Discovery of novel biomarkers and phenotypes by semantic technologies

Trugenberger, Carlo A; Wälti, Christoph; Peregrim, David; Sharp, Mark E; Bureeva, Svetlana

doi:10.1186/1471-2105-14-51

BMC Bioinformatics

Table 3 PubMed results with highest confidence levels

From: Discovery of novel biomarkers and phenotypes by semantic technologies

*Row*	*Term (A)*	*Relationship (B)*	*Object (C)*	*Conf% (D)*	*#Docs (E)*	*PMIDs (F)*
1	glycemic control	BiomarkerFor	Diabetes	70.3	1122	20110333, 20128112, 20149122,
2	Insulin	PhenoTypeOf	Diabetes	68.3	5000	19995096, 20017431, 20043582,
3	Proinsulin	BiomarkerFor	Diabetes	67.8	105	16108846, 9405904, 20139232,
4	TNF alpha inhibitor	PhenoTypeOf	Diabetes	67.1	245	9506740, 20025835, 20059414,
5	anhydroglucitol	BiomarkerFor	Diabetes	67.1	10	20424541, 20709052, 21357907,
6	linoleic acid	BiomarkerFor	Diabetes	67.1	61	20861175, 20846914, 15284064,
7	palmitic acid	BiomarkerFor	Diabetes	67.1	24	20861175, 20846914, 21437903,
8	pentosidine	BiomarkerFor	Diabetes	67.1	13	21447665, 21146883, 17898696,
9	uric acid	BiomarkerFor	Obesity	66.8	433	10726195, 19428063, 10904462,
10	proatrial natriuretic peptide	BiomarkerFor	Obesity	66.6	4	14769680, 18931036, 17351376,
11	ALT values	BiomarkerFor	Diabetes	66.3	2	20880180, 19010326
12	adrenomedullin	BiomarkerFor	Diabetes	64.3	7	21075100, 21408188, 20124980,
13	fructosamin	BiomarkerFor	Diabetes	64.2	59	20424541, 21054539, 18688079,
14	TNF alpha inhibitor	BiomarkerFor	Diabetes	62.1	245	9506740, 20025835, 20059414,
15	uric acid	BiomarkerFor	Diabetes	61.8	259	21431449, 20002472, 20413437,
16	monoclonal antibody	BiomarkerFor	Obesity	61.7	41	14715842, 21136440, 21042773,
17	Insulin level QTL	PhenoTypeOf	Obesity	61.2	1167	16614055, 19393079, 11093286,
18	stimulant	BiomarkerFor	Obesity	61.2	646	18407040, 18772043, 10082070,
19	IL-10	BiomarkerFor	Obesity	60.9	120	19798061, 19696761, 20190550,
20	central obesity	PhenoTypeOf	Diabetes	59.5	530	16099342, 17141913, 15942464,
21	lipid	BiomarkerFor	Obesity	59.5	4279	11596664, 12059988, 12379160,
22	urine albumin screening	BiomarkerFor	Diabetes	59.0	95	20886205, 19285607, 20299482,
23	tyrosine kinase inhibitor	BiomarkerFor	Obesity	58.8	83	18814184, 9538268, 15235125,
24	TNF alpha inhibitor	BiomarkerFor	Obesity	58.0	785	20143002, 20173393, 10227565,
25	fas	BiomarkerFor	Obesity	57.7	179	12716789, 17925465, 19301503,
26	leptin	PhenoTypeOf	Diabetes	57.6	870	11987032, 17372717, 18414479,
27	ALT values	BiomarkerFor	Obesity	57.4	8	16408483, 19010326, 17255837,
28	lipase	BiomarkerFor	Obesity	56.8	356	16752181, 17609260, 20512427,
29	insulin resistance	PhenoTypeOf	Obesity	55.8	5000	20452774, 20816595, 21114489,
30	chronic inflammation	PhenoTypeOf	Diabetes	55.7	154	15643475, 18673007, 18801863,

Highest confidence level scoring biomarker/phenotype candidates discovered by InfoCodex text mining of the experimental PubMed collection. The identified candidate terms appear in column A, with their relationship to diabetes or obesity in columns B-C. The confidence level, in column D (the descending sort key), is normalized on a scale in which the maximum of 100% is the score of the manually curated reference biomarkers/phenotypes. In column E are the numbers of documents in which a given candidate term appears. Column F displays the PubMed IDs of the most relevant PubMed documents for purposes of manual SME review. Note that the same term can have multiple entries since it can have different relationships (biomarker for diabetes, phenotype for obesity, etc.).

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ISSN: 1471-2105

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