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Contact us cbioc@asu.edu

News:

Aug 23, 2007:
New version 2.3.1 of IE plug-in solves problem of PMID not loading. PubMed changes to its URL caused it.

Jul 17, 2007:
All interactions from IntAct are now integrated into CBioC.

June 23, 2006:
See "Annotate While You Read" in Science Magazine's NetWatch.

June 1, 2006:
New feature: display facts from multiple PMIDs by entering a comma-separated list in the search box.

In Brief

CBioC (Beta) allows extraction and collaboration for data curation.

After install, loads when you visit PubMed.

Gets interactions from PubMed abstracts.

Allows you to vote and modify extracted data.

Also shows data from BIND, DIP, MINT, GRID, IntAct.

Links:

- BioAI Group
- CSE Dep.
- ASU
- PubMed

Functionality

CBioC presents a new approach to the curation problem using mass collaboration, allowing the community of researchers that writes and reads the biomedical texts to contribute to the curation process on a voluntary basis.

Researchers can correct information that is automatically extracted from the biomedical texts, vote on the accuracy of the extraction and rate the reliability of the extracted facts based on the evidence presented by the author.

We present here an overview of the different functions available in CBioC. You can click on the images to see it full size.

Running CBioC

CBioC runs as a web browser extension, not as a stand-alone application. This means it will only run within your browser when the browser is active.

When you visit the Entrez (PubMed) web site, CBioC automatically opens within a "web band" at the bottom of the main browser window in either Microsoft's Internet Explorer or Mozilla's Firefox. CBioC will "wait" until you display an abstract from the PubMed website.

Displaying data

When you search the PubMed database and display a particular abstract, CBioC will automatically display the interactions found in the CBioC database related to the abstract you are viewing. If the abstract has not been processed by CBioC before, the automatic extraction system will run "on the fly".

After the extracted interactions, CBioC also displays interactions found for the article in publicly accessible databases. The "CBioC Statistics" box displayed in the entry page will tell you how many interactions from each database are included in CBioC.

Searching

A powerful feature of CBioC is its search function. As a registered CBioC user, you can search our database for all facts related to a particular protein, gene, disease, or interaction word by simply typing the relevant term in the Search box within the CBioC web band. CBioC will automatically expand your search term with known synonyms of the term. You must be logged in to access the advanced search functions.

You can also display the facts available for a set of abstracts by typing a comma-separated list of their PMIDs in the search box. The search box also lets you see all the facts we have from a particular database by typing its name, such as "BIND" or "MINT".

Voting, modifying, and adding

As a registered CBioC user, you can vote on the accuracy of an extraction, modify the interactions, or add interactions that the extraction system missed. You must be logged in to access any of these functions.

If the interaction seems correctly extracted, click the "Yes" button to approve. Otherwise, you can vote "No" or modify the data. The percentage of the "Yes" votes is displayed as a proportional green bar under "% Acceptance".

To modify an interaction, click on its "Modify" button. The data fields will open for you to change the data. Click "Submit" when you are done. Your screen id is displayed in the "Source" column, and the previous data is accessible by clicking on the "History" link.

Similarly, to add an interaction present in the abstract or within the text of the article, enter the correct information in the last row. Click "Add" when you are done. Your screen id will be displayed in the "Source" column, and the information will be subject to the community vote.