The Open Biological and Biomedical Ontologies (OBO) Foundry is a group of people dedicated to build and maintain
ontologies
In computer science and information science, an ontology encompasses a representation, formal naming, and definition of the categories, properties, and relations between the concepts, data, and entities that substantiate one, many, or all domains ...
related to the life sciences. The OBO Foundry establishes a set of principles for ontology development for creating a suite of interoperable reference ontologies in the biomedical domain. Currently, there are more than a hundred ontologies that follow the OBO Foundry principles.
The OBO Foundry effort makes it easier to integrate biomedical results and carry out analysis in bioinformatics. It does so by offering a structured reference for terms of different research fields and their interconnections (ex: a
phenotype
In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological pr ...
in a
mouse model
A model organism (often shortened to model) is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the working ...
and its related phenotype in
zebrafish
The zebrafish (''Danio rerio'') is a freshwater fish belonging to the minnow family (Cyprinidae) of the order Cypriniformes. Native to South Asia, it is a popular aquarium fish, frequently sold under the trade name zebra danio (and thus often ca ...
).
Introduction
The Foundry initiative aims at improving the integration of data in the life sciences. One approach to integration is the annotation of data from different sources using
controlled vocabularies
Control may refer to:
Basic meanings Economics and business
* Control (management), an element of management
* Control, an element of management accounting
* Comptroller (or controller), a senior financial officer in an organization
* Controlling ...
. Ideally, such controlled vocabularies take the form of
ontologies
In computer science and information science, an ontology encompasses a representation, formal naming, and definition of the categories, properties, and relations between the concepts, data, and entities that substantiate one, many, or all domains ...
, which support logical reasoning over the data annotated using the terms in the vocabulary.
The formalization of concepts in the biomedical domain is especially known via the work of the
Gene Ontology
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and ge ...
Consortium, a part of the OBO Foundry. This has led to the development of certain proposed principles of good practice in ontology development, which are now being put into practice within the framework of the Open Biomedical Ontologies consortium through its OBO Foundry initiative. OBO ontologies form part of the resources of the
National Center for Biomedical Ontology The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing, and is funded by the NIH. Among the goals of the NCBO are to provide tools for discovery and access of biomedical ontologies, which are a t ...
, where they form a central component of the NCBO's BioPortal.
Open Biological and Biomedical Ontologies
The Open Biological and Biomedical Ontologies (OBO; formerly Open Biomedical Ontologies) is an effort to create
ontologies
In computer science and information science, an ontology encompasses a representation, formal naming, and definition of the categories, properties, and relations between the concepts, data, and entities that substantiate one, many, or all domains ...
(
controlled vocabularies
Control may refer to:
Basic meanings Economics and business
* Control (management), an element of management
* Control, an element of management accounting
* Comptroller (or controller), a senior financial officer in an organization
* Controlling ...
) for use across biological and medical domains.
A subset of the original OBO ontologies has started the OBO Foundry, which leads the OBO efforts since 2007.
The creation of OBO in 2001 was largely inspired by the efforts of the
Gene Ontology
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and ge ...
project. OBO forms part of the resources of the
U.S.
The United States of America (U.S.A. or USA), commonly known as the United States (U.S. or US) or America, is a country primarily located in North America. It consists of 50 states, a federal district, five major unincorporated territori ...
National Center for Biomedical Ontology The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing, and is funded by the NIH. Among the goals of the NCBO are to provide tools for discovery and access of biomedical ontologies, which are a t ...
(NCBIO) and a central element of the NCBO's BioPortal. It is an initiative led by the OBO Foundry.
Rules for participation
The OBO Foundry is open to participations of any interested individuals. Ontologies that intend to be officially part of the OBO Foundry have to adhere to the OBO principles and pass a series of reviews done by the members, when "the Foundry coordinators serve as analogs of journal editors". There are ontologies that follow OBO principles but are not officially part of OBO, such as eagle-i's Reagent Application Ontology. and the Animals in Context Ontology.
An integration into OBO of the OntoClean's theory of rigidity has been proposed as a step to standardize candidate ontologies. This integration would make it easier to develop software to automatically check candidates.
Tools
The OBO Foundry community is also dedicated to developing tools to facilitate creating and maintaining ontologies. Most ontology developers in OBO use the Protégé ontology editor and the
Web Ontology Language
The Web Ontology Language (OWL) is a family of knowledge representation languages for authoring ontologies. Ontologies are a formal way to describe taxonomies and classification networks, essentially defining the structure of knowledge for vario ...
(OWL) for building ontologies. To facilitate
command line
A command-line interpreter or command-line processor uses a command-line interface (CLI) to receive commands from a user in the form of lines of text. This provides a means of setting parameters for the environment, invoking executables and pro ...
management of ontologies in a Protégé- and OWL-compatible format, the OBO Foundry has developed the tool ROBOT (ROBOT is an OBO Tool). ROBOT aggregates functions for routine tasks in ontology development, is open source, and can be used either via the command line or as a library for any language on the Java Virtual Machine.
Other tool related to the OBO effort is OBO-Edit, an ontology editor and reasoner funded by the
Gene Ontology Consortium
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and ge ...
. There are also plugins for OBO-Edit which facilitate the development of ontologies, such as the semi-automatic ontology generator DOG4DAG.
The OBO file format
The OBO file format is a biology-oriented language for building ontologies. It is based on the principles of Web Ontology Language (OWL).
As a community effort, standard common mappings have been created for lossless roundtrip transformations between Open Biomedical Ontologies (OBO) format and OWL. The research contains methodical examination of each of the constructs of OBO and a layer cake for OBO, similar to the Semantic Web stack.
OBO Foundry Ontologies
The initial set of OBO Foundry ontologies was composed by mature ontologies (such as the
Gene Ontology
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and ge ...
, GO, and the
Foundational Model of Anatomy
The Foundational Model of Anatomy Ontology (FMA) is a reference ontology for the domain of Human anatomy. It is a symbolic representation of the canonical, phenotypic structure of an organism; a spatial-structural ontology of anatomical entities a ...
, FMAO), by mergers of previously existing ontologies (ex: the Cell Ontology, CL, formed from different dedicated ontologies, and related parts on GO and FMAO) and by development of new ontologies based on its principles.
The original set of ontologies also included the Zebrafish Anatomical Ontology (a part of the
Zebrafish Information Network The Zebrafish Information NetworkZFIN is an online biological database of information about the zebrafish (''Danio rerio''). The zebrafish is a widely used model organism for genetic, genomic, and developmental studies, and ZFIN provides an integr ...
), the
CheBI
Chemical Entities of Biological Interest, also known as ChEBI, is a chemical database and ontology of molecular entities focused on 'small' chemical compounds, that is part of the Open Biomedical Ontologies (OBO) effort at the European Bioinf ...
Sequence Ontology
The Sequence Ontology (SO) is an ontology
In metaphysics, ontology is the philosophy, philosophical study of being, as well as related concepts such as existence, Becoming (philosophy), becoming, and reality.
Ontology addresses questions ...
, the
Ontology for Biomedical Investigations
The Ontology for Biomedical Investigations (OBI) is an open-access, integrated ontology for the description of biological and clinical investigations. OBI provides a model for the design of an investigation, the protocols and instrumentation used, ...
A number of different OBO Foundry ontologies have also been integrated to the
Wikidata
Wikidata is a collaboratively edited multilingual knowledge graph hosted by the Wikimedia Foundation. It is a common source of open data that Wikimedia projects such as Wikipedia, and anyone else, can use under the CC0 public domain license ...
knowledge graph. This has led to the integration of OBO structured ontologies to data from other, non-OBO databases . For example, the integration of the Human Disease Ontology to Wikidata has enabled its link to the description of cell-lines from the resource Cellosaurus. One of the goals of the integration of OBO Foundry to Wikidata has been to lower the barriers for non-ontologists to contribute to and use ontologies. Wikidata is arguably easier to understand and use than the traditional ontology models (which require a high degree of specific expertise).
Principles
Summary of OBO Foundry Principles for development of an OBO-compatible life sciences
ontology
In metaphysics, ontology is the philosophical study of being, as well as related concepts such as existence, becoming, and reality.
Ontology addresses questions like how entities are grouped into categories and which of these entities exi ...
:
Openness
The ontologies are openly available and have to be released under either the license CC-BY 3.0 or under the public domain (
CC0
A Creative Commons (CC) license is one of several public copyright licenses that enable the free distribution of an otherwise copyrighted "work".A "work" is any creative material made by a person. A painting, a graphic, a book, a song/lyric ...
). The openness of the ontologies has enabled, for example, the import of terms from the
Gene Ontology
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and ge ...
(one of the ontologies that follow OBO Principles) to the
Wikidata
Wikidata is a collaboratively edited multilingual knowledge graph hosted by the Wikimedia Foundation. It is a common source of open data that Wikimedia projects such as Wikipedia, and anyone else, can use under the CC0 public domain license ...
project.
Common format
The ontologies have to be available in a common
formal language
In logic, mathematics, computer science, and linguistics, a formal language consists of words whose letters are taken from an alphabet and are well-formed according to a specific set of rules.
The alphabet of a formal language consists of sy ...
. In practice, that means that ontologies that are part of the OBO foundry need to describe items unsing the formats OWL/ OWL2 or
OBO
Obo is the capital of Haut-Mbomou, one of the 14 Prefectures of the Central African Republic, prefectures of the Central African Republic. It is close to the Pole of inaccessibility#Africa, African Pole of Inaccessibility.
Poste Airport is loca ...
CHEBI
Chemical Entities of Biological Interest, also known as ChEBI, is a chemical database and ontology of molecular entities focused on 'small' chemical compounds, that is part of the Open Biomedical Ontologies (OBO) effort at the European Bioinf ...
, GO, PRO) and a local numeric identifier within the ontology. The choice of a numerical ID was made in order to improve maintenance and evolution of the resources. In order to participate in OBO Foundry, ontologies have to be orthogonal and the concepts it models must be unique within OBO, so each concept has a single Uniform Resource Identifier (URI). New ontologies have, then, to reuse work done in other efforts.
Despite the ideal of uniqueness of terms and interoperability, in practice, this is difficult to enforce, leading to the occurrence of term duplication. Furthermore, some ontologies do not reuse terms or even reuse terms inappropriately.
Versioning
Ontologies evolve in time, refining concepts and descriptions according to advances in the knowledge of their specific domains. In order to ensure that new versions are updated, but tools that use older version of the ontologies are still function, OBO enforces a system of versioning systems, with each ontology version receiving a unique identifier, either in the format of a date or a numbering system, and metadata dags.
Scope
The ontologies should have a clearly specified scope (the domain it intends to cover).
Have textual definitions
The ontologies should have textual definitions for each item, in a
human-readable
A human-readable medium or human-readable format is any encoding of data or information that can be naturally read by humans.
In computing, ''human-readable'' data is often encoded as ASCII or Unicode text, rather than as binary data. In most c ...
way. That means that beside the alphanumeric identification for each item, they should be described in natural language by logical affirmations following the Aristotelian logic in a way that is unique within the ontology.
Standardized relations and the Relation Ontology (RO)
The ontologies should use relations between items from the Relations Ontology (RO). This ensures that different ontologies can integrated seamlessly, which is specially important for logical inference.
The Relation Ontology (RO) is an
ontology
In metaphysics, ontology is the philosophical study of being, as well as related concepts such as existence, becoming, and reality.
Ontology addresses questions like how entities are grouped into categories and which of these entities exi ...
designed to represent the relationships between different biomedical concepts. It describes rigorously relations like "part_of", "located_in" and "preceded_by" that are reused by many OBO Foundry ontologies.
Documentation
OBO ontologies need to be thoroughly documented. Frequently this is done via
GitHub
GitHub, Inc. () is an Internet hosting service for software development and version control using Git. It provides the distributed version control of Git plus access control, bug tracking, software feature requests, task management, continu ...
The ontologies should be useful for multiple different people, and ontology developers should document the evidence of use. This criterion is important for the review process. Examples of use include linking to terms by other ontologies, use in semantic web projects, use in
annotation
An annotation is extra information associated with a particular point in a document or other piece of information. It can be a note that includes a comment or explanation. Annotations are sometimes presented in the margin of book pages. For anno ...
s or other research applications.
Openness to collaborations
The ontologies should be developed in a way that allows collaborations with other OBO Foundry members.
Locus of authority
The ontologies should have one person responsible for the ontology who mediates interaction with the community.
Naming conventions
Naming conventions for OBO ontologies aim at making primary labels unambiguous and unique inside the ontology (and preferably, inside OBO). Labels and synonyms should be written in English, avoiding the use of
underscore
An underscore, ; also called an underline, low line, or low dash; is a line drawn under a segment of text. In proofreading, underscoring is a convention that says "set this text in italic type", traditionally used on manuscript or typescript a ...
s and
camel case
Camel case (sometimes stylized as camelCase or CamelCase, also known as camel caps or more formally as medial capitals) is the practice of writing phrases without spaces or punctuation. The format indicates the separation of words with a single ...
. OBO lacks a mechanism for multilingual support, in contrast to
Wikidata
Wikidata is a collaboratively edited multilingual knowledge graph hosted by the Wikimedia Foundation. It is a common source of open data that Wikimedia projects such as Wikipedia, and anyone else, can use under the CC0 public domain license ...
, which allows labels in different systems. The naming system in OBO is based on a series of surveys at cataloguing naming conventions of current ontologies, as well as discover issues relating to these conventions.
Maintenance
The ontologies should be updated with regards to changes in scientific consensus. The OBO Foundry defines scientific consensus as "multiple publications by independent labs over a year come to the same conclusion, and there is no or limited (<10%) dissenting opinions published in the same time frame."
Gene Ontology Consortium
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and ge ...
*
Sequence Ontology
The Sequence Ontology (SO) is an ontology
In metaphysics, ontology is the philosophy, philosophical study of being, as well as related concepts such as existence, Becoming (philosophy), becoming, and reality.
Ontology addresses questions ...
*
Generic Model Organism Database
The Generic Model Organism Database (GMOD) project provides biological research communities with a toolkit of open-source software components for visualizing, annotating, managing, and storing biological data. The GMOD project is funded by the Unit ...
Ontology for Biomedical Investigations
The Ontology for Biomedical Investigations (OBI) is an open-access, integrated ontology for the description of biological and clinical investigations. OBI provides a model for the design of an investigation, the protocols and instrumentation used, ...
CHEBI
Chemical Entities of Biological Interest, also known as ChEBI, is a chemical database and ontology of molecular entities focused on 'small' chemical compounds, that is part of the Open Biomedical Ontologies (OBO) effort at the European Bioinf ...
archive.org
The Internet Archive is an American digital library with the stated mission of "universal access to all knowledge". It provides free public access to collections of digitized materials, including websites, software applications/games, music, ...