Gene prioritization and clustering by multi-view text mining

BMC Bioinformatics

Table 1 Overview of the controlled vocabularies applied in the multi-view approach.

No.	CV	Number of terms in CV	Number of indexed terms
1	eVOC	1659	1286
2	eVOC anatomical system	518	401
3	eVOC cell type	191	82
4	eVOC human development	658	469
5	eVOC mouse development	369	298
6	eVOC pathology	199	166
7	eVOC treatment	62	46
8	GO	37069	7403
9	GO biological process	20470	4400
10	GO cellular component	3724	1571
11	GO molecular function	15282	3323
12	KO	1514	554
13	LDDB	935	890
14	MeSH	29709	15569
15	MeSH analytical	3967	2404
16	MeSH anatomy	2467	1884
17	MeSH biological	2781	2079
18	MeSH chemical	11824	6401
19	MeSH disease	6717	4001
20	MeSH organisms	4586	1575
21	MeSH psychiatry	1463	907
22	MPO	9232	3446
23	OMIM	5021	3402
24	SNOMED	311839	27381
25	SNOMED assessment scale	1881	810
26	SNOMED body structure	30156	2865
27	SNOMED cell	1224	346
28	SNOMED cell structure	890	498
29	SNOMED disorder	97956	13059
30	SNOMED finding	51159	3967
31	SNOMED morphologic abnormality	6903	2806
32	SNOMED observable entity	11927	3119
33	SNOMED procedure	69976	9575
34	SNOMED product	23054	1542
35	SNOMED regime therapy	5362	1814
36	SNOMED situation	9303	2833
37	SNOMED specimen	1948	742
38	SNOMED substance	33065	8948
39	Uniprot	1618	520
40	Merge-9	372527	50687
41	Merge-4	363321	48326
42	Concept-4	1420118	44714
43	No-voc	-	259815

The versions of bio-ontologies and MEDLINE repository adopted in the indexing process are mentioned in the text. The Number of indexed terms of controlled vocabularies reported in this table are counted on indexing results of human related publications only so their numbers are smaller than those in our earlier work [2], which were counted on all species appeared in GeneRIF. The Number of terms in CV are counted on the vocabularies independently from the indexing process. The numbers of terms of Merge-9, Merge-4 and Concept-4 are counted on text mining results of all species occurring in GeneRIF.

ISSN: 1471-2105