An ontology for the formalization and visualization of scientific knowledge

by   Vincenzo Daponte, et al.
University of Geneva

The construction of an ontology of scientific knowledge objects, presented here, is part of the development of an approach oriented towards the visualization of scientific knowledge. It is motivated by the fact that the concepts that are used to organize scientific knowledge (theorem, law, experience, proof, etc.) appear in existing ontologies but that none of these ontologies is centered on this topic and presents them in a simple and easily understandable organization. This ontology has been constructed by 1) selecting concepts that appear in high level ontologies or in ontologies of knowledge objects of specific fields and 2) by interviewing scientists in different fields. We have aligned this ontology with some of the sources used, which has allowed us to verify its consistency with respect to them. The validation of the ontology consists in using it to formalize knowledge from various sources, which we have begun to do in the field of physics.



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1 Motivations

The access to scientific knowledge, whether general or factual, must necessarily involve a visual, auditory or other presentation that appeals to one or more senses of the human being. If we are interested in the visual presentation of knowledge, we notice that the natural written language occupies a predominant place in it but that other graphic forms (notations, mathematical and chemical formulas, diagrams, tables, forms, hypertexts, etc.) play an important role in facilitating the performance of various intellectual tasks (calculation, comparison, deduction, etc.).

The general framework in which our work is carried out is the study of techniques for visualizing scientific knowledge and in particular their formal specification with the purpose of building visualization tools that are adapted to the tasks of the scientific user. Indeed, experience shows that there is not an optimal visualization technique but that the effectiveness of each technique depends on the context and objectives of the user (see, for example [Card1999]).

To formally represent the notion of visualization technique it is necessary, according to the reference model proposed by [Chi2000], To formally represent the notion of visualization technique, it is necessary to define an abstract model of the data to be visualized, an abstract model of the visual objects and an application of the data model in the abstract visual model. In the case of the visualization of scientific knowledge, it is therefore necessary to create an abstract model of the scientific knowledge to be visualized. Our goal is to provide a formalization of visualization that applies to any science, so we decided to build an ontology of the knowledge structuring objects used in the various sciences. Such an ontology will make it possible to model the knowledge to be visualized in the form of instances of the classes of this ontology, according to the diagram in figure 1.

Figure 1: Adaptation of the [Chi2000] model to the visualization of scientific knowledge

If sciences vary according to their objects of study (differentiable functions, butterflies, human societies, elementary particles,…), they also have their own concepts to structure the knowledge produced. Mathematics produces theorems, corollaries, lemmas, conjectures, proofs, whereas physics speaks about laws, principles, measures, experimental results or anthropology produces observations, theories, explanatory hypotheses, methods. In addition, each science has developed a set of formalisms (i.e. linguistic constructs) to express and process this knowledge: chemical formulae and equations, mathematical formulae, flow diagrams, interaction diagrams, syntactic trees, etc. and a set of knowledge production techniques: experimentation, formal reasoning, surveys, observations, etc. However, it can be seen that the vocabulary for classifying scientific knowledge objects is limited and that several terms often cover similar concepts. Therefore, we can think of building a central ontology composed of a small number of classes of scientific objects. The knowledge to be visualized can then be represented as instances of these classes.

In the rest of this article we will begin by examining the work that focuses on the representation of scientific knowledge and those that, while somewhat related, can provide important elements. We will then present the method used to create a first version of the SKOO ontology of scientific knowledge objects and the ontology obtained. We will then present the first evaluations we have carried out. In the conclusion we will give perspectives on the practical use of this ontology and on the continuation of the evaluation and development of the ontology.

2 State of the art

To our knowledge, there is currently no ontology whose field is the conceptualization of objects used to represent or structure scientific knowledge in general. It should also be noted that works on the epistemology of science do not generally address this general ontological question but deal either with a particular science or a particular aspect of science. On the other hand, this ontological work was carried out in knowledge engineering for some specific fields.

The OMDoc ontology core presented in ([lange2013ontologies]) presents a model of mathematical knowledge in the form of knowledge items that are types of mathematical objects, theories or statements, which can be of the Assertion, Proof, Definition, Axion, etc. type. In addition, there are relationships between these types of elements, such as the Proof-Assertion proves relationship. Although this ontology is dedicated to mathematics, it can easily be extended to other sciences.

The SIO (Semanticscience Integrated Ontology) ontology, [Dumontier2014], is a higher level ontology that essentially aims to represent biomedical knowledge. The primary purpose of SIO is to describe complex biomedical objects (with component-composite relationships) and the processes in which they are involved or the (experimental) procedures applied to them. However, in the SIO description class, there are many concepts used to structure scientific knowledge: argument, belief, conclusion, evidence, hypothesis,… However, unlike OMDoc, there are no specific relationships between these concepts, but they can be linked to the objects they describe. SIO also describes the linguistic, mathematical and media objects that support knowledge.

The notion of experimental scientific process is at the heart of the EXPO system ([soldatova2006ontology]). It combines SUMO ontology ([niles2001towards, )]) with subject-specific ontologies of experiments by formalizing the generic concepts of experimental design, methodology and results representation. EXPO aims to describe different experimental domains and to provide a formal description of the experiences for analysis, annotation and sharing of results.

We can also consider what has been done in scientific knowledge bases, such as Gene Ontology ([ashburner2000gene]), OntoMathPro ([nevzorova2014ontomath]) or FMA ([Rosse2007]) that aim to represent the current state of our knowledge in a field. They generally consist of a terminology part that organizes very precisely the concepts of the domain and a part composed of assertions (statements) that represent our knowledge about these concepts. In Gene Ontology (GO), statements are called "annotations". They typically link a gene and a term from the GO ontology (for example, to indicate that the gene has a certain function). The statements are qualified by a type of proof (experimental, phytogenetic inference, automatic inference, etc.). In OntoMathPro ([nevzorova2014ontomath]) the terminology levels and assertions do exist but are not structurally separated. Thus Stokes’ theorem (assertion) is not an instance but a subclass of the Theorem

class. Similarly, as a first level subclass of Mathematical knowledge object we find both Theorem and Tensor. There is therefore an aggregation of the objects describing the knowledge and the objects of the domain on which we are working.

It should also be noted that there are ontologies whose sole purpose is to list and classify the subject-specific objects or to create a domain terminology (SWEET, ScienceWISE, etc.). In general, these ontologies are not interested in knowledge structuring objects.

On the other hand, a lexical ontology such as WordNet contains a large number of concepts such as theorem, law, definition, hypothesis, corollary. However, it should be noted that these concepts are not organized in a way that can be directly used. For example, we have the hyperonymic relationship chains


whereas from a formal point of view a corollary is a theorem. In other words, an ontology of scientific knowledge objects cannot be extracted by the simple projection of a part of WordNet. The same is true for other higher-level ontologies (SUMO, CyC,…)

3 Construction of the SKOO ontology

To build the ontology of Scientific Knowledge Objects Ontology (SKOO)111 we applied the following process:

  1. We collected a set of terms used to structure knowledge in different scientific fields. This was done by consulting books (textbooks, forms, “handbooks” monographs) in biochemistry, physics, mathematics, linguistics, sociology; interviews with scientists from different fields; analysis of the terminology level of scientific knowledge bases and ontologies (Gene Ontology, OntoMathPro,…)

  2. To build the upper level of ontology we first associated the highlighted terms with equivalent or more general “synsets” of WordNet. Then we used the DOLCE ontology, already aligned with WordNet, to find higher-level concepts.

  3. Finally, we have defined relationships between higher-level concepts based on relationships found in scientific ontologies, in particular OMDoc, and by specialization of certain high-level DOLCE relationships.

Figure 2 shows the upper level of the ontology obtained and its links with DOLCE and WordNet. We describe below the interpretation of each of its classes.

Figure 2: Structure of the top level of the SKOO ontology.

The items of scientific knowledge are all the objects that serve to structure the expression of scientific knowledge. They may be objects, such as theorems, laws (physical, chemical), models or methods that carry knowledge in themselves in the Platonic sense of true and justified belief. But they can also be “auxiliary” objects such as definitions, examples, evidence, hypotheses, problems. These objects correspond to the objects of the description class of the ontology DOLCE ([masolo2003wonderweb]).


The purpose of this class is to group all forms of expression of knowledge elements, whether linguistic or in the form of diagrams, schemas, formulas, etc.. This is a subclass of the DOLCE ontology information-object class ([masolo2003wonderweb]), and its main class Sci-linguistic-object is a subclass of the DOLCE linguistic-object class ([masolo2003wonderweb]). This class aims to include all forms and methods of expressing the concepts used to represent knowledge of the disciplines under consideration.


This class represents the activities, in the sense of activity (hyponym of human activity) in WordNet, that are used to generate elements of scientific knowledge. These activities may be experimental (process, experimentation, observation), but also empirical (conducting surveys) or formal (formally proving, calculating). The precise description of activities, in particular experimentation, is not defined in this ontology because it is already covered by other ontologies, such as SIO and EXPO.


represents all objects about which scientific knowledge is expressed. This class serves as an anchor point for classes describing the objects studied in specific fields. When using ontology in practice, the principle is to import an ontology of objects from the scientific domain concerned and create subsumption axioms for its higher level classes.

Figure 3: The higher levels of the subclasses of Sci-activity, Sci-knowledge-items and Sci-information-object.

4 Evaluation

We conducted two types of evaluations, consistency and capacity. In addition to the internal consistency of the ontology, to give an indication of the external consistency (relative to other ontologies), the ontology has been aligned with the OMDoc, DOLCE and WordNet ontologies. To do this, we translated the OMDoc and WordNet concepts into OWL classes, then created correspondence axioms of the owl:subClassOf and owl:EquivalentClass types between them and SKOO. Table 1 shows some of these axioms. We then verified the consistency of the ontologies obtained by merging SKOO, the three ontologies and the correspondence axioms (but without correspondence between DOLCE, WordNet and OMDoc).

Sci-knowledge-items MathKnowledgeItem description
Statement Statement statement
Theory Theory theory theory
Assertion Assertion assertion
Axiom Axiom axiom
Definition Definition definition
Proof Proof proof
Sci-activity activity
Process activity process
Sci-information-object information-object
Table 1: Correspondence between SKOO and OMDoc, DOLCE, WordNet classes.

To evaluate the capabilities of ontology we must verify whether, given a system of visualization of scientific knowledge, ontology makes it possible to create an appropriate abstract model for this knowledge. In the case of structured and homogeneous knowledge bases, such as Gene Ontology annotations or mathematical forms, it is easy to check the adequacy of the ontology. Indeed, this knowledge generally corresponds to statements that can be theorems. On the other hand, the case of knowledge expressed in texts is more complex. We carried out a first test by taking as a visualization system a part of an accelerator physics book ([wille2000physics]). We have modeled different concepts from the different sections of Chapter 3, in particular, the main concept expressed in Section 3.2, the complete Section 3.6 of this book (dispersion and momentum compaction factor) and a theorem used in Section 3.8 as SKOO class instances. Figure 4 shows the modeling of a physical law (Law instance) represented by an equation (Equation instance) and also the modeling of a theorem (Theorem instance) and a notation (Notation instance) used to represent a particular concept. It should be noted that in the relationships shown in this figure, the hasIndividual relationship is used by Protégé to associate the type of instance (the class) with the instance itself.

Figure 4: Some concepts contained in several sections of Chapter 3 of ([wille2000physics]) expressed as instances of SKOO ontology.

5 Conclusions and future work

We presented the construction of the first version of the SKOO ontology whose purpose is to provide a general model for the modeling of scientific knowledge to be visualized (according to the diagram of [Chi2000]). Although the concepts represented in this ontology all exist in other ontologies, none of them are grouped in such a way that they can be directly used to represent scientific knowledge. Hence the interest of the SKOO ontology. The ontology was aligned with reference ontologies to verify with a reasoner that they did not contradict them. On the other hand, we have begun to validate the capacity of this ontology to model the knowledge represented in existing knowledge bases, which does not pose any particular problem, and the knowledge represented in (hyper)texts, which is more difficult, especially for texts in the human and social sciences. After having carried out a test on a part of a physics book, we will undertake tests on books from the humanities and social sciences.

The next step in this work will be to fully model various existing knowledge visualization systems. To do this, we will use the SPARQL language to specify transformations from a knowledge model (expressed with SKOO) to a model of visualization objects (including lists, trees, graphs, texts, geometric shapes, etc.). This will validate the complete model for specifying visualization techniques. From there it will be possible to create a visualization generation system from their specification and use it to create new visualization techniques and test them with users.

During this work we realized that the interest of this ontology goes beyond the mere visualization of knowledge. It is applicable, for example, in the context of the search for precise information or automatic reasoning on large bodies of scientific knowledge.


This work has been enriched by the valuable advice and experience of Giuseppe Cosenza and Jean-Pierre Hurni, whom the authors would like to thank.