文章：ARDB-Antibiotic Resistance Genes Database

年份：2009

ARDB的建立过程：

第一步：每种抗性基因的代表序列确定。First, the sequence of an experimentally confirmed respresentative was identified for every type of resistance, based on literature searches and meta-information provided by the NCBI protein database.

第二步：根据代表序列去查找相似序列。These representative resistance genes were then used to 'fish out' additional homologues using similarity searches against the NCBI nr database. The similarity cutoff was set at 80% unless a different value was recommended in the literature for aspecific resistance type. 最终获得13254 protein sequences putatively involved in antibiotic resistance.

第三步：对查到的13254条序列进行合并去冗余和清洗。We filtered this set by removing vector sequences in a non-redundant set of 6206 proteins. 如此得到6206条，进一步处理，This set was further refined by removing incomplete sequences, thereby yielding a core set of 4554 antibiotic resistance proteins. 最终得到4554条。

第四步：对得到的序列进行注释。Each sequence was associated with correponding CDD, COG, ontology and source organism information.

第五步：对序列进行分组和抗性机理等信息的添加。Furthermore, the genes were grouped into resistance types, corresponding to clusters of genes with similar resistance profiles, operon membership and mechanism of action. In addition, basic information about known antibiotics was extracted from KEGG DRUG, PubChem, PubMed MeSH database and the Chemical Entities of Biological Interest ontology.

最终，该数据库包含，ARDB contains resistance information for 13293 genes, 377 types, 257 antibiotics, 632 genomes, 933 species and 124 genera.

这个数据库的特点：

1）主要是靠文献、数据库检索，对比分析和整理得到的，为此工作量很大，导致数据库在2009年后就未有新的更新。resistance profile, is mostly 'paper-bound' made the construction of ARDB both difficult and time-consuming. To compile, confirm and validate this collection of data, several textbooks and several hundred journal articles were searched and summarized.

2）除抗性基因外，还包括了12个药物作用靶点，因为它的变化会引起抗性。12 additional drug targets have also been included into ARDB with relevant information [16S rRNA, 23s rRNA, gyrA, gyrB, parC, parE, rpoB, katG, pncA, embB, forP, fdr], whose modification has been shown to confer resistance.