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Francesco Vitali edited this page Mar 23, 2018 · 28 revisions

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. In ontological jargon we can identify some main components and features. Here we will use a classical example in ontological field, an extract from this guide, to illustrate the component of an ontology and to provide practical directions.

Classes: are the concepts in a domain of discourse. For example, if our domain of discourse is represented by wine and winery, the “wine” class would represent all possible wines. In an ontology, classes are organized in a hierarchical structure of subclasses and superclasses. Subclasses of a certain class represent concepts that are more specific than their superclass. For example, we can divide the class of all wines into red, white, and rosé wines (i.e. the main wine styles). The raw organization of classes and subclasses represents the “skeleton” of the ontology, indicating the basic relationships that connect the classes of the ontology. In a structure like this, classes at various depth in the hierarchy can be identified, form the broader top-level concepts (i.e. wine, a class which comprises all the wines) to the most granular ones at the bottom level (i.e. a Red Bordeaux is a sub-class of Red wine, which in turn is a subclass of Wine).

In ontological jargon:

Instances: while classes of the ontology should have universal meaning, to define concepts universally applicable, instances of a class represent specific individuals of that class, which cannot have universal meaning. In our wine example, the red Bordeaux produced by a certain winery, or the red Bordeaux in this glass of wine, are instances of the Red Bordeaux subclass.

Properties: classes, subclasses and their individuals, are the concepts of the domain of discourse that the ontology is representing. Properties describes the various features and attributes of those concept and how they relate to each other’s. The basic type of properties, which has been already introduced in the example above, are those specifying the super and subclass relationships among classes. Formally, those properties would be read as “is_a” property connecting each subclass to its superclass For the purposes of organising the concepts in biomedical and scientific domain ontologies, the Basic Formal Ontology (BFO) comes handy (http://ifomis.uni-saarland.de/bfo/). The BFO is a small, general and genuinely upper-level, ontology aiming at dividing the reality in defined classes, wich could be applied to any domain of discourse. 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 (http://ontology.buffalo.edu/bfo/BFO2.png), 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. In this way, the BFO could constitute the top level classes of any ontology as, regardless of the scope, all of them describe the same general reality. Briefly, BFO organisation of reality is as follows:

  • 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. Continuant can be divided in:

      • independent continuant - never depends on any other entity
      • generically dependent continuant - i.e. it depends on one or more other entities.
      • specifically dependent continuant - 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. An example of occurrent is:

      • process - an occurrent that has a temporal actualisation and, at some point in time, it depends on some material entity.

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)

Reading list

Link to external material

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