science

OBO Foundry

OBO Foundry is a science topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand OBO Foundry rather than just read about it. In short: The Open Biological and Biomedical Ontologies (OBO) Foundry is a group of people who build and maintain ontologies 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.

Key takeaways

OBO Foundry belongs to science; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect OBO Foundry to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of OBO Foundry from memory before moving on to harder problems.

Reference excerpt

The Open Biological and Biomedical Ontologies (OBO) Foundry is a group of people who build and maintain ontologies 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 a mouse model and its related phenotype in zebrafish).

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. Ideally, such controlled vocabularies take the form of ontologies, 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 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, 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 (controlled vocabularies) 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 project. OBO forms part of the resources of the U.S. National Center for Biomedical Ontology (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 (OWL) for building ontologies. To facilitate command line 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. 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, GO, and the Foundational Model of Anatomy, 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 CheBI ontology, the Disease Ontology, the Plant Ontology, the Sequence Ontology, the Ontology for Biomedical Investigations and the Protein Ontology. The number of ontologies in OBO has grown to the order of hundreds, and they are gathered in the list of OBO Foundry ontologies.

OBO Foundry and Wikidata A number of different OBO Foundry ontologies have also been integrated to the Wikidata 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:

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). The openness of the ontologies has enabled, for example, the import of terms from the Gene Ontology (one of the ontologies that follow OBO Principles) to the Wikidata project.

Common format The ontologies have to be available in a common formal language. In practice, that means that ontologies that are part of the OBO foundry need to describe items unsing the formats OWL/OWL2 or OBO using a RDF/XML syntax to maximize interoperability.

Orthogonality

… excerpt ends here. Continue reading the full article.

Worked examples

Example 1 — a first encounter with OBO Foundry

Start with the simplest possible case. Write down what OBO Foundry claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In science, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to OBO Foundry before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about OBO Foundry ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of OBO Foundry

In research: OBO Foundry appears in science research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses OBO Foundry in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: OBO Foundry is common in secondary-school and first-year university syllabi. It links to neighbouring topics Bioinformatics, Health standards, Medical classification, so understanding it makes those chapters shorter.
In everyday life: Look for OBO Foundry outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study OBO Foundry in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what OBO Foundry means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain OBO Foundry out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is OBO Foundry in simple terms?

Why does OBO Foundry matter?

Because it connects several science ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study OBO Foundry?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on OBO Foundry.