G language Bookmarklet

G-language Bookmarklet

Overview

G-language Bookmarklet is a visual gateway to numerous biological resources, implemented as an interactive ring menu. Call up the bookmarklet from any web page after selecting a keyword of interest from the web page.

Since it is more easily to see an actual example, click on the following link. Then bookmark the following link to open it up on any web page.

Bookmark this or this one (without audio) or this one (open new window)

Use Safari 4, Firefox 3.5 or above for full functionality.

Controls

• Invoking the ring: click on the bookmarklet from your browser. Highlight a text within the web page before invoking the ring to use the word for querying. Otherwise a prompt window comes up, where you can type in the query keyword.
• Rotating the ring: use mouse scroll wheels, LEFT/RIGHT keys, or two-finger rotation gesture on iPad/iPhone.
• Selecting an item: click on an icon to select, and click again to open up, or press ENTER.
• Reverting the ring: press UP key, or pinch-in gesture on iPad/iPhone.
• Freeing the ring: move the mouse cursor away, press ESCAPE, right click, or pinch-out gesture on iPad/iPhone.

Ring contents

From the top icon in clockwise order, the icons represent the following:

• Wikipedia: search Wikipedia (English) with the given keyword. (jumps immediately to Wikipedia site)
• Eijiro: search Eijiro (Japanese-English dictionary) with the given keyword. (jumps immediately to Eijiro site)
• Google: search Google with the given keyword. (jumps immediately to Google site)
• PubMed: search PubMed with the given keyword. (jumps immediately to PubMed site)
• NCBI: search NCBI Entrez with the given keyword. You can select the database in the second-level ring.
• Genome Net/KEGG: search KEGG with given keyword. Second-level ring will come up showing results of search in KEGG, and with the third-level ring, you can find entries linked to the selected entry in KEGG.
• EMBL - EB-eye: search EMBL databases through EB-eye search engine with given keyword. You can select the database in the second-level ring.
• Bio2RDF: search bio2rdf with the given keyword. It queries with SPARQL in the background, showing you the available predicates in the second-level ring.
• Reflect.ws: sends the current web page to reflect.ws for the text mining and annotation of biological terms. Reflect.ws highlights the biological terms within a web page, and the highlighted terms are clickable for further information retrieval.
• G-language REST Services: select an analysis function in the G-language REST Service, first by selecting the analysis category from the second-level ring, and then selecting the analysis function that you would like to execute.
• EMBOSS REST Services: select a program in EMBOSS REST Service, first by selecting the analysis category from the second-level ring, and then selecting the program that you would like to execute. This service also includes 40 tools from Keio Bioinformatics Web Services.
• BLAST Search: you can select amino acid or nucleotide sequence to start with, which will automatically run BLAST search against Swissprot database on the first hand.

Customized Ring Generator

You can also create your own customized and personalized ring using this tool. http://www.g-language.org/cube/generator/

Simply change the URLs and descriptions to suit your needs and to change the icons, drag&drop to reorder the list, and add or delete the ring items. You can choose from a collection of ring items to include in your own personalized ring.

Shortcut

In Safari, bookmarks placed on the bookmark-bar can be opened using Command + number. So if you place the G-language Bookmarklet to be the left-most bookmark on the bookmark bar, you can press Command + 1 to invoke the ring anytime.

Alternatively, in MacOS X, you can assign keyboard shortcuts from the "Keyboard" preferences panel in the System Preferences. Here you can set your own key combination to load a bookmark.

Supported Browsers

G-language Bookmarklet utilizes several features of HTML5 (round-rect elements, drop-shadow effects, and Audio() class). In order to use full functionality, use Firefox 3.5 or above, or Safari 4 or above.

Chrome works ok but without the sound effects (Chrome does not have codec for WAV files).

Internet Explorer has poor support for correct HTML/Javascript/CSS, and does not support HTML5 audio. We have no plans to support/test on IE, but G-language Bookmarklet should basically work.

Known Issues

• G-language Bookmarklet fails to load on pages using frames.

History

• 2010.12.22 version 0.7 Custom Ring Generator, direct link to search results page for Entrez search
• 2010.11.08 version 0.6 release (new window support, ring items for Mashup Awards 6th)
• 2010.07.05 Reflect.ws support
• 2010.02.12 First public release

License

G-language Bookmarklet is provided under the MIT License.

Development Philosophy and To Dos

You can find these information at the BioHackathon2010 site.

Acknowledgements

The basic idea of ring menu comes from the "Ring Command" interface of the game "Secrets of Mana" (聖剣伝説2 by SQUARE ENIX CO. LTD.

Basic javascript implementation of the Ring Command is adopted from the NavigationRing.

Sound for the Ring Command is taken from SKLaunch.