Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment

Table 4 Higher Taxa Queries.

QUERY	Trees Returned using TreeBASE	Trees Returned using TCl-Db with Sp2000 Hierarchy	Trees Returned using TCl-Db with ITIS Hierarchy	Trees Returned using TCl-Db with NCBI Hierarchy
Diptera	7	X	111	106
Lepidoptera	5	41	39	71
Carnivora	12	49	49	65
Animalia	1	954	856	0
Solanaceae	9	80	80	80
Rosaceae	1	42	42	38
Felidae	7	10	10	15
Vertebrata	3	0	408	443
Fungi	8	807	389	814
Crustacea	2	0	47	38
Chordata	1	433	411	446
Metazoa	5	0	0	1,014
Poaceae	11	100	100	95
Rodentia	9	100	100	102
Chlorophyceae	6	50	66	50
Cnidaria	3	75	78	79
Arthropoda	5	404	284	371
Primates	7	61	61	61
Aves	8	91	91	87
Reptilia	1	74	74	0
Coleoptera	3	67	45	49
Cetacea	16	47	17	47
Bacteria	2	55	13	35
Ascomycota	9	549	273	540
Archaea	4	X	0	15
Mollusca	14	75	86	93
Mammalia	12	224	212	221
Fabaceae	11	151	143	151
Asteraceae	11	127	127	156
Insecta	2	325	238	301

Expanding query terms hierarchically increases the number of trees returned from TreeBASE. The first column shows the count of trees found in TreeBASE. The remaining columns show the number of trees returned using hierarchical query expansion on TreeBASE using Sp2000, ITIS and NCBI classifications. The table highlights the importance of including more than one hierarchy. For instance, the query 'Metazoa' returns no data when using the ITIS or Sp2000, and 1014 when using NCBI. Also, for 'Fungi' we see that NCBI and ITIS differ. In some cases the hierarchical query failed, denoted with an X. For example, as the term 'Archaea' is both a genus and superkingdom in SP2K, the hierarchical query fails.