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Related Concept Videos

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.
Synthetic Biology02:55

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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In-situ Hybridization02:31

In-situ Hybridization

In situ hybridization (ISH) is a technique used to detect and localize specific DNA or RNA molecules in cells, tissue, or tissue sections using a labeled probe. The technique was first used in 1969 for the investigation of nucleic acids. It is currently an essential tool in scientific research and clinical settings, especially for diagnostic purposes.
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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...

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Related Experiment Video

Updated: Jun 22, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
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Published on: February 8, 2017

PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction.

Martin Krallinger1, Carlos Rodriguez-Penagos, Ashish Tendulkar

  • 1Structural Biology and Biocomputing programme, Spanish National Cancer Center (CNIO), Melchor Fernandez Almagro 3, Madrid, 28029, Spain. mkrallinger@cnio.es

Nucleic Acids Research
|June 13, 2009
PubMed
Summary

PLAN2L is a new web system that uses text mining to help researchers find information on the plant Arabidopsis thaliana. It efficiently retrieves data on genes, proteins, and biological processes from scientific literature.

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Area of Science:

  • Plant biology
  • Bioinformatics
  • Computational biology

Background:

  • Growing need for literature mining to supplement bioinformatics data.
  • Existing methods may not efficiently integrate diverse biological information.
  • Plant model organism research, specifically Arabidopsis thaliana, requires systematic data access.

Purpose of the Study:

  • Introduce PLAN2L, a web-based system for literature mining in plant biology.
  • Facilitate efficient retrieval of genetic, cellular, and molecular information for Arabidopsis thaliana.
  • Enable systematic analysis of complex biological relationships from scientific text.

Main Methods:

  • Integration of text mining and information extraction techniques.
  • Development of a web-based online search system (PLAN2L).
  • Querying capabilities for single entities and predefined pairs of entities.

Main Results:

  • Systematic retrieval of information on Arabidopsis thaliana genetics, cellular, and molecular aspects.
  • Efficient access to data on protein interactions, gene regulation, and sub-cellular locations.
  • Identification of literature-derived relations and textual evidence for queried biological topics.

Conclusions:

  • PLAN2L enhances information retrieval for Arabidopsis thaliana research.
  • The system supports the analysis of diverse biological topics and relationships.
  • PLAN2L provides a valuable, freely accessible resource for the scientific community.