=Paper=
{{Paper
|id=Vol-2285/ICBO_2018_paper_16
|storemode=property
|title=A Falsification Approach to Create and Check Ontology Definitions
|pdfUrl=https://ceur-ws.org/Vol-2285/ICBO_2018_paper_16.pdf
|volume=Vol-2285
|authors=Citlalli Mejía,Julio Collado-Vides
|dblpUrl=https://dblp.org/rec/conf/icbo/MejiaC18
}}
==A Falsification Approach to Create and Check Ontology Definitions==
https://ceur-ws.org/Vol-2285/ICBO_2018_paper_16.pdf
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA 1
A Falsification approach to create and check ontology
definitions
Citlalli Mejía-Almonte, Julio Collado-Vides
Computational Genomics Program
Center for Genomic Sciences, UNAM
Cuernavaca, México
Abstract— One of the most important features of ontological
representation of knowledge is the possibility of creating formal II. METHODS
definitions that allow automatic reasoning. Reasoning in Ontological primitive classes are described only by
ontologies is based on symbolic logic representation. This necessary conditions, whereas defined classes are described by
requires that ontological definitions state either necessary necessary and sufficient conditions [6]. Necessary and
conditions or necessary and sufficient conditions. Here we
sufficient conditions are explained in terms of the conditional
propose a manual approach to review the necessity and
sufficiency of ontological definitions that can be used to analyze logical relation. Let A be a class or concept and let P be some
the most prominent concepts of a domain. property. There are many language items to refer to this [7]:
• A only if P; if A, then P; P is necessary for A; and A is
Keywords—falsification; ontology definition; necessary and sufficient for P.
sufficient conditions
Any of these statements means that all instances of A
I. INTRODUCTION satisfy property P, or that for all objects of the universe, if
some satisfies P then it is an instance of A. When this logical
Since the publication of the Gene Ontology, Biomedical condition holds in both directions, that is:
ontologies have thrived. As a result, a growing number of
ontologies are created to represent all aspects of the biological • A is necessary and sufficient condition for B and B is
world. Currently there are 182 ontologies in OntoBee [1] and necessary and sufficient condition for A
716 in BioPortal [2], the OBO foundry [3] and the NCBO [4] We say that A means B, or A is equivalent to B. This
ontology repositories respectively. Some of these ontologies relation of equivalency is the one we look for to make
are foundational, for they are species-independent models ontological definitions.
aimed to be reused in or extended by species-specific
ontologies. Although categorization of ontologies into species Necessity of P is proved by demonstrating that all instances
dependent and species independent is not straightforward if of A have property P. However, demonstration of necessity is
authors have not established it in the scope description, we epistemologically impossible in experimental sciences, even
found 57 species-independent, 36 taxonomically restricted (at assuming an agent with the complete knowledge of the current
higher taxonomic ranges), 19 whose scope does not include state of affairs. Thus, we took a falsification approach [8].
biological entities, and 63 species-specific ontologies in
OntoBee. When authors did not specify taxonomic range, this • We can disprove sufficiency by finding some object that
classification was based on the next criteria: species- has property P and does not belong to A.
independent if the ontology includes classes representing • We can disprove necessity by finding some instance of A
organisms of more than one kingdom, and species-specific if that does not hold property P.
the ontology is human-centric.
Based on this, we propose the following workflow to
This large set of computational models can provide the analyze necessity and sufficiency of proposed definitions:
means for automatic reasoning to generate mechanistic
hypothesis for the biomedical research [5]. However, • Retrieve definitions from diverse sources such as the
foundational, species-independent ontologies must have formal literature and extant ontologies.
definitions general enough to support pertinent inferences
throughout all kingdoms of life. • Based on the retrieved definitions, generate a list of the
Here we present a manual approach to check the suitability commonly used properties to define these concepts.
of necessity and sufficiency of ontological definitions for the
current state of affairs in biological sciences. This allowed us • Search counter examples for definitions to discard
to find out that if we consider natural language definitions of necessity or sufficiency of the defining properties.
extant foundational ontologies as necessary and sufficient
conditions, some prokaryotic instances may be left out.
ICBO 2018 August 7-10, 2018 1
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA 2
• Keep those properties that were not falsified to generate a We are currently applying this approach to generate an
new definition. ontology on prokaryotic gene regulation. In the process, we are
reviewing the applicability of definitions of the existing
III. RESULTS ontologies. This step-by-step workflow can ease up the
involvement of domain-experts in the generation of logically-
As a matter of example, we apply this approach to the sound ontological definitions based on ontological realism.
definition of bacterial promoter in the sequence ontology (SO) However, we have not planned any training session to help
[9]. The following are the two relevant definitions extracted other groups to check their ontological definitions.
from this ontology in July 2018:
IV. LIMITATIONS
• Promoter: A regulatory_region composed of the TSS(s)
and binding sites for TF_complexes of the basal This approach can be useful to apply OBO principle of
transcription machinery maintenance [3]. However, as it requires huge human effort,
we believe it could be applied in a top-down approach to check
o Bacterial RNA-polymerase promoter: A DNA for the necessity and sufficiency of the most general or
sequence to which bacterial RNA polymerase prominent concepts of a domain.
binds, to begin transcription.
ACKNOWLEDGMENT
Bacterial RNA-polymerase promoter is a subclass of
promoter. Thus, the list of properties that define a Bacterial C.M.A. is a doctoral student from Programa de Doctorado
RNA-polymerase promoter is: en Ciencias Biomédicas, UNAM, receives fellowship 576333
from CONACYT and received financial aid from Programa de
• has part some TSS Apoyos para Estudios de Posgrado (PAEP) for this conference.
• has part some basal TF binding sites
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