DefiningImageAccess/Tool/Connotea
From ImageWeb
| DefiningImageAccess/Tool/Connotea | |
|---|---|
| Link:=http://www.connotea.org/}} | |
| Status:=Active}} | |
| JISCTool:=False}} | |
| Focus:=Metadata creation and Annotation}} | |
| [[Publishes::{{{Publishes}}}]]}} | |
| [[Uses::{{{Uses}}}]]}} | |
| RelatedTo::DefiningImageAccess/Tool/TaggingTool}} | |
| [[Partner::{{{Partner}}}]]}} | |
| [[Contact::{{{Contact}}}]]}} | |
| Defining Image Access | DefiningImageAccess/RelatedWork |
Connotea
Free online reference management for all researchers, clinicians and scientists
- http://www.connotea.org/
- http://blogs.nature.com/wp/nascent/2006/10/connotea_is_a_database_1.html - not only a bookmark list - can also be used as a database.
Developed by Nature Publishing Group, and inspired by social bookmarking sites such as del.icio.us and flickr. Browse web for paper, then click bookmarklet in browser. Connotea harvests URL and passes it to the citation module, which harvests PUBMED ID, title, etc.
Connotea allows users to tag freely. Tags are public-facing by default, but can be made private or embargoed (e.g. for journalists researching stories). Connotea can be used to supplement or replace a conventional desktop bibliographic information manager (e.g. Endnote).
Connotea tags are the primary means of navigating boookmarked sites - all bookmarks must have at least one tag. Some tag names are reserved. Machine tags can be used, distinguished by namespace prefixes, e.g. geo:lat=2, geo:long=y (not a standard, but stolen from Flickr), as used in Declan Butler's mashup of Avian flu papers with Google earth (http://declanbutler.info/blog/?p=58; http://www.nature.com/nature/journal/v439/n7072/full/439006a.html).
Similar systems: CiteULike, Bibsonomy, FURL etc. These are not designed for academic use. The following text taken from e-mail on this subject from Euan Adie to David Shotton, 29th January 2007:
"Connotea is open source (but run commercially, at the end of the day – we’ve tried bringing ads in, for example). One of the ideas behind being open source is that if NPG ever decides to stop supporting Connotea, the codebase and data can all be transferred elsewhere. Bibsonomy isn’t open source. Possibly the biggest single difference - Connotea has an API to allow 3rd party applications read/write access to tags & bookmarks – this is how the Eprints integration and various Greasemonkey plugins work. Bibsonomy doesn’t. Connotea has a small but active group of people using the API in cool ways – there are PubMed mashups, library visualizations etc. Connotea uses citation modules that, given an URL, return a citation. The user doesn’t need to look around for the ‘save to citation manager’ link or similar. To add citations to Bibsonomy, you need to find the relevant BibTeX (in most cases, I think that they’re now bringing in scrapers/citation modules too). Groups and friends features are better on Bibsonomy (Connotea is currently lacking in this regard)."
Has human readable/hackable URLs: e.g. connotea.org/tag/bioinformatics, connotea.org/user/euanadie, etc. REST-based API, returns XML, open to all users. Full site functionality exposed via API. Can view, add, remove one's own posts, and can view posts by others.
Robert Muetzelfeldt's MultiGuise: Stores environmental models in XML, and output styles in which these are to be displayed (tables, code, etc.) in XSLT. Retrieves data from Connotea, splits into models and style sheets, then use style sheet to apply to document and get display for user. Advantages: all data storage is on Connotea, which also undertakes functions of user authentication and spam filtering.
Notes based on meeting notes: Meetings/20070209/DefiningImageAccess-ToolsAndTechnologies#Connotea_as_a_database
Software evaluation
An experiment is performed by using the "Piglet Squid" images from the Serpent project. These images are used as they were provided with rich, domain-specific metadata on the Serpent project web site.
The experiment annotates 5 piglet squid images using Connotea:
- http://serpent.eprints.org/281/
- http://serpent.eprints.org/282/
- http://serpent.eprints.org/283/
- http://serpent.eprints.org/284/
- http://serpent.eprints.org/285/
The metadata are archived in a local XSL file.
By using Connotea, each image is annotated in terms of its:
- Classification
- Site
- Countries
- Deposited By
For the classification information, several terms at different levels of the classification hierarchy are used as the tags. For example, both "Mollusca" and "Cranchiidae" (a kind of Mollusca) are used to annotate each image.
The result of this simple experiment shows that:
- it is very quick and easy to use Connotea to annotate the Web pages publishing these images and then browse them by the tags;
- through the Connotea Web interface, external data sources (e.g. publications) can be discovered and linked with our image metadata. For example, publications about Mollusca are also linked with the squid images. This brings a mash-up between Image Web and Publication Web.
Todo:
- experiment with mashing up the biological metadata about the squids with other biological data sources. Need to consult David for this.
- experiment with mashing up the geographic metadata with Google Earth or Frappr.
Experiment with Hui Hua's annotations
Using Connotea's Web API:
- get all the tags used by Hui: http://www.connotea.org/data/tags/user/huihua
- get all the posts(bookmarks events) created by Hui: http://www.connotea.org/data/user/huihua
- get all the bookmarks created by Hui: http://www.connotea.org/data/bookmarks/user/huihua
This returns raw RDF/XML metadata about HuiHua's annotations. They should be able to be imported into Jena using the model loader.
