000000000011111111112222222222333333333344444444445The maximum-length legal spans in this example are from bytes 0-4, 8-29, and 39-50. Our legalspans.txt file would include the following data:
012345678901234567890123456789012345678901234567890
Aaa. <p> Bbbbb <b>cc</b> ddd. <p><p><p> Eee ff ggg.
12345 0 5Let's consider the span 8-29 further. This is a maximum-length legal span because there is an HTML paragraph tag on either side of it. If a system nominates a passage that exceeds these boundaries, it will be disqualified for further analysis or judgment. But anything within the maximum-length legal span, e.g. 8-19, 18-19, or 18-28, could be nominated or relevant passages.
12345 8 22
12345 39 12
Biological object (1..many) <--relationship--> Biological process (1..many)The biological object might be genes, proteins, gene mutations, etc. The biological process can be physiological processes or diseases. The relationships can be anything, but are typically verbs such as causes, associated with, or phosphorylates. We determined four out of the five GTTs from 2005 could be reformulated into the above structure, with the exception of the first GTT asking procedures or methods. The patterns for doing this from the GTTs were based on the examples in the following table:
GTT | Question Pattern | Example |
Find articles describing the role of a gene involved in a given disease. | What is the role of gene in disease? | What is the role of DRD4 in alcoholism? |
Find articles describing the role of a gene in a specific biological process. | What effect does gene have on biological process? | What effect does the insulin receptor gene have on tumorigenesis? |
Find articles describing interactions (e.g., promote, suppress, inhibit, etc.) between two or more genes in the function of an organ or in a disease. | How do genes interact in organ function? | How do HMG and HMGB1 interact in hepatitis? |
Find articles describing one or more mutations of a given gene and its biological impact. | How does a mutation in gene influence biological process? | How does a mutation in Ret influence thyroid function? |
160 12474524 1 1.0 1572 27 tag1Runs were submitted using the form in the active participants area of the NIST TREC Web site: http://ir.nist.gov/trecsubmit/g.html. The following link has a Perl script that checks your run to insure it is in the proper format: http://trec.nist.gov/act_part/scripts/06.scripts/check_genomics.pl. It does not check to see whether your spans are "legal," as defined above.
160 12513833 2 0.373 1698 54 tag1
160 12517948 3 0.222 99 159 tag1
161 12531694 1 0.907 232 38 tag1
161 12545156 2 0.456 789 201 tag1
160 12474524 1572 27 MeSH1;MeSH2
160 12513833 1698 54 MeSH1;MeSH3
160 12517948 99 159 MeSH4
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
12 |
13 |
14 |
15 |
16 |
17 |
18 |
19 |
20 |
21 |
A |
b |
b |
c |
c |
c |
d |
d |
d |
e |
e |
f |
f |
||||||||
G |
h |
h |
i |
i |
i |
j |
j |
j |
k |
k |
l |
l |
m |
m |
||||||
N |
o |
o |
p |
p |
q |
s |
s |
t |
t |
t |
u |
|||||||||
V |
w |
|||||||||||||||||||
X |
x |
x |
y |
y |
z |
z |
z |
Document |
Passage |
Aspect |
D1 |
P1 |
A1 |
D2 |
P2 |
A2 |
D3 |
P3 |
NR |
D1 |
P4 |
A3 |
D4 |
P5 |
A4 |
D1 |
P6 |
A1 |
D5 |
P7 |
NR |
D2 |
P8 |
A2 |
D6 |
P9 |
A5 |
Passage |
Chars in
passage |
Relevant
chars in passage |
CCR |
CCP |
A bb ccc ddd ee ff | 18 |
12 |
12/40 = 0.3 |
12/18 = 0.67 |
G hh iii jjj kk ll mm | 21 |
0 |
12/40 = 0.3 |
12/39 = 0.31 |
N oo pp q ss ttt u | 18 |
18 |
30/40 = 0.75 |
30/57 = 0.53 |
V w | 3 |
0 |
30/40 = 0.75 |
30/60 = 0.5 |
Xxx yy zzz | 10 |
0 |
30/40 = 0.75 |
30/70 = 0.43 |
Rank |
Aspect |
1 |
A1 |
2 |
A2 |
3 |
NR |
4 |
A3 |
5 |
A4 |
6 |
NR |
7 |
A5 |
Rank |
Document |
1 |
D1 |
2 |
D2 |
3 |
D3 |
4 |
D4 |
5 |
D5 |
6 |
D6 |
7 |
D7 |