Abstract
In the previous chapter we were able to automatically process structured data to retrieve biomedical text about any chemical compound, such as caffeine. This chapter will provide a step-by-step introduction to how we can process that text using shell script commands, specifically extract information about diseases related to caffeine. The goal is to equip the reader with an essential set of skills to extract meaningful information from any text.
Highlights
In the previous chapter we were able to automatically process structured data to retrieve biomedical text about any chemical compound, such as caffeine
The goal is to equip the reader with an essential set of skills to extract meaningful information from any text
When searching for mentions of malignant hyperthermia, we may be interested in finding mentions using related expressions, such as: Malignant hyperthermia (MH) – acronym Malignant hyperthermia susceptibility (MHS) – acronym for malignant hyperthermia susceptible
Summary
We used the grep command in the last chapter to find a disease in the text, since grep receives as argument a pattern to find an exact match in the text, like any search functionality provided by conventional text editors. We may need to search for multiple patterns even when interested in a single disease. When searching for mentions of malignant hyperthermia, we may be interested in finding mentions using related expressions, such as: MH – acronym MHS – acronym for malignant hyperthermia susceptible. Since we already know how to deal with multiple patterns by using the -e option, we may solve this problem by executing:
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