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Extracting Recipes from Chemical Academic Papers

Extracting Recipes from Chemical Academic Papers. Lei Luo. Extracting Recipes from Chemical Academic Papers. Chemicals Extraction Tools Results Comparison Future Work Recipes Extraction Sample Results Future Work. C hemicals Extraction. Tools Brat ChemTagger ChemDataExtractor.

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Extracting Recipes from Chemical Academic Papers

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  1. Extracting Recipes from Chemical Academic Papers Lei Luo

  2. Extracting Recipes from Chemical Academic Papers • Chemicals Extraction • Tools • Results Comparison • Future Work • Recipes Extraction • Sample Results • Future Work

  3. Chemicals Extraction • Tools • Brat • ChemTagger • ChemDataExtractor

  4. Chemicals Extraction • Brat • Web-based tool for text annotation; that is, for adding notes to existing text documents. • Needs to define three things: • Top level annotation definition. • Second level annotation definition. • Original text file. • Needs manual annotation.

  5. Brat • Top level annotation

  6. Brat • Second level annotation

  7. Brat • Original text file

  8. Brat • Result

  9. Chemicals Extraction • ChemTagger • Phrase-based semantic NLP tool for parsing the language of chemical experiments. • Takes a string as input and produces an XML document as output. • Uses a combination of OSCAR4, domain-specific regex and English taggers to identify parts-of-speech.

  10. ChemTagger • Web-based interface

  11. ChemTagger • Web-based interface

  12. ChemTagger • Local

  13. ChemTagger • Result – XML & Chemicals

  14. Chemicals Extraction • ChemDataExtractor • Able to automatically extract chemical names, properties, and spectra from scientific papers. • Uses machine learning, custom dictionaries, and rule-based parsing grammars. • Able to resolve data interdependencies. • Extracts data from tables.

  15. ChemDataExtractor • Web-based interface

  16. ChemDataExtractor • Local

  17. ChemTagger vs ChemDataExtractor • Example 1

  18. ChemTagger vs ChemDataExtractor • Example 2

  19. ChemTagger vs ChemDataExtractor • Example 3

  20. ChemTagger vs ChemDataExtractor • Example 4

  21. ChemTagger vs ChemDataExtractor • Results • ChemTagger identifies chemicals and the properties. ChemDataExtractor tags chemicals. • ChemTagger gives repetitive chemicals. • ChemTagger also tags non-chemicals. • ChemDataExtractor seems to be able to handle unclean text better than ChemTagger.

  22. Chemicals Extraction • Near Future Work • Clean the results and combine. • Chemical entities verification. • Accuracy assessment.

  23. Recipes Extraction • Sample Recipe

  24. Recipes Extraction • Future Work • More literature review. • From a large number of papers we can get many different recipes for the making the same chemical. • For each paper we can extract chemicals and synthesis parameters.

  25. Recipes Extraction • Future Work • Build a database for chemicals. • Use data mining to see under which condition the chemical is more likely to be produced. • use machine learning models by providing examples of synthesis parameters and synthesis outcomes. Then, make prediction.

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