Negation in Ontologies

Inconsistencies, Negations and Changes in Ontologies
Proceeding of the 21st National Conference on Artificial Intelligence, Boston, US, July 16-20, 2006. AAAI.
Giorgos Flouris, Zhisheng Huang, Jeff Z. Pan, Dimitris Plexousakis, Holger Wache

An introduction to Description Logics and Ontology Languages
Magdalena Ortiz
June 2016

Das Nicht im Satz

Combining Ontologies with Rules (Two Different Worlds?)


    • Viruses do not have any capacity for locomotion and, therefore, the collision event is simply a random process determined by diffusion.
      {Sherris Medical Microbiology, 7e © 2018 > Chapter 6: Viruses—Basic Concepts > VIRUS REPLICATION CYCLE Adsorption or Attachment}
    • a significant difference between Na+ and Ca2+ is the absence of Ca2+ reabsorption in the collecting duct.
      {The Big Picture Physiology: Medical Course & Step 1 Review, 2e © 2020 > Chapter 6: Renal Physiology and Acid-Base Balance > RENAL CALCIUM HANDLING}
    • It lacks diuretic effect, apparently because it lacks a sulfonamide group.
      {MeSH > diazoxide}
    • Penicillamine is an α-amino acid metabolite of penicillin, although it has no antibiotic properties.
      {, 2021}
    • somatic sensation refers to the sensations of touch or pressure, vibration, joint position, pain, and temperature, and to more complex functions that rely on these primary sensory modalities (eg, two-point discrimination, stereognosis, graphesthesia);
      it excludes special senses such as smell, vision, taste, and hearing.
      {Clinical Neurology, 11e © 2021}
    • Anaerobic bacteria are not associated with spontaneous bacterial peritonitis.
      {Current Medical Diagnosis & Treatment 2021 > 15-09: Spontaneous Bacterial Peritonitis}
    • The left dorsalis pedis and posterior tibialis pulses were not palpable.
      {Patient Management in the Telemetry/Cardiac Step-Down Unit © 2020 > Ch 8: Peripheral Artery Disease}
    • Ultrasound showed no evidence of cholecystitis.
      {Textbook of Complex General Surgical Oncology, © 2018}


No todo conocimiento puede codificarse

Reconocemos que no todo conocimiento puede codificarse.
(La complejidad del conocimiento: el conocimiento tacito frente al explicito. p. 37)

Smart Things to Know About Knowledge Management
Thomas M. Koulopoulus and Carl Frappaolo

Knowledge Management, 2nd Edition
Carl Frappaolo
March 2006, Capstone


Ontology > Exception

apicoplasts have been detected in all apicomplexan parasites studied, with the exception of Cryptosporidium

DNA viruses replicate in the nucleus by using host RNA polymerase for transcription and either host or viral DNA polymerase for replication (exception are poxviruses that replicate in the cytoplasm).
Sherris Medical Microbiology, 7e ©2018 > Chapter 6: Viruses—Basic Concepts

Most RNA viruses replicate in the cytoplasm—the immediate site of entry with the exception of influenza viruses and the retroviruses that replicate in the nucleus.
Sherris Medical Microbiology, 7e ©2018 > Chapter 6: Viruses—Basic Concepts


Ontology resources

Symptom ontology

The DBpedia Ontology (2014)
accessed: January 3, 2015

cited by:
Stanford, June 2012





Merriam-Webster Medical Dictionary

============================================= => 13,200 pages

ChEBI Ontology
accessed: 2020




intramembranous ossification

The Dictionary of Cell and Molecular Biology



Movie “Bloodshot”:
– They are in my blood?
– They are your blood.

accessed: March 2021
For both terms and relational expressions in BFO, we distinguish between primitive and defined. ‘Entity’ is an example of one such primitive term.
Primitive terms in a highest-level ontology such as BFO are terms that are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms.”

A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity.

There are multiple grand truths

Structure Data 2014: Democratizing Artificial Intelligence with APIs
Apr 11, 2014
If you think Siri is smart, you haven’t seen anything yet. Hear how APIs are putting cutting-edge capabilities in deep learning, cognitive computing and artificial intelligence into the hands of developers everywhere.
Elliot Turner — CEO, AlchemyAPI
Stephen Gold — VP, WW Marketing and Sales Operations, Watson Solutions, IBM Software Group

00:40 cognition as a service
02:05 programatic computing
04:00 in congnitive systems, there is no absolute outcome
05:00 the grand truth
05:40 context is key. You can have multiple grand truths, depending on the situation. Vampires are real in certain contexts, but they’re not in others.

“… the data, which in the end would form the ‘grand truth’ that Watson would regard as baseline facts.”

There seems to be no term in the NN literature for the set of all cases that you want to be able to generalize to. Statisticians call this set the “population”. Tsypkin (1971) called it the “grand truth distribution,” but this term has never caught on.
Tsypkin, Y. (1971), Adaptation and Learning in Automatic Systems, NY: Academic Press.

the notion of context as a critical feature to understanding anything. Bateson (1979) was adamant in making the point that “without context, words and actions have no meaning at all” (p. 16).
Words and actions need to be situated in one or more relevant and meaningful contexts, in order to develop any degree of complex understandings.
The use of metapatterns for research into complex systems of teaching, learning, and schooling. Part II: Applications.
Bloom, Jeffrey W., & Volk, Tyler. (2007).
Complicity: An International Journal of Complexity and Education. 4(1): 45—68.

Category Theory for Scientists

Category Theory for Scientists
David I. Spivak
MIT. 2013

Department of Mathematics
Spring 2013

Book (Sept 2013)


nLab > Category Theory
Dec. 2014