Genomics Article Search

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Genomics Article Search

• Group 3
• -Adjoa, Alexia, Carmon, Nick, and Shelley-

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Our Websitehttp//unix.aml.yorku.ca8080/w04_g3/
indexSearch.html
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How to Split the XML Dataset

• We separated the articles in the dataset from
  between opening and closing PubmedArticle tags.
• This creates 1139 XML documents.
• In these XML documents, they call on a XSL
  stylesheet.

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Technology Used

• Java
• HTML
• XML
• XSL
• Perl

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How to Parse and Extract Keywords and PMIDs

• We used DOM to parse the text contents within the
  XML documents.
• First step in parsing, we extracted the text
  within the XML tags.
• Second step was string tokenizing the words and
  PMIDs separately.
• Third step was to attach the document ID for each
  term.

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How to Sort

• We used Perl scripting to sort the tokenized
  terms.
• The terms appear in alphabetical and numerical
  order.

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How We Built the Two-Level Index

• We used the data structure of TreeMaps to help
  build the two-level index.
• We chose to use TreeMaps because elements inside
  are sorted in order (according to the key) in an
  ascending order at all times
• They stored the keys (words and numbers), and
  their corresponding values (document IDs or
  pointers to them).

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How We Built the Two-Level Index (contd)

• A TreeMap which stores each keyword (or PMID)
  with the beginning and end pointers to the
  positions of their document IDs is written into
  in the text file as the lexicon / first level
  index
• All the document numbers are then written into
  another text file to form the second level index
  or postings file.

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How to Search

• The servlet class gets the keyword or PMID from
  the form and tries to find a match in the lexicon
  (text file).
• If a match is found, it takes the document IDs
  position pointers and retrieves the corresponding
  document IDs from the postings file.
• It then returns hyperlinks of all the matching
  XML documents to the user.
• If no match is found, it returns the user to a
  search page to try again.

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• DEMO

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Questions, Comments??