BarCamb Connotea by Ian Mulvany

Slide 1: Getting more out of social bookmarking sites for science Ian Mulvany, Web Publishing, Nature Publishing Group. i.mulvany@nature.com

Slide 2: 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

Slide 3: 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

Slide 4: 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

Slide 5: 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

Slide 6: 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

Slide 7: 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

Slide 8: Connotea front page, blog, community pages.

Slide 9: user home page, toolbox, on right user tags related tags related users, groups

Slide 10: 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

Slide 11: 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.

Slide 12: 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??

Slide 13: 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

Slide 14: 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

Slide 15: 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

Slide 16: “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

Slide 17: “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

Slide 18: “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

Slide 19: “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

Slide 20: “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

Slide 21: sample rss output

Slide 22: http://mekentosj.com/ Example of interaction using the api A. Griekspoor’s papers

Slide 23: 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

Slide 24: http://baoilleach.blogspot.com/2007/06/add-to-connotea-from-journal-pages.html Provides a Digg-like number next to DOI’s

Slide 25: http://baoilleach.blogspot.com/2007/06/add-to-connotea-from-journal-pages.html Clicking on the icon allows quick adding to connotea library

Slide 26: http://baoilleach.blogspot.com/2007/06/add-to-connotea-from-journal-pages.html Some fine-tuning required with lots of tags

Slide 27: 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

Slide 28: 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

Slide 29: http://apps.similette.com/multiguise/ http://www.itfutures.ed.ac.uk/robert_muetzelfeldt_synopsis.htm MultiGuise model view

Slide 30: 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.

Slide 31: 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.

Slide 32: 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.

Slide 33: 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.

Slide 34: Future? what about the future? We want to make connotea a good recommendation engine for science

Slide 35: Graph Analysis? Text Text Text Connotea is a graph. It should be possible to use this property to do collaborative filtering

Slide 36: 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

Slide 37: The End!

Slide 38: Other Topics ✦ Tagging tool ✦ groups ✦ hub med, post genomic ✦ nature network ✦ document recommendation ✦ open source ✦ offline-online ✦ synchronizing citations ✦ better everything

Slide 39: 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

Slide 40: That’s really the End!

Slide 41: <?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