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Connotea Tools

This page is a list of tools which Connotea users have created to work with Connotea. If you have created a Connotea tool, please feel free to post it here so that other users can find it. You might also like to post a message to the Connotea discussion list to tell other users about it and get feedback from them. If you would like to create your own tools, but need help or inspiration, please also feel free to post to the discussion list to talk about your ideas.

XML

Created by User:robertm

* MultiGuise is an application for applying an XSLT stylesheet to an XML document. To support this, MultiGuise has a higher-level concept of a 'package', where one package references a compatible set of XML documents and XSLT stylesheets. Each package is itself an XML document, which can be bookmarked in Connotea. When MultiGuise starts up, it automatically goes to Connotea to pull out the titles for all bookmarked packages. Thus, new packages can be added by anyone, from any field, just as documents and stylesheets can be added.

A package is tagged with multiguise_package

The purpose of MultiGuise is primarily to allow the sharing and viewing of systems biology models.
More information can be found here

Greasemonkey

Most of the tools below require Firefox and the Greasemonkey extension. Unfortunately there is no Greasemonkey equivalent for Internet Explorer.

Contributed tools

Created by User:baoilleach?

Add to Connotea, a Greasemonkey script using the API, which allows you to to easily bookmark a paper on Connotea by adding a Connotea logo next to every DOI. A useful feature is the ability to quickly select from tags that you have already used. The "Add to Connotea" script also displays a count of the number of people who have already bookmarked a particular paper. If you click on this number, it will bring you to the Connotea page for that paper from where you can travel to related papers. See this post on baoilleach's blog for more details.

Created by User:lindenb

Connotea Client: An alternative way of bookmarking PubMed articles in Connotea. You can search PubMed from within the application, and can easily use MeSH terms or words from an article abstract as tags.
Connotea Explorer: Helps you visualise and explore the contents of Connotea using a treemap algorithm. It allows you to navigate through the articles and links in the database using the tags that have been applied to them. This java tool was later transformed into a dynamic javascript page available at http://www.urbigene.com/cx2/connotea.xhtml.
PubMed2Connotea: A Greasemonkey script for Firefox which works with PubMed, and inserts "Add to Connotea" links next to articles in the search results page. Also works with Opera.
Connotea Search within Firefox: Allows Firefox users to search Connotea directly from the browser's toolbar
AnnoConnotea. AnnoConnotea? acts as a bridge between Connotea (used as an Annotea Server) and Annozilla allowing scientist to see and share comments about a web site/a paper. It can also be used to send a new bookmark to Connotea.
A GreaseMonkey Script to Display SVG TreeMaps of Tags Greasemonkey user script which alters the content of the web page when browsing connotea by inserting a treemap of the current tags using SVG.

Created by User:shoomchool

PubConn: Doing a search in PubMed and interesting to know if any of the search results has been bookmarked in Connotea? Pubconn is a Firefox extension that integrates the functionality of Connotea within Pubmed.

Created by User:petahopkins

Two plugins created by User:petahopkins are available from mozdev.org - mycroft.

From hubmed

This greasemonkey script adds links from connotea.org/tag/whatever to del.icio.us/tag/whatever.
http://hublog.hubmed.org/archives/001373.html A TouchGraph? applet of the items and tags in a user's Connotea library.
A greasemonkey script to copy your recent Del.icio.us bookmarks to Connotea.

Created by User:euanadie

Greasemonkey script to add comment icons next to papers that have been discussed by science bloggers.
Basic Word integration - as long as you're using Office 2007
Add five star ratings to your bookmarks with another Greasemonkey script.
Form to copy your last 100 delicious bookmarks to Connotea.

Created by User:ben

Ruby script to copy your Connotea bookmarks into Del.icio.us

Created by User:kokstitan?

Perl script to copy your Del.icio.us bookmarks to Connotea.

Created by User:scilib

A Feedflare Unit, for adding a bookmark to Connotea. (FeedFlare is an add-in technology from Feedburner, that is now also supported in Typepad.) You can use the XML file for the unit itself, my posting about it is Science Library Pad: Connotea FeedFlare Unit.

Created by User:morgan

Connotea Advanced Search is a simple web form that can perform advanced searches on Connotea bookmarks.

Created by User:astraw

connoshow is a WordPress plugin to show a Connotea bookmark's title and create links to it in the content of a blog entry.

Created by User:bgood

ED, the EntityDescriber comprises two Greasemonkey scripts that facilitate the use of terms from existing controlled vocabularies as your tags. Use MeSH, the gene ontology or any other public, shared vocabulary to improve the organization of your tag collection. Take advantage of the hierarchical structure of these resources when interacting with your library. Contribute to the semantic web.

Created by User:egonwillighagen

Molecule tagging. If you tag the rdf pages of molecules from the open molecules web page then the tags you use for the page will now appear on the page. Egon has more information at his blog. The current syntax seems to follow this structure: http://rdf.openmolecules.net/?info:inchi/InChI=1/CH4/h1H.

Created by User:Stervbo?

Mozilla Connotea Info Protocol Handler is an extension for Firefox, which registers 'info:' as a protocol in Firefox and allows for opening the info:pmid/ or info:doi/ in a new tab or window. The extension is based on Mark Donoghue's Mozilla Handle/DOI Protocol Handler