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Thomas edited this page Jan 10, 2015 · 16 revisions

Scheme

From the user's interface (UI), SEARCH QUERY(SQ) are passed onto the Learning module
The Learning module returns a list of literature (with title, abstract, and other info)
User provides feedback (boolean: Yay or nay, along with Journal_Name) back to the Learning Module
Repeat Step 2 based on feedback

Dependencies:

In respect to python module:

Biopython
Beautiful Soup to support scholar.py

Required dataset:

Gene Ontology

Module

Learning Module:

keeps track all of the user's feedback

Google Scholar API

i.e. python scholar.py -A "-p90 -WAF1 +p53"

Limitations: Some of the abstracts are shortened and it only looks up to top 20 articles.
input : Query keyword (str)
Output: Title, citations, Years
Status: Completed

NCBI Journal search module

dependencies : Bio-python module
input: Journal_title (str)
output: abstract, Keywords

Gene Ontology (GO) search module

function: parse the GO's obo file
input : keyword [str], degree of association [int]
output : a list of synonyms within given degree of association [comma-separated]

Gene Homology explore module

purpose: this module returns a list of homologous genes
input: GENE Name, species
output: genes (ranked by similarity, besides its own)

GEO explore module

SCOP (structural Classification module)