The Ontology for Biomedical Investigations (OBI) is an open access, integrated ontology

Ontology

Ontology is the philosophical study of the nature of being, existence or reality as such, as well as the basic categories of being and their relations...

 for the description of biological and clinical investigations. OBI provides a model for the design of an investigation, the protocols

Protocol (natural sciences)

In the natural sciences a protocol is a predefined written procedural method in the design and implementation of experiments. Protocols are written whenever it is desirable to standardize a laboratory method to ensure successful replication of results by others in the same laboratory or by other...

 and instrumentation

Instrumentation

Instrumentation is defined as the art and science of measurement and control of process variables within a production, or manufacturing area....

 used, the materials

Biomaterial

A biomaterial is any matter, surface, or construct that interacts with biological systems. The development of biomaterials, as a science, is about fifty years old. The study of biomaterials is called biomaterials science. It has experienced steady and strong growth over its history, with many...

 used, the data generated and the type of analysis

Data analysis

Analysis of data is a process of inspecting, cleaning, transforming, and modeling data with the goal of highlighting useful information, suggesting conclusions, and supporting decision making...

 performed on it. The project is being developed as part of the OBO Foundry

OBO Foundry

The Open Biomedical Ontologies Foundry is a collaborative experiment involving developers of science-based ontologies...

 and as such adheres to all the principles therein such as orthogonal coverage (i.e. clear delineation from other foundry member ontologies) and the use of a common formal language. In OBI the common formal language used is the Web Ontology Language

Web Ontology Language

The Web Ontology Language is a family of knowledge representation languages for authoring ontologies.The languages are characterised by formal semantics and RDF/XML-based serializations for the Semantic Web...

 (OWL). As of March 2008, a pre-release version of the ontology was made available at the project's SVN repository

Scope of the Ontology

The Ontology for Biomedical Investigations (OBI) addresses the need for controlled vocabularies to support integration and joint ("cross-omics") analysis of experimental data, a need originally identified in the transcriptomics domain by the FGED Society, which developed the MGED Ontology as an annotation resource for microarray data. OBI uses the Basic Formal Ontology

Basic Formal Ontology

The Basic Formal Ontology is a formal ontological framework developed by Barry Smith and his associates that consists in a series of sub-ontologies at different levels of granularity...

 upper level ontology

Upper ontology (computer science)

In information science, an upper ontology is an ontology which describes very general concepts that are the same across all knowledge domains. The most important function of an upper ontology is to support very broad semantic interoperability between a large number of ontologies accessible...

 as a means of describing general entities that do not belong to a specific problem domain. As such, all OBI classes are a subclass of some BFO class.

The ontology has the scope of modeling all biomedical investigations and as such contains ontology terms for aspects such as:

• biological material - for example blood plasma
  Blood plasma
  Blood plasma is the straw-colored liquid component of blood in which the blood cells in whole blood are normally suspended. It makes up about 55% of the total blood volume. It is the intravascular fluid part of extracellular fluid...
  
  
• instrument (and parts of an instrument therein) - for example DNA microarray
  DNA microarray
  A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome...
  
  , centrifuge
  Centrifuge
  A centrifuge is a piece of equipment, generally driven by an electric motor , that puts an object in rotation around a fixed axis, applying a force perpendicular to the axis...
  
  
• information content - such as an image or a digital information entity such as an electronic medical record
  Electronic medical record
  An electronic medical record is a computerized medical record created in an organization that delivers care, such as a hospital or physician's office...
  
  
• design and execution of an investigation (and individual experiments therein) - for example study design
  Study design
  Clinical study design is the formulation of trials and experiments in medical and epidemiological research, sometimes known as clinical trials. Many of the considerations here are shared under the more general topic of design of experiments but there can be others, in particular related to patient...
  
  , electrophoresis
  Electrophoresis
  Electrophoresis, also called cataphoresis, is the motion of dispersed particles relative to a fluid under the influence of a spatially uniform electric field. This electrokinetic phenomenon was observed for the first time in 1807 by Reuss , who noticed that the application of a constant electric...
  
   material separaition
• data transformation (incorporating aspects such as data normalization and data analysis) - for example principal components analysis
  Principal components analysis
  Principal component analysis is a mathematical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of uncorrelated variables called principal components. The number of principal components is less than or equal to...
  
   dimensionality reduction, mean
  Mean
  In statistics, mean has two related meanings:* the arithmetic mean .* the expected value of a random variable, which is also called the population mean....
  
   calculation

Less 'concrete' aspects such as the role a given entity may play in a particular scenario (for example the role of a chemical compound in an experiment) and the function of an entity (for example the digestive function of the stomach to nutriate the body) are also covered in the ontology.

OBI Consortium

The MGED Ontology was originally identified in the transcriptomics domain by the FGED Society and was developed to address the needs of data integration. Following a mutual decision to collaborate, this effort later became a wider collaboration between groups such as FGED, PSI and MSI in response to the needs of areas such as transcriptomics, proteomics

Proteomics

Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...

 and metabolomics

Metabolomics

Metabolomics is the scientific study of chemical processes involving metabolites. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles...

and the FuGO (Functional Genomics Investigation Ontology) was created. This later became the OBI covering the wider scope of all biomedical investigations.

As an international, cross-domain initiative, the OBI consortium draws upon a pool of experts from a variety of fields, not limited to biology. The current list of OBI consortium members is available at the OBI consortium website. The consortium is made up of a coordinating committee which is a combination of two subgroups, the Community Representative (those representing a particular biomedical community) and the Core Developers (ontology developers who may or may not be members of any single community). Separate to the coordinating committee is the Developers Working Group which consists of developers within the communities collaborating in the development of OBI at the discretion of current OBI Consortium members.

External links

• The OBI Consortium project homepage http://obi-ontology.org/
• The OBI Consortium SVN Repository homepage http://obi.svn.sourceforge.net/viewvc/obi/
• The OBI Consortium mailing list homepage http://obi-ontology.org/page/Mailing_lists