candida albicans is the most common fungal pathogen causing invasive and bloodstream infections in immunocompromised patients , although in recent years , several non - albicans species and other yeasts have also emerged as major opportunistic pathogens ( 1,2 ) .
studies in the us identify candida glabrata as the second most common candida species involved in invasive fungal infections .
moreover , antifungal drug resistance , especially to azoles , is common among c. glabrata clinical strains isolated from patients with prior azole treatment ( 1 ) .
the availability of genome sequences for these pathogenic fungi has made it possible to study genes that play a role in pathogenesis and drug resistance in candida species , thereby increasing our understanding of the mechanisms of virulence in fungal pathogens .
the candida genome database ( cgd , http://www.candidagenome.org/ ) is an online resource for the scientific research community studying fungal molecular biology and pathogenesis .
the primary mission of cgd is to facilitate and accelerate candida research by providing both an extensively curated compendium of candida gene , protein and sequence information , and easy - to - use web - based tools for accessing , analyzing and exploring these data . when the cgd project began in 2004 , our initial efforts focused on curation of c. albicans , because it is the best - characterized species of the group and has the largest corpus of gene - specific scientific literature .
we have now expanded the scope of the project to include other candida species , and provide an extensive suite of tools and resources that have been redesigned to facilitate the analysis of multiple species concurrently .
the cgd locus summary page ( lsp ) has been updated with information about the identity of orthologous genes in c. glabrata , and with orthology - based functional predictions and gene descriptions .
we currently display both manual and computational gene , protein and sequence information about c. albicans and the recently added species , c. glabrata .
we also provide genomic and protein sequence downloads and blast ( 3 ) resources for multiple candida species and strains , including c. albicans strains sc5314 ( 4 ) and wo-1 ( 5 ) , c. dubliniensis ( 6 ) , c. guilliermondii ( 5 ) , c. lusitaniae ( 5 ) , c. parapsilosis ( 5 ) , c. tropicalis ( 5 ) , debaryomyces hansenii ( 7 ) and lodderomyces elongisporus ( 5 ) .
we will be adding curated information for all these other candida species in the future .
we also have an extensive suite of online user documentation , and provide advice and user support by e - mail at candida-curator@lists.stanford.edu .
at cgd , phd level curators perform ongoing manual curation of the scientific literature to collect , organize , summarize and present a comprehensive picture of each characterized gene .
manual curation includes the recording of gene names , addition and updates to our summary gene descriptions , capture of mutant phenotype data and the assignment of relevant go annotations with evidence and citations .
the manual curation of the previously published literature pertaining to genes of c. albicans and c. glabrata is now complete ( table 1 ) .
we have combed the scientific literature for gene - specific information and gene bibliographies ; gene ontology ( go ) annotations describing the function , role and localization of gene products ; and mutant phenotypes .
these are now reported in cgd for all of the genes for which this information is available . at this time , there are 6203 predicted c. albicans protein - encoding genes localized to chromosomes in the current ( assembly 21 ) reference gene set , 22% with manually annotated gene and protein information . for c. glabrata
, the reference annotation set contains 5212 predicted genes , each of which has a lsp ( figure 1 ) , and 3% of which have manually curated annotations .
cgd now includes a detailed genome snapshot for c. glabrata in addition to c. albicans , which provides a graphical and tabular summary of information about the total number of chromosomal features and feature types , changes to the reference sequence and a distribution of gene products by functional categories and cellular localization ( figure 2 ) . 

lsps for both c. albicans and c. glabrata now feature new expanded orthology information sections , orthology - based description lines for uncharacterized genes , orthology - based go term predictions and protein domain - based go term predictions . 

pie chart from the cgd genome snapshots , comparing the current extent of the characterization of the predicted protein - coding genes in the c. albicans and c. glabrata genomes .
dubious have no experimental characterization and appear to be indistinguishable from random non - coding sequences ( 5 ) . 

table 1.cgd curation statisticscandida albicanscandida glabratanumber of orfs61085212number of trnas156230verified orfs1403178uncharacterized orfs47055034dubious orfs152n / amanual go annotations46974689features with manual go annotations13  7072622orthology - based go annotations13  24619  655features with orthology - based go annotations30994157protein - domain ( interpro)-based go annotations60485087features with protein - domain ( interpro)-based go annotations29632583features with orthology - based description lines13523982 updates to the cgd locus summary page ( lsp ) .
lsps for both c. albicans and c. glabrata now feature new expanded orthology information sections , orthology - based description lines for uncharacterized genes , orthology - based go term predictions and protein domain - based go term predictions .
pie chart from the cgd genome snapshots , comparing the current extent of the characterization of the predicted protein - coding genes in the c. albicans and c. glabrata genomes .
dubious have no experimental characterization and appear to be indistinguishable from random non - coding sequences ( 5 ) .
cgd curation statistics in addition , cgd curators have composed in - depth descriptive locus summaries for 272 selected c. albicans genes , which , in contrast to the very concise locus descriptions , are more detailed enumerations of the characteristics of each gene , presented in a bullet - point format on the cgd lsps . they provide additional experimental details and gene regulatory information that can not be accommodated within the space limits of the locus description line .
these lists are displayed in the locus summary section located near the bottom of the page and are fully searchable through the cgd text search tool .
the curation of the entire body of scientific literature for these organisms is a large and ongoing endeavor as new papers are published , and we welcome suggestions from users as to papers that should be prioritized or other data that should be included .
we greatly appreciate the beneficial interactions with members of the candida research community who have already volunteered to review specific lsps and provide feedback on the curation content for specific genes .
the comments we have received have resulted in refinement of description lines , improvements to phenotype and go annotations , and addition of new references that we had not encountered in our literature searches  improvements that benefit the entire community of cgd users .
cgd was originally modeled after the saccharomyces genome database ( sgd ) ( 8) , a database that provides the saccharomyces cerevisiae reference sequence with literature curation , and gene , protein and sequence analysis tools for the s. cerevisiae research community .
sgd , and initially cgd , were designed to store and display data for only a single species at a time . to accommodate the incorporation of additional species in the database , user interface and analysis tools , significant design modifications to the software and
the cgd search tools , such as quick search , text search , gene / sequence resources , ortholog search and pattern match have been redesigned to search multiple species . in order to accommodate search results for multiple species ,
the new results page for the cgd quick search and text search tools now displays three sections .
search results that apply to all species ( e.g. go terms , authors and reference information , colleagues ) are displayed at the top , with sections for species - specific search results displayed below .
all of the tools that perform species- or sequence - specific searches ( e.g. gene / sequence resources , pattern match , advanced search , batch download , restriction mapper , go term finder , go slim mapper ) have been updated , and they now prompt users to select the species of interest .
the ortholog search now retrieves ortholog and best - hit matches among all of the species in cgd and sgd ( currently c. albicans , c. glabrata and s. cerevisiae ) .
blast searches at cgd have also been redesigned to allow queries against any combination of the several candida species for which we have complete sequence sets ( c. albicans , c. glabrata , c. dubliniensis , c. guilliermondii , c. lusitaniae , c. parapsilosis , c. tropicalis , debaryomyces hansenii and lodderomyces elongisporus ) .
in addition , the curation tools have been extensively modified to facilitate the curation of multiple species .
each gene in cgd is represented on a lsp , which is the central organizing unit of the cgd web site .
the lsp contains the basic information that describes the gene and provides access to tools for retrieval , analysis and visualization of gene data .
lsps for each c. albicans and c. glabrata gene now feature an expanded orthology section , by which the lsps of each c. albicans gene are hyperlinked to the lsps of their c. glabrata orthologs , and vice versa .
the lsp for c. glabrata genes also provide external links to gene pages available at ge nolevures ( http://www.genolevures.org/cagl.html # ) this section also serves as a gateway to information about the orthologs in saccharomyces cerevisiae , providing hyperlinks to the lsp of each ortholog in the sgd .
including s. cerevisiae ortholog information is especially useful for the c. glabrata lsps : the evolutionary divergence between c. glabrata and s. cerevisiae is considerably more recent ( 100 - 300 million years ago ) ( 7,9 ) than the divergence between these two species and c. albicans ( 700 - 800 million years ago ) ( 10 ) , and thus c. glabrata shares a larger number of orthologs with s. cerevisiae than with c. albicans , 4372 and 3201 , respectively ( as predicted by inparanoid ) .
to define orthology relationships , we use the inparanoid algorithm , which identifies reciprocal best blast hits between species ( 11 ) . these mappings and links
are updated quarterly in order to reflect changes in gene models and annotations at cgd and sgd .
in addition to the new orthology relationships displayed in cgd , another level of similarity - based information is provided via the new protein tab on the lsp of each protein - coding gene ( figure 3 ) .
this tab opens the protein information page that provides descriptions and a graphical display of conserved protein domains and motifs identified using interproscan software ( 12,13 ) .
the protein information pages also display the structure of the most similar protein in the protein data bank ( 14 ) , and contain information about the predicted protein length , molecular weight , sequence and a link to a table of calculated physicochemical properties . 

the protein information page provides data including structural information inferred from homologs in pdb ( rcsb protein data bank ) , an interactive domains / motifs browser , protein sequence and physicochemical property details , blastp search against other cgd sequences and links to external protein resources such as uniprot .
the protein information page provides data including structural information inferred from homologs in pdb ( rcsb protein data bank ) , an interactive domains / motifs browser , protein sequence and physicochemical property details , blastp search against other cgd sequences and links to external protein resources such as uniprot .
the go is a structured vocabulary that is used to describe three aspects of gene products : their molecular function or activity , the broader biological process in which they participate , and the cellular location in which they reside ( 15 )
. a gene product can be annotated with any number of terms about any of the three aspects , depending on the available data .
each go term assignment is associated with an evidence code that describes the type of data the assignment is based on , and with a reference to its source .
the go is in wide use in genomic research and because it is rigorously structured , it ensures consistency in capturing of functional information about genes from different organisms and thus enables reliable analysis of biological significance of genomic data ( 1521 ) . for the fully curated species , c. albicans and c. glabrata ,
all of the available gene - related literature pertaining to these two species has been read and all possible go assignments from these papers have been made . to augment the manual curation , we have leveraged the orthology relationships to infer go annotations for genes having an experimentally characterized ortholog in sgd or cgd .
predictions for c. albicans are made based on s. cerevisiae and c. glabrata orthologs , whereas predictions for c. glabrata are based on orthologs from s. cerevisiae and c. albicans . despite the evolutionary distances between c. albicans , c. glabrata and s. cerevisiae
, the use of orthology relationships to infer go annotations between c. albicans and c. glabrata allow the transfer of a significant number of important pathogenesis - related terms to be transferred between these two fungal pathogens .
candidate go annotations to be used as the basis for these inferences are limited to those with experimental evidence , i.e. associated with evidence codes of  inferred from direct assay ( ida) ,  inferred from physical interaction ( ipi) ,  inferred from genetic interaction ( igi) , or  inferred from mutant phenotype ( imp). any annotations that are themselves predicted in s. cerevisiae or in candida , either based on sequence similarity or by some other methods , are excluded from this group to avoid transitive propagation of predictions .
also excluded from the predicted annotation set are annotations that are redundant with existing , manually curated annotations , or those that assign a related but less specific go term other than candidate annotations .
these orthology - based go assignments are associated with evidence code  inferred from electronic annotation ( iea) and displayed with the source species and gene name they are derived from along with a hyperlink to the appropriate lsp at cgd or sgd .
cgd has also taken advantage of protein domain and motif homology to assign go annotations for c. albicans and c. glabrata genes .
we systematically predict conserved domains in cgd protein sequences using interproscan ( 12 ) , and then use the interpro - to - go mappings ( 12,13 ) provided by the go consortium to provide molecular function annotations for those proteins .
these annotations are assigned the evidence code iea and are displayed with the interpro identifier of the protein that serves as the basis for the annotation .
the identifier is linked to the embl - ebi database to provide access to more extensive information about each structural domain .
we have also used the trnascan - se software to predict trna genes , and have inferred predicted go annotations for these trnas ( 22 ) .
the new annotations that have been transferred from s. cerevisiae to c. albicans and c. glabrata , and between c. albicans and c. glabrata , are summarized in table 1 .
in addition to having the evidence code iea , all these orthology - based annotations are identified as being derived computationally , rather than manually extracted from the scientific literature .
predictions are updated several times a year to make sure they remain current with annotation updates and new curation in cgd , sgd and in the protein domain datasets .
now that all literature - based go assignments for c. albicans and c. glabrata , and all orthology - based and protein domain - based predictions have been made , we consider curation of both species to be  go - complete. for the remaining uncharacterized genes , we have explicitly assigned 
unknown annotations to indicate that to the best of our knowledge no data are available .
we have also used the multispecies information to create informative descriptions for those candida genes that lack any experimental characterization , and which therefore have no literature - based description on the lsp , incorporating orthology relationships and orthology - based functional predictions into the gene description in cases where there would otherwise be no information available .
additional cgd resources for the candida research community include a new collection of bibliographies on topics relevant to candida biology , which is accessible under  community resources from the navigation sidebar on the cgd home page .
these highlights in candida biology contain lists of important references , including many key reviews , and are designed to provide an overview of selected subject areas in c. albicans and c. glabrata biology .
as new species are curated at cgd , highlights in candida biology will expand to include bibliographies on these species as well .
we have also curated a directory of strains , which provides descriptions and references for commonly used candida laboratory strains , along with a lineage diagram that graphically depicts the relationship among these strains .
this resource is especially important for researchers because differences in strain background are known to have a significant impact on observed mutant phenotypes . in some cases ,
genes have been found to be lethal in one genetic background while successful gene disruption is possible in another .
an example of this is the c. albicans ume6 gene , for which homozygous mutants are viable in the sn152 genetic background ( 23 ) yet inviable in the bwp17 strain background ( 24 ) . because of its importance , we also provide all available strain background information along with all of the curated phenotypes for each gene .
additional cgd resources for the candida research community include a new collection of bibliographies on topics relevant to candida biology , which is accessible under  community resources from the navigation sidebar on the cgd home page .
these highlights in candida biology contain lists of important references , including many key reviews , and are designed to provide an overview of selected subject areas in c. albicans and c. glabrata biology .
as new species are curated at cgd , highlights in candida biology will expand to include bibliographies on these species as well .
we have also curated a directory of strains , which provides descriptions and references for commonly used candida laboratory strains , along with a lineage diagram that graphically depicts the relationship among these strains .
this resource is especially important for researchers because differences in strain background are known to have a significant impact on observed mutant phenotypes . in some cases ,
genes have been found to be lethal in one genetic background while successful gene disruption is possible in another .
an example of this is the c. albicans ume6 gene , for which homozygous mutants are viable in the sn152 genetic background ( 23 ) yet inviable in the bwp17 strain background ( 24 ) . because of its importance , we also provide all available strain background information along with all of the curated phenotypes for each gene .
now that the underlying database has been re - tooled to accommodate the curation of multiple species , we will add curated information for other candida - related species including c. dubliniensis , c. guilliermondii , c. lusitaniae , c. parapsilosis , c. tropicalis , debaryomyces hansenii and lodderomyces elongisporus . in order to facilitate navigation across multiple genomes ,
we will provide links to an interactive comparative visualization tool , which will allow users to explore ortholog clusters in their genomic context .
recent advances in genomics technologies have created a deluge of information that poses a significant challenge of making all these data organized and readily available to researchers . we have adapted our genome browser , gbrowse , to enable users to visualize unannotated transcripts in c. albicans that have been identified by rnaseq ( 2527 ) .
these transcripts are aligned to the reference genome and displayed alongside the existing set of features in the reference annotation .
we will further develop and/or integrate existing software to incorporate and visualize more types of data and more data sets from high - throughput studies .
funding for open access charge : national institute of dental and craniofacial research at the us national institutes of health ( grant no .
 the candida genome database ( cgd , http://www.candidagenome.org/ ) is an internet - based resource that provides centralized access to genomic sequence data and manually curated functional information about genes and proteins of the fungal pathogen candida albicans and other candida species . as the scope of candida research , and the number of sequenced strains and related species , has grown in recent years 
 , the need for expanded genomic resources has also grown . to answer this 
 need , cgd has expanded beyond storing data solely for c. albicans , now integrating data from multiple species . 
 herein we describe the incorporation of this multispecies information , which includes curated gene information and the reference sequence for c. glabrata , as well as orthology relationships that interconnect locus summary pages , allowing easy navigation between genes of c. albicans and c. glabrata . 
 these orthology relationships are also used to predict go annotations of their products . 
 we have also added protein information pages that display domains , structural information and physicochemical properties ; bibliographic pages highlighting important topic areas in candida biology ; and a laboratory strain lineage page that describes the lineage of commonly used laboratory strains . 
 all of these data are freely available at http://www.candidagenome.org/. we welcome feedback from the research community at candida-curator@lists.stanford.edu . 
INTRODUCTION
LITERATURE CURATION FOR MULTIPLE 
TOOLS FOR SEARCH AND DISPLAY OF MULTISPECIES INFORMATION IN CGD
LEVERAGING MULTISPECIES INFORMATION IN CGD: HOMOLOGY-BASED FUNCTIONAL PREDICTIONS
CURATED INFORMATIONAL PAGES AT CGD
FUTURE DIRECTIONS
FUNDING