genome - scale transcriptional regulatory network ( trn ) for any specific microbial organism is a critical component on the way to the next big milestone in system biology  building an integrated metabolic and regulatory model that can accurately predict cellular growth phenotypes .
several approaches and associated web resources have been developed for genome - wide reconstruction of metabolic pathways for a number of microbial genomes .
biocyc maintains an encyclopedia of experimentally defined metabolic pathways in model organisms and uses it for reconstruction of metabolism in other sequenced genomes ( 1 ) .
model seed allows user to submit any complete genome to the annotation pipeline to generate a draft metabolic model ( 2 ) . at the same time , the large - scale trns so far are available only for a limited number of model organisms , such as escherichia coli ( 3 ) , bacillus subtilis ( 4 ) , corynebacterium glutamicum ( 5 ) and mycobacterium tuberculosis ( 6 ) .
a fundamental difference between the reconstruction of trns and metabolic pathways is that regulatory interactions are much less conserved across bacterial genomes than metabolic pathways ( 7 ) . to address the challenging problem of propagation of regulatory interactions between distant genomes
, we recently developed a strategy enabling the genomic reconstruction of large - scale trns in diverse microbial genomes ( 8) .
the bacterial species tree is subdivided into small taxonomic families , and a subset of 512 representative genomes is selected for each family ; then the comparative genomics techniques are used to reconstruct a collection of reference regulons in these genomes . at the next stage ,
these reference regulons are used for an automatic annotation of regulatory interactions in the remaining genomes from the same taxonomic group . in 200910 , with a goal of building collections of taxonomy - specific reference regulons , we developed two web resources for large - scale inference and analysis of regulatory interactions in prokaryotes : the regprecise database ( http://regprecise.lbl.gov ) to capture and visualize manually curated regulons ( 9 ) and the regpredict web server ( http://regpredict.lbl.gov ) for fast and accurate regulon reconstruction ( 8) . the community - based approach for regulon reconstruction implemented in the regpredict web server enabled fast accumulation of a large number of curated regulatory interactions ( 1013 ) .
the current release of regprecise 2.0 captures the detailed descriptions of 1000 regulogs controlled by protein transcription factors ( tfs ) in 13 taxonomic groups of bacteria ( 147 genomes total ) and 400 regulogs controlled of conserved ribonucleic acid ( rna ) regulatory motifs ( e.g. riboswitches ) in 22 taxonomic groups ( 255 genomes total ) .
the total number of effectors of analyzed regulators in regprecise exceeds 200 and includes the following major classes of metabolites : amino acids , carbohydrates , nucleotides , lipids and fatty acids , co - enzymes , peptides and antibiotics , secondary metabolites and inorganic chemicals . beside tf regulons ,
the last release of regprecise includes a large collection of curated regulons controlled by rna regulatory elements ( such as riboswitches ) annotated by the regpredict web server using rna models from the rfam database ( 14 ) .
we anticipate that the content of regprecise database will continue fast growing due to large - scale regulon annotation projects conducted by scientific community using regpredict .
regprecise serves as a core resource on transcriptional regulation for the microbial domain of the doe systems biology knowledgebase ( 15 ) , a community - driven cyber infrastructure for sharing and integrating data and analytical tools to accelerate predictive biology . in the context of this project
, we developed a comprehensive set of restful web services for programmatic access to the whole scope of transcriptional regulatory data provided by regprecise .
the hierarchical organization of the regprecise database has three major levels : i ) a regulon , ii ) a regulog and iii ) a collection of regulogs .
a regulon is the basic unit of regprecise that represents a set of genes in a particular genome that are co - regulated by the same tf or rna regulatory motif .
the major types of output in the regprecise web services application programming interface ( api ) are represented by six objects that provide the detailed information about reconstructed regulatory interactions ( figure 1 ) . the regulon object
, being a basic unit , provides the general description of regulon , including the name of genome , the common name of regulator , its protein family and predicted effector molecule and the metabolic pathway ( or biological process ) controlled by the regulator .
the regulationtype property of the regulon object identifies the type of mechanism of regulation , which is either by transcription factor ( tf ) or by rna regulatory element ( rna ) .
the regulator object represents the actual gene encoding tf and provides its gene name , locus tag and vimssid [ gene identifier in microbesonline ( 16 ) database ] . in rare cases
, comparative genomics does not allow unambiguous selection of true cognate regulator between several homologous tfs .
in this case , more than one regulator can be assigned to a particular regulon . in the case of regulation by rna elements
the gene object represents a regulated gene and provides general information , such as gene name , locus tag , gene vimssid and function .
the site object represents either tf - binding site or rna regulatory element and provides its sequence , score , position relative to the translational gene start and downstream gene identifiers . 

the regulog object combines several regulons , controlled by orthologous regulators , that were reconstructed in a set of closely related genomes .
similar to the regulon object , the general information about regulator , effector and metabolic pathway is available for the regulog object . in addition
, the taxonname property describes the name of ncbi taxon representing all genomes analyzed in a given regulog .
finally , the regulogcollection object represents the highest level in the regprecise hierarchical data organization .
there are six types of collections available in regprecise : by taxonomy , orthologous tf , tf family , rna regulatory family , effector molecule of a regulator and regulated metabolic pathway .
the collectiontype property of the regulogcollection object encodes the type of collection and can possess one of the following values : 
pathway. several types of collections , such as collection by effector and by metabolic pathway , have two - level hierarchical structure , and thus , the classname property representing the upper level is provided in addition to the collection name .
the developed web services api enables programmatic access to the whole content of the regprecise database .
the api is implemented as a set of restful web services providing data in either javascript object notation ( json ) or extensible markup language ( xml ) , two of the most popular formats . the base uniform resource locator ( url ) for all web services is http://regprecise.lbl.gov / services / rest/. the current version of regprecise web services api includes 14 resources that can be classified into four categories ( table 1 ) .
the core resources provide access to the regulators ( genes encoding either tfs or rna motifs ) , target regulated genes and sites ( either tf - binding sites or rna regulatory elements ) .
these three resources together provide complete information about the content of a particular regulon and can be queried by regulon identifier . at the same time , if a user is interested in all genes regulated by orthologs of a particular tf in a group of closely related genomes , the genes resource can be queried by an identifier of a corresponding regulog .
the regulog and regulon resources can be used to obtain summary information about the intrinsic attributes of a regulog / regulon , such as the associated metabolic pathway ( or biological process ) , effector molecules , the regulation mode ( activation or repression ) , the regulation type ( tf or rna ) and regulator family . 

table 1.list of resources available in regprecise web services api 1.0resourcesdescriptioncore resources  /regulatorsrepresents a list of analyzed regulators that belong to either a given regulon or regulog . 
/genesrepresents a list of regulated genes that belong to either a given regulon or regulog . 
/sitesrepresents a list of tf - binding sites or rna regulatory elements that belong to either a given regulon or regulog . 
/regulonrepresents a regulon.navigation resources  /regulogcollectionsrepresents various types of regulog classifications : by taxonomic group , orthologous tf , tf family , rna regulatory element , metabolic pathway or biological process , effector molecule or environmental signal . 
/regulogsrepresents a list of regulogs in a collection of a given type and identifier . 
/regulonsrepresents a list of regulons in either a particular regulog or a genome.statistics resources  /regulogcollectionstatsrepresents general statistics on regulog collections of a particular type . 
/genomestatsrepresents general statistics on genomes that have at least one reconstructed regulon.utility resources  /searchregulonssearch regulons by the name or locus tag of either regulator or target regulated genes . 
/releaserepresents the version and the release date of the current version of regprecise . list of resources available in regprecise web services api 1.0 the navigation resources allow traversing through the hierarchical organization of the regprecise data ( table 1 ) . the list of the available regulog collections can be retrieved for each of these types using the regulogcollections resource .
subsequently , the list of regulogs that belong to a particular collection can be obtained by the regulogs resource .
it is important that the collection identifiers are unique only within the space of regulog collections of a particular type .
thus in addition to these identifiers , it is necessary to provide the type of a collection as a parameter in a query .
finally , a list of regulons analyzed for a particular tf of rna motif in a set of closely related genomes can be accessed by the regulons resource given regulog identifier .
the alternative navigation route starts from a list of genomes that have at least one reconstructed regulon .
the same regulons resource can be used to get a list of all reconstructed regulons for a particular genome . to get an overview of the regprecise content
, we developed two resources providing the general statistics for regulog collections ( regulogcollectionstats resource ) and genomes ( genomestats resource ) .
the statistics includes the number of genomes , reconstructed regulogs , regulons , and regulatory sites for the tfs and rna elements .
finally , the utility resources allow for searching for regulons by locus tags of the target regulated genes or tfs ( searchregulons resource ) .
the searchextregulons resource takes ncbi taxonomy i d of a genome and comma - separated list of gene locus tags and returns the non - redundant list of regulons that contain at least one of the provided genes .
in particular , this resource can be used for automatic validation of gene clusters reconstructed by the analysis of expression data . the current version of the regprecise database underlying the web services api can be obtained by the release resource .
first , we provide a template program in perl that can be run to access several of the web services and parse the output data .
the program is organized in two perl scripts : ( i ) regpreciseadapter.pma perl module that provides access to the individual web services and ( ii ) regulons.plan example of workflow that can be implemented using a combination of several web services .
both scripts can be easily modified to access all the web services available . at the same time , each web service is accompanied with an example of accessing api using curl command - line tool .
in this study , we provide two examples of the possible scenarios of using regprecise web services api . scenario 1obtaining information on a trn available for a particular genome . to check the availability of regulatory interactions for a given genome
, the user can query the genomes resource . by analyzing the output for the presence of the ncbi taxonomy i d of the genome of interest
for instance , the ncbi taxonomy i d of shewanella baltica os155 is 325240 , which corresponds to the internal genome identifier genomeid  =  7 .
the list of all reconstructed regulons in this genome can be retrieved by querying regulons?genomeid  =  7 .
analysis of the regulationtype property of each regulon in the output will show that 63 regulons are regulated by tfs , whereas 14 regulons are controlled by rna regulatory elements . among tf - operated regulons , the tryptophane regulon trpr has regulonid  =  6378 .
scenario 2obtaining all genes that are regulated by a particular rna motif in any genome .
analysis of the regulogcollections?collectiontype  =  rnafam query output identifies the corresponding regulog collection ( collectionid  =  25 ) .
list of all reconstructed regulogs in this collection can be retrieved by querying regulogs?collectiontype  =  rnafam&collectionid  =  25 . finally , by iterating through each regulog
, the complete list of genes regulated by fmn riboswitch can be retrieved by genes resource by providing regulog identifier as a parameter , e.g. genes?regulogid  =  1450 .
we are currently working on the automatic conservative propagation of all regulons inferred in the reference set of genomes to all closely related genomes from the same taxonomic group .
we will develop new web services to enable programmatic access to the results of propagation .
this work was supported by the office of science , office of biological and environmental research , of the us department of energy ( doe ) under contract no .
[ de - ac02 - 05ch11231 ] , as part of the doe systems biology knowledgebase , and under contract no .
[ de - sc0004999 ] with sanford - burnham medical research institute and lawrence berkeley national laboratory , as part of genomic science program .
 web services application programming interface ( api ) was developed to provide a programmatic access to the regulatory interactions accumulated in the regprecise database ( http://regprecise.lbl.gov ) , a core resource on transcriptional regulation for the microbial domain of the department of energy ( doe ) systems biology knowledgebase . 
 regprecise captures and visualize regulogs , sets of genes controlled by orthologous regulators in several closely related bacterial genomes , that were reconstructed by comparative genomics . 
 the current release of regprecise 2.0 includes > 1400 regulogs controlled either by protein transcription factors or by conserved ribonucleic acid regulatory motifs in > 250 genomes from 24 taxonomic groups of bacteria . 
 the reference regulons accumulated in regprecise can serve as a basis for automatic annotation of regulatory interactions in newly sequenced genomes . 
 the developed api provides an efficient access to the regprecise data by a comprehensive set of 14 web service resources . 
 the regprecise web services api is freely accessible at http://regprecise.lbl.gov/regprecise/services.jsp with no login requirements . 
INTRODUCTION
DATA TYPES AND ORGANIZATION
WEB SERVICES API
USE CASES
FUTURE DEVELOPMENT
FUNDING