TBMap: a taxonomic perspective on the phylogenetic database TreeBASE

BMC Bioinformatics

Table 2 Effectiveness of string and hierarchical queries

TreeBASE studies retrieved by text and hierarchical queries
Rank	Term	Frequency	tax_id	Text	Hierarchical
1	homo sapiens	9700	9606	22	25
2	mammalia	5028	40674	7	69
3	Fungi	1875	4751	6	440
4	angiosperms	1825	3398	8	470
5	pine	1772
6	carnivora	1723	33554	6	18
7	maple	1666
8	acer	1618	4022	5	7
9	chordata	1373	7711	1	140
10	Agaricus bisporus	1286	5341	17	18
11	Homo	1212	9605	1	26
12	oak	1103
13	Cetacea	1006	9721	9	15
14	bacteria	988	2	2	21
15	pinus	973	3337	4	14
16	Candida albicans@	963	5476	21	21
17	human	951	9606		25
18	Zea mays	929	4577	13	17
19	donoghue	914		-	-
20	jody hey	901		-	-
21	Aves	888	8782	5	28
22	quercus	865	3511	1	3
23	chase	804		-	-
24	Hibbett	803		-	-
25	drosophila	792	7215	3	15
26	Drosophila melanogaster	727	7227	13	13
27	Nematoda@	649	6231	3	29
28	arthropoda	648	6656	5	148
29	primates	619	9443	2	28
30	mollusca	610	6447	4	38
Total		45211		158	1628

For the 30 most common query terms entered by users of TreeBASE between December 1998 to March 2006, the table shows the frequency of that term, the NCBI taxonomy tax_id (where applicable), and the number of studies retrieved by a SQL text query and by a hierarchical query using a nested sets representation of the NCBI classification (Fig. 3). Queries in boldface are vernacular names that are also present in the NCBI taxonomy database. Two queries used the '@' symbol, which TreeBASE treats as a wild-card. For those terms the corresponding SQL text query used the '%' wild-card.

ISSN: 1471-2105