many primary biological databases are dedicated to providing annotation for a specific type of biological molecule such as a clone , transcript , gene or protein ( eg the national center for biotechnology information [ ncbi ] entrez gene database provides annotation for genes , whereas uniprotkb provides this for proteins ) . other types of secondary databases provide relevant information about the attributes of these molecules , such as pathway , function(s ) or structural information ( eg the kyoto encyclopedia of genes and genomes [ kegg ] and protein data bank [ pdb ] . often , these databases provide limited cross - references for interoperation between databases . thus , enhanced mapping between these databases is required to facilitate the correlation of independent experimental datasets , which can be provided by identifier ( i d ) mapping services . i d mapping services are tools to connect one type of database i d to the corresponding i d in another database . this mapping includes three types of relationships : one - to - one , one - to - many and many - to - many . one - to - many and many - to - many relationships are required to account for biological processes such as alternative splicing , resulting in one gene giving rise to multiple transcripts , the presence of several isoforms of a single protein and other similar processes occurring in a cell . also , gene expression datas such as microarray datas are known to have multiple probes targeting a single transcript and vice versa ( eg affymetrix probes , which can be described by many - to - many relationships ) . thus , mapping ids of multiple databases to one another facilitates the correlation of different types of ' omics ' datasets which , in turn , might provide meaningful insights into the biological processes occurring in a cell . the seven i d converters that are discussed in detail in this review were selected to represent the majority of i d converters -- as well as major biological databases -- used in high - throughput genomics and proteomics datasets . they have many common features , such as : ( i ) supporting one - to - many and many - to - many relationships ; ( ii ) providing mapping counts , and the details of the database ids used as a ' bridge ' to link to target database ids ; ( iii ) providing a web - based graphical user interface ( gui ) which allows submission of a single i d or a batch search for multiple ids ; and ( iv ) the output database ids are hyperlinked to their original database for reference . link to web interface of various i d converters these i d converters also differ in a number of ways , such as in the availability of ( i ) type of query input ; ( ii ) target output databases ; ( iii ) species ; ( iv ) data sources -- and therefore coverage of the genome or proteome of a particular species ; ( v ) ease of use ; ( vi ) database update frequency ; ( vii ) possible conversion types ( eg protein - to - gene , gene - to - transcripts etc . ) ; ( viii ) speed of conversion ; ( ix ) a detailed help section or tutorial describing the intended use of the application ; and ( x ) an algorithm for mapping database ids . in general , these services establish mapping links using existing cross - references or by using sequence alignment information to determine the match . fewer i d converters have their own published algorithm for establishing the mapping , in addition to using the existing cross - references . many of the i d converters provide a web - based intuitive user interface , generally having three components : input types ( ie query databases ) , output types ( ie target databases ) and the species under consideration . it provides the option for several query and target databases for human , mouse and rat species . the output can be customised by selecting from a number of output databases which are divided into several logical levels , such as gene , gene clone , protein and functional annotation . further , detailed references are provided for the resultant output ids by hyperlinking them to their original data sources . a detailed list of input / output databases , availability and other pertinent features can be found in table 2 . a useful piece of information provided on the interface itself includes the specific version that was used as the data source for individual databases . this is of importance , considering the frequent updates of sequence databases and the increasing novel findings about the biological molecules in the respective research areas . comparison of various i d converters all input i d types are potential output i d types as well ( eg ) : as in i d mapping by uniprot . in some cases , however , there are additional output i d types available to choose from which are not available as input i d using that particular converter . such output i d types are mentioned in parentheses and are indicated as ' additional output ' ( eg ) as in clone / gene i d converter , gui graphical user interface . it supports almost all organisms , with monthly updates , and maps approximately 90 database sources , including primary sequence databases and secondary functional / structural annotation databases . thus , the input and output database option is divided into uniprot , other sequence database , three - dimensional structure , protein - protein interaction , protein family / group , two - dimensional gel , genome annotation , organism specific gene database , phylogenomics , enzyme and pathway and gene expression , and other database types which are listed in table 2 . the output is provided in the form of a tab - delimited table indicating the ids in the query that could be mapped to those in the target databases , along with a list of unique target database ids and a list of those ids that could not be mapped . i d mapping by uniprot also provides an application programming interface ( api ) for programmatic access , as well as file transfer protocol ( ftp ) downloads if the user wishes to have a local i d mapping service for large datasets ( > 100,000 ids ) . matchminer is tool that provides a clean interface with an interesting batchmerge option , along with interactive lookup and batch lookup . interactive lookup and batch lookup can be used for generic i d conversion for single and multiple query input , respectively . the batch merge option is intended to be used to merge an input of two different query database i d lists into a single list , by determining which of the ids from the two lists refers to the same gene or biological entity . in the i d conversion html output , hyperlinks are provided from each output i d to the original database for some ( eg entrez gene , unigene ) , but not all , databases ( eg affymetrix ) . also , matchminer follows a hierarchy of source reliability while searching for an i d and specifies the source database in the output ; for example , if the input i d is a genbank accession , then the algorithm first searches for the i d from university of california santa cruz ( ucsc ) -known genes . if this is not found , only then it does search through unigene and then ucsc expressed sequence tags ( ests ) . details of hierarchy of source reliability for all source databases can be found in the original article on matchminer . another unique feature of matchminer is that it provides a command line interface option for querying , which can be useful in cases where matchminer is to be integrated as a part of a pipeline or as a filtering step in a workflow . thus , matchminer provides certain unique features that can be useful for specialised i d conversion needs . most of the i d converters use the available data sources to create mapping ; however , the david gene i d conversion tool[12 - 14 ] uses its own knowledge base , which is based on the david gene concept ,   in addition to the primary entrez- and uniprot - based mapping . the data source used by this tool includes 20 main gene / protein i d types , in addition to other secondary i d types . it also has the capability to handle a mixture of i d types in case of ' unsure ' input i d type . the output yields summary statistics for conversion , including i d count , presence in david database and conversion status as successful or otherwise , with possible choices for ambiguities , such as when the input i d may not belong to the database as specified by the user but may exist as an i d in another database . biodbnet provides a converter ' db2db ' which has wide coverage of databases , including 153 database i d types including genes , proteins , pathways and other biological concepts as their data source . it also provides other menu options for i d conversion , such as ' dbfind ' , when the input i d type is unknown , ' dbwalk ' , where the user can direct the type of conversion and the intermediate databases to ' walk ' through , ' dbreport ' , which provides an all - inclusive search , one i d to all other available ids / annotations available . likewise , g : convert , which is a part of g : profiler ,   provides mappings which are mainly based on the ensembl database ,   created through a three - level index of gene , transcript and protein ensembl ids . by contrast , the cross - reference navigation server ( cronos ) provides mappings which are based on primary resources such as uniprot , refseq and ensembl . these mappings are validated by eliminating ambiguous gene names , which provide an all - inclusive search of one i d to all other available ids / annotations available . this review is by no means comprehensive , but is intended to be representative of the currently available i d converters . thus , there are several other i d converters that are part of other integrative analysis systems which are not reviewed here but might be of interest to researchers -- such as babelomics ,   biomart ,   i d converter system ,   bridgedb etc . many of the users provide their feedback after using these tools at internet forums ( eg http://biostar.stackexchange.com/questions/22/gene-id-conversion-tool ) . comparisons are made using a test set of ids to test the performance of different i d converters ( eg http://www.scribd.com/doc/18966500/id-converters-test ) that might aid in the selection of an appropriate i d converter . such comparative analysis is not presented in this review , as the intended use of each of the i d converters is different and each has its own unique features which may not be measured by direct comparison . it is , however , recommended that one should base the choice of an i d converter application on the researcher 's conversion needs ; for example , the availability of the required input and output i d type , acceptable mapping algorithm and database update frequency , which are described in this review and summarised in table 2 , as well as other factors that might be of interest for the biological experiment being conducted . the authors thank the nancy and stephen grand philanthropic foundation , myeloma institute for research and therapy , uams , multiple myeloma research foundation and the idea networks of biomedical research excellence ( inbre ) program of the national center for research resources .
many primary biological databases are dedicated to providing annotation for a specific type of biological molecule such as a clone , transcript , gene or protein , but often with limited cross - references . 
 therefore , enhanced mapping is required between these databases to facilitate the correlation of independent experimental datasets . 
 for example , molecular biology experiments conducted on samples ( dna , mrna or protein ) often yield more than one type of ' omics ' dataset as an object for analysis ( eg a sample can have a genomics as well as proteomics expression dataset available for analysis ) . thus , in order to map the two datasets , the identifier type from one dataset is required to be linked to another dataset , so preventing loss of critical information in downstream analysis . 
 this identifier mapping can be performed using identifier converter software relevant to the query and target identifier databases . 
 this review presents the publicly available web - based biological database identifier converters , with comparison of their usage , input and output formats , and the types of available query and target database identifier types .