Annotation-based feature extraction from sets of SBML models

Alm, Rebekka; Waltemath, Dagmar; Wolfien, Markus; Wolkenhauer, Olaf; Henkel, Ron

doi:10.1186/s13326-015-0014-4

Journal of Biomedical Semantics

Table 1 Extracted features for different sets (CC, RS1, RS2 and BMDB), methods and feature size

From: Annotation-based feature extraction from sets of SBML models

5 Features	Method 2				Method 4
	CC	RS1	RS2	BMDB	CC	RS1	RS2	NFKB
	33285	24870	24870	24870	22563	22563	26816	24870
	33302	33302	33302	33302	33608	26082	33695	26082
ChEBI	33304	33304	33304	33304	33694	33241	47019	33241
	35701	33582	33582	33582	37096	33695	61120	33695
	36357	36357	36357	36357	37787	61120	63367	61120
*avg depth*	5.4	4.2	4.4	4.2	7.2	5.6	8.2	5.4
	8152	3674	3674	3674	22411	3674	3674	3674
	9987	8152	5575	8152	30163	5575	9987	5575
GO	44699	9987	8152	9987	51726	6810	22607	9987
	65007	44699	9987	44699	65009	9987	43170	43170
	71840	51234	44699	65007	71822	43170	71822	71822
*avg depth*	2	1.8	1.8	1.8	4.4	2.2	3.6	2.6
	003	064	231	003	009	009	009	003
	236	231	245	064	231	064	167	009
SBO	374	240	247	231	252	176	240	064
	375	241	291	236	336	252		167
	545	545	545	545				240
*avg depth*	2.4	2.4	2.4	2	4	4.3	3.5	3
15 Features	Method 2				Method 4
	CC	RS1	RS2	BMDB	CC	RS1	RS2	BMDB
	16646	18059	18059	18059	22563	22563	24875	24835
	24651	24835	24835	24835	33608	24835	25107	24870
	25367	24870	24870	24870	33694	25741	26816	26082
	25699	25367	25367	25367	37096	26082	33252	33241
	25741	25806	26082	26082	37787	33241	33620	33259
	26082	26082	33259	33241		33252	33636	33636
	33241	26835	33304	33259		33259	33695	33695
ChEBI	33839	33241	33581	33285		33608	35155	35155
	35701	33259	33674	33304		33695	35569	35569
	36358	33285	33839	33674		35701	47019	35701
	36606	33674	35701	33839		61120	61120	47019
	51143	33694	37577	35701		63367	63161	61120
	63161	35701	50906	50906		64709	63367	63161
	63299	51143	51143	51143				63367
	64709	64709	64709	64709				64709
*avg depth*	5.9	5.3	4.8	4.8	7.2	5.4	7.0	6.3
	3674	3674	3674	3674	216	3674	3674	3674
	5575	5575	5575	5575	4693	5575	5834	5575
	6807	6807	6807	8152	5575	6810	6826	9987
	9056	9056	9056	9987	22411	9987	8943	43170
	9058	9058	9058	32501	30163	16088	9987	71822
	40007	44237	32501	32502	32268	43170	22607
	44237	44238	44237	40007	45750	45750	43170
GO	44238	44699	44238	44699	51726		71822
	44699	44710	44699	48511	65009
	50896	48511	44710	50896	71822
	51234	50896	50896	51234
	65007	51234	51234	51704
	71704	65007	65007	65007
	71840	71704	71704	71840
		71840	71840
*avg depth*	2.3	2.3	1.9	1.8	4.1	2.1	3.0	2.6
	009	064	016	003	009	009	009	003
	177	177	017	064	231	064	167	009
	179	179	046	241	252	176	240	064
	180	180	153	245	336	252		167
	181	182	156	247				240
	182	185	231	253
	205	205	241	285
SBO	245	241	245	290
	253	247	247	291
	290	250	253	374
	291	253	290	375
	308	285	291	405
	342	290	308	409
	360	377	360	412
	374	545	380	545
*avg depth*	4.6	4.5	3.7	3.3	4	4.3	3.5	3

The upper table shows a maximum of five features, the bottom table 15 features, respectively. IDs are shortened (e.g. SBO:0000064 is represented by 064) and ordered ascending. The average depth (avg) of features per ontology is emphasized for the test sets.

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ISSN: 2041-1480

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