the arrayexpress archive of functional genomics data is one of the major international repositories for functional genomics high - throughput data . since 2003 ( 1 ) , the database has grown to 15  000 experiments comprised of 425  000 assays . during this period , the technology used to generate functional genomics data has changed from microarray - based experiments to high - throughput sequencing . to address this , we have developed and integrated submissions of high - throughput sequencing data with the european genome - phenome archive ( ega ) ( lappalainen , i . et al . , submitted ) and the european nucleotide archive ( ena ) ( 2 ) . other important developments are the inclusion of all gene expression omnibus ( geo ) array - based data and a new data exchange agreement with the geo ( 3 ) for high - throughput sequencing data , a new advanced query capability supporting ontology - based queries over the entire archive contents . the european bioinformatics institute 's gene expression atlas ( gxa ) ( 4 ) is now a separate resource from the archive and is linked from the arrayexpress graphical user interface . adjusting arrayexpress to accept and display high - throughput sequencing experiments alongside existing array data is one of the major recent developments . we have worked closely with other resources at european bioinformatics institute , specifically the ena and ega , who archive short - read data for multi - species and potential human identifiable data , respectively . as outlined in minseqe guidelines ( minimum information about a high throughput sequencing experiment , http://www.mged.org/minseqe ) , the provision of raw sequence data is insufficient to describe comparative experiments such as rna - seq ; metadata describing the experimental conditions and processed data are necessary to interpret the experiment . there are parallels to the provision of metadata for microarray - based experiments ( in addition to the raw data files , e.g. cel files ) ; therefore , the mage - tab ( 5 ) data representation format is both an appropriate and an easy to use format for describing these experiments . submission of high - throughput sequencing data are now supported by the mage - tab template generation system ( 6 ) . this allows users to generate and complete a taxon - specific tab - delimited template which describes their experiment and to supply related data files by ftp or aspera . where raw data are available these are integrated into the ena at the point of submission , and both arrayexpress experiment accessions and ena identifiers for sequences are returned to the user by arrayexpress curators . exceptions to this process are submissions with human data which are potentially identifiable , e.g. sequence of human patients . these data are submitted direct to the ega in mage - tab format , raw data are retained by the ega and summary - level data which meet ethical requirements for release are released to arrayexpress . sequencing - based experiments in arrayexpress now have clickable links from the user interface to the ena sequence archive to raw data files , and links are also provided in the mage - tab . work is in progress to develop an automated bioconductor ( 7 ) package to identify , extract and reprocess rna - seq data for inclusion in the gxa . arrayexpress provides rich metadata for samples and experiments , these are typically provided as free - text name value pairs , e.g. disease state , invasive ductal carcinoma . to enable semantic queries ( for instance , to find all cancer - related data sets even if they were not annotated as leukemia ) , we have developed open source software that allows for query expansion based on the experiment factor ontology ( efo ) ( 8) . efo is a data - driven application ontology developed to describe the sample attributes and experimental variables in functional genomics data sets . for example ,  retrieve all experiments where one or more samples is annotated as cancer , or a subtype of cancer returns 21  083 assays , without the ontology support and 49  729 assays using subsumption queries for known subtypes of cancer . the query results are visualized with yellow matching original input , green matching synonyms and red matching child terms . the ontology is visualized as a tree on query and users are provided with autocomplete options based on its content . additionally , the interface has been modified so that experiments can be queried by assay types ( array / high - throughput sequencing ) , source ( geo / arrayexpress ) and molecule ( dna / rna ) . arrayexpress has been importing selected geo ( 3 ) data sets ( gds ) in order to provide unified queries across public data and for integration with european bioinformatics institute databases such as ensembl ( 9 ) . to date more than 12  000 geo - derived experiments and associated array designs are available , import of all geo data will be complete by the end of 2010 . selected gds are re - annotated , subjected to quality control and integrated into the gxa . a data exchange agreement between geo and arrayexpress is now in place for high - throughput sequencing data and all htp sequencing data submitted to geo are present in arrayexpress . software developed tools for curation processes are publicly available ; recent software releases include a lexical mapping application , zooma ( http://zooma.sf.net ) , the ontocat ontology query service ( http://ontocat.sf.net ) , a canonical mage - tab parser ( http://limpopo.sf.net ) , mage - tab format conversion tools ( http://tab2mage.sf.net ) and a mage - tab importer for bioconductor ( 10 ) . arrayexpress will be closely integrated with a new biosample database at the european bioinformatics institute ( ebi ) ( http://www.ebi.ac.uk/biosamples ) . this database will store the sample descriptions for all the samples referenced by any of the databases . samples can be pre - submitted and will be linked to ebi databases where related data exist . for example , 1000 genomes , coriell cell lines or hapmap samples have records in the ena , ega and arrayexpress . this new resource is being developed in conjunction with the ncbi and data exchange is planned . the replacement of existing mage - om centric architecture ( 11 ) with mage - tab - based infrastructure is ongoing and data migration is underway . this effort will significantly simplify all internal data management tasks and will benefit the users in improved data load times , faster issuing of accession numbers , faster data exchange with geo and improved query interfaces . the existing browse user interface will be maintained , as will current programmatic access and ftp site structure to ensure minimum disruption for users . adjusting arrayexpress to accept and display high - throughput sequencing experiments alongside existing array data is one of the major recent developments . we have worked closely with other resources at european bioinformatics institute , specifically the ena and ega , who archive short - read data for multi - species and potential human identifiable data , respectively . as outlined in minseqe guidelines ( minimum information about a high throughput sequencing experiment , http://www.mged.org/minseqe ) , the provision of raw sequence data is insufficient to describe comparative experiments such as rna - seq ; metadata describing the experimental conditions and processed data are necessary to interpret the experiment . there are parallels to the provision of metadata for microarray - based experiments ( in addition to the raw data files , e.g. cel files ) ; therefore , the mage - tab ( 5 ) data representation format is both an appropriate and an easy to use format for describing these experiments . submission of high - throughput sequencing data are now supported by the mage - tab template generation system ( 6 ) . this allows users to generate and complete a taxon - specific tab - delimited template which describes their experiment and to supply related data files by ftp or aspera . where raw data are available these are integrated into the ena at the point of submission , and both arrayexpress experiment accessions and ena identifiers for sequences exceptions to this process are submissions with human data which are potentially identifiable , e.g. sequence of human patients . these data are submitted direct to the ega in mage - tab format , raw data are retained by the ega and summary - level data which meet ethical requirements for release are released to arrayexpress . sequencing - based experiments in arrayexpress now have clickable links from the user interface to the ena sequence archive to raw data files , and links are also provided in the mage - tab . work is in progress to develop an automated bioconductor ( 7 ) package to identify , extract and reprocess rna - seq data for inclusion in the gxa . arrayexpress provides rich metadata for samples and experiments , these are typically provided as free - text name value pairs , e.g. disease state , invasive ductal carcinoma . to enable semantic queries ( for instance , to find all cancer - related data sets even if they were not annotated as leukemia ) , we have developed open source software that allows for query expansion based on the experiment factor ontology ( efo ) ( 8) . efo is a data - driven application ontology developed to describe the sample attributes and experimental variables in functional genomics data sets . for example ,  retrieve all experiments where one or more samples is annotated as cancer , or a subtype of cancer returns 21  083 assays , without the ontology support and 49  729 assays using subsumption queries for known subtypes of cancer . the query results are visualized with yellow matching original input , green matching synonyms and red matching child terms . the ontology is visualized as a tree on query and users are provided with autocomplete options based on its content . additionally , the interface has been modified so that experiments can be queried by assay types ( array / high - throughput sequencing ) , source ( geo / arrayexpress ) and molecule ( dna / rna ) . arrayexpress has been importing selected geo ( 3 ) data sets ( gds ) in order to provide unified queries across public data and for integration with european bioinformatics institute databases such as ensembl ( 9 ) . to date more than 12  000 geo - derived experiments and associated array designs are available , import of all geo data will be complete by the end of 2010 . selected gds are re - annotated , subjected to quality control and integrated into the gxa . a data exchange agreement between geo and arrayexpress is now in place for high - throughput sequencing data and all htp sequencing data submitted to geo are present in arrayexpress . software developed tools for curation processes are publicly available ; recent software releases include a lexical mapping application , zooma ( http://zooma.sf.net ) , the ontocat ontology query service ( http://ontocat.sf.net ) , a canonical mage - tab parser ( http://limpopo.sf.net ) , mage - tab format conversion tools ( http://tab2mage.sf.net ) and a mage - tab importer for bioconductor ( 10 ) . arrayexpress will be closely integrated with a new biosample database at the european bioinformatics institute ( ebi ) ( http://www.ebi.ac.uk/biosamples ) . this database will store the sample descriptions for all the samples referenced by any of the databases . samples can be pre - submitted and will be linked to ebi databases where related data exist . for example , 1000 genomes , coriell cell lines or hapmap samples have records in the ena , ega and arrayexpress . this new resource is being developed in conjunction with the ncbi and data exchange is planned . the replacement of existing mage - om centric architecture ( 11 ) with mage - tab - based infrastructure is ongoing and data migration is underway . this effort will significantly simplify all internal data management tasks and will benefit the users in improved data load times , faster issuing of accession numbers , faster data exchange with geo and improved query interfaces . the existing browse user interface will be maintained , as will current programmatic access and ftp site structure to ensure minimum disruption for users . european molecular biology laboratory , the european commission ( sling grant agreement number 226073 , gen2phen grant agreement number 200754 ) ; us national institutes of health ( the national human genome research institute , the national institute of biomedical imaging and bioengineering and the national cancer institute ) ( grant number p41 hg003619 ) . funding for open access charge : european molecular biology laboratory functional genomics team budget . conflict of interest statement .
the arrayexpress archive ( http://www.ebi.ac.uk/arrayexpress ) is one of the three international public repositories of functional genomics data supporting publications . 
 it includes data generated by sequencing or array - based technologies . 
 data are submitted by users and imported directly from the ncbi gene expression omnibus . the arrayexpress archive is closely integrated with the gene expression atlas and the sequence databases at the european bioinformatics institute . 
 advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease , cell types and anatomy .