Table 1

Explanation of the scoring functions evaluated.

Scoring Method

Description


Cosine Distance of Term Frequency-Inverse Document Frequency

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Cosine Distance of p-values

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Cosine Distance of term fractions

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Sum of the log of combined p-values

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Sum of the differences of log p values

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L2 of log-p of overlapping terms only

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L2 of term fractions of overlapping terms only

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L2 of log of p-values

<a onClick="popup('http://www.biomedcentral.com/1755-8794/6/S2/S3/mathml/M17','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1755-8794/6/S2/S3/mathml/M17">View MathML</a>


L2 of p-values

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L2 of term fractions

<a onClick="popup('http://www.biomedcentral.com/1755-8794/6/S2/S3/mathml/M19','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1755-8794/6/S2/S3/mathml/M19">View MathML</a>


L2 of term frequency

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Term Coverage

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Term Overlap

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Number of Drug MeSH Terms

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Number of Disease MeSH Terms

<a onClick="popup('http://www.biomedcentral.com/1755-8794/6/S2/S3/mathml/M24','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1755-8794/6/S2/S3/mathml/M24">View MathML</a>


M refers to the set of all MeSH terms, C and D refer to the MeSH terms for the drug and disease profile respectively. c(i), cf(i), cp(i) and ci(i) refer to the frequency, term fraction, hypergeometric p-value and term frequency-inverse document frequency for the MeSH term i of the drug profile. d(i), df(i), dp(i) and di(i) refer to the frequency, term fraction, hypergeometric p-value and term frequency-inverse document frequency for the MeSH term i of the disease profile.

Cheung et al. BMC Medical Genomics 2013 6(Suppl 2):S3   doi:10.1186/1755-8794-6-S2-S3

Open Data