ReviewBriefings in bioinformatics2021
An extensive review of tools for manual annotation of documents.
Review in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 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
28 citing papers in PubMed.
- SPELL: A scalable NLP method using regular expressions and large language models for clinical information extraction.Computer methods and programs in biomedicine · 2026Article
- A Sentence Classification-Based Medical Status Extraction Pipeline for Electronic Health Records: Institutional Case Study.JMIR medical informatics · 2026Article
- Large language models for structured cardiovascular data extraction: a foundation for scalable research and clinical applications.European heart journal. Digital health · 2026Article
- Leveraging artificial intelligence for efficient microbial production.Bioresource technology · 2026Review
- AI in biocuration: challenges, opportunities, and a roadmap for sustainable integration.Bioinformatics advances · 2026Article
- Autogenerating a Domain-Specific Question-Answering Data Set from a Thermoelectric Materials Database to Enable High-Performing BERT Models.Journal of chemical information and modeling · 2025Article
- Multicriteria Optimization of Language Models for Heart Failure With Preserved Ejection Fraction Symptom Detection in Spanish Electronic Health Records: Comparative Modeling Study.Journal of medical Internet research · 2025Article
- Multimodal identification of a rare head and neck cancer patient cohort in the clinical data warehouse of Greater Paris Teaching Hospital.ESMO real world data and digital oncology · 2025Article
- PretoxTM: a text mining system for extracting treatment-related findings from preclinical toxicology reports.Journal of cheminformatics · 2025Article
- LSD600: the first corpus of biomedical abstracts annotated with lifestyle-disease relations.Database : the journal of biological databases and curation · 2025Article
- Lightweight technology stacks for assistive linked annotations.Genomics & informatics · 2024Article
- LLM-AIx: An open source pipeline for Information Extraction from unstructured medical text based on privacy preserving Large Language Models.medRxiv : the preprint server for health sciences · 2024Article
- BioKC: a collaborative platform for curation and annotation of molecular interactions.Database : the journal of biological databases and curation · 2024Article
- MetaTron: advancing biomedical annotation empowering relation annotation and collaboration.BMC bioinformatics · 2024Article
- A case study in applying artificial intelligence-based named entity recognition to develop an automated ophthalmic disease registry.Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie · 2023Article
- Web-Based Application Based on Human-in-the-Loop Deep Learning for Deidentifying Free-Text Data in Electronic Medical Records: Development and Usability Study.Interactive journal of medical research · 2023Article
- Inter-rater agreement for the annotation of neurologic signs and symptoms in electronic health records.Frontiers in digital health · 2023Article
- Linguistic and ontological challenges of multiple domains contributing to transformed health ecosystems.Frontiers in medicine · 2023Article
- MedTator: a serverless annotation tool for corpus development.Bioinformatics (Oxford, England) · 2022Article
- TAX-Corpus: Taxonomy based Annotations for Colonoscopy Evaluation.Biomedical engineering systems and technologies, international joint conference, BIOSTEC ... revised selected papers. BIOSTEC (Conference) · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationAnnotation tools are applied to build training and test corpora, which are essential for the development and evaluation of new natural language processing algorithms. Further, annotation tools are also used to extract new information for a particular use case. However, owing to the high number of existing annotation tools, finding the one that best fits particular needs is a demanding task that requires searching the scientific literature followed by installing and trying various tools.
methodsWe searched for annotation tools and selected a subset of them according to five requirements with which they should comply, such as being Web-based or supporting the definition of a schema. We installed the selected tools (when necessary), carried out hands-on experiments and evaluated them using 26 criteria that covered functional and technical aspects. We defined each criterion on three levels of matches and a score for the final evaluation of the tools.
resultsWe evaluated 78 tools and selected the following 15 for a detailed evaluation: BioQRator, brat, Catma, Djangology, ezTag, FLAT, LightTag, MAT, MyMiner, PDFAnno, prodigy, tagtog, TextAE, WAT-SL and WebAnno. Full compliance with our 26 criteria ranged from only 9 up to 20 criteria, which demonstrated that some tools are comprehensive and mature enough to be used on most annotation projects. The highest score of 0.81 was obtained by WebAnno (of a maximum value of 1.0).
Indexed as
Identifiers
What Socratic 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 Socratic graph.