Negative findings in electronic health records and biomedical ontologies: a realist approach

PURPOSE—A substantial fraction of the observations made by clinicians and entered into patient records are expressed by means of negation or by using terms which contain negative qualifiers (as in “absence of pulse” or “surgical procedure not performed”). This seems at first sight to present problems for ontologies, terminologies and data repositories that adhere to a realist view and thus reject any reference to putative non-existing entities. Basic Formal Ontology (BFO) and Referent Tracking (RT) are examples of such paradigms. The purpose of the research here described was to test a proposal to capture negative findings in electronic health record systems based on BFO and RT. METHODS—We analysed a series of negative findings encountered in 748 sentences taken from 41 patient charts. We classified the phenomena described in terms of the various top-level categories and relations defined in BFO, taking into account the role of negation in the corresponding descriptions. We also studied terms from SNOMED-CT containing one or other form of negation. We then explored ways to represent the described phenomena by means of the types of representational units available to realist ontologies such as BFO. RESULTS—We introduced a new family of ‘lacks’ relations into the OBO Relation Ontology. The relation lacks_part, for example, defined in terms of the positive relation part_of, holds between a particular p and a universal U when p has no instance of U as part. Since p and U both exist, assertions involving ‘lacks_part’ and its cognates meet the requirements of positivity. CONCLUSION—By expanding the OBO Relation Ontology, we were able to accommodate nearly all occurrences of negative findings in the sample studied

Lexical typology : a programmatic sketch

The present paper is an attempt to lay the foundation for Lexical Typology as a new kind of linguistic typology.1 The goal of Lexical Typology is to investigate crosslinguistically significant patterns of interaction between lexicon and grammar

Relational vs Adverbial Conceptions of Phenomenal Intentionality

This paper asks whether phenomenal intentionality (intentionality that arises from phenomenal consciousness alone) has a relational structure of the sort envisaged in Russell’s theory of acquaintance. I put forward three arguments in favor of a relation view: one phenomenological, one linguistic, and one based on the view’s ability to account for the truth conditions of phenomenally intentional states. I then consider several objections to the relation view. The chief objection to the relation view takes the form of a dilemma between Platonic and Aristotelian conceptions of the properties constitutive of the contents of phenomenally intentional states on this view: the Aristotelian view seems unable to account for all the apparent contents of phenomenally intentional states, but the Platonic view seems to be ontologically unacceptable. I also consider other objections from physicalism, phenomenology, and epistemology