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Escape Excel: A tool for preventing gene symbol and accession conversion errors.

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Summary

Excel corrupts gene symbols and other text data. Escape Excel is an open-source tool that prevents this by escaping text, ensuring data integrity in scientific analyses and publications.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Data Science

Background:

  • Microsoft Excel's automatic conversion of text to numerical formats corrupts gene symbols and database accessions.
  • This data corruption issue affects approximately 20% of scientific papers with supplementary gene lists.
  • Erroneous conversions lead to irreversible loss of critical textual information.

Purpose of the Study:

  • To introduce Escape Excel, an open-source tool designed to prevent Microsoft Excel's erroneous text-to-number conversions.
  • To provide a reliable method for preserving the integrity of gene symbols and other alphanumeric data during Excel import.
  • To mitigate widespread data corruption in scientific literature.

Main Methods:

  • Developed Escape Excel as an open-source tool available in multiple formats.
  • Implemented Escape Excel as a Perl script, Windows Excel Add-In, OS X application, web server, and Galaxy interface.
  • Provided accessible test implementations via web interfaces for user convenience.

Main Results:

  • Escape Excel successfully detects and escapes problematic text strings, preventing unwanted conversions.
  • The tool handles date-like strings, time-like strings, leading zeros, and long alphanumeric identifiers.
  • Generated escaped text files ensure safe and accurate data importation into Excel.

Conclusions:

  • Escape Excel effectively safeguards against Excel's data corruption of scientific text.
  • Increased awareness and use of text escaping tools like Escape Excel can reduce corrupted data in publications.
  • This tool promotes greater accuracy and reliability in bioinformatics and data analysis workflows.