The BKL Ontology Tool- Biology Simplified
If time equals money, then the right search tool and data structure can make all the difference.
The Problem
Literature searches consume valuable time and resources. Available tools are often cumbersome to use, and even worse, the final search results are often unreliable because the searches were based on limited information or unstructured data. Such incomplete or flawed results lead to an even greater consumption of time and resources.
The Solution
Reliable Data with a Searchable Structure
The structured content of the BIOBASE Knowledge Library and its unique BKL Retriever platform offers a solution so that you can quickly, easily and reliably answer complex biological questions.
The strength of BIOBASE’s data mining solutions is based on:
- Extensive and comprehensive information derived from abstracts and full-text articles
- Structured data using controlled vocabularies
- Reliable, expert manual curation as opposed to error-prone text mining and/or predictions
Retrieve sets of proteins based on shared characteristics
If your goal is to identify proteins relevant to your research based on their functional characteristics, the BKL Ontology tool provides a simple solution.
Overview
The figure below illustrates how a user can generate highly defined protein sets based on protein characteristics using the BKL Ontology tool.
Identification of potential Parkinson’s Disease (PD) markers, which share structural characteristics, and which are already known pharmaceutical targets.
Other ways you can use the BKL Ontology tool:
- Learn which genes or proteins are overexpressed in Alzheimer’s disease patients.
- Identify how many genes or proteins are expressed in pancreatic islet cells only.
- Explore which pathways are targets for methotrexate.
- Find which liver proteins have been shown to be targets of statins.
- Discover which proteins are associated with both multiple sclerosis (MS) and lupus.
Gene Set Analysis
If your goal is to better understand an experimental gene set generated in your lab, the BKL Ontology tool can provide quick answers.
Overview
Easily characterize a set of genes obtained from an experiment, or perform statistical analyses of defined gene sets to identify over represented biological processes, diseases, phenotypes, expression patterns, pathways, and more which may provide insight into biological events associated with your gene set.
A gene set can be the result of a search you’ve performed, or it can be an uploaded list of genes that you provide as the results of a microarray or other high-throughput data experiment. For user-uploaded gene sets, a wide range of identifiers is supported including Affymetrix, Agilent, Entrez Gene, and UniProt.
Ontology Tool at a Glance
The Ontology tool allows users to drill through extensive BIOBASE hierarchies, or to use a simple Term Lookup.
Examples of searchable hierarchies are:
- Pharmaceuticals
- Disease
- Pathway
- Gene Ontology
- Domains
- Expression (e.g. cell type, tissue, location, stage, conditions)
- Phenotype (e.g. mutation type, phenotype)
- Modifications
- Interacting proteins
- Transcription factors
- Attributes (e.g. molecular weight, pI)
Example Workflow
Perhaps you want to determine which targets of simvastatin are also involved in inflammatory response, since statins have a secondary, anti-inflammatory effect.
Step One: Search for Targets of Simvastatin
Use the term lookup to search for simvastatin, select the term in the dropdown menu, and click “Focus on term”.
Step Two: Search for the Biological Process Term "Inflammatory Response"
Step Three: View the List of Fourteen Targets of Simvastatin that Are Involved in Inflammatory Response
Step Four: Visualize Pathways, with Simvastatin Targets Highlighted, in the Pathfinder
The BKL Ontology tool allows you to answer simple questions such as:
- What drugs interact with my gene or protein of interest?
- What diseases are associated with my gene or protein of interest?
- In which tissues is a gene or protein expressed or not expressed?
- What pathways interact with a drug target or targets?
- How are my proteins of interest modified?
Term Statistics Analysis
The Ontology tool allows you to run statistical analysis on a gene set resulting from a user-defined search, or on your own uploaded gene set, in order to identify biological processes, domains, families, tissue localization, experimental conditions, pathways or other experimentally relevant associations which provide insight into biological processes, tissues, or events likely affected by your protein set.
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