• Corpus ID: 4442123

"Lmo-2 interacts with elf-2" - On the Meaning of Common Statements in Biomedical Literature

  title={"Lmo-2 interacts with elf-2" - On the Meaning of Common Statements in Biomedical Literature},
  author={Stefan Schulz and Ludger Jansen},
Statements about the behavior of biological entities, e.g. about the interaction between two proteins, abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that is necessary to take into account in the practice of biomedical ontology engineering. Several concurring formalizations are proposed. Emphasis is… 
Spatial location and its relevance for terminological inferences in bio-ontologies
The proposed formalism allows to deal consistently with "role propagation along non-taxonomic hierarchies" in biomedical ontologies and seems to be suitable for the redesign of compositional hierarchies in (bio)medical terminology systems.
Concept Systems and Ontologies: Recommendations for Basic Terminology.
  • G. Klein, Barry Smith
  • Computer Science
    Transactions of the Japanese Society for Artificial Intelligence = Jinko Chino Gakkai ronbunshi
  • 2010
This paper proposes to use the term "concept" in the context of producing defined professional terminologies with one specific and consistent meaning which is proposed for adoption as the agreed meaning of the term in future terminological research, and specifically in the development of formal terminologies to be used in computer systems.


Relations in biomedical ontologies
A methodology for providing consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation is advanced.
Thesaurus or Logical Ontology, Which One Do We Need for Text Mining?
This work argues that a thesaurus (i.e. an organised collection of terms enriched with relations) is more useful for text mining applications than formal ontologies, and proposes a text-centered approach for knowledge sharing, as an alternative to formal ontology.
Biomedical ontologies: What part-of is and isn't
From GENIA to BIOTOP - Towards a Top-Level Ontology for Biology
This work introduces BIOTOP, an upper ontology of physical continuants in the domain of biology, with a coverage similar to the GENIA ontology, and uses OWL-DL as a formal knowledge representation language and may thus use a terminological reasoner for classification in order to check and maintain consistency during the ontology engineering phase.
Ontological Categories in GOL
The present paper gives an overview about the basic categories of the GOL-ontology and a proposal for an integrated family of top-level ontologies and will be applied to several fields of medicine, in particular to the field of Clinical Trials.
The Ontology of Tendencies and Medical Information Sciences
In order to develop the ontology of tendencies for use in the representation of medical knowledge, tendencies are compared with other kinds of entities possessing the
Sweetening Ontologies with DOLCE
In this paper we introduce the DOLCE upper level ontology, the first module of a Foundational Ontologies Library being developed within the WonderWeb project. DOLCE is presented here in an intuitive
Granularity, scale and collectivity: When size does and does not matter
The Cornucopia of Formal-Ontological Relations
The paper presents a new method for generating typologies of formal-ontological relations. The guiding idea is that formal relations are those sorts of relations which hold between entities which are
The Description Logic Handbook: Theory, Implementation, and Applications
This new edition of The Description Logic Handbook provides a thorough account of the subject, covering all aspects of research in this field, namely: theory, implementation, and applications.