Resistance and Sensitivity: genomic interactions of cancer drugs

Work for Galvanize capstone project

Steps:

1. Read PDF files to txt (console based)

2. Create dictionaries:

• Gene dictionary: genes have multiple names - associate all names to standard name
• Drug dictionary: drugs have multiple names - associate all names to standard name

3. Tokenize txt files:

• divide text into sentences
• sentences to word lists
• lower case words
• filter tokens for stop words or punctuation
• break hyphenated words
• identify gene names and translate to standard name
• identify drug names and translate to standard name
• stem words

4. Read and process data:

• Create document matrix
  • Use count vectorizer - does word occur in sentence or not
• Create vocabulary
• Create list of academic papers where sentences are found
• Create list of evidence sentence
• Use document matrix to create gene/drug network interaction matrix
• Create ditionary to associate genes and drugs to their indices in different matrices

5. Functionality:

• Use gene/drug network matrix to:
  • Generate networks of gene/drug interactions
  • Parse literature for evidence of gene/drug network interactions
  • Predict novel gene/drug interactions