Knowledge Representation and Management, It’s Time to Integrate!Findings from the IMIA Yearbook Section on Knowledge Representation and Management
11 September 2017 (online)
Objectives: To select, present, and summarize the best papers published in 2016 in the field of Knowledge Representation and Management (KRM).
Methods: A comprehensive and standardized review of the medical informatics literature was performed based on a PubMed query.
Results: Among the 1,421 retrieved papers, the review process resulted in the selection of four best papers focused on the integration of heterogeneous data via the development and the alignment of terminological resources. In the first article, the authors provide a curated and standardized version of the publicly available US FDA Adverse Event Reporting System. Such a resource will improve the quality of the underlying data, and enable standardized analyses using common vocabularies. The second article describes a project developed in order to facilitate heterogeneous data integration in the i2b2 framework. The originality is to allow users integrate the data described in different terminologies and to build a new repository, with a unique model able to support the representation of the various data. The third paper is dedicated to model the association between multiple phenotypic traits described within the Human Phenotype Ontology (HPO) and the corresponding genotype in the specific context of rare diseases (rare variants). Finally, the fourth paper presents solutions to annotation-ontology mapping in genome-scale data. Of particular interest in this work is the Experimental Factor Ontology (EFO) and its generic association model, the Ontology of Biomedical AssociatioN (OBAN).
Conclusion: Ontologies have started to show their efficiency to integrate medical data for various tasks in medical informatics: electronic health records data management, clinical research, and knowledge-based systems development.
- 1 Griffon N, Charlet J, Darmoni S. Knowledge representation and management: towards an integration of a semantic web in daily health practice. Yearb Med Inform 2013; 08: 155-8.
- 2 Griffon N, Charlet J, Darmoni SJ. Managing free text for secondary use of health data. Yearb Med Inform 2014; 09: 167-9.
- 3 Charlet J, Darmoni SJ. Knowledge Representation and Management. From Ontology to Annotation. Findings from the Yearbook 2015 Section on Knowledge Representation and Management. Yearb Med Inform 2015; 10 (01) 134-6.
- 4 Soualmia LF, Charlet J. Efficient Results in Semantic Interoperability for Health Care. Findings from the Section on Knowledge Representation and Management. Yearb Med Inform. 2016 01 184-7.
- 5 Lamy J-B, Séroussi B, Griffon N, Kerdelhué G, Jaulent M-C, Bouaud J. Toward a formalization of the process to select IMIA Yearbook best papers. Methods Inf Med 2015; 54 (02) 135-44.
- 6 Sarntivijai S, Vasant D, Jupp S, Saunders G, Bento AP, Gonzalez D. et al. Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation. J Biomed Semantics 2016; 07: 8.
- 7 Banda JM, Evans L, Vanguri RS, Tatonetti NP, Ryan PB, Shah NH. A curated and standardized adverse drug event resource to accelerate drug safety research. Sci Data 2016; 03: 160026.
- 8 Bauer CR, Ganslandt T, Baum B, Christoph J, Engel I, Lobe M. et al. Integrated Data Repository Toolkit (IDRT). A Suite of Programs to Facilitate Health Analytics on Heterogeneous Medical Data. Methods Inf Med 2016; 55 (02) 125-35.
- 9 Greene D, NIHR BioResource, Richardson S, Turro E. Phenotype Similarity Regression for Identifying the Genetic Determinants of Rare Diseases. Am J Hum Genet 2016; 98 (03) 490-9.
- 10 Blank CE, Cui H, Moore LR, Walls RL. MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. J Biomed Semantics 2016; 07: 18.
- 11 Detwiler LT, Mejino JL, Brinkley JF. From frames to OWL2: Converting the Foundational Model of Anatomy. Artif Intell Med 2016; 69: 12-21.
- 12 Hayman GT, Laulederkind SJ, Smith JR, Wang SJ, Petri V, Nigam R. et al. The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database. Database (Oxford). 2016 2016.
- 13 Hochheiser H, Castine M, Harris D, Savova G, Jacobson RS. An information model for computable cancer phenotypes. BMC Med Inform Decis Mak 2016; 16 (01) 121.
- 14 Hoffman JM, Dunnenberger HM, Kevin JHicks, Caudle KE, Whirl MCarrillo, Freimuth RR. et al. Developing knowledge resources to support precision medicine: principles from the Clinical Pharmacogenetics Implementation Consortium (CPIC). J Am Med Inform Assoc 2016; 23 (04) 796-801.
- 15 Johnson SG, Speedie S, Simon G, Kumar V, Westra BL. Application of An Ontology for Characterizing Data Quality For a Secondary Use of EHR Data. Appl Clin Inform 2016; 07 (01) 69-88.
- 16 Jupp S, Burdett T, Welter D, Sarntivijai S, Parkinson H, Malone J. Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates. J Biomed Semantics 2016; 07: 17.
- 17 Klann JG, Abend A, Raghavan VA, Mandl KD, Murphy SN. Data interchange using i2b2. J Am Med Inform Assoc 2016; 23 (05) 909-15.
- 18 Saunders CJ, Jalali MSefid Dashti, Gamieldien J. Semantic interrogation of a multi knowledge domain ontological model of tendinopathy identifies four strong candidate risk genes. Sci Rep 2016; 06: 19820.
- 19 Thanintorn N, Wang J, Ersoy I, Al-Taie Z, Jiang Y, Wang D. et al. Rdf Sketch Maps - Knowledge Complexity Reduction for Precision Medicine Analytics. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing 2016; 21: 417-28.
- 20 Workman TE, Fiszman M, Cairelli MJ, Nahl D, Rindflesch TC. Spark, an application based on Serendipitous Knowledge Discovery. J Biomed Inform 2016; 60: 23-37.
- 21 Banda JM, Evans L, Vanguri RS, Tatonetti NP, Ryan PB, Shah NH. Data from: A curated and standardized adverse drug event resource to accelerate drug safety research. Dryad Data Repository. 2016 http://dx.doi.org/10.5061/dryad.8q0s4.
- 22 Rosenbloom ST, Carroll RJ, Warner JL, Matheny ME, Denny JC. Representing Knowledge Consistently Across Health Systems. Yearb Med Inform. 2017: 139-47.