DeepSearch v0

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Introduction

Below are some sample questions for the CLEF 2012 pilot task on Alzheimer's disease.

We approach the task using the technique of "index expansion", which is the dual to query expansion. Query expansions adds terms to the query in order to achieve better recall, but this often results in poorer precision, since a lot of noise is introduced because of term polysemy. Index expansion instead adds variants of terms to the index, for example synonyms and hypernyms. This introduces much less noise, since if the variant term is used in the query, then it is relevant and the match wil be successfull. On the other hand, inappropriate terms will not be used in the queries and hence their presence in the index will not affect negativey the results. The only drawback of the approach is that the size of the index increases, but this is a minor issue, since the index is compressed and disk space is cheap. In other wrds we trade space for speed and accuracy, which is akin to the technique of "database denoralization".

The index is also enriched with information extracted from linguistc analysis of the documents. The index in fact can be seen as a multilayer index, where each layer represents a type of annotation. The layers are:

form
the original text
lemma
the lemma of each word
POS
the POS of each word
head
the governor of each word
deprel
the dependency relation of each word wth its governor
lemma
the lemmas of each word
synonyms
list of synonyms for each word
hypernyms
list of hypernyms for each word

The questions have been parsed and from the parse tree a query in the DeepSearch query language has been generated. To each of these questions one of the multiple possible answers has been added. Those queries which obtain an answer with the highest score are considered to be the correct answer.

Question 1

Which entity does allosterically regulate insulin degrading enzyme activity?
  1. AD ne:protein|dep:nsubj OR lemma:regulate OR dep:dobj|activity OR insulin-degrading-enzyme
  2. Ab ne:protein|dep:nsubj OR lemma:regulate OR dep:dobj|activity OR insulin-degrading-enzyme
  3. somatostatin ne:protein|dep:nsubj OR lemma:regulate OR dep:dobj|activity OR insulin-degrading-enzyme
  4. microglia cells ne:protein|dep:nsubj OR lemma:regulate OR dep:dobj|activity OR insulin-degrading-enzyme
  5. mRNA ne:protein|dep:nsubj OR lemma:regulate OR dep:dobj|activity OR insulin-degrading-enzyme

Question 2

Which peptide hormone is the positive transcriptional regulator of IDE?
  1. Ab dep:amod|peptide OR dep:nsubj|hormone OR lemma:regulate dep:dobj|IDE
  2. somatostatin dep:amod|peptide OR dep:nsubj|hormone OR lemma:regulate dep:dobj|IDE
  3. BV-2 dep:amod|peptide OR dep:nsubj|hormone OR lemma:regulate dep:dobj|IDE
  4. AD dep:amod|peptide OR dep:nsubj|hormone OR lemma:regulate dep:dobj|IDE
  5. mRNA dep:amod|peptide OR dep:nsubj|hormone OR lemma:regulate dep:dobj|IDE

QUESTION 3

In which cell line was the gene expression regulation of IDE characterized ?
  1. mouse dep:prep_in OR regulation OR lemma:regulate IDE gene expression
  2. astrocytes dep:prep_in OR regulation OR lemma:regulate IDE gene expression
  3. microglia dep:prep_in OR regulation OR lemma:regulate IDE gene expression
  4. BV-2 dep:prep_in OR regulation OR lemma:regulate IDE gene expression
  5. beta-amyloid dep:prep_in OR regulation OR lemma:regulate IDE gene expression

QUESTION 4

Which method was applied to measure the quantity of IDE mRNA in the gene regulation experiments described in the paper ?
  1. ELISA lemma:apply OR lemma:measure OR dep:dobj|quantity IDE mRNA lemma:experimen
  2. siRNA lemma:apply OR lemma:measure OR dep:dobj|quantity IDE mRNA lemma:experimen
  3. RealTime PCR lemma:apply OR lemma:measure OR dep:dobj|quantity IDE mRNA lemma:experimen
  4. Western Blotting lemma:apply OR lemma:measure OR dep:dobj|quantity IDE mRNA lemma:experimen
  5. IgG antibody lemma:apply OR lemma:measure OR dep:dobj|quantity IDE mRNA lemma:experimen

QUESTION 5

What regulates the production of neprilysin ?
  1. A.5.1 # somatostatin A.5.2 # NEP A.5.3 # enzyme A.5.4 # matrix metalloproteinase A.5.5 # microglia

QUESTION 6

What kind of glial cell is able to phagocyte b-amyloid ?
  1. A.6.1 # neprilysin A.6.2 # siRNA A.6.3 # brain A.6.4 # culture medium A.6.5 # microglia

QUESTION 7

What is the major protease produced by microglia responsible for degrading A ?
  1. A.7.1 # Ab A.7.2 # cells A.7.3 # IDE A.7.4 # extracellular A.7.5 # beta-amyloid

QUESTION 8

What substance exhibited a similar effect on IDE secretion as achieved by somatostatin ?
  1. A.8.1 # octreotide A.8.2 # analogue A.8.3 # endogenous modulator A.8.4 # substrate A.8.5 # beta-amyloid

QUESTION 9

What are the sst receptors that are expressed on rat astrocytes ?
  1. A.9.1 # SSTR-2 , SSTR-3 and SSTR-4 A.9.2 # SSTR-1 , SSTR-2 and SSTR-4 A.9.3 # somatostatin A.9.4 # microglia A.9.5 # rat

QUESTION 10

What method was used to inhibit the expression of IDE ?
  1. A.10.1 # Western blot A.10.2 # microglia A.10.3 # positive modulation A.10.4 # siRNA A.10.5 # culture medium

Please send comments to Giuseppe Attardi.