Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Tagging and Fusion Proteins01:24

Tagging and Fusion Proteins

7.3K
Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...
7.3K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

19.5K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
19.5K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

242
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
242
Proteomics01:33

Proteomics

8.4K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
8.4K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

MetaTron: advancing biomedical annotation empowering relation annotation and collaboration.

BMC bioinformatics·2024
Same author

Building a large gene expression-cancer knowledge base with limited human annotations.

Database : the journal of biological databases and curation·2023
Same author

Modelling digital health data: The ExaMode ontology for computational pathology.

Journal of pathology informatics·2023
Same author

Empowering digital pathology applications through explainable knowledge extraction tools.

Journal of pathology informatics·2022
Same author

Unleashing the potential of digital pathology data by training computer-aided diagnosis models without human annotations.

NPJ digital medicine·2022
Same author

Search, access, and explore life science nanopublications on the Web.

PeerJ. Computer science·2021

Related Experiment Video

Updated: Oct 9, 2025

A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts
07:50

A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts

Published on: September 20, 2018

16.1K

MedTAG: a portable and customizable annotation tool for biomedical documents.

Fabio Giachelle1, Ornella Irrera1, Gianmaria Silvello2

  • 1Department of Information Engineering, University of Padua, Padua, Italy.

BMC Medical Informatics and Decision Making
|December 19, 2021
PubMed
Summary

MedTAG is a free, open-source biomedical annotation tool that streamlines the creation of training data for Named Entity Recognition and Linking (NER+L) algorithms. It supports physicians and experts in annotating clinical reports efficiently.

Keywords:
Biomedical annotation toolsDigital healthEntity extractioneHealth

More Related Videos

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
09:29

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Published on: May 15, 2019

19.8K
Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging ESI
13:06

Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging ESI

Published on: September 24, 2015

10.2K

Related Experiment Videos

Last Updated: Oct 9, 2025

A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts
07:50

A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts

Published on: September 20, 2018

16.1K
Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
09:29

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Published on: May 15, 2019

19.8K
Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging ESI
13:06

Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging ESI

Published on: September 24, 2015

10.2K

Area of Science:

  • Biomedical Informatics
  • Natural Language Processing

Background:

  • Developing Named Entity Recognition and Linking (NER+L) algorithms in the biomedical domain is hindered by a lack of sufficient annotated data.
  • Manual annotation by experts is expensive and time-consuming, limiting the progress of NLP in this field.

Purpose of the Study:

  • To introduce MedTAG, a novel collaborative biomedical annotation tool.
  • To support, organize, and accelerate the manual annotation process for biomedical documents.

Main Methods:

  • MedTAG is presented as an open-source, platform-independent, and freely distributable tool.
  • Its features are demonstrated through its application in annotating over seven thousand clinical reports in histopathology.
  • A comparative analysis of MedTAG against established tools like BioQRator, ezTag, MyMiner, and tagtog is performed.

Main Results:

  • MedTAG was successfully used by physicians and experts to manually annotate a substantial volume of clinical reports.
  • The tool demonstrated a user-friendly interface and efficient annotation capabilities.
  • MedTAG was highlighted as one of the few open-source tools with an open license and easy cross-platform installation.

Conclusions:

  • MedTAG was designed adhering to key requirements for manual annotation tools, including availability, distributability, installability, workability, and schematic design.
  • The tool meets a significant majority (20 out of 22) of criteria from a recent review of annotation tools.
  • MedTAG offers a valuable, efficient, and accessible solution for biomedical data annotation.