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Welcome to The Ontology for Nutritional Studies (ONS) wiki pages!

Here you will find useful information and training to start using, downloading, browsing and even contributing to expanding the ONS ontology. Most of the documentation is summarised and put together from external resources, whom shall go the credits.

What is an ontology?

An ontology is defined as a formal representation of the knowledge in a certain reality (i.e. a certain domain of knowledge), in a way that different people - and, notably, computers - can understand the concepts it contains and learn about the reality that is being represented. Ontologies consist of defined classes of entities, typically structured within a knowledge hierarchy where concepts are connected by standardised semantic relationships (i.e. "is-a", "part-of") formally specifying knowledge relations such as generalisations of specifications of the reality of interest.

example

In ontological jargonjargon:

• Classes are the concepts in a domain of discourse
• Subclasses of a class represent concepts that are more specific than the superclass. For example, we can divide the class of all wines into red, white, and rosé wines.
• Instances of a class represent specific objects of that class, for example Amarone is an Italian wine.
• Roles are properties of a concept, or its instances, describing various features and attributes of the concept, for example the taste or the winery producer.
• Role restrictions are used to describe limitations of the concept properties

For the purposes of organising the concepts in biomedical and scientific domain ontologies, the Basic Formal Ontology (BFO) comes handy. It does not contain physical, chemical, biological or other terms which would properly fall within the coverage domains of the special sciences. The structure of BFO, which indeed counts only 35 classes, is based on a division of entities into two disjoint categories of continuant and occurrent, the former comprehending for example objects and spatial regions, the latter comprehending processes conceived as extended through (or as spanning) time.

BFO organisation of knowledge entities:

• entity - anything that exists or has existed or will exist.
  • continuant - an entity that persists, endures, or continues to exist through time while maintaining its identity.
    • independent continuant - never depends on any other entity
    • generically dependent occurrent - i.e. it depends on one or more other entities.
    • specifically dependent occurrent - meaning it has a dependance, at a certain time, on some other specific independent entity.
  • occurrent - is the philosophical development of a process that at any real point in time, like a snapshot, can be observed only for the part actually happening at that time.
    • process - an occurrent that has a temporal actualisation and, at some point in time, it depends on some material entity.

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TASKS

When dealing with an ontology, and ONS is one of a kind, the following common tasks will get you started.

• TASK 1. Browse and lookup ONS concepts online or with a Spreadsheet

• TASK 2. Browsing and making changes to ONS locally

  • Basic Protègè usage
  • Download and browse ONS on you PC

• TASK 3. Contribute to ONS

  • Propose a change via issue tracker (preferred method)
  • Propose changes via pull requests (experienced users)

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Reading list

Link to external material