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LinkDB specifications


Unique identifier OMICS_21251
Name LinkDB
Restrictions to use None
Community driven No
Data access File download, Browse, Application programming interface
User data submission Not allowed
Maintained Yes

Publication for LinkDB

LinkDB citations


Innate Multigene Family Memories Are Implicated in the Viral Survivor Zebrafish Phenotype

PLoS One
PMCID: 4535885
PMID: 26270536
DOI: 10.1371/journal.pone.0135483

[…] ne in and, to obtain the corresponding zebrafish accession numbers in, following previously described methods []. Zebrafish accession numbers were extracted from the WIKI pathways at pathways […]


TogoTable: cross database annotation system using the Resource Description Framework (RDF) data model

Nucleic Acids Res
PMCID: 4086138
PMID: 24829452
DOI: 10.1093/nar/gku403

[…] ublication, geography, media and government databases.There are several ID conversion tools such as the UniProt ID mapping tool (), DAVID ID conversion tool (), Protein Identifier Cross-Reference (), LinkDB () and Hyperlink Management System and Converter System (). Whereas these tools provide ID conversion service between biological databases, TogoTable provides not only ID conversion but also th […]


Catalytic residues in hydrolases: analysis of methods designed for ligand binding site prediction

J Comput Aided Mol Des
PMCID: 3032897
PMID: 21104192
DOI: 10.1007/s10822-010-9402-0
call_split See protocol

[…] lar enzyme class: hydrolases. The polypeptide chains were selected form the literature entries of CSA (version 2.2.9) []. Firstly, the Enzyme Commission (EC) numbers were found for the entries, using LinkDB method of KEGG API []. For the entries that failed to obtain an EC number, id mapping from the Protein Data Bank (PDB) to the UniProtKB (UP), available on the UniProt web page [] was performed […]


Comparative genomics of metabolic networks of free living and parasitic eukaryotes

BMC Genomics
PMCID: 2858753
PMID: 20356377
DOI: 10.1186/1471-2164-11-217

[…] ] and supplemented with data kindly provided by H. Ma and A.P. Zeng (German Research Center for Biotechnology, Braunschweig, Germany). Organism-specific enzyme lists were also obtained from KEGG, via LinkDB. The networks were reconstructed as directed graphs, but for all subsequent analyses treated as undirected. The basic network properties such as average connectivity or network diameter were de […]


Atlas – a data warehouse for integrative bioinformatics

BMC Bioinformatics
PMCID: 554782
PMID: 15723693
DOI: 10.1186/1471-2105-6-34

[…] can be stored in their own fields in the database, permitting 'substring' operations to extract parts of the sequence that span a particular feature type using SQL. Systems like EnsMart [] and DBGET/LinkDB [] provide data in a relational form, such that the power of SQL is at users' disposal. EnsMart's relational back-end provides users with the ability to construct intricate queries on the data […]


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LinkDB institution(s)
Institute for Chemical Research, Kyoto University, Uji, Japan; Nihon Silicon Graphics Cray K.K., Yokohama, Japan; Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan; National Institute for Basic Biology, Okazaki, Japan; Tsukuba Research Center, Real World Computing Partnership, Tsukuba, Japan; Institute for Chemical Research, Kyoto University, Uji, Japan
LinkDB funding source(s)
Supported by a Grant-in-Aid for Scientific Research on Priority Areas, “Genome Science”, from the Ministry of Education, Science, Sports and Culture of Japan.

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