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

Classification of Systems-I

Classification of Systems-I

Linearity is a system property characterized by a direct input-output relationship, combining homogeneity and additivity.
Homogeneity dictates that if an input x(t) is multiplied by a constant c, the output y(t) is multiplied by the same constant. Mathematically, this is expressed as:

Classification of Systems-II

Classification of Systems-II

Continuous-time systems have continuous input and output signals, with time measured continuously. These systems are generally defined by differential or algebraic equations. For instance, in an RC circuit, the relationship between input and output voltage is expressed through a differential equation derived from Ohm's law and the capacitor relation,

Microbial Classification System

Microbial Classification System

Classification is the process of organizing organisms into hierarchically inclusive groups based on their phenotypic similarities or evolutionary relationships. A species comprises one or more strains, and closely related species are grouped into genera. Genera are further classified into families, families into orders, orders into classes, and so forth, up to the domain level, which is the broadest taxonomic rank derived from a combination of phenotypic and genotypic data.The nomenclature of...

Applications of Molecular Taxonomy

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...

Evolutionary Relationships through Genome Comparisons

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...

The Tree of Life - Bacteria, Archaea, Eukaryotes

The Tree of Life - Bacteria, Archaea, Eukaryotes

The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both extant and...

You might also read

Related Articles

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

Sort by

Same author

Generative language models exhibit social identity biases.

Nature computational science·2024

Same author

Internet Healthcare Policy Analysis, Evaluation, and Improvement Path: Multidimensional Perspectives.

Healthcare (Basel, Switzerland)·2023

Same author

Solidification Behavior of Dy-Tb-Fe Alloys through Experimental Study and Thermodynamic Calculation.

Materials (Basel, Switzerland)·2023

Same author

Theoretical Study on Cooperation Catalysis of Chiral Guanidine/ Copper(I) in Asymmetric Azide-Alkyne Cycloaddition/[2 + 2] Cascade Reaction.

The Journal of organic chemistry·2023

Same author

Risk factors for severe COVID-19 outcomes: a study of immune-mediated inflammatory diseases, immunomodulatory medications, and comorbidities in a large US healthcare system.

medRxiv : the preprint server for health sciences·2023

Same author

Optimization of Profile Control and Oil Displacement Scheme Parameters Based on Deep Deterministic Policy Gradient.

ACS omega·2023

Search research articles

Related Experiment Video

Updated: Jun 4, 2026

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

Towards classifying species in systems biology papers using text mining.

Qi Wei¹, Nigel Collier

¹Department of Informatics, The Graduate University for Advanced Studies (Sokendai), 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo. collier@nii.ac.jp.

BMC Research Notes

|February 8, 2011

Summary

This summary is machine-generated.

Automated text mining can now classify molecular biology documents by organism. This study optimized models for fly, mouse, and yeast, achieving high accuracy, especially with full-text articles.

More Related Videos

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

Related Experiment Videos

Last Updated: Jun 4, 2026

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

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

Area of Science:

Bioinformatics
Computational Biology
Text Mining

Background:

High-throughput methods have generated vast molecular biology literature.
Automated text mining aims to structure this data, but organism classification remains a challenge.
Current database curation relies heavily on manual effort.

Purpose of the Study:

To compare supervised models for classifying documents by organism.
To optimize automated organism detection in scientific literature.
To evaluate performance on abstracts and full-text articles for model organisms.

Main Methods:

Comparative analysis of eight supervised machine learning models.
Utilized features such as gene names, organism frequency, MeSH headings, and term-species associations.
Tested models on a corpus of 10,000 abstracts and full papers for fly, mouse, and yeast.

Main Results:

The best model achieved high F-scores: 97.1% for fly, 88.6% for mouse, and 85.5% for yeast.
Term-species associations significantly improved classification performance.
Full-text articles consistently yielded better results than abstracts across all tested organisms.

Conclusions:

An optimized system for automatically detecting the primary organism in full-text articles (fly, mouse, yeast) was developed.
The approach demonstrated high accuracy and effectiveness.
The method is expected to be adaptable for classifying other organism types.