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Populous: a tool for building OWL ontologies from templates
BMC Bioinformatics
|March 1, 2012
Summary
Populous is a new tool that simplifies ontology creation for life scientists. It allows domain experts to contribute knowledge through familiar spreadsheet-like forms, facilitating broader community involvement in building scientific ontologies.
Area of Science:
- Life Sciences
- Bioinformatics
- Computational Biology
Background:
- Ontologies are crucial for standardizing life science data interpretation.
- Emerging ontology-based applications require tools for domain expert knowledge contribution.
- Barriers hinder domain expert engagement in ontology development, necessitating novel solutions.
Purpose of the Study:
- To introduce Populous, a tool designed to facilitate ontology content gathering.
- To enable domain experts to contribute knowledge without direct interaction with complex ontological representations.
- To lower barriers for scientists to participate in ontology development.
Main Methods:
- Populous utilizes a table-based form interface for knowledge input.
- Columns in the forms are constrained by existing ontologies.
- Populated tables are mapped to patterns for automatic ontology content generation.
- Forms can be exported as spreadsheets for user familiarity.
Main Results:
- Populous simplifies the knowledge acquisition phase of ontology development.
- It separates knowledge gathering from conceptualization and axiomatization.
- The tool provides a user-friendly interface familiar to biologists, such as spreadsheets.
Conclusions:
- Populous aids in the mass production of ontology content by engaging a wider scientific community.
- It serves as a complementary platform to standard ontology editing tools.
- The tool effectively addresses the knowledge gathering bottleneck in ontology development.
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Overview
Concepts and Prototypes
The human nervous system handles vast amounts of information by translating sensory stimuli into neural impulses, which the brain processes, creating thoughts expressed through language or stored as memories. The brain also synthesizes information from emotions and memories, which significantly influence thoughts and behaviors. This intricate process creates a comprehensive mental picture.
The brain organizes this information using concepts, which are mental categories grouping linguistic data,...
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Schemata
A schema is a mental construct that organizes related concepts, allowing the brain to process information efficiently. Upon activation, schemata facilitate assumptions about people or objects.
Two types of schemata are:
Two types of schemata are:
Schemas
A schema is a mental construct consisting of a cluster or collection of related concepts (Bartlett, 1932). There are many different types of schemata, and they all have one thing in common: schemata are a method of organizing information that allows the brain to work more efficiently. When a schema is activated, the brain makes immediate assumptions about the person or object being observed.
Population Growth
Population size is dynamic, increasing with birth rates and immigration, and decreasing with death rates and emigration. In ideal conditions with unlimited resources, populations can increase exponentially, which plots as a J-shaped growth rate curve of population size against time. This type of curve is characteristic of newly-introduced invasive species, or populations that have suffered catastrophic declines and are rebounding.
Gene Families
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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