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

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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.

You might also read

Related Articles

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

Sort by
Same author

The integrated stress response contributes to tRNA synthetase-associated peripheral neuropathy.

Science (New York, N.Y.)·2021
Same author

Mouse Genome Informatics: Mapping/Homology Data.

TheScientificWorldJournal·2018
Same author

Gene Ontology annotations and resources.

Nucleic acids research·2012
Same author

The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology.

Nucleic acids research·2004
Same author

Systems biology of the 2-cell mouse embryo.

Cytogenetic and genome research·2004
Same author

Initial healing rates of venous ulcers: are they useful as predictors of healing?

American journal of surgery·2004
Same journal

Development of CypriSSR: a genome-wide, chromosome-level microsatellite database for multiple cyprinidae species.

Database : the journal of biological databases and curation·2026
Same journal

KitBase Expanded: An Integrated Genomic and Phenotypic Resource for 3,268 Fast-Neutron-Irradiated Rice Mutants.

Database : the journal of biological databases and curation·2026
Same journal

PhaLP 2.0: extending the community-oriented phage lysin database with a SUBLYME pipeline for metagenomic discovery.

Database : the journal of biological databases and curation·2026
Same journal

A similarity metric, rubric, and unified hierarchy for biomedical publication types and study designs.

Database : the journal of biological databases and curation·2026
Same journal

GUTAID: a curated database linking gut microbial antigens to autoimmune mechanisms.

Database : the journal of biological databases and curation·2026
Same journal

Rosetta Statements: simplifying FAIR knowledge graph construction with a user-centred approach.

Database : the journal of biological databases and curation·2026
See all related articles

Related Experiment Video

Updated: Jun 16, 2026

Cloud-Based Phrase Mining and Analysis of User-Defined Phrase-Category Association in Biomedical Publications
09:20

Cloud-Based Phrase Mining and Analysis of User-Defined Phrase-Category Association in Biomedical Publications

Published on: February 23, 2019

Integrating text mining into the MGI biocuration workflow.

K G Dowell1, M S McAndrews-Hill, D P Hill

  • 1The Jackson Laboratory, Mouse Genome Informatics, 600 Main Street, Bar Harbor, ME 04609-1500, USA and University of Maine, Graduate School of Biomedical Sciences, Barrows Hall, Orono, ME 04469, USA.

Database : the Journal of Biological Databases and Curation
|February 17, 2010
PubMed
Summary
This summary is machine-generated.

Text mining tools can streamline biomedical literature curation for model organism databases (MODs). Pilot projects with Open Biomedical Annotator and ProMiner show potential for semi-automated gene indexing.

More Related Videos

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
05:47

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems

Published on: June 13, 2025

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
07:35

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

Published on: October 13, 2023

Related Experiment Videos

Last Updated: Jun 16, 2026

Cloud-Based Phrase Mining and Analysis of User-Defined Phrase-Category Association in Biomedical Publications
09:20

Cloud-Based Phrase Mining and Analysis of User-Defined Phrase-Category Association in Biomedical Publications

Published on: February 23, 2019

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
05:47

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems

Published on: June 13, 2025

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
07:35

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

Published on: October 13, 2023

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Extracting data from biomedical literature is a major challenge for genomics resources.
  • Existing biological natural language processing (bioNLP) tools are difficult to integrate into model organism database (MOD) workflows and have high error rates.

Purpose of the Study:

  • To identify and evaluate dictionary-based text mining tools for integration into the Mouse Genome Informatics (MGI) biocuration workflow.
  • To streamline gene indexing and other curation tasks within the MGI system.

Main Methods:

  • Searched for dictionary-based text mining tools suitable for MGI's biocuration workflow.
  • Evaluated pilot projects using NCBO's Open Biomedical Annotator and Fraunhofer SCAI's ProMiner.
  • Defined performance metrics and success criteria for tool evaluation.

Main Results:

  • Identified a shortlist of potential text mining tools for further evaluation.
  • Demonstrated the potential of semi-automated processes for biomedical literature curation.
  • Highlighted the challenges of adapting existing bioNLP solutions to MOD curation needs.

Conclusions:

  • Semi-automated text mining holds promise for improving the efficiency of biomedical literature curation.
  • Further incorporation of text mining tools can aid in gene indexing and data extraction for genomics resources.
  • Successful integration requires tools adaptable to existing curation workflows and scientific literature formats.