Relevant bibliographies by topics / Clinical annotations

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Clinical annotations'

Author: Grafiati
Published: 16 November 2024
Last updated: 31 July 2025

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Journal articles on the topic "Clinical annotations"

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Yost, Shawn, Márton Münz, Shazia Mahamdallie, Anthony Renwick, Elise Ruark, and Nazneen Rahman. "Clinical Annotation Reference Templates: a resource for consistent variant annotation." Wellcome Open Research 3 (November 14, 2018): 146. http://dx.doi.org/10.12688/wellcomeopenres.14924.1.

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Annotating the impact of a variant on a gene is a vital component of genetic medicine and genetic research. Different gene annotations for the same genomic variant are possible, because different structures and sequences for the same gene are available. The clinical community typically use RefSeq NMs to annotate gene variation, which do not always match the reference genome. The scientific community typically use Ensembl ENSTs to annotate gene variation. These match the reference genome, but often do not match the equivalent NM. Often the transcripts used to annotate gene variation are not pro
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Anderson, Matthew, Salman Sadiq, Muzammil Nahaboo Solim, et al. "Biomedical Data Annotation: An OCT Imaging Case Study." Journal of Ophthalmology 2023 (August 22, 2023): 1–9. http://dx.doi.org/10.1155/2023/5747010.

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In ophthalmology, optical coherence tomography (OCT) is a widely used imaging modality, allowing visualisation of the structures of the eye with objective and quantitative cross-sectional three-dimensional (3D) volumetric scans. Due to the quantity of data generated from OCT scans and the time taken for an ophthalmologist to inspect for various disease pathology features, automated image analysis in the form of deep neural networks has seen success for the classification and segmentation of OCT layers and quantification of features. However, existing high-performance deep learning approaches r
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Cronkite, David, Bradley Malin, John Aberdeen, Lynette Hirschman, and David Carrell. "Is the Juice Worth the Squeeze? Costs and Benefits of Multiple Human Annotators for Clinical Text De-identification." Methods of Information in Medicine 55, no. 04 (2016): 356–64. http://dx.doi.org/10.3414/me15-01-0122.

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SummaryBackground: Clinical text contains valuable information but must be de-identified before it can be used for secondary purposes. Accurate annotation of personally identifiable information (PII) is essential to the development of automated de-identification systems and to manual redaction of PII. Yet the accuracy of annotations may vary considerably across individual annotators and annotation is costly. As such, the marginal benefit of incorporating additional annotators has not been well characterized.Objectives: This study models the costs and benefits of incorporating increasing number
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Park, Jimyung, Seng Chan You, Eugene Jeong, et al. "A Framework (SOCRATex) for Hierarchical Annotation of Unstructured Electronic Health Records and Integration Into a Standardized Medical Database: Development and Usability Study." JMIR Medical Informatics 9, no. 3 (2021): e23983. http://dx.doi.org/10.2196/23983.

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Background Although electronic health records (EHRs) have been widely used in secondary assessments, clinical documents are relatively less utilized owing to the lack of standardized clinical text frameworks across different institutions. Objective This study aimed to develop a framework for processing unstructured clinical documents of EHRs and integration with standardized structured data. Methods We developed a framework known as Staged Optimization of Curation, Regularization, and Annotation of clinical text (SOCRATex). SOCRATex has the following four aspects: (1) extracting clinical notes
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Yssel, Anna E. J., Shu-Min Kao, Yves Van de Peer, and Lieven Sterck. "ORCAE-AOCC: A Centralized Portal for the Annotation of African Orphan Crop Genomes." Genes 10, no. 12 (2019): 950. http://dx.doi.org/10.3390/genes10120950.

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ORCAE (Online Resource for Community Annotation of Eukaryotes) is a public genome annotation curation resource. ORCAE-AOCC is a branch that is dedicated to the genomes published as part of the African Orphan Crops Consortium (AOCC). The motivation behind the development of the ORCAE platform was to create a knowledge-based website where the research-community can make contributions to improve genome annotations. All changes to any given gene-model or gene description are stored, and the entire annotation history can be retrieved. Genomes can either be set to “public” or “restricted” mode; anon
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Keegan, Niamh M., Samantha E. Vasselman, Ethan Barnett, et al. "Clinical annotations for prostate cancer research: Defining data elements, creating a reproducible analytical pipeline, and assessing data quality." Journal of Clinical Oncology 40, no. 6_suppl (2022): 64. http://dx.doi.org/10.1200/jco.2022.40.6_suppl.064.

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64 Background: Routine clinical data from the electronic medical record are indispensable for retrospective and prospective observational studies and clinical trials. Their reproducibility is often not assessed. We sought to develop a prostate cancer-specific database with a defined source hierarchy for clinical annotations and to evaluate data reproducibility. Methods: At a comprehensive cancer center, we designed and implemented a clinical database for men with prostate cancer and clinical-grade paired tumor–normal sequencing for whom we performed team-based retrospective clinical data annot
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Moore, Jill E., Xiao-Ou Zhang, Shaimae I. Elhajjajy, et al. "Integration of high-resolution promoter profiling assays reveals novel, cell type–specific transcription start sites across 115 human cell and tissue types." Genome Research 32, no. 2 (2021): 389–402. http://dx.doi.org/10.1101/gr.275723.121.

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Accurate transcription start site (TSS) annotations are essential for understanding transcriptional regulation and its role in human disease. Gene collections such as GENCODE contain annotations for tens of thousands of TSSs, but not all of these annotations are experimentally validated nor do they contain information on cell type–specific usage. Therefore, we sought to generate a collection of experimentally validated TSSs by integrating RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression (RAMPAGE) data from 115 cell and tissue types, which resulted in a collection of
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de Bruijn, Ino, Xiang Li, Onur Sumer, et al. "Abstract 1156: Genome Nexus: A comprehensive resource for the annotation and interpretation of genomic variants in cancer." Cancer Research 82, no. 12_Supplement (2022): 1156. http://dx.doi.org/10.1158/1538-7445.am2022-1156.

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Abstract Interpreting genomic variants in tumor samples presents a challenge in research and the clinical setting. A major barrier is that information about variants is fragmented across disparate databases, and aggregating information from these requires building extensive infrastructure. To this end, we have developed Genome Nexus, a one stop shop for variant annotation, equipped with a powerful API for bulk annotation of variants and a user friendly interface for cancer researchers. Genome Nexus is available at https://www.genomenexus.org. It a) aggregates variant information from a large n
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Queirós, Pedro, Polina Novikova, Paul Wilmes, and Patrick May. "Unification of functional annotation descriptions using text mining." Biological Chemistry 402, no. 8 (2021): 983–90. http://dx.doi.org/10.1515/hsz-2021-0125.

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Abstract A common approach to genome annotation involves the use of homology-based tools for the prediction of the functional role of proteins. The quality of functional annotations is dependent on the reference data used, as such, choosing the appropriate sources is crucial. Unfortunately, no single reference data source can be universally considered the gold standard, thus using multiple references could potentially increase annotation quality and coverage. However, this comes with challenges, particularly due to the introduction of redundant and exclusive annotations. Through text mining it
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Bax, Martin, Hilary Hart, and Sue Jenkins. "Annotations." Developmental Medicine & Child Neurology 23, no. 1 (2008): 92–95. http://dx.doi.org/10.1111/j.1469-8749.1981.tb08450.x.

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Dissertations / Theses on the topic "Clinical annotations"

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Agarwal, Navneet. "Autοmated depressiοn level estimatiοn : a study οn discοurse structure, input representatiοn and clinical reliability". Electronic Thesis or Diss., Normandie, 2024. http://www.theses.fr/2024NORMC215.

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Compte tenu de l'impact sévère et généralisé de la dépression, des initiatives de recherche significatives ont été entreprises pour définir des systèmes d'évaluation automatisée de la dépression. La recherche présentée dans cette thèse tourne autour des questions suivantes qui restent relativement inexplorées malgré leur pertinence dans le domaine de l'évaluation automatisée de la dépression : (1) le rôle de la structure du discours dans l'analyse de la santé mentale, (2) la pertinence de la représentation de l'entrée pour les capacités prédictives des modèles de réseaux neuronaux, et (3) l'im
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Weng, Chunhua. "Supporting collaborative clinical trial protocol writing through an annotation design /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/7155.

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Velupillai, Sumithra. "Shades of Certainty : Annotation and Classification of Swedish Medical Records." Doctoral thesis, Stockholms universitet, Institutionen för data- och systemvetenskap, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-74828.

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Access to information is fundamental in health care. This thesis presents research on Swedish medical records with the overall goal of building intelligent information access tools that can aid health personnel, researchers and other professions in their daily work, and, ultimately, improve health care in general. The issue of ethics and identifiable information is addressed by creating an annotated gold standard corpus and porting an existing de-identification system to Swedish from English. The aim is to move towards making textual resources available to researchers without risking exposure
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Kholghi, Mahnoosh. "Active learning for concept extraction from clinical free text." Thesis, Queensland University of Technology, 2017. https://eprints.qut.edu.au/112420/1/Mahnoosh_Kholghi_Thesis.pdf.

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This thesis is a step towards automating information extraction from clinical free-text. It establishes a Cost-efficient Enhanced Active Learning framework to significantly reduce annotation cost, while ensuring high-quality extracted information. The practical significance of this research is three-fold: (1) benefitting the overall patient healthcare by facilitating downstream eHealth workflows such as supporting clinical information processing and efficient decision making, (2) benefitting the research in medical informatics by facilitating the development of rich annotated corpora from clin
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Hallier, Andrea Rae. "Variant-curation and database instantiation (Variant-CADI): an integrated software system for the automation of collection, annotation and management of variations in clinical genetic testing." Thesis, University of Iowa, 2016. https://ir.uiowa.edu/etd/2218.

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One of the tools a clinician has in disease diagnosis and treatment is genetic testing. To generate value in genetic testing, the link between genetic variants and disease must be discovered, documented, and shared within the community. Working with two existing genomic variation tools, Kafeen and Cordova, a new set of features referred to as Variant-Curation and Database Instantiation (Variant-CADI) was identified, designed, implemented and integrated into the existing Cordova system to unite data collection, management and distribution into one cohesive tool accessible through user interface
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Ghous, Hamid. "Building a robust clinical diagnosis support system for childhood cancer using data mining methods." Thesis, 2016. http://hdl.handle.net/10453/90061.

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University of Technology Sydney. Faculty of Engineering and Information Technology.<br>Progress in understanding core pathways and processes of cancer requires thorough analysis of many coding and noncoding regions of the genome. Data mining and knowledge discovery have been applied to datasets across many industries, including bioinformatics. However, data mining faces a major challenge in its application to bioinformatics: the diversity and dimensionality of biomedical data. The term ‘big data’ was applied to the clinical domain by Yoo et al. (2014), specifically referring to single nucleoti
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"Genome annotation and identification of blood invasiveness genetic determinants in Salmonella Typhimurium clinical isolates from Hong Kong." 2013. http://library.cuhk.edu.hk/record=b5549745.

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食物中毒感染是常見但非常重要的全球性公共健康問題。沙門氏鼠傷寒桿菌乃常被分離出來的細菌性病原體之一。隨著實驗室參考菌株LT2的基因組序列於2001年被發表之後，另外9個沙門氏鼠傷寒菌菌株的基因序列均已陸續進行測序。最近，本實驗室亦對十個本地沙門氏鼠傷寒菌臨床分離菌株的基因序列進行了測序。為了為這些基因組序列提供高品質的註釋，我們把預測的基因組提交到質量控制工具GenePRIMP以識別有潛在錯誤或異常的預測基因。本研究針對血液分離菌株78896和糞便分離菌株1047518的GenePRIMP報告進行人工檢查，並對每個菌株超過270個的基因進行了修訂。此外，本研究亦對上述的10個本地菌株進行了功能註釋。註釋項目包括沙門氏菌致病島（SPIs）、致病因子、tRNA和非編碼小分子RNA、噬菌體和CRISPRs結構等基因組及致病元素。 KEGG通路則提供了進一步的功能註釋。<br>本研究同時對本地的血液和糞便分離菌株，連同國外的臨床分離菌株，進行了廣泛的比對，用以識別全身性沙門氏菌感染的潛在遺傳因素。 本研究進行了以下基因分析：（1）多位點序列分型（MLST）；（2）在小鼠全身性感染中涉及的主調控因子和關鍵元素; 及（3）人類腸胃道感染中涉及的基因。然而，這些分析產生只能對全身性沙門氏菌感染提供有限的見解。然而，透過使用RAST註釋系統，我們於其中三個血液分離菌株中發現了一個的額外的螯鐵蛋白a
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Books on the topic "Clinical annotations"

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American Medical Association. Council on Ethical and Judicial Affairs. Code of medical ethics: Current opinions with annotations. 2nd ed. AMA Press, 2004.

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American Medical Association. Council on Ethical and Judicial Affairs. Code of medical ethics: Current opinions with annotations. 2nd ed. AMA Press, 2006.

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American Medical Association. Council on Ethical and Judicial Affairs. Code of medical ethics: Current opinions with annotations. 2nd ed. The Association, 2000.

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American Medical Association. Council on Ethical and Judicial Affairs. Code of medical ethics: Current opinions with annotations. The Association, 1998.

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Oliver J. Bear Don't Walk. Inferring Race and Ethnicity from Clinical Notes: Annotation, Model Auditing, and Ethical Implications. [publisher not identified], 2022.

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Billroth, Christian Albert Theodor. Clinical Surgery, Extracts From the Reports of Surgical Practice, 1860-1876, Tr. and Ed., With Annotations, by C.T. Dent. Arkose Press, 2015.

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Affa, AMA Council on Ethical and Judicial, and American Medical Association. Code of Medical Ethics 2004-2005: Current Opinions with Annotations (Code of Medical Ethics). American Medical Association Press, 2004.

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Clinical Surgery. Extracts From the Reports of Surgical Practice Between the Years 1860-1876. Translated From the Original, and Edited, With Annotations, by C. T. Dent. Franklin Classics, 2018.

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Clinical Surgery. Extracts from the Reports of Surgical Practice Between the Years 1860-1876. Translated from the Original, and Edited, with Annotations, by C. T. Dent. Creative Media Partners, LLC, 2023.

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Billroth, Theodor. Clinical Surgery. Extracts from the Reports of Surgical Practice Between the Years 1860-1876. Translated from the Original, and Edited, with Annotations, by C. T. Dent. Franklin Classics Trade Press, 2018.

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Book chapters on the topic "Clinical annotations"

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Rahman, Fahrurrozi, and Juliana Bowles. "Semantic Annotations in Clinical Guidelines." In From Data to Models and Back. Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-70650-0_12.

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Del Rio, Mauro, Luca Lianas, Oskar Aspegren, et al. "AI Support for Accelerating Histopathological Slide Examinations of Prostate Cancer in Clinical Studies." In Lecture Notes in Computer Science. Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-13321-3_48.

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AbstractWhile studies in pathology are essential for the progress in the diagnostic and prognostic techniques in the field, pathologist time is becoming an increasingly scarce resource, and can indeed become the limiting factor in the feasibility of studies to be performed. In this work, we demonstrate how the Digital Pathology platform by CRS4, for supporting research studies in digital pathology, has been augmented by the addition of AI-based features to accelerate image examination to reduce the pathologist time required for clinical studies. The platform has been extended to provide comput
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Petit, Olivier, Nicolas Thome, Arnaud Charnoz, Alexandre Hostettler, and Luc Soler. "Handling Missing Annotations for Semantic Segmentation with Deep ConvNets." In Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support. Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-030-00889-5_3.

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Płaczek, Aleksander, Alicja Płuciennik, Mirosław Pach, Michał Jarząb, and Dariusz Mrozek. "The Role of Feature Selection in Text Mining in the Process of Discovering Missing Clinical Annotations – Case Study." In Beyond Databases, Architectures and Structures. Paving the Road to Smart Data Processing and Analysis. Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-19093-4_19.

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Cai, Jinzheng, Youbao Tang, Le Lu, et al. "Accurate Weakly-Supervised Deep Lesion Segmentation Using Large-Scale Clinical Annotations: Slice-Propagated 3D Mask Generation from 2D RECIST." In Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-030-00937-3_46.

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Savova, Guergana, Sameer Pradhan, Martha Palmer, Will Styler, Wendy Chapman, and Noémie Elhadad. "Annotating the Clinical Text – MiPACQ, ShARe, SHARPn and THYME Corpora." In Handbook of Linguistic Annotation. Springer Netherlands, 2017. http://dx.doi.org/10.1007/978-94-024-0881-2_52.

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Kuroda, Makoto, and Keiichi Hiramatsu. "Genome Sequencing and Annotation." In Genomics, Proteomics, and Clinical Bacteriology. Humana Press, 2004. http://dx.doi.org/10.1385/1-59259-763-7:029.

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Bergelson, Mira B., and Mariya V. Khudyakova. "Narrative discourse segmentation in clinical linguistics." In Studies in Corpus Linguistics. John Benjamins Publishing Company, 2020. https://doi.org/10.1075/scl.94.08ber.

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Abstract This chapter deals with segmentation, definition of basic units and annotation of the first corpus of Russian narratives by individuals with brain damage – people with aphasia and right hemisphere damage – and neurologically healthy speakers. We show that parameters such as pause length and intonation contours cannot be used for segmentation of impaired speech. Instead, they use syntactic criteria for the identification of the basic, or – as they are called in this paper – elementary discourse units (EDUs). The Russian CliPS (Clinical Pear Stories) corpus contains multi-layer annotati
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Tinhofer, Ingeborg, Ulrich Keilholz, and Damian Rieke. "How to Standardize Molecular Profiling Programs for Routine Patient Care." In Critical Issues in Head and Neck Oncology. Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-23175-9_4.

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AbstractManagement of patients with advanced cancer includes individualized treatment recommendations guided by molecular profiles. Refined complex molecular and immunological diagnostics are developed in parallel to the rapidly growing number of targeted therapies for defined genetic alterations and novel immunotherapies. For adequate counseling, patients are presented to Molecular Tumor Boards within the framework of precision oncology programs established at virtually all large cancer centers worldwide. The annotation and clinical interpretation of molecular pathology results are carried ou
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Bayo-Montón, Jose Luis, Begoña Martínez-Salvador, Carlos Fernández-Llatas, and Mar Marcos. "Structural and Semantic Enrichment of Models for the Interactive Discovery of Clinical Processes." In Lecture Notes in Business Information Processing. Springer Nature Switzerland, 2025. https://doi.org/10.1007/978-3-031-82225-4_32.

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Abstract Process Mining (PM) is a relatively new field which provides techniques to analyze business processes in different areas. In the field of Medicine, PM seeks to infer clinical processes from the data routinely collected during healthcare activities. In most frameworks, workflows are used to represent the results obtained by PM techniques. A problem with these workflows is that their structure is complex and not always easy to understand and hence to exploit by the clinician. A different problem, related to Clinical Practice Guidelines (CPGs), is that their development is mostly manual.
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Conference papers on the topic "Clinical annotations"

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Duong, Thanh, and Thanh Thieu. "OncoNLP: Cancer Comprehend Annotation - a Pipeline for Cancer Phenotype and Clinical Extraction." In 2024 IEEE EMBS International Conference on Biomedical and Health Informatics (BHI). IEEE, 2024. https://doi.org/10.1109/bhi62660.2024.10913931.

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Aich, Ankit, Avery Quynh, Pamela Osseyi, et al. "Using LLMs to Aid Annotation and Collection of Clinically-Enriched Data in Bipolar Disorder and Schizophrenia." In Proceedings of the 10th Workshop on Computational Linguistics and Clinical Psychology (CLPsych 2025). Association for Computational Linguistics, 2025. https://doi.org/10.18653/v1/2025.clpsych-1.15.

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Ruder, Deniss, Andero Uusberg, and Kairit Sirts. "Assessing the Reliability and Validity of GPT-4 in Annotating Emotion Appraisal Ratings." In Proceedings of the 10th Workshop on Computational Linguistics and Clinical Psychology (CLPsych 2025). Association for Computational Linguistics, 2025. https://doi.org/10.18653/v1/2025.clpsych-1.1.

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Velupillai, Sumithra. "Semantic annotations in clinical documentation." In the third workshop. ACM Press, 2010. http://dx.doi.org/10.1145/1871962.1871968.

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Vizza, Patrizia, Giuseppe Tradigo, Elvis Kallaverja, Maria Giulia Cristofaro, Giuseppe Lucio Cascini, and Pierangelo Veltri. "Annotations for clinical data enrichment." In 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2021. http://dx.doi.org/10.1109/bibm52615.2021.9669480.

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Robinson, Gain, Lin Li, Yimin Zhu, et al. "Deep learning-based automated lung tumor segmentation in mouse preclinical micro-CT scans with limited annotations." In Clinical and Biomedical Imaging, edited by Barjor S. Gimi and Andrzej Krol. SPIE, 2024. http://dx.doi.org/10.1117/12.3006521.

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Galveia, Jose N., Antonio Travassos, and Luis A. da Silva Cruz. "An Ophthalmology Clinical Decision Support System Based on Clinical Annotations, Ontologies and Images." In 2018 IEEE 31st International Symposium on Computer-Based Medical Systems (CBMS). IEEE, 2018. http://dx.doi.org/10.1109/cbms.2018.00024.

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Llorca, Ignacio, Florian Borchert, and Matthieu-P. Schapranow. "A Meta-dataset of German Medical Corpora: Harmonization of Annotations and Cross-corpus NER Evaluation." In Proceedings of the 5th Clinical Natural Language Processing Workshop. Association for Computational Linguistics, 2023. http://dx.doi.org/10.18653/v1/2023.clinicalnlp-1.23.

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Roy, Sharmili, Michael S. Brown, and George L. Shih. "Extracting volumetric information from standard two-dimensional radiological annotations within the clinical workflow." In 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW). IEEE, 2012. http://dx.doi.org/10.1109/bibmw.2012.6470226.

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Schäfer, Henning, Ahmad Idrissi-Yaghir, Peter Horn, and Christoph Friedrich. "Cross-Language Transfer of High-Quality Annotations: Combining Neural Machine Translation with Cross-Linguistic Span Alignment to Apply NER to Clinical Texts in a Low-Resource Language." In Proceedings of the 4th Clinical Natural Language Processing Workshop. Association for Computational Linguistics, 2022. http://dx.doi.org/10.18653/v1/2022.clinicalnlp-1.6.

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Reports on the topic "Clinical annotations"

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Xu, Chao, Walter Forkel, Stefan Borgwardt, Franz Baader, and Beihai Zhou. Automatic Translation of Clinical Trial Eligibility Criteria into Formal Queries. Technische Universität Dresden, 2019. http://dx.doi.org/10.25368/2023.224.

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Selecting patients for clinical trials is very labor-intensive. Our goal is to develop an automated system that can support doctors in this task. This paper describes a major step towards such a system: the automatic translation of clinical trial eligibility criteria from natural language into formal, logic-based queries. First, we develop a semantic annotation process that can capture many types of clinical trial criteria. Then, we map the annotated criteria to the formal query language. We have built a prototype system based on state-of-the-art NLP tools such as Word2Vec, Stanford NLP tools,
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