BarCamb Connotea by Ian Mulvany

Getting more out of social bookmarking sites

for science

Ian Mulvany, Web Publishing, Nature Publishing Group. [email protected]

mailto:[email protected]

mailto:[email protected]

The first bookmarking site was delicious

now there are a few offerings for science, key feature is abilityto 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 rightuser tagsrelated tagsrelated 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 ontags 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 userhas 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/science2.0+citation

http://www.connotea.org/user/IanMulvany/tag/science

Example of calls to query the data, html output

http://www.connotea.org/data/user/IanMulvany/tag/science2.0+citation






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

Example of API calls

http://www.connotea.org/user/IanMulvany/tag/scifoo%0D

http://www.connotea.org/user/IanMulvany/tag/scifoo%0D









“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


Java



Java

Python



Java

Python

Perl



Java

Python

PerlRuby


sample rss output

http://mekentosj.com/

Example of interaction using the api

A. Griekspoor’s papers

http://mekentosj.com

http://mekentosj.com

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




Provides a Digg-like number next to DOI’s




Clicking on the icon allows quick adding to connotea library




Some fine-tuning required with lots of tags



http://www.itfutures.ed.ac.uk/robert_muetzelfeldt_synopsis.htm

http://apps.similette.com/multiguise/

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







MultiGuise chains these documents together to present different viewson the documents.

MultiGuise Summary View







MultiGuise model view







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 greasemonkeyto extend the suggested tags to fixed ontologies.

This is quite a new add on.










Ontological tags can be colour coded.










There are many ontologies to choose from.







Future?

what about the future?

We want to make connotea a good recommendation engine for science

TextTextText

Graph Analysis?

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

Information bottleneckCollaborative Filtering

Citation Network AnalysisPattern Burst Detection

Propagating Particle SwarmPCA

Page Rank

Does anyone have any experience with any of the following?

propogating particle swarm - rodriguez and bollen lnal 2001Information Bottleneck - Tishby, also paper by WigginsPage 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> </dcterms:URI> </uri> </Post></rdf:RDF>hyperlink

back

Sample rdf output from Connotea

http://usefulchem.blogspot.com/2007/08/first-scifoo-lives-on-session.html

http://usefulchem.blogspot.com/2007/08/first-scifoo-lives-on-session.html

Technology

BarCamb Connotea by Ian Mulvany