Jill L. Wegrzyn et al. 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 [3]. This organization allows for a combination of internal curation as well as third-party submissions to validate and maintain current content. 2.2.1. Species module Individual species and colleague databases exist in the Tree- Genes schema and are well integrated with other database modules. Species is a manually curated database of 222 mem- bers of the Pinaceae family. It is currently being expanded to encompass more forest trees. 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 extended taxonomy [4] provide direct access to publicly available sequence sets. 2.2.2. Colleague module 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. 2.2.3. Comparative maps module The comparative map module is displayed through a mod- iﬁed version of Cmap [2]. Cmap is one component of the larger Generic Model Organism Database (GMOD) toolkit [5]. 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 indi- viduals 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. The ﬁnal map display is highly interactive. 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, col- league, 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. 3 2.2.4. Literature module The Literature module is responsible for performing regu- lar and automated searches of major relevant publication repositories including Pubmed [6] 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. These submit- ted publications undergo the same process of keyword gen- eration. 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. 2.2.5. Expressed sequence tags module The TreeGenes EST pipeline and database apply a combina- tion 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. [7]. (3) Sequence clustering con- sists of assembling high-quality sequences to produce longer transcripts and reduce overall redundancy. This occurs via two rounds of Cap3 [8] processing. (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 [9]. In general, searches are performed against the Genbank nr protein database [4], 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 Ontol- ogy (GO) [10] (with preference given to Plant GO [11] hits when available), KEGG for metabolic pathways [12], Enzyme Commission (EC) [13], and InterPro [14] for conserved protein domains (which includes CDD [15], SMART [16], and Pfam [17]). The ﬁnal stage and optional stage of the processing pipeline involves submission to Genbank [4] following the approval of the owner. Users can login in and view the original EST data, the cleansed data and the