Efforts to Link Ecological Metadata with Bacterial Gene Sequences at the Sapelo Island Microbial Observatory Wade M. Sheldon Mary Ann Moran James T. Hollibaugh

Genetic Sequence Databases  Major informatics success story  Large repositories for nucleotide sequences (e.g. GenBank/EMBL/NDDJ ~16M)  Automated and web-based data submission - required as part of publication process  Standardized alignment/search tools support use for classification  Numerous ‘environmental sequences’ – ecologists now using to study biogeography, community structure, eco-physiology

Problems with GenBank  Metadata voluntary – limited in scope  Title (definition), authors, key words, comments, literature citation  Many sequences unpublished, undescribed  Quality control standards poorly enforced  No direct way to provide links to ancillary data (URLs not officially supported, often removed)  Very inefficient and often impossible for investigators to obtain ecological context information, even from journals  Comparisons of matched taxa by traits not possible

Consequence  Tremendous amount of bacterial sequence data relevant to microbial ecologists  No established interface

Example – Insufficient Metadata

Sapelo Island Microbial Observatory (  MObs – NSF-funded network of sites or "microbial observatories" established to discover novel microorganisms, microbial consortia, communities, activities and other novel properties, and to study their roles in diverse environments  Projects supported are expected to establish or participate in an established, Internet-accessible knowledge network to disseminate the information resulting from these activities  SIMO - Investigating the diversity of prokaryotes, their physiological and genetic characteristics, and their biogeochemical activities in a salt marsh/estuarine ecosystem in the southeastern U.S.  Knowledge networks:  GenBank  GCE-LTER IS  SIMO 16S rRNA Database

SIMO 16S rRNA Database  Purpose: LIMS, research tool, data dissemination  Designed to store sequence data and all supporting SIMO research information  Hierarchical structure modeled after research workflow  Metadata on site geography, sample collection, all methodology, personnel, ancillary measurements  Extensive content control, error checking  Links to information in external databases (RDP II, GenBank, GCE-LTER)  Queries by phylogenic and/or ecological characteristics

Conceptual Diagram of the SIMO Database

List-based data entry linked to metadata tables

Controlled vocabulary supports finely-targeted queries Automatic hyperlinks provide links to tasks

List-based queries also simplify public interface

Phylogenetic and ecological characteristics combined dynamically to create overview and query interface

SIMO Metadata  Metadata primarily stored in managed lists, linked to records by foreign key fields  Scalable design – details can be added independently without altering data records  Complete metadata for sequences generated by relational joins  Links to external metadata in GCE-LTER database adds site geography, research history, long-term environmental characteristics

Metadata Standards  No existing standard for environmental sequence metadata  Sequence formats (FASTA, BIOML, BSML) designed for data parsing, sequence annotation  SIMO metadata currently displayed in summary form on sequence detail pages  Exploring adopting emerging standards like EML

Sequence Details

Future Directions  Incorporating batch upload features for library submissions  Integrating database with ‘RDP SeqMatch Agent’ programs for automatic phylogenetic analysis, sequence annotation  Provide full metadata in formatted/printable and parsable ASCII formats (XML)  Participate in Entrez Link-Out to provide links to SIMO sequence entries from GenBank