Table 2

Taxonomic annotations obtained from source databases

Database

Taxonomy

data format

Structures with

taxonomic annotation

Unique species

names or IDs

Unique NCBI

taxonomy IDs


BCSDB

NCBI ID

6747

451

451

CarbBank

free text

13521

2471

1594

CFG

free text

2966

273

240

GlycoBase (Lille)

free text

178

13

13

GLYCOSCIENCES.de

NCBI ID

5384

312

312


Five source databases provided taxonomic annotations in the format listed. For each database the numbers listed are: total structures with taxonomic annotations (column 3), unique species names or IDs found (column 4), and unique NCBI taxonomy IDs remaining after data integration and standardization in GlycomeDB (column 5). The large difference between the number of free-text names and assigned NCBI IDs is a result of the usage of different names for the same species and names which could not be translated to NCBI taxonomy IDs.

Ranzinger et al. BMC Bioinformatics 2008 9:384   doi:10.1186/1471-2105-9-384

Open Data