Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Anatomical Terminology

Anatomical Terminology

Knowledge of anatomy is essential to understand human biology and medicine. Anatomists and health care professionals use standard terminology to describe the human body with more precision and no ambiguity. Anatomical terms have mostly Greek and Latin-derived roots. Because these languages are rarely used in conversation, the meaning of words remains the same. Each term is made up of a root in between the prefixes and suffixes. The root of a term often refers to an organ, tissue, or condition,...

Protein-Protein Interfaces

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

Protein Families

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...

Protein Families

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...

Proteomics

Proteomics

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 proteomics...

Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

You might also read

Related Articles

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

Sort by

Same author

Enhancing the quality and trustworthiness of large language model-generated summaries of clinical oncology literature.

JAMIA open·2026

Same author

Supporting the working life exposome: Annotating occupational exposure for enhanced literature search.

PloS one·2024

Same author

Predicting potential target genes in molecular biology experiments using machine learning and multifaceted data sources.

iScience·2024

Same author

Knowledge-enhanced Graph Topic Transformer for Explainable Biomedical Text Summarization.

IEEE journal of biomedical and health informatics·2023

Same author

Contextualized medication event extraction with levitated markers.

Journal of biomedical informatics·2023

Same author

A Novel Automated Approach to Mutation-Cancer Relation Extraction by Incorporating Heterogeneous Knowledge.

IEEE journal of biomedical and health informatics·2022

Search research articles

Related Experiment Video

Updated: Jul 2, 2026

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

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

Published on: October 13, 2023

FACTA: a text search engine for finding associated biomedical concepts.

Yoshimasa Tsuruoka¹, Jun'ichi Tsujii, Sophia Ananiadou

¹School of Computer Science, The University of Manchester, Manchester, UK. yoshimasa.tsuruoka@manchester.ac.uk

Bioinformatics (Oxford, England)

|September 6, 2008

Summary

This summary is machine-generated.

FACTA is a text search engine that indexes biomedical concepts for efficient retrieval from MEDLINE abstracts. It enhances searching by pre-indexing concepts, providing immediate results and aiding in the discovery of associations.

More Related Videos

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

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

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

Published on: June 13, 2025

Related Experiment Videos

Last Updated: Jul 2, 2026

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

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

Published on: October 13, 2023

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

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

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

Published on: June 13, 2025

Area of Science:

Biomedical Informatics
Text Mining
Information Retrieval

Background:

MEDLINE abstracts contain vast amounts of biomedical information.
Efficiently searching and browsing these abstracts is crucial for researchers.
Existing systems may lack advanced concept indexing capabilities.

Purpose of the Study:

To introduce FACTA, a novel text search engine for MEDLINE abstracts.
To enhance the browsing of biomedical concepts within search results.
To provide immediate and flexible search result delivery.

Main Methods:

FACTA pre-indexes both words and biomedical concepts (genes, diseases, chemicals).
Concepts are identified using data from biomedical databases and thesauri (UniProt, UMLS, KEGG, DrugBank).
Search queries can be flexible, including keywords or Boolean combinations.

Main Results:

FACTA presents retrieved concepts in a ranked tabular format based on co-occurrence statistics.
The system allows users to view snippets for textual evidence of term-concept associations.
FACTA delivers immediate results even for large document sets.

Conclusions:

FACTA offers an efficient method for searching and exploring biomedical concepts in MEDLINE.
The pre-indexing of concepts improves search flexibility and result delivery speed.
This tool facilitates the discovery of relationships between biomedical terms and concepts.