Pubconn

This page describes Pubconn, an open-source extension for Mozilla Firefox that integrates the functionality of Connotea within Pubmed.

Install Pubconn from here (version 2007.12.05).
You will probably need to save the xpi file first and then drag and drop it into an open Firefox window.

Please note that the current version of Pubconn does not automatically check for updates. So remember to visit this page periodically to grab the latest version of the extension.

If you are a heavy user of Pubmed, and are using Connotea to organize/share your bookmarks, and to see what sort of stuff other people are bookmarking, this extension might be helpful for you.

Different scenarios in which Pubconn might prove useful:

- When you are doing a Pubmed search, you are interested to see if other people have bookmarked any of the papers you have in your search results. Currently, you should query Connotea for each and every record returned by Pubmed. Using Pubconn, any of the Pubmed records that have been bookmarked are highlighted within your search results.

- You are doing a search in Pubmed and find an article familiar to you. Have you bookmarked this paper before? Currently, the best way to do this is to have a Connotea page open and search for the Pubmed record in your bookmarks (e.g. using PMID), or press the 'add to Connotea' button to see if you have already bookmarked that paper; the latter option is severly limited due to Buggotea . Using Pubconn, your bookmarked records in Pubmed are highlighted and the tags and descriptions you have provided for the bookmarked are displayed next to the Pubmed record.

- You are doing a literature review in a collaborative project with several other people, you have created a user group in Connotea and are bookmarking relevant papers in that group. When you start searching, you are interested in knowing whether a particular paper has already been reviewed by one of your teammates. Using Pubconn, all the bookmarks highlighted by your colleagues are highlighted.

Pubconn works in two different modes: offline and online:

Online mode: In this mode, whenever a page containing Pubmed search results is loaded, Pubconn interrogates Connotea to see if any of the Pubmed records in the page has been bookmarked in Connotea. If a record has a matched bookmark on Connotea, the information retrieved from Connotea (bookmark creator(s), tags, and descriptions) are displayed within the Pubmed record.

Offline mode: In this mode, you first download a set of bookmarks (e.g. your own bookmarks) into the memory. Pubconn is notified whenever a Pubmed search result is loaded and immediately starts finding matches between Pubmed records and stored Connotea bookmarks. Matching is performed using Pubmed Id (PMID), and optionally, it can be performed using citation data such as authors and journal name (so if you have bookmarked a paper on the nature website Pubconn should be able to find its corresponding Pubmed record).

Using Pubconn

Pubconn is an extension for Firefox, so you need to have Firefox installed on your computer. After installing the extension and restarting Firefox, you can adjust Pubconn's settings by right-clicking on Pubconn bar on the Firefox status bar and then clicking on settings. By default, Pubconn starts in the online mode.

You can communicate with Pubconn through the Pubmed search box. Pubconn adds a 'Pubconn' button on the right side of the search box. By pressing this button, the text written in the search box is processed by Pubconn (instead of being passed to Pubmed). Pubconn syntax is similar to Pubmed search queries.

Online mode

In this mode, you just use Pubmed as usual. The Pubconn panel in the statusbar shows whether any record has been matched in the search results in the Pubmed. For example, type the following search term in the Pubmed search box:

Wilkinson md

and press Enter (or the Go button). Pubconn should find 7 matches (at the time of editing this page) in the first page of the results.

*Sometimes Pubconn panel in the statusbar remains in the authentication, waiting for reply, or loading(1) for a long time (due to an error in communication with Connotea). Just repeat your Pubmed search if this happened.

By default, Pubconn searches the entire database of Connotea for any match. You can limit the scope of the online search using the SET command (see below)

Offline mode

* To set Pubconn to offline mode, right-click on the Pubconn panel and click the offline menu item.

In the offline mode, a set of bookmarks must first be loaded into the memory. In order to make this more intuituve for Pubmed users, Pubconn uses a syntax similar to Pubmed search tags. Here are a few examples:

Example 1: Suppose you want to load all the bookmarks that are tagged as 'Antigen' into the memory. Go to Pubmed main page and type in the search box:

Antigen[tag]

and press the Pubconn button. The Pubconn status bar will display the progress of downloading bookmarks from connotea. If you have not entered your Connotea user name and password in Pubconn settings, you will be asked to log-in at this point. When the communication is finished, the Pubconn status bar shows the number of bookmarks downloaded into the memory.

In the above example, the field descriptor Tag indicates that all the bookmarks tagged as Antigen should be downloaded.

Now type

list

in the searchbox and press the Pubconn button again. A list of Pubmed IDs of all bookmarks appears in the search box. Now press Enter or click on the Go button to get the list of all bookmarks in Pubmed.

Example 2: Suppose you want to load all your bookmarks that are tagged as 'Genetics' into the memory. In the search box, you should type:

genetics[tag] me

and press the Pubconn button. Again, the Pubconn status bar will display the progress of downloading bookmarks from Connotea.

The keyword me here means that the search should be performed in the user's own set of bookmarks.

Example 3: Loading all bookmarks by user shoomchool tagged as Canada:

shoomchool[user] Canada[tag]

Again, the field descriptor "user" restricts the dataset to shoomchool's bookmarks and "tag" restrics bookmarks to those which are tagged as Canada.

Example 4: Loading all bookmarks that are tagged as both genetics and bioinformatics:

genetics[tag] AND bioinformatics[tag]

or

genetics+bioinformatics[tag]

or

genetics bioinformatics[tag]

Example 5: Loading all bookmarks tagged Canada or Iran:

Iran[tag] OR Canada[tag]

Note: Combination of a user and a tag field is always AND, while combination of two user fields or two tags can be either AND or OR. No operand betweenn two search terms implies an AND search.

Search within bookmarks
You can use the keyword FIND to search for a simple string withing the stord bookmarks (currently, Pubconn does not search within the bookmarks matched for the records in the current pubmed page, but rather the search is done on the stored bookmark set. As an example, download the set of bookmarks specified in Example 1 and type the following command in the search box:

find receptor

and press the Pubconn button. The PMIDs of the matched records appears in the search box and you can see the records by pressing the Go button.

Online mode & the SET command
In the online mode, Pubconn will search the entire database of bookmarks in Connotea for Pubmed records displayed in the browser. However, by using the set command, you are able to limit the search to a specific set of bookmarks. For example, if you wand Pubconn to search only within your own set of bookmarks, you should type:

set me

and press the Pubconn button. The syntax is the same as the syntax in the offline mode, with the addition of the SET command in the beginning.

* All the functionality of Pubconn in the offline mode is also available in the online mode. Taht is, you can download and keep a set of bokmarks into memory (and use them by commands like FIND and LIST). However, in the online mode, Pubmed search results are only matched against the online bookmarks not the stored ones.

List of Pubconn field descriptors

* I do not know how to write the bracket characters in a table in this wiki page, instead parenthesis are used. It should be replaced with openning and closing brackets.

List of Pubconn commands

Technical description

offline mode
Pubconn generates a URI string for each query it receives. For example, when Pubconn is in the offline mode, the following URIs are generated and submitted to Connotea for the examples 1-4 described above:

Example 1: http://www.connotea.org/data/tag/antigen/
Example 2: http://www.connotea.org/data/user/%user%/tag/genetics/
Example 3: http://www.connotea.org/data/user/shoomchool/tag/canada/
Example 4: http://www.connotea.org/data/tag/genetics+bioinformatics/
Example 5: http://www.connotea.org/data/tag/Iran/Canada

online mode
In the online mode, the Pubconn command you use does not result in any bookmarks being downloaded and stored locally. Instead, the command acts as a filtering criterion for all subsequent bookmark matching.

Suppose your Pubmed search has returned two citations. Pubconn performs a free text search in Connotea with the search term being the PMID of the two records:

http://www.connotea.org/data/bookmarks/?q=PMID1/PMID2

If you type the following command in search box:

set asthma[tag] me

All subsequent requests to Connotea are limited to those created by you that are tagges as Asthma. for example, for the same two records above, the following URI is sent to Connotea:
http://www.connotea.org/data/bookmarks/user/%user%/tag/asthma/?q=PMID1/PMID2

Notice that unlike the iffline mode, in which posts are loaded, in the online mode, bookmarks are requested.

Pubconn and Buggotea

Pubconn is alsmost totally unaffected by Buggotea: In the offline mode, matches between Pubmed records and Connotea bookmarks are made by PMID, so the URI dies not matter at all. In the online mode, Pubconn interrogates Connotea with PMIDs of records in the page NOT BY THEIR URIs, therefore, all bookmarks associated with a Pubmed record are retrieved, regardless of their URIs.

By using the "Add to Connotea" icon that Pubconn adds to each record (instead of connotea's bookmarklet), or its equivalent item in its popupp menu (invoked by right-cliking on PubConn panel in the statusbar), a stripped, standard URI is submitted to Connotea, again a protective measure against Buggotea. In addition, if PubConn could find a match created by you for a Pubmed record, it will update this stripped URI with the URI you havce used before, so you will not create a new bookmark by clicking this icon if you have done this before, instead you will see and can edit your previous bookmark.

User feedback

Please feel free to update this section with regard to any problems or suggestions you you have about Pubcconn.

You can also email me at msafavi at interchange dot ubc dot ca