# Presentation: 378962

## OBO FOUNDRY– A FAMILY OF REFERENCE ONTOLOGIES

**Cell Ontology**
**cell types from**
**prokaryotes to mammals****  **

**Chemical Entities of**
**Biological Interest**
**Molecular entities which are**
**used to intervene in the**
**process of living organisms  **

**Foundational**
**Model of Anatomy**
**structure of the human body**

**Functional Genomics**
**Investigation Ontology**** **
**design, protocol, instrumentation,**
**data, and analysis applied in**
**functional genomics investigations **

**Gene Ontology**
**cellular components, molecular**
**functions, biological processes in all organisms **

**Protein Ontology**
**protein types and**
**modifications classified on**
**the basis of evolutionary**
**principles **

**Relation Ontology**
**Relations between universals**
**and instances in biomedical ontologies**

- Sequence Ontology
**features and properties**
**of nucleic sequences **

**RNA Ontology**
**three-dimensional RNA structures**
**and homologous sequence**
**alignments and associated**
**attributes and processes **

**OBO FOUNDRY MEMBERS**

**INTRODUCTION**
- The National Center for Biomedical Ontology (http://bioontology.org) is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists funded by the NIH Roadmap to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. One goal of the center is to propagate best practices and quality control methods that will improve the utility increase the lasting value of biomedical ontologies that are developed, and allow for greater interoperability between them.

**THE BABEL PROBLEM**
- The value of scientific data is greatly enhanced when it exists in a form which allows it to be integrated with other data. One route to integration is through the annotation of data using common controlled vocabularies or ‘ontologies’. A variety of terminology resources have been assembled, often these are homegrown solutions that are tied to the specific needs of the designers who developed them. These has lead to the following situation:
- 	1.	Many controlled vocabularies have grown in an ad hoc way 		without clear boundaries and design principles.
- 	2. 	The existing ontologies are of uneven quality.
- 	3.	The reusability of many controlled vocabularies is limited.
- 	4.	The ontologies don’t cover the biomedical domain in a 		systematic way.
- 	5.	The semantic relations (e.g. is_a, part_of) are used 		inconsistently within the same ontologies as well as across 		different ontologies.
- 	6.	Ontologies overlap and use inconsistent terminology.
- Consequently, a Babylonian problem arises: there are many ontologies each of which assigns semantic content to its terms in its own idiosyncratic way. This problem thwart not only the integration of data but also the exploitation of ontologies for purposes of reasoning.

**OBJECTIVE**
- The OBO Foundry is a collaborative experiment to overcome the Babel problem. It involves a group of leading ontology developers who have agreed in advance to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies within the broader OBO framework, and also to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain. In particular, these principles ensure that the ontologies which are part of the Foundry are not tailored to a specific problem, but can be used as a reference ontology for the community. Further, the ontologies do not overlap, their terms are well defined, and the semantic relations are used consistently across the ontologies. The objective is to establish a family of interoperable, high-quality reference ontologies to be used in the annotation of biomedical data.

**OBO FOUNDRY PRINCIPLES**
**Availability and Community Collaboration**
- 	1.	The ontology is open and available to be used by all without 	any constraint other than (a) its origin must be 	acknowledged and (b) it is not to be altered and 	subsequently redistributed except under a new name and 	with different identifiers.
- 	2.	The ontology is developed in a collaborative effort.
- 	3.	The ontology has a plurality of independent users.
**Formal Structure and Scope**
- 	4.	The ontology has a clearly specified and clearly delineated 	subject-matter.
- 	5. 	The ontology uses relations which are unambiguously 	defined following the pattern of definitions laid down in the 	OBO Relation Ontology.
- 	6.	The ontology is in, or can be expressed in, a common 	formal language.
**Documentation and Maintenance**
- 	7.	The ontology has documentation that is clearly written for 	non-experts in ontologies.
- 	8.	The ontology includes textual definitions for all terms.
- 	9.	The ontology provider has procedures for identifying 	distinct 	successive versions.
- 	10.	The ontology possesses a unique identifier space within 	OBO.

**OBO FOUNDRY– A FAMILY OF REFERENCE ONTOLOGIES**
- Fabian Neuhaus, Barry Smith

- University at Buffalo