TY - JOUR AU - Mahner, M. AU - Kary, M. PY - 1997 DA - 1997// TI - What exactly are genomes, genotypes and phenotypes? And what about phenomes? JO - J Theor Biol VL - 186 UR - https://doi.org/10.1006/jtbi.1996.0335 DO - 10.1006/jtbi.1996.0335 ID - Mahner1997 ER - TY - JOUR AU - Hoehndorf, R. AU - Oellrich, A. AU - Rebholz-Schuhmann, D. PY - 2010 DA - 2010// TI - Interoperability between phenotype and anatomy ontologies JO - Bioinformatics. VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq578 DO - 10.1093/bioinformatics/btq578 ID - Hoehndorf2010 ER - TY - JOUR AU - Uciteli, A. AU - Groß, S. AU - Kireyev, S. AU - Herre, H. PY - 2011 DA - 2011// TI - An ontologically founded architecture for information systems in clinical and epidemiological research JO - J Biomed Semantics VL - 2 UR - https://doi.org/10.1186/2041-1480-2-S4-S1 DO - 10.1186/2041-1480-2-S4-S1 ID - Uciteli2011 ER - TY - JOUR AU - Scheuermann, R. H. AU - Ceusters, W. AU - Smith, B. PY - 2009 DA - 2009// TI - Toward an ontological treatment of disease and diagnosis JO - Summit Translat Bioinforma VL - 2009 ID - Scheuermann2009 ER - TY - JOUR AU - Deans, A. R. AU - Lewis, S. E. AU - Huala, E. AU - Anzaldo, S. S. AU - Ashburner, M. AU - Balhoff, J. P. PY - 2015 DA - 2015// TI - Finding our way through phenotypes JO - PLoS Biol VL - 13 UR - https://doi.org/10.1371/journal.pbio.1002033 DO - 10.1371/journal.pbio.1002033 ID - Deans2015 ER - TY - JOUR AU - Robinson, P. N. PY - 2012 DA - 2012// TI - Deep phenotyping for precision medicine JO - Hum Mutat VL - 33 UR - https://doi.org/10.1002/humu.22080 DO - 10.1002/humu.22080 ID - Robinson2012 ER - TY - JOUR AU - Mo, H. AU - Thompson, W. K. AU - Rasmussen, L. V. AU - Pacheco, J. A. AU - Jiang, G. AU - Kiefer, R. PY - 2015 DA - 2015// TI - Desiderata for computable representations of electronic health records-driven phenotype algorithms JO - J Am Med Inform Assoc JAMIA VL - 22 UR - https://doi.org/10.1093/jamia/ocv112 DO - 10.1093/jamia/ocv112 ID - Mo2015 ER - TY - JOUR AU - Köhler, S. AU - Vasilevsky, N. A. AU - Engelstad, M. AU - Foster, E. AU - McMurry, J. AU - Aymé, S. PY - 2017 DA - 2017// TI - The human phenotype ontology in 2017 JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1039 DO - 10.1093/nar/gkw1039 ID - Köhler2017 ER - TY - JOUR AU - Hoehndorf, R. AU - Schofield, P. N. AU - Gkoutos, G. V. PY - 2011 DA - 2011// TI - PhenomeNET: a whole-phenome approach to disease gene discovery JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkr538 DO - 10.1093/nar/gkr538 ID - Hoehndorf2011 ER - TY - JOUR AU - Loebe, F. AU - Stumpf, F. AU - Hoehndorf, R. AU - Herre, H. PY - 2012 DA - 2012// TI - Towards improving phenotype representation in OWL JO - J Biomed Semantics VL - 3 UR - https://doi.org/10.1186/2041-1480-3-S2-S5 DO - 10.1186/2041-1480-3-S2-S5 ID - Loebe2012 ER - TY - JOUR AU - Gehring, S. AU - Eulenfeld, R. PY - 2018 DA - 2018// TI - German medical informatics initiative: unlocking data for research and health care JO - Methods Inf Med VL - 57 UR - https://doi.org/10.3414/ME18-13-0001 DO - 10.3414/ME18-13-0001 ID - Gehring2018 ER - TY - JOUR AU - Semler, S. C. AU - Wissing, F. AU - Heyder, R. PY - 2018 DA - 2018// TI - German medical informatics initiative JO - Methods Inf Med VL - 57 UR - https://doi.org/10.3414/ME18-03-0003 DO - 10.3414/ME18-03-0003 ID - Semler2018 ER - TY - STD TI - Winter A, Stäubert S, Ammon D, Aiche S, Beyan O, Bischoff V, et al. Smart Medical Information Technology for Healthcare (SMITH). Methods Inf Med. 2018;57(S 01):e92–105. ID - ref13 ER - TY - STD TI - Meineke FA, Stäubert S, Löbe M, Uciteli A, Löffler M. Design and concept of the SMITH phenotyping pipeline. Stud Health Technol Inform. 2019;267:164–72. ID - ref14 ER - TY - STD TI - HL7 FHIR. https://www.hl7.org/fhir/. Accessed 12 Aug 2020. UR - https://www.hl7.org/fhir/ ID - ref15 ER - TY - STD TI - FHIR Search. https://www.hl7.org/fhir/search.html. Accessed 12 Aug 2020. UR - https://www.hl7.org/fhir/search.html ID - ref16 ER - TY - STD TI - ART-DECOR®. https://www.art-decor.org/. Accessed 12 Aug 2020. UR - https://www.art-decor.org/ ID - ref17 ER - TY - STD TI - Kerndatensatz | Medizininformatik-Initiative. https://www.medizininformatik-initiative.de/de/kerndatensatz. Accessed 12 Aug 2020. UR - https://www.medizininformatik-initiative.de/de/kerndatensatz ID - ref18 ER - TY - STD TI - Hoehndorf R, Ngomo A-CN, Herre H. Developing consistent and modular software models with ontologies. In: Fujita H, Marik V, editors. New trends in software methodologies, tools and techniques: proceedings of the eighth SoMeT_09: IOS Press; 2009. p. 399–412. ID - ref19 ER - TY - STD TI - Herre H. General Formal Ontology (GFO): a foundational ontology for conceptual modelling. In: Poli R, Healy M, Kameas A, editors. Theory and applications of ontology: computer applications. Netherlands: Springer; 2010. p. 297–345. ID - ref20 ER - TY - STD TI - Herre H. Towards a new foundational ontology of properties, attributives and data. In: Borgo S, Ferrario R, Masolo C, Vieu L, editors. Ontology makes sense - essays in honor of Nicola Guarino: IOS Press; 2019. p. 194–210. https://doi.org/10.3233/978-1-61499-955-3-194. ID - ref21 ER - TY - JOUR AU - Uciteli, A. AU - Neumann, J. AU - Tahar, K. AU - Saleh, K. AU - Stucke, S. AU - Faulbrück-Röhr, S. PY - 2017 DA - 2017// TI - Ontology-based specification, identification and analysis of perioperative risks JO - J Biomed Semantics VL - 8 UR - https://doi.org/10.1186/s13326-017-0147-8 DO - 10.1186/s13326-017-0147-8 ID - Uciteli2017 ER - TY - STD TI - OWL API. http://owlcs.github.io/owlapi/. Accessed 12 Aug 2020. UR - http://owlcs.github.io/owlapi/ ID - ref23 ER - TY - STD TI - HermiT Reasoner. http://www.hermit-reasoner.com/. Accessed 12 Aug 2020. UR - http://www.hermit-reasoner.com/ ID - ref24 ER - TY - STD TI - Openllet Reasoner. https://github.com/Galigator/openllet. Accessed 12 Aug 2020. UR - https://github.com/Galigator/openllet ID - ref25 ER - TY - STD TI - Dropwizard. https://www.dropwizard.io. Accessed 12 Aug 2020. UR - https://www.dropwizard.io ID - ref26 ER - TY - STD TI - Klimaschewski U. EvalEx - Java expression evaluator. https://github.com/uklimaschewski/EvalEx. Accessed 12 Aug 2020. UR - https://github.com/uklimaschewski/EvalEx ID - ref27 ER - TY - JOUR AU - Lampert, T. AU - Müters, S. AU - Stolzenberg, H. AU - Kroll, L. E. PY - 2014 DA - 2014// TI - Measurement of socioeconomic status in the KiGGS study: first follow-up (KiGGS wave 1) JO - Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz VL - 57 UR - https://doi.org/10.1007/s00103-014-1974-8 DO - 10.1007/s00103-014-1974-8 ID - Lampert2014 ER - TY - STD TI - Obesity: preventing and managing the global epidemic (Report of a WHO Consultation). World Health Organization (WHO); 2000. http://www.who.int/entity/nutrition/publications/obesity/WHO_TRS_894/en/. Accessed 12 Aug 2020. UR - http://www.who.int/entity/nutrition/publications/obesity/WHO_TRS_894/en/ ID - ref29 ER - TY - STD TI - Waist circumference and waist-hip ratio: report of a WHO Expert Consultation. World Health Organization (WHO); 2008. http://www.who.int/nutrition/publications/obesity/WHO_report_waistcircumference_and_waisthip_ratio/en/. Accessed 12 Aug 2020. UR - http://www.who.int/nutrition/publications/obesity/WHO_report_waistcircumference_and_waisthip_ratio/en/ ID - ref30 ER - TY - STD TI - Loeffler M, Engel C, Ahnert P, Alfermann D, Arelin K, Baber R, et al. The LIFE-Adult-Study: objectives and design of a population-based cohort study with 10,000 deeply phenotyped adults in Germany. BMC Public Health. 2015;15:691. ID - ref31 ER - TY - STD TI - SPSS Software. https://www.ibm.com/analytics/spss-statistics-software. Accessed 12 Aug 2020. UR - https://www.ibm.com/analytics/spss-statistics-software ID - ref32 ER - TY - JOUR AU - Vincent, J. -. L. AU - Moreno, R. AU - Takala, J. AU - Willatts, S. AU - Mendonça, A. D. AU - Bruining, H. PY - 1996 DA - 1996// TI - The SOFA (sepsis-related organ failure assessment) score to describe organ dysfunction/failure JO - Intensive Care Med VL - 22 UR - https://doi.org/10.1007/BF01709751 DO - 10.1007/BF01709751 ID - Vincent1996 ER - TY - STD TI - FHIR Subscription. https://www.hl7.org/fhir/subscription.html. Accessed 12 Aug 2020. UR - https://www.hl7.org/fhir/subscription.html ID - ref34 ER - TY - STD TI - Automatic Layout | yEd. https://yed.yworks.com/support/tutorial/apply_layout.html. Accessed 12 Aug 2020. UR - https://yed.yworks.com/support/tutorial/apply_layout.html ID - ref35 ER - TY - STD TI - yEd Graph Editor. http://www.yworks.com/yed. Accessed 12 Aug 2020. UR - http://www.yworks.com/yed ID - ref36 ER - TY - STD TI - Type 2 Diabetes Mellitus | PheKB. https://phekb.org/sites/phenotype/files/T2DM-algorithm.pdf. Accessed 12 Aug 2020. UR - https://phekb.org/sites/phenotype/files/T2DM-algorithm.pdf ID - ref37 ER - TY - STD TI - Leipzig Health Atlas: Ontological Modelling of T2DM Phenotype using Phenotype Manager (PhenoMan). https://health-atlas.de/lha/81CQ04CX4Q-9. Accessed 12 Aug 2020. UR - https://health-atlas.de/lha/81CQ04CX4Q-9 ID - ref38 ER - TY - JOUR AU - Fernández-Breis, J. T. AU - Maldonado, J. A. AU - Marcos, M. AU - Legaz-García, M. AU - Moner, D. AU - Torres-Sospedra, J. PY - 2013 DA - 2013// TI - Leveraging electronic healthcare record standards and semantic web technologies for the identification of patient cohorts JO - J Am Med Inform Assoc VL - 20 UR - https://doi.org/10.1136/amiajnl-2013-001923 DO - 10.1136/amiajnl-2013-001923 ID - Fernández-Breis2013 ER - TY - STD TI - openEHR. https://www.openehr.org/. Accessed 12 Aug 2020. UR - https://www.openehr.org/ ID - ref40 ER - TY - JOUR AU - Papež, V. AU - Denaxas, S. AU - Hemingway, H. PY - 2018 DA - 2018// TI - Evaluation of semantic web Technologies for Storing Computable Definitions of electronic health records Phenotyping algorithms JO - AMIA Annu Symp Proc VL - 2017 ID - Papež2018 ER - TY - JOUR AU - Pathak, J. AU - Bailey, K. R. AU - Beebe, C. E. AU - Bethard, S. AU - Carrell, D. C. AU - Chen, P. J. PY - 2013 DA - 2013// TI - Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium JO - J Am Med Inform Assoc VL - 20 UR - https://doi.org/10.1136/amiajnl-2013-001939 DO - 10.1136/amiajnl-2013-001939 ID - Pathak2013 ER - TY - STD TI - QDM - Quality Data Model. https://ecqi.healthit.gov/qdm. Accessed 12 Aug 2020. UR - https://ecqi.healthit.gov/qdm ID - ref43 ER - TY - STD TI - HQMF - Health Quality Measure Format. https://ecqi.healthit.gov/hqmf. Accessed 12 Aug 2020. UR - https://ecqi.healthit.gov/hqmf ID - ref44 ER - TY - JOUR AU - Pacheco, J. A. AU - Rasmussen, L. V. AU - Kiefer, R. C. AU - Campion, T. R. AU - Speltz, P. AU - Carroll, R. J. PY - 2018 DA - 2018// TI - A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record environments JO - J Am Med Inform Assoc VL - 25 UR - https://doi.org/10.1093/jamia/ocy101 DO - 10.1093/jamia/ocy101 ID - Pacheco2018 ER - TY - STD TI - KNIME. https://www.knime.com/. Accessed 12 Aug 2020. UR - https://www.knime.com/ ID - ref46 ER - TY - JOUR AU - Hochheiser, H. AU - Castine, M. AU - Harris, D. AU - Savova, G. AU - Jacobson, R. S. PY - 2016 DA - 2016// TI - An information model for computable cancer phenotypes JO - BMC Med Inform Decis Mak VL - 16 UR - https://doi.org/10.1186/s12911-016-0358-4 DO - 10.1186/s12911-016-0358-4 ID - Hochheiser2016 ER - TY - JOUR AU - Haarbrandt, B. AU - Jack, T. AU - Marschollek, M. PY - 2016 DA - 2016// TI - Automated transformation of openEHR data instances to OWL JO - Stud Health Technol Inform VL - 223 ID - Haarbrandt2016 ER - TY - JOUR AU - Rosse, C. AU - Mejino, J. L. V. PY - 2003 DA - 2003// TI - A reference ontology for biomedical informatics: the foundational model of anatomy JO - J Biomed Inform VL - 36 UR - https://doi.org/10.1016/j.jbi.2003.11.007 DO - 10.1016/j.jbi.2003.11.007 ID - Rosse2003 ER - TY - JOUR AU - Washington, N. L. AU - Haendel, M. A. AU - Mungall, C. J. AU - Ashburner, M. AU - Westerfield, M. AU - Lewis, S. E. PY - 2009 DA - 2009// TI - Linking human diseases to animal models using ontology-based phenotype annotation JO - PLoS Biol VL - 7 UR - https://doi.org/10.1371/journal.pbio.1000247 DO - 10.1371/journal.pbio.1000247 ID - Washington2009 ER - TY - STD TI - FHIRPath - FHIR v4.0.1. https://www.hl7.org/fhir/fhirpath.html. Accessed 12 Aug 2020. UR - https://www.hl7.org/fhir/fhirpath.html ID - ref51 ER - TY - STD TI - Clinical Quality Language (CQL). https://cql.hl7.org/. Accessed 12 Aug 2020. UR - https://cql.hl7.org/ ID - ref52 ER - TY - STD TI - FHIR Profiling. https://www.hl7.org/fhir/profiling.html. Accessed 12 Aug 2020. UR - https://www.hl7.org/fhir/profiling.html ID - ref53 ER -