the treegenes database is a resource for all forest trees , however work 
 to date has focused on specific members of the pinaceae family .
pinaceae is one 
 of eight families of the order coniferales ( conifer ) and includes 10 genera and 
 approximately 220 species .
species of pinaceae are commercially important to 
 the forest industry and are used for building , packaging , and paper products 
 worldwide .
because of the very large size and complexity of the conifer genomes 
 ( 1040 gb ) , greater emphasis has been placed on the expressed portion of the 
 genome .
the principal species 
 represented include six members of the genus pinus ( taeda , elliottii , radiata , pinaster , sylvestris and lambertiana ) , two species from other 
 genera of the pinaceae ( picea abies and pseudotsuga menzeisii ) , and one 
 member of another family of conifer ( cryptomeria 
 japonica cupressaceae ) .
recent work 
 has also focused on integrating resources for members of populus and 
 eucalyptus .
developing genetic resources for these organisms improve the 
 genetic understanding individual member species within the same families or 
 genera .
the rapid rate in 
 which genetic data is being generated from large - scale est and resequencing 
 projects has required corresponding growth in relational databases and 
 associated computational tools .
the ability to 
 combine data from different sources facilitates interpretation and potentially 
 allows stronger inferences to be made . when information from several different 
 databases is required , the assembly of data into a format suitable for querying 
 is a challenge .
the development of systems for the integration and combined 
 analysis of diverse data remains a priority in bioinformatics .
the treegenes database helps 
 researchers efficiently analyze , access , integrate , and apply the data .  
this paper will navigate through the dendrome 
 ( http://dendrome.ucdavis.edu/ ) and treegenes ( http://dendrome.ucdavis.edu/treegenes/ ) interfaces as well as the 
 types of data that can be accessed through these resources .
the dendrome pages are entry points to valuable 
 links , community projects , information forums , custom tools , and the treegenes 
 database ( http://dendrome.ucdavis.edu/resources/ ) 
 ( figure 1 ) .  
the resources 
 available include custom blast and fasta services for sequence similarity 
 searches .
these services directly access all publicly available sequence data 
 as well as custom est or related databases . 

users can submit requests for the generation and submission of a 
 searchable database to this repository .
an area for the retrieval and 
 submission of custom scripts developed in the community of general use for the 
 manipulation of genetic data exists . 

this interface allows authors to post and make available scripts and 
 more advanced programs that they have designed including relevant 
 documentation .
the tools pages are 
 internally curated and provide information on open source and freeware software 
 packages that are relevant to the processing , availability , and analysis of 
 data presented in the treegenes database .
links pages allow users to submit to and describe online resources and projects 
 relevant to the research community .
the links are submitted into one or more 
 relevant genomic categories and are available immediately in the 
 repository.forms are present through the dendrome site in order to encourage users to modify , add , and correct a variety of information .
the dendrome pages are the primary source 
 of useful information for the research community such as upcoming events , 
 research opportunities , and the community - curated repository of links . in 
 addition
, a discussion forum has recently been implemented to encourage users 
 to submit questions and comments on the database as well as participate in 
 general discussions of conifer genomics .
the related dendrome plone 
 ( http://dendrome.ucdavis.edu/tgplone ) , based on the plone 3.0 content 
 management platform ( http://plone.org/ ) , 
 provides a user friendly environment for investigators to share and obtain 
 information relating to a variety of projects .
treegenes   ( http://dendrome.ucdavis.edu/treegenes/ ) functions through a semi - automated postgresql 
 version 8.1.4-based 
 database that consists of modules to hold a broad range 
 of data and information for trees .
this system has a front end consisting of 
 perl 5.8.5 scripts running in a linux / apache / php environment .
the database is 
 organized into ten different modules that are highly connected in order to ease 
 access and analysis of the data ( figure 2 ) .
the sequencing 
 and primers module contains sequences from the resequencing efforts as well as 
 data describing how the sequences were generated and parameters used in their 
 alignment and analysis .
the species module holds the taxonomy information and 
 the colleague module contains information on laboratories and individuals . 

there is a comparative map module that uses cmap   to hold and view genetic 
 maps , map relations , and molecular markers .
the literature module stores 
 publications . the est module stores sequence and annotation information and 
 ties into an automated pipeline that allows users to submit sequences for 
 processing , analysis , and genbank submission .
treegenes is being expanded to 
 include more extensive genotype and phenotype data utilizing data models from 
 the germinate database .
this organization allows for a combination of 
 internal curation as well as third - party submissions to validate and maintain 
 current content .
individual species and colleague 
 databases exist in the treegenes schema and are well integrated with other 
 database modules .  
the species module contains detailed information for each entry 
 including range maps and multiple images for each tree .  
internal connections to the researchers who 
 study each species , moreover , relevant publications are available in the detail 
 view .   external links to ncbi s
the colleague database is a 
 semi - automated directory of nearly 2 000 researchers and 730 
 organizations .  
the colleague interfaces 
 allow users to add , modify , and remove the contact information of both the 
 users themselves and their respective organizations .  
the interface offers the user the ability to 
 query researchers who focus on particular species in addition to their specific 
 research interests .
cmap is one component of the larger generic 
 model organism database ( gmod ) toolkit . 

this package has the ability to compare across genetic , sequence , and 
 physical maps .   at this time , treegenes 
 only contains genetic maps .  
the 
 interactive display allows individuals to select single maps and continue to 
 add additional linkage groups from any species to build a comparative 
 view .  
maps can be selected by specific 
 linkage groups or they can be queried by their features .  
treegenes currently houses features ( marker 
 types ) for over 50 genetic maps including aflp , estp , isozyme , ssr , rapd , and 
 rflp .
selecting specific features 
 allows for the display of marker information and sequence information .  
detail views also include links to internal 
 databases within treegenes including species , literature , colleague , est , qtls , 
 and pcr primer information ( figure 3 ) .  
a 
 standardized nomenclature has been developed to describe each potential map 
 feature .  
custom scripts exist to 
 generate and enforce this documented nomenclature during the import 
 process .  
this internal validation allows 
 for name - based correspondences ( markers ) to be annotated .  
these correspondences can be easily viewed 
 during comparisons of the maps themselves as well as cmap s matrix view .
the literature module is 
 responsible for performing regular and automated searches of major relevant publication 
 repositories including pubmed   and biosis according to a compiled list of 
 keywords .  
treegenes organizes these 
 publications , creates a list of searchable keywords , and builds internal 
 relations to provide a centralized forest genetics publication repository .  
this resource can be queried on many levels 
 and allows for a customized subscription to preview recently added 
 publications .  
in addition to querying 
 public repositories , treegenes has a unique feature that allows for the 
 submission of manuscripts by the author . 

in addition to the 
 submission of new publications , authors are encouraged to submit supplemental 
 information .  
each detail view provides 
 automated external linking in addition to the opportunity to provide sequence data , raw mapping files , or accession numbers from 
 public database submissions .  
this is the 
 primary mechanism by which the curators can organize the information and 
 further populate the related modules . 

all standardized nomenclatures are enforced during submission including 
 accessions ids and treegenes comparative mapping nomenclature .
the treegenes est pipeline and database   apply a combination of custom and open - source tools integrated into a 
 fully automated processing pipeline ( figure 4 ) . 

the processing occurs at five unique stages and allows users to either 
 original tracefiles or fasta files .  
in 
 the latter case , the quality scores are unable to be considered in the 
 processing .  
( 1 ) specific est 
 nomenclature is enforced during submission of the initial trace files or fasta 
 text files .
( 2 ) tracefiles are processed 
 to identify a filtered , high - quality clone library as determined by ewing et al . .  
( 3 ) sequence clustering consists of assembling 
 high - quality sequences to produce longer transcripts and reduce overall 
 redundancy .  
( 4 ) annotation 
 involves pairwise comparisons of the est clone library and the est contig 
 consensus sequences . sequence identification and annotation
is provided by a 
 series of blast homology searches ( parallel and priority blast ) against 
 user - defined and publicly available sequence databases implemented with ncbi s 
 blast .   in general , searches are 
 performed against the genbank nr protein database , however users may select 
 custom datasets .
the unigene dataset is derived by selecting the clone that best represents each contig and 
 the singletons that have unique or no matches are further annotated .  
this level of annotation consists of gene 
 ontology ( go )   ( with preference given to plant go   hits when 
 available ) , kegg for metabolic pathways , enzyme commission ( ec ) , and 
 interpro   for conserved protein domains ( which includes cdd , smart 
 , and pfam ) .  
the final stage 
 and optional stage of the processing pipeline involves submission to genbank 
  following the approval of the owner .
users can login in and view the 
 original est data , the cleansed data and the analysis results .
tables , 
 formatted text , and links are provided for viewing summary and detailed 
 information .
submission includes the generation , formatting , and actual 
 submission of the required flat files . 

since the treegenes database is home to many species , the database is 
 organized to maintain independent species and project sets while search 
 interfaces have been developed to support comparative queries .
the sample tracking , primers , sequencing , and genotype 
 modules are currently accessible through an interactive interface that includes 
 a growing library of predefined queries ( figure 5 ) . each template provides a 
 simplified view of an underlying query by means of a text description and one 
 or more searchable fields .
the recent increase in high - throughput sequencing 
 projects encouraged the development of interfaces capable of dealing with the 
 analysis of large amounts of data .   in 
 short , researchers can query thousands of sequences in a single operation .
the desktop 
 style interface assists with these searches and allows users to customize their 
 results and organize data views .
data types 
 available here currently include ests , est annotation , tracefiles , snps , primer 
 sequences , and resequenced amplicons ( including dna extraction and tree sample 
 information )   ( http://dendrome.ucdavis.edu/interface/ ) . 

this interface currently accesses information for over 40 000 ests and nearly 8 000 resequenced amplicons .
the dendrome project and 
 the treegenes database are publicly available and can be accessed at http://dendrome.ucdavis.edu/.   from the website , there is access to help in 
 the form of tutorials and a user manual .
we 
 encourage researchers to actively participate in making dendrome and treegenes 
 more accessible by submitting data and providing feedback on general usability . 

we are interested in being able to provide a unique resource to the community , 
 which is fully dependent on individual submissions .
treegenes has a robust 
 interface to submit a variety of information including sequence data and 
 comparative mapping files through the literature database .
more information on 
 this resource can be found in http://dendrome.ucdavis.edu / treegenes / literature/. the discussion forum available through the dendrome project 
 website provides an opportunity for users to submit suggestions on improvements 
 or additions to the community resources .
this feedback form will automatically send us the inquiry , making it easier to 
 give an accurate response .
further information is available by joining one of 
 the treegenes electronic mailing lists ( details on the website ) or by email to 
 info@treegenes.ucdavis.edu .
the structure of treegenes permits researchers to rapidly accumulate a 
 wealth of information about a particular object or set of objects .
this 
 flexible design facilitates the formulation of new hypotheses for refining 
 subsequent investigations .
in addition to refinement and extension of smaller 
 scale investigations , treegenes can also facilitate more comprehensive 
 approaches by allowing the investigation of interactions among datasets .
future plans include incorporating 
 standardized gene ontology to describe phenotypic traits unique to forest 
 trees .
in addition , robust databases will be available for the submission and 
 visualization of snp and expression data . 

the advanced workspace interface will be expanded to accommodate both of 
 these data types as well as tools to ease the analysis and comparison of this 
 information . with an emphasis on meaningful data acquisition and interface 
 design
, treegenes continues to serve a critical role in the efficient storage 
 and analysis of data by the forest genetics community .
 the dendrome project and associated treegenes database serve the forest genetics research community through a curated and integrated web - based relational database . 
 the research community is composed of approximately 2 000 members representing over 730 organizations worldwide . 
 the database itself is composed of a wide range of genetic data from many forest trees with focused efforts on commercially important members of the pinaceae family . 
 the primary data types curated include species , publications , tree and dna extraction information , genetic maps , molecular markers , ests , genotypic , and phenotypic data . 
 there are currently ten main search modules or user access points within this postgresql database . 
 these access points allow users to navigate logically through the related data types . 
 the goals of the dendrome project are to ( 1 ) provide a comprehensive resource for forest tree genomics data to facilitate gene discovery in related species , ( 2 ) develop interfaces that encourage the submission and integration of all genomic data , and to    ( 3 ) centralize and distribute existing and novel online tools for the research community that both support and ease analysis .   
 recent developments have focused on increasing data content , functional annotations , data retrieval , and visualization tools .   
 treegenes was developed to provide a centralized web resource with analysis and visualization tools to support data storage and exchange . 
1. INTRODUCTION
2. CONTENT AND ORGANIZATION
3. AVAILABILITY, DATA SUBMISSION,
FEEDBACK, AND SUPPORT
4. FUTURE DEVELOPMENT