ArticleDatabase : the journal of biological databases and curation2014
Automated semantic annotation of rare disease cases: a case study.
Article in Database : the journal of biological databases and curation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed.
- AutoPCR: automated phenotype concept recognition by prompting.Bioinformatics (Oxford, England) · 2026Article
- Synonym Augmentation for Rare Disease Identification in Unstructured Data.medRxiv : the preprint server for health sciences · 2026Article
- Finding Case Report Nuggets: A Web-Based Tool for Mining and Enhancing the Value of Clinical Case Reports.medRxiv : the preprint server for health sciences · 2025Article
- FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology.Bioinformatics (Oxford, England) · 2024Article
- Enhancing phenotype recognition in clinical notes using large language models: PhenoBCBERT and PhenoGPT.Patterns (New York, N.Y.) · 2024Article
- Term-BLAST-like alignment tool for concept recognition in noisy clinical texts.Bioinformatics (Oxford, England) · 2023Article
- PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology.Journal of biomedical informatics · 2022Article
- PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology.Bioinformatics (Oxford, England) · 2021Article
- Diagnosis of Rare Diseases: a scoping review of clinical decision support systems.Orphanet journal of rare diseases · 2020Article
- ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis.Genetics in medicine : official journal of the American College of Medical Genetics · 2019Article
- Identifying Clinical Terms in Medical Text Using Ontology-Guided Machine Learning.JMIR medical informatics · 2019Article
- A manual corpus of annotated main findings of clinical case reports.Database : the journal of biological databases and curation · 2019Article
- PubCaseFinder: A Case-Report-Based, Phenotype-Driven Differential-Diagnosis System for Rare Diseases.American journal of human genetics · 2018Article
- An ontology-aware integration of clinical models, terminologies and guidelines: an exploratory study of the Scale for the Assessment and Rating of Ataxia (SARA).BMC medical informatics and decision making · 2017Article
- A new synonym-substitution method to enrich the human phenotype ontology.BMC bioinformatics · 2017Article
- Phenotypic Analysis of Clinical Narratives Using Human Phenotype Ontology.Studies in health technology and informatics · 2017Article
- Identifying Human Phenotype Terms by Combining Machine Learning and Validation Rules.BioMed research international · 2017Article
- Capturing phenotypes for precision medicine.Cold Spring Harbor molecular case studies · 2015Article
- Automatic concept recognition using the human phenotype ontology reference and test suite corpora.Database : the journal of biological databases and curation · 2015Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationAs the number of clinical reports in the peer-reviewed medical literature keeps growing, there is an increasing need for online search tools to find and analyze publications on patients with similar clinical characteristics. This problem is especially critical and challenging for rare diseases, where publications of large series are scarce. Through an applied example, we illustrate how to automatically identify new relevant cases and semantically annotate the relevant literature about patient case reports to capture the phenotype of a rare disease named cerebrotendinous xanthomatosis.
resultsOur results confirm that it is possible to automatically identify new relevant case reports with a high precision and to annotate them with a satisfactory quality (74% F-measure). Automated annotation with an emphasis to entirely describe all phenotypic abnormalities found in a disease may facilitate curation efforts by supplying phenotype retrieval and assessment of their frequency. Availability and Supplementary information: http://www.usc.es/keam/Phenotype Annotation/. Database URL: http://www.usc.es/keam/PhenotypeAnnotation/
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.