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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.
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Enabling a fast annotation process with the Table2Annotation tool.

Pierre Larmande1,2, Kazim Muhammed Jibril2

  • 1DIADE, Univ. Montpellier, IRD, Montpellier, France.

Genomics & Informatics
|July 8, 2020
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Summary
This summary is machine-generated.

This study introduces Table2Annotation, a tool for semantic annotation of scientific spreadsheets. It enhances resource discoverability by linking concepts to text, improving information retrieval.

Keywords:
bioinformaticsontologiessemantic annotation

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Area of Science:

  • Information Science
  • Bioinformatics
  • Computational Biology

Background:

  • Semantic annotation links concepts to natural language, improving resource searchability.
  • Information retrieval systems benefit from semantic annotation for query augmentation.

Purpose of the Study:

  • To identify ontological concepts within scientific text in spreadsheets.
  • To develop and evaluate a tool for semantic annotation of spreadsheet data.

Main Methods:

  • Developed a versatile tool, Table2Annotation, capable of processing diverse spreadsheet formats.
  • Integrated the NCBO Annotator API (National Center for Biomedical Ontology) from BioPortal for enhanced semantic annotation.
  • Applied semantic annotation to scientific text embedded in spreadsheets.

Main Results:

  • Table2Annotation demonstrates efficiency in handling various spreadsheet types.
  • The tool exhibits strengths in speed, robust error handling, and accurate complex concept matching.
  • Successfully enhanced semantic annotation capabilities for spreadsheet data.

Conclusions:

  • Table2Annotation effectively addresses the challenge of semantic annotation in scientific spreadsheets.
  • The tool improves the accessibility and searchability of information within tabular scientific data.
  • Integration with BioPortal's NCBO Annotator API expands semantic capabilities for structured data.