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Annotating Logical Forms for EHR Questions

Kirk Roberts, Dina Demner-Fushman
Finally, logical forms are created using a lambda calculus representation. We use a corpus of 446 questions asking for patient-specific information.  ...  The goal is to provide the training data necessary for semantic parsers to automatically convert EHR questions into a structured query.  ...  Conclusion We have described the creation of a corpus of EHR questions annotated with logical forms.  ... 
pmid:28503677 pmcid:PMC5428549 fatcat:vov3s7pcrrbxjai34kkohnowfa

Using FHIR to Construct a Corpus of Clinical Questions Annotated with Logical Forms and Answers

Sarvesh Soni, Meghana Gudala, Daisy Zhe Wang, Kirk Roberts
2020 AMIA Annual Symposium Proceedings  
This paper describes a novel technique for annotating logical forms and answers for clinical questions by utilizing Fast Healthcare Interoperability Resources (FHIR).  ...  Directly annotating questions with logical forms is a challenging task and involves a time-consuming step of concept normalization annotation.  ...  The text box for simple logical form is used for entering the logical form for the constructed question.  ... 
pmid:32308918 pmcid:PMC7153115 fatcat:bmpwmzhdzja2nbds5wdzfuq2ey

A Semantic Parsing Method for Mapping Clinical Questions to Logical Forms

Kirk Roberts, Braja Gopal Patra
2018 AMIA Annual Symposium Proceedings  
This paper presents a method for converting natural language questions about structured data in the electronic health record (EHR) into logical forms.  ...  When combined with a module for converting a logical form into an EHR-dependent query, this high-precision approach allows for a question answering system to provide a user with a single, verifiably correct  ...  We have previously described the structure of the logical form 23 as well as an annotated corpus of <question,logical form> pairs 15 .  ... 
pmid:29854217 pmcid:PMC5977685 fatcat:cihjbholczd7bf2vcyrkxhq7lu

DrugEHRQA: A Question Answering Dataset on Structured and Unstructured Electronic Health Records For Medicine Related Queries [article]

Jayetri Bardhan, Anthony Colas, Kirk Roberts, Daisy Zhe Wang
2022 arXiv   pre-print
Our goal is to provide a benchmark dataset for multi-modal QA systems, and to open up new avenues of research in improving question answering over EHR structured data by using context from unstructured  ...  (EHR).  ...  tables of MIMIC-III for QA. emrKBQA contains 940,000 questions, logical forms and answers which uses the structured records of MIMIC-III.  ... 
arXiv:2205.01290v1 fatcat:3vuetxqyqbcnzmdduc7cofttiq

Knowledge Graph-based Question Answering with Electronic Health Records [article]

Junwoo Park, Youngwoo Cho, Haneol Lee, Jaegul Choo, Edward Choi
2021 arXiv   pre-print
Question Answering (QA) is a widely-used framework for developing and evaluating an intelligent machine.  ...  EHR data are typically stored in a relational database, which can also be converted to a directed acyclic graph, allowing two approaches for EHR QA: Table-based QA and Knowledge Graph-based QA.  ...  Thus, we assume that SPARQL may be the more suitable logical form than SQL for the NLQ2Query task.  ... 
arXiv:2010.09394v2 fatcat:fkqpgyxxbneldhr6ymcmpx3yba

A Patient-Screening Tool for Clinical Research Based on Electronic Health Records Using OpenEHR: Development Study

Mengyang Li, Hailing Cai, Shan Nan, Jialin Li, Xudong Lu, Huilong Duan
2021 JMIR Medical Informatics  
The widespread adoption of electronic health records (EHRs) has facilitated the secondary use of EHR data for clinical research. However, screening eligible patients from EHRs is a challenging task.  ...  In addition, we demonstrated a promising solution for secondary use of EHR data using openEHR, which can be referenced by other researchers.  ...  Form-based query interfaces, such as Informatics for Integrating Biology & the Bedside (i2b2) [13] , provide a promising direction for queries on EHRs.  ... 
doi:10.2196/33192 pmid:34673526 pmcid:PMC8569542 fatcat:jrk7klly7bhylhgtcnb74czpbq

An ontology-based methodology for the migration of biomedical terminologies to electronic health records

Barry Smith, Werner Ceusters
2005 AMIA Annual Symposium Proceedings  
We accordingly describe a new framework for the treatment of both generals and particulars in biomedical information systems that is designed: 1) to provide new opportunities for the sharing and management  ...  We argue that this is not so, and that, if the EHR of the future is to fulfill its promise, then the foundations of both EHR architectures and biomedical terminologies need to be reconceived.  ...  Acknowledgments Work on this paper was carried out under the auspices of the Wolfgang Paul Program of the Humboldt Foundation and the Volkswagen Foundation Project "Forms of Life".  ... 
pmid:16779131 pmcid:PMC1560617 fatcat:cbpyzjevqjfizggec2vfasysuq

Natural Language Processing for Mimicking Clinical Trial Recruitment in Critical Care: A Semi-automated Simulation Based on the LeoPARDS Trial [article]

Hegler Tissot, Anoop Shah, Ruth Agbakoba, Amos Folarin, David Brealey, Steve Harris, Richard Dobson, Folkert Asselbergs
2019 biorxiv/medrxiv   pre-print
We manually reviewed clinical records for a random sample of additional patients identified by the algorithm but not identified for screening in the original trial.  ...  Automated review of electronic health records has been explored as a way of identifying trial participants, but much of the information is in unstructured free text rather than a computable form.  ...  Use of EHR data with NLP could also be used to extract participant data for the trial case report forms.  ... 
doi:10.1101/19005603 fatcat:agloqpm3qrddxizrgy3yiynjse

Discovering and Comparing Relational Knowledge, the Example of Pharmacogenomics

Pierre Monnin
2018 International Conference Knowledge Engineering and Knowledge Management  
Pharmacogenomics (PGx) studies the influence of the genome in drug response, with knowledge units of the form of ternary relationships genomic variation -drug -phenotype.  ...  Acknowledgments I would like to thank my supervisors Adrien Coulet and Amedeo Napoli and my co-authors Clément Jonquet, Joël Legrand, Mario Lezoche and Andon Tchechmedjiev for our on-going work.  ...  The ontology and the encoding for provenance metadata were validated by answering competency questions.  ... 
dblp:conf/ekaw/Monnin18 fatcat:vtgfjv3c2fffhb6t37dmxqblje

Ontology Middleware for Integration of IoT Healthcare Information Systems in EHR Systems

Abdullah Alamri
2018 Computers  
Most EHR systems have not been designed for integration with IoT technology; they have been designed to be more patient-centric management systems. The use of the IoT in EHR remains a long-term goal.  ...  Healthcare sectors have been at the forefront of the adoption and use of IoT technologies for efficient healthcare diagnosis and treatment.  ...  of patients' health information, the next logical step is to integrate wearables and other monitoring devices in EHR for enhancing healthcare.  ... 
doi:10.3390/computers7040051 fatcat:6em5gvccnfh2lg5sjp5iqlp7wy

Multi-source development of an integrated model for family health history

Elizabeth S Chen, Elizabeth W Carter, Tamara J Winden, Indra Neil Sarkar, Yan Wang, Genevieve B Melton
2014 JAMIA Journal of the American Medical Informatics Association  
First, clinical notes from multiple resources were annotated for FHH information. Second, questions and responses for family members in patient-facing FHH tools were examined.  ...  Lastly, elements defined in FHH-related specifications were extracted for several standards development and related organizations.  ...  for Fletcher Allen Health Care.  ... 
doi:10.1136/amiajnl-2014-003092 pmid:25336591 pmcid:PMC5901119 fatcat:4ztcsxrgprbdpkge4phlgykbk4

Conceptual Design, Implementation, and Evaluation of Generic and Standard-Compliant Data Transfer into Electronic Health Records

Rogério Blitz, Martin Dugas
2020 Applied Clinical Informatics  
annotated clinical documentation.  ...  Objectives The objective of this study is the conceptual design, implementation and evaluation of a system for generic, standard-compliant data transfer into electronic health records (EHRs).  ...  Clinical data are provided in the ODM format for efficient Generalizability of the Study The conversion of EHRs to semantically annotated, structured patient records is a decisive step for the implementation  ... 
doi:10.1055/s-0040-1710023 pmid:32462639 pmcid:PMC7253309 fatcat:ua2fxzumxrf4li22itv5wii5oa

SNOMED CT's Ontological Commitment

Stefan Schulz, Ronald Cornet
2009 Nature Precedings  
SNOMED CT is a clinical terminology that describes the meaning of terms by logical axioms.  ...  We argue that a clear understanding of to what kind of entities SNOMED CT concepts extend is crucial for the proper use and maintenance of SNOMED CT.  ...  Even the EHR interpretation makes sense here, as it is plausible that all records annotated by Tetralogy of Fallot should by considered as being annotated by Pulmonic Valve Stenosis.  ... 
doi:10.1038/npre.2009.3465.1 fatcat:ovphbl43pfezrj36dhdq2navoq

IMIA LaMB WG event: 'Biomedical Semantics in the Big Data Era', Workshop at MEDINFO 2015 – São Paulo,Brazil

Roland Cornet, Stephane Meystre, Stefan Schulz, Patrick Ruch, Tomasz Adamusiak, Laszlo Balkanyi, Jianying Hu
2019 Zenodo  
knowledge and information, by Stefan Schulz - Deep question-answering for biomedical decision support, by Patrick Ruch - Feature extraction for predictive modeling, by Jianying Hu - Connecting structured  ...  This document set document has (1) all the presentation materials: - Introduction, by Ronald Cornet - From free text to ontology, by Stephane Meystre - Bridging natural and formal languages for representing  ...  An extract, load, and transform approach separated original annotations in the EHR from the mapping process and allowed for continuous updates as the terminologies were updated.  ... 
doi:10.5281/zenodo.3398964 fatcat:ksn3rajzs5earbjd3kczdvrwdi

Learning to Ask Like a Physician [article]

Eric Lehman, Vladislav Lialin, Katelyn Y. Legaspi, Anne Janelle R. Sy, Patricia Therese S. Pile, Nicole Rose I. Alberto, Richard Raymund R. Ragasa, Corinna Victoria M. Puyat, Isabelle Rose I. Alberto, Pia Gabrielle I. Alfonso, Marianne Taliño, Dana Moukheiber (+6 others)
2022 arXiv   pre-print
We also train baseline models for trigger detection and question generation (QG), paired with unsupervised answer retrieval over EHRs.  ...  Existing question answering (QA) datasets derived from electronic health records (EHR) are artificially generated and consequently fail to capture realistic physician information needs.  ...  The authors would like to thank Sierra Tseng for feedback on a draft of this manuscript, as well as Melina Young and Maggie Liu for their help in designing some of the figures.  ... 
arXiv:2206.02696v1 fatcat:bqqanoqajbdb3dinpe5n4lkdke
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