caBIO Home Page

caBIO Portal

Overview

caBIO is a resource that integrates biomedical data on genes, proteins, clinical protocols, disease ontologies, pharmacological agents, pathways, and other entities with annotations, controlled vocabularies, and metadata models originating from twenty-three data sources, including the Cancer Gene Index, the Pathway Interaction Database, and the University of California, Santa Cruz Distributed Annotation System.

The caBIO Portal provides a graphical user interface (GUI) which Home Page allows you to browse the entire caBIO object model. Thus, you may use this tool to view all Cancer Gene Index data and to find how these genes, diseases, and compounds relate to pathways, clinical protocols, and other biomedical and biological entities.

Specifically, you can use this interface to uncover fact-based associations between genes and diseases or genes and compounds. In addition, you can evaluate the evidence from which these associations were extracted and the codes and details that describe these associations. Other annotations, such as sentence status flags, negation indicators, cell line indicators, and organism are also accessible through the Portal.

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If you are not already familiar with these concepts, stop! It is highly recommended that you instead use the caBIO Portlet Templated Search tool and refer to its step-by-step end user documentation. If you still would prefer to use a caBIO Portal tool, first refer to the section Getting Started with the caBIO Object ModelsHome Page, and then proceed slowly and with caution.

caBIO Home Page Search Tools

The caBIO Home Page PORTAL SCREENSHOT HERE!Unlike the caBIO Portlet Templated Search with is relatively simple to use but only exposes gene terms, their associated disease or compound term, and PubMed identifiers for the gene-disease or gene-compound evidence, the caBIO Portal allows you to view all Cancer Gene Index and other data through two search tools - a Google ^TM -like Freestyle Lexical Mine and Search for Biological Entities.

The Freestyle Lexical functionalities return Mine tool returns any caBIO object with data an attribute that match matches your search term. Associations between classes are represented as links (generally , often as accessor or "getter" methods , such as getGene or getDiseaseOntology) , that you can click to walk the caBIO object model. In doing so, you not only can find relationships among Cancer Gene Index data, but also with these data and related objects of type Protein (the product of many Cancer Gene Index gene terms), Pathway (what pathway the gene is in and if it is altered in a disease), Clinical Protocols, and many otherscaBIO objects.

The Search for Biological Entities tool, on the other hand, has an class-based search interface that also allows you to limit your search results to a specific object type. This tool still allows you to navigate through the caBIO object model, but gives you a single "point" from which to being doing so.

Because you must click on hyperlinks in at least two to or three objects links for each gene-disease or gene-compound association in order to uncover relevant all of the Cancer Gene Index data you would like to see, it can be quite tedious to compile even a relatively modest list of genes associated with a disease or compound. Even with the time-consuming click throughs to navigate the caBIO object model, it is still much faster to use the caBIO Portal than it is to use traditional methods of uncovering all of the genes associated with a disease or compound (e.g., a search and review for such relationships (for example, searching for and reviewing hundreds or even thousands of articles in PubMed).

Selecting the Right caBIO

Home Page Tool for You

The caBIO Portal Home Page Freestyle Lexical Mine and Search for Biological Entities tools both retrieve caBIO objects, but have vastly different GUIsdiffer in their search interfaces, the types of retrieved objects, and distinct differences in how results are formattedresult formatting.

• If you want to explore Cancer Gene Index data and how it is associated with other data in caBIO, refer to the step-by-step guide for the caBIO Portal Home Page Freestyle Lexical Mine. This is the recommended caBIO Portal tool for most end users!
• If you want to view retrieve only specific types of objects related to Cancer Gene Index in the search results or to use a class-oriented search interface, you may refer to the step-by-step guide for the caBIO Portal Home Page Search for Biological Entities tool.