/
scifoo
http://www.connotea.org/data/user/IanMulvany/tag/
science
http://www.connotea.org/data/user/IanMulvany/tag/
science2.0+citation
Example of API calls

“After you make an API, the first thing people want to do is
write a wrapper in their favorite language”
API now has 4 wrapper libraries

“After you make an API, the first thing people want to do is
write a wrapper in their favorite language”
Java
API now has 4 wrapper libraries

“After you make an API, the first thing people want to do is
write a wrapper in their favorite language”
Java
Python
API now has 4 wrapper libraries

“After you make an API, the first thing people want to do is
write a wrapper in their favorite language”
Java
Python
Perl
API now has 4 wrapper libraries

“After you make an API, the first thing people want to do is
write a wrapper in their favorite language”
Java
Python
Ruby
Perl
API now has 4 wrapper libraries

sample rss output

http://mekentosj.com/
Example of interaction using the api
A. Griekspoor’s papers

http://baoilleach.blogspot.com/2007/06/add-to-connotea-from-journal-pages.html
Another sample using the api
Many tools can be seen at http://www.connotea.org/wiki/ConnoteaTools

http://baoilleach.blogspot.com/2007/06/add-to-connotea-from-journal-pages.html
Provides a Digg-like number next to DOI’s

http://baoilleach.blogspot.com/2007/06/add-to-connotea-from-journal-pages.html
Clicking on the icon allows quick adding to connotea library

http://baoilleach.blogspot.com/2007/06/add-to-connotea-from-journal-pages.html
Some fine-tuning required with lots of tags

http://apps.similette.com/multiguise/
http://www.itfutures.ed.ac.uk/robert_muetzelfeldt_synopsis.htm
Robert Muetzelfeldt has produced an interesting use for connotea
This sort of use is a good example of how people may adapt an open system
XML as a backbone
Connotea links XML documents across the web

http://apps.similette.com/multiguise/
http://www.itfutures.ed.ac.uk/robert_muetzelfeldt_synopsis.htm
MultiGuise chains these documents together to present dierent views
on the documents.
MultiGuise Summary View

http://apps.similette.com/multiguise/
http://www.itfutures.ed.ac.uk/robert_muetzelfeldt_synopsis.htm
MultiGuise model view

http://apps.similette.com/multiguise/
http://www.itfutures.ed.ac.uk/robert_muetzelfeldt_synopsis.htm
MultiGuise Graph Simulator view
You can create any view you like, and make it available to MultiGuise by
bookmarking the XML document appropriately in Connotea.

http://www.connotea.org/wiki/User:MrED
http://www.connotea.org/wiki/EntityDescriber
http://i9606.blogspot.com/2007/08/connotea-semantic-web-ed.html
Another example of a tool built on top of Connotea
The Entity describer uses the RDF output and greasemonkey
to extend the suggested tags to fixed ontologies.
This is quite a new add on.

http://www.connotea.org/wiki/User:MrED
http://www.connotea.org/wiki/EntityDescriber
http://i9606.blogspot.com/2007/08/connotea-semantic-web-ed.html
Ontological tags can be colour coded.

http://www.connotea.org/wiki/User:MrED
http://www.connotea.org/wiki/EntityDescriber
http://i9606.blogspot.com/2007/08/connotea-semantic-web-ed.html
There are many ontologies to choose from.

Future?
what about the future?
We want to make connotea a good recommendation engine for science

Graph Analysis?
Text
Text
Text
Connotea is a graph.
It should be possible to use this property to do collaborative filtering

Citation Analysis?
Eigenfactor.org use the graph properties of the references to try to provide
better analysis of the weighting of citations.
Add in reading lists from connotea and one could begin to provide
tailored paper reccomendations

The End!

Other Topics
✦ Tagging tool
✦ groups
✦ hub med, post genomic
✦ nature network
✦ document recommendation
✦ open source
✦ offline-online
✦ synchronizing citations
✦ better everything

Does anyone have any experience with any of the following?
Information bottleneck
Collaborative Filtering
Citation Network Analysis
Pattern Burst Detection
Propagating Particle Swarm
PCA
Page Rank
propogating particle swarm - rodriguez and bollen lnal 2001
Information Bottleneck - Tishby, also paper by Wiggins
Page Reank, Folk Rank paper by Gerd Stumme

That’s really the End!

<?xml version=\"1.0\"?>
<rdf:RDF
xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"
xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\"
xmlns:dc=\"http://purl.org/dc/elements/1.1/\"
xmlns:dcterms=\"http://purl.org/dc/terms/\"
xmlns:prism=\"http://prismstandard.org/namespaces/1.2/basic/\"
xmlns:foaf=\"http://xmlns.com/foaf/0.1/\"
xmlns=\"http://www.connotea.org/2005/01/schema#\">
<Post rdf:about=\"http://www.connotea.org/user/IanMulvany/uri/
1f079ccb3687202fdaa517d5245b5588\">
<title>First SciFoo Lives On Session</title>
<dc:subject>secondlife</dc:subject>
<dc:subject>scifoo</dc:subject>
<userBookmarkID>576893</userBookmarkID>
<dc:creator>IanMulvany</dc:creator>
<private>0</private>
<created>2007-08-21T15:46:38Z</created>
<updated>2007-08-21T15:46:38Z</updated>
<uri>
<dcterms:URI rdf:about=\"http://usefulchem.blogspot.com/2007/08/first-scifoo-lives-on-
session.html\">
<dc:title>Useful Chemistry: First SciFoo Lives On Session</dc:title>
<link>http://usefulchem.blogspot.com/2007/08/first-scifoo-lives-on-session.html</link>
<hash>1f079ccb3687202fdaa517d5245b5588</hash>
<citation>
<rdf:Description>
<citationID>582573</citationID>
<prism:title>First SciFoo Lives On Session</prism:title>
<foaf:maker>
<foaf:Person>
<foaf:name>Jean-Claude Bradley</foaf:name>
</foaf:Person>
</foaf:maker>
<dc:date>2007-08-20T00:00:00Z</dc:date>
<journalID>546903</journalID>
<prism:publicationName>Useful Chemistry</prism:publicationName>
</rdf:Description>
</citation>
back
</dcterms:URI>
</uri>
</Post>
</rdf:RDF>hyperlink
Sample rdf output from Connotea