Efforts to Link Ecological Metadata with Bacterial Gene Sequences at the

Sapelo Island Microbial Observatory

Wade M. SheldonWade M. SheldonMary Ann MoranMary Ann Moran

James T. HollibaughJames T. Hollibaugh

Genetic Sequence Databases Major informatics success storyMajor informatics success story Large repositories for nucleotide sequences (e.g. Large repositories for nucleotide sequences (e.g.

GenBank/EMBL/NDDJ ~16M)GenBank/EMBL/NDDJ ~16M) Automated and web-based data submission - Automated and web-based data submission -

required as part of publication processrequired as part of publication process Standardized alignment/search tools support use for Standardized alignment/search tools support use for

classificationclassification Numerous ‘environmental sequences’ – ecologists Numerous ‘environmental sequences’ – ecologists

now using to study biogeography, community now using to study biogeography, community structure, eco-physiologystructure, eco-physiology

Problems with GenBank Metadata voluntary – limited in scopeMetadata voluntary – limited in scope

Title (definition), authors, key words, comments, Title (definition), authors, key words, comments, literature citationliterature citation

Many sequences unpublished, undescribedMany sequences unpublished, undescribed Quality control standards poorly enforcedQuality control standards poorly enforced No direct way to provide links to ancillary data No direct way to provide links to ancillary data

(URLs not officially supported, often removed)(URLs not officially supported, often removed) Very inefficient and often impossible for investigators to Very inefficient and often impossible for investigators to

obtain ecological context information, even from journalsobtain ecological context information, even from journals Comparisons of matched taxa by traits not possibleComparisons of matched taxa by traits not possible

Consequence

Tremendous amount of bacterial sequence Tremendous amount of bacterial sequence data relevant to microbial ecologistsdata relevant to microbial ecologists

No established interfaceNo established interface

Example – Insufficient Metadata

Sapelo Island Microbial Observatory (http://simo.marsci.uga.edu)

MObs – NSF-funded network of sites or "microbial MObs – NSF-funded network of sites or "microbial observatories" established to discover novel microorganisms, observatories" established to discover novel microorganisms, microbial consortia, communities, activities and other novel microbial consortia, communities, activities and other novel properties, and to study their roles in diverse environmentsproperties, and to study their roles in diverse environments

Projects supported are expected to establish or participate in Projects supported are expected to establish or participate in an established, Internet-accessible knowledge network to an established, Internet-accessible knowledge network to disseminate the information resulting from these activitiesdisseminate the information resulting from these activities

SIMO - Investigating the diversity of prokaryotes, their SIMO - Investigating the diversity of prokaryotes, their physiological and genetic characteristics, and their physiological and genetic characteristics, and their biogeochemical activities in a salt marsh/estuarine ecosystem biogeochemical activities in a salt marsh/estuarine ecosystem in the southeastern U.S.in the southeastern U.S.

Knowledge networks:Knowledge networks: GenBankGenBank GCE-LTER ISGCE-LTER IS SIMO 16S rRNA DatabaseSIMO 16S rRNA Database

SIMO 16S rRNA Database Purpose: LIMS, research tool, data disseminationPurpose: LIMS, research tool, data dissemination Designed to store sequence data and all supporting SIMO Designed to store sequence data and all supporting SIMO

research informationresearch information Hierarchical structure modeled after research workflowHierarchical structure modeled after research workflow Metadata on site geography, sample collection, all Metadata on site geography, sample collection, all

methodology, personnel, ancillary measurementsmethodology, personnel, ancillary measurements Extensive content control, error checkingExtensive content control, error checking Links to information in external databases (RDP II, Links to information in external databases (RDP II,

GenBank, GCE-LTER)GenBank, GCE-LTER) Queries by phylogenic and/or ecological characteristicsQueries by phylogenic and/or ecological characteristics

Conceptual Diagram of the SIMO DatabaseSecondary/

External DataPrimary DataMetadata

Samples

Organisms

Sequences

PhylogeneticComparisons

Environment

Methodology

Study Site

Methodology

Methodology

Methodology

PhylogeneticGroups

Other Analyses

GenBank

GCE-LTER

Ancillary Data

RDP II

List-based data entry linked to metadata tables

Controlled vocabulary supports finely-targeted queriesAutomatic 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 Metadata primarily stored in managed lists, linked

to records by foreign key fieldsto records by foreign key fields Scalable design – details can be added Scalable design – details can be added

independently without altering data recordsindependently without altering data records Complete metadata for sequences generated by Complete metadata for sequences generated by

relational joinsrelational joins Links to external metadata in GCE-LTER Links to external metadata in GCE-LTER

database adds site geography, research history, database adds site geography, research history, long-term environmental characteristicslong-term environmental characteristics

Metadata Standards No existing standard for environmental sequence No existing standard for environmental sequence

metadatametadata Sequence formats (FASTA, BIOML, BSML) Sequence formats (FASTA, BIOML, BSML)

designed for data parsing, sequence annotationdesigned for data parsing, sequence annotation SIMO metadata currently displayed in summary SIMO metadata currently displayed in summary

form on sequence detail pagesform on sequence detail pages Exploring adopting emerging standards like EMLExploring adopting emerging standards like EML

Sequence Details

Future Directions Incorporating batch upload features for library Incorporating batch upload features for library

submissionssubmissions Integrating database with ‘RDP SeqMatch Agent’ Integrating database with ‘RDP SeqMatch Agent’

programs for automatic phylogenetic analysis, programs for automatic phylogenetic analysis, sequence annotationsequence annotation

Provide full metadata in formatted/printable and Provide full metadata in formatted/printable and parsable ASCII formats (XML)parsable ASCII formats (XML)

Participate in Entrez Link-Out to provide links to Participate in Entrez Link-Out to provide links to SIMO sequence entries from GenBankSIMO sequence entries from GenBank