DeprecatedEntityDescriber

Here is some information about the first version of the EntityDescriber, released circa August, 2007. For information on the current version (circa Spring 2008), please see the new project website or the EntityDescriber wiki page. A manuscript describing this project is available on Nature Precedings.

These installation instructions may or may not work. Although we'd suggest using the new version, you are welcome to try these user scripts out or take them and modify them for your own purposes. If you would like to keep using these as they are, please contact me and I will try to accommodate you (or convince you to start using the new one).

Installing E.D. - 1) Get Firefox . 2) Install GreaseMonkey 3) Install the E.D. scripts: for adding tags and for browsing your tag library.

Using E.D. when adding a bookmark (this may still work)

1. Install it as above
2. Press your "Add To Connotea" button on your browser.
3. Press the "Add Vocab" link on the left
4. Select an ontology from the list to see how it works
5. Pick a color for it. This is the color the terms from the ontology will appear in your type-ahead. You can change it later.
6. Press the "Add Controlled Vocabulary" button on the bottom
7. Click in the Tags input area and start typing. The type-ahead will scan through the terms in all of the vocabularies that you have selected.
8. Select some terms and press the "Add to my library" button as usual

This second script will definitely not work anymore, if you would like it to, please contact me

Using E.D. when browsing a Connotea user's library

1. Make sure you have the browse script installed.
2. Navigate to the library page of a user that has added some tags with E.D. See MrED for example.
3. If you can't find anyone, add some tags of your own as above and go to your own library page.
4. You will see what will hopefully be a self-explanatory dark blue box labeled "Filter by Vocab" appear on the left of the screen underneath the little box that provides the type-ahead interface into the tag's used in the library. As it suggests, you can filter the tag list by vocabulary.
5. You may notice the little "Expand" check box at the bottom of the blue box. When that is checked, two things are happening:
• The tag list is populated by the tags in the selected vocab as well as terms that are broader than them.
• When you click on one of the terms, the request to connotea includes the union of all of the narrower terms than the one you clicked on.

This means that if you tagged something with 'neo-cortex' from MeSH, filtered by MeSH, and turned expand on, you would see tags like 'brain' even if you never typed them. When you clicked on them, you would get to the posts that used the narrower term - in this case, neo-cortex.

What was E.D. doing?

• When you added a bookmark with E.D. installed, your bookmark is posted to Connotea as usual. All the tags from your vocabularies and from the tags you type go into the Connotea database as normal tags.
• In addition, if the 'keep private' box was not checked, the tagging event is stored on our database (Jena, RDF, accessible via Joseki endpoint listed below). Otherwise, ED doesn't store anything. Thus, you could use ED to organize a private list by using its access to a particular set of vocabularies without having the contents of the list in the public domain. We do hope however, that you choose to keep most of your bookmarks public.
• This is a public resource. The data that goes into ED is shared just like the public data on Connotea.

It lets us:

• see how people like ED
• provide users access to "semantic queries" like the brain example above (in development)

Please feel free to edit this page with your thoughts on and experiences with ED.

ED is a product of Eddie Kawas and Benjamin Good of the Wilkinson Laboratory