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A domain-specific annotation framework and expert-annotated corpus for structured analysis of German HNSCC pathology reports.

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Τίτλος: A domain-specific annotation framework and expert-annotated corpus for structured analysis of German HNSCC pathology reports.
Συγγραφείς: Gubik S; Department of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany. gubik_s@ukw.de., Seger F; Department of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany., Vollmer A; Department of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany., Hörner M; Department of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany., Renner T; Department of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany., Kohlhepp L; CAIDAS (Center of AI and Data Science), University Würzburg, Würzburg, Germany., Manthey M; Institute of Pathology, University of Würzburg, Würzburg, Germany., Müller-Richter U; Department of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany., Kübler A; Department of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany., Hackenberg S; Department of Otorhinolaryngology, Plastic, Aesthetic, and Reconstructive Head and Neck Surgery, University Hospital Würzburg, Würzburg, Germany., Hartmann S; Department of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany.
Πηγή: BMC research notes [BMC Res Notes] 2026 Sep 21; Vol. 19 (1). Date of Electronic Publication: 2026 Sep 21.
Τύπος έκδοσης: Journal Article
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: Biomed Central Country of Publication: England NLM ID: 101462768 Publication Model: Electronic Cited Medium: Internet ISSN: 1756-0500 (Electronic) Linking ISSN: 17560500 NLM ISO Abbreviation: BMC Res Notes Subsets: MEDLINE
Imprint Name(s): Original Publication: London : Biomed Central, 2008.
Ιατρικοί όροι (MeSH): Head and Neck Neoplasms*/pathology , Squamous Cell Carcinoma of Head and Neck*/pathology , Data Mining*/methods , Natural Language Processing*, Humans ; Germany
Περίληψη: Objective: To develop and empirically characterize a domain-specific, block-structured annotation schema and an expert-annotated reference corpus for German-language head and neck squamous cell carcinoma (HNSCC) pathology reports.
Results Description: We retrieved 631 pathology reports from 145 patients treated at University Hospital Würzburg between January 2021 and March 2024 and split them at the patient level into training, validation, and evaluation subsets. Reports were manually annotated using a hierarchical, span-based schema supporting overlapping and nested annotations. The resulting corpus contains 45 unique labels organized into clinically meaningful blocks and an average of 37-39 annotations per report across subsets. Label frequencies and normalized category distributions were broadly comparable across the three subsets. Fine-grained labels were predominantly applied within their designated blocks, indicating adherence to the intended block structure. The corpus provides a domain-specific reference resource for developing and evaluating structured information-extraction approaches for German HNSCC pathology reports.
(© 2026. The Author(s).)
Competing Interests: Declarations. Ethics approval and consent to participate: This study was conducted in accordance with the Declaration of Helsinki and approved by the Ethics Committee of the University of Würzburg (approval number: 20.02.2024/ag). Consent for publication: Not applicable. The manuscript does not contain any individual person’s data in any form (including individual details, images, or videos). Competing interests: The authors declare no competing interests.
References: N Engl J Med. 2016 Nov 10;375(19):1856-1867. (PMID: 27718784)
N Engl J Med. 2020 Jan 2;382(1):60-72. (PMID: 31893516)
J Clin Med. 2019 Jul 09;8(7):. (PMID: 31324026)
Methods Inf Med. 2018 May;57(1):e22-e29. (PMID: 29801178)
J Clin Oncol. 2015 Oct 10;33(29):3235-42. (PMID: 26351338)
Acad Radiol. 2023 Jun;30(6):1141-1147. (PMID: 35909050)
J Clin Pathol. 2025 Jan 17;78(2):135-138. (PMID: 39304201)
CA Cancer J Clin. 2018 Nov;68(6):394-424. (PMID: 30207593)
BMC Med Inform Decis Mak. 2022 Apr 15;22(1):102. (PMID: 35428335)
Contributed Indexing: Keywords: Annotation schema; Clinical natural language processing; German medical texts; Head and neck cancer; Information extraction; Medical text mining; Pathology reports; TNM classification
Entry Date(s): Date Created: 20260922 Date Completed: 20260922 Latest Revision: 20260924
Update Code: 20260924
PubMed Central ID: PMC13595725
DOI: 10.1186/s13104-026-08024-w
PMID: 42768362
Βάση Δεδομένων: MEDLINE
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  Data: A domain-specific annotation framework and expert-annotated corpus for structured analysis of German HNSCC pathology reports.
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  Data: <searchLink fieldCode="AU" term="%22Gubik+S%22">Gubik S</searchLink>; Department of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany. gubik_s@ukw.de.<br /><searchLink fieldCode="AU" term="%22Seger+F%22">Seger F</searchLink>; Department of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany.<br /><searchLink fieldCode="AU" term="%22Vollmer+A%22">Vollmer A</searchLink>; Department of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany.<br /><searchLink fieldCode="AU" term="%22Hörner+M%22">Hörner M</searchLink>; Department of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany.<br /><searchLink fieldCode="AU" term="%22Renner+T%22">Renner T</searchLink>; Department of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany.<br /><searchLink fieldCode="AU" term="%22Kohlhepp+L%22">Kohlhepp L</searchLink>; CAIDAS (Center of AI and Data Science), University Würzburg, Würzburg, Germany.<br /><searchLink fieldCode="AU" term="%22Manthey+M%22">Manthey M</searchLink>; Institute of Pathology, University of Würzburg, Würzburg, Germany.<br /><searchLink fieldCode="AU" term="%22Müller-Richter+U%22">Müller-Richter U</searchLink>; Department of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany.<br /><searchLink fieldCode="AU" term="%22Kübler+A%22">Kübler A</searchLink>; Department of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany.<br /><searchLink fieldCode="AU" term="%22Hackenberg+S%22">Hackenberg S</searchLink>; Department of Otorhinolaryngology, Plastic, Aesthetic, and Reconstructive Head and Neck Surgery, University Hospital Würzburg, Würzburg, Germany.<br /><searchLink fieldCode="AU" term="%22Hartmann+S%22">Hartmann S</searchLink>; Department of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany.
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  Data: Objective: To develop and empirically characterize a domain-specific, block-structured annotation schema and an expert-annotated reference corpus for German-language head and neck squamous cell carcinoma (HNSCC) pathology reports.<br />Results Description: We retrieved 631 pathology reports from 145 patients treated at University Hospital Würzburg between January 2021 and March 2024 and split them at the patient level into training, validation, and evaluation subsets. Reports were manually annotated using a hierarchical, span-based schema supporting overlapping and nested annotations. The resulting corpus contains 45 unique labels organized into clinically meaningful blocks and an average of 37-39 annotations per report across subsets. Label frequencies and normalized category distributions were broadly comparable across the three subsets. Fine-grained labels were predominantly applied within their designated blocks, indicating adherence to the intended block structure. The corpus provides a domain-specific reference resource for developing and evaluating structured information-extraction approaches for German HNSCC pathology reports.<br /> (© 2026. The Author(s).)
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  Data: Declarations. Ethics approval and consent to participate: This study was conducted in accordance with the Declaration of Helsinki and approved by the Ethics Committee of the University of Würzburg (approval number: 20.02.2024/ag). Consent for publication: Not applicable. The manuscript does not contain any individual person’s data in any form (including individual details, images, or videos). Competing interests: The authors declare no competing interests.
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  Data: N Engl J Med. 2016 Nov 10;375(19):1856-1867. (PMID: <searchLink fieldCode="PM" term="%2227718784%22">27718784)</searchLink><br />N Engl J Med. 2020 Jan 2;382(1):60-72. (PMID: <searchLink fieldCode="PM" term="%2231893516%22">31893516)</searchLink><br />J Clin Med. 2019 Jul 09;8(7):. (PMID: <searchLink fieldCode="PM" term="%2231324026%22">31324026)</searchLink><br />Methods Inf Med. 2018 May;57(1):e22-e29. (PMID: <searchLink fieldCode="PM" term="%2229801178%22">29801178)</searchLink><br />J Clin Oncol. 2015 Oct 10;33(29):3235-42. (PMID: <searchLink fieldCode="PM" term="%2226351338%22">26351338)</searchLink><br />Acad Radiol. 2023 Jun;30(6):1141-1147. (PMID: <searchLink fieldCode="PM" term="%2235909050%22">35909050)</searchLink><br />J Clin Pathol. 2025 Jan 17;78(2):135-138. (PMID: <searchLink fieldCode="PM" term="%2239304201%22">39304201)</searchLink><br />CA Cancer J Clin. 2018 Nov;68(6):394-424. (PMID: <searchLink fieldCode="PM" term="%2230207593%22">30207593)</searchLink><br />BMC Med Inform Decis Mak. 2022 Apr 15;22(1):102. (PMID: <searchLink fieldCode="PM" term="%2235428335%22">35428335)</searchLink>
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