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

@article{citeulike:1195416, abstract = {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.}, address = {Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, NY, USA(1).}, author = {Ceusters, Werner and Elkin, Peter and Smith, Barry }, citeulike-article-id = {1195416}, doi = {10.1016/j.ijmedinf.2007.02.003}, issn = {1386-5056}, journal = {Int J Med Inform}, keywords = {medicine, negation}, month = {March}, posted-at = {2007-10-24 14:08:03}, priority = {2}, title = {Negative findings in electronic health records and biomedical ontologies: A realist approach.}, url = {http://dx.doi.org/10.1016/j.ijmedinf.2007.02.003}, year = {2007} }

TY - JOUR ID - citeulike:1195416 L3 - citeulike-article-id:1195416 TI - Negative findings in electronic health records and biomedical ontologies: A realist approach. JF - Int J Med Inform AD - Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, NY, USA(1). SN - 1386-5056 N2 - 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. KW - medicine KW - negation AU - Ceusters, Werner AU - Elkin, Peter AU - Smith, Barry PY - 2007/03/16/ UR - http://dx.doi.org/10.1016/j.ijmedinf.2007.02.003 ER -