1. TreeGenes & Tripal treegenesdb.org Emily Grau
-Total time alloted: 15 minutes (10-12 minutes talking time? Also the last presentation, so time might be squeezed from other talks)
-How much background detail to give?
Outline
What TG is:
History
Userbase?
Data we hold:
# of species—many!
Data types
Data sources:
Primary databases
Users!
Tools we offer
GMOD
Custom development: DiversiTree and CartograTree
Transition to Chado & Tripal:
Challenges:
25 years of data in custom schema  chado
Advantages:
Future stuff:
Tripal Gateway will allow us to expand resources we offer to users!
Connect HWG, GDR, TG
Workflows + HPC resources (will we tie this in to CartograTree, give users greater control, offer multistep workflows?)
New user submission module (!!!!!), plan to develop module for others to use(?)
treegenesdb.org
Emily Grau
Department of Ecology & Evolutionary Biology
University of Connecticut, Storrs CT

2. TreeGenes Database: History
treegenesdb.org
Began as the Dendrome project (USDA funded initiative) in 1993 to hold forest tree genetic maps and associated markers
One of the 1st UDSA funded databases on the internet
Schema has been changing and evolving ever since
Start of the history slide
Number of users
Organizations
Countries represented
Awstats or Google
History
Overview
yr started
comparative maps
expanded to seq (sanger) -> next gen -> association (environment)

3. TreeGenes Database: History
treegenesdb.org
Began to hold forest tree genetic maps and associated markers
Expanded to other data types
Sequence
Reseqeuncing, Large-Scale Genotyping, Transcriptomics/Expression
Full Genome Sequences
Analysis and Visualization Tools
Ability for users to mine the data
Resources for the user community
Literature, Colleagues
Start of the history slide
Number of users
Organizations
Countries represented
Awstats or Google
History
Overview
yr started
comparative maps
expanded to seq (sanger) -> next gen -> association (environment)

4. TreeGenes Database: Users
treegenesdb.org
2,086 users from 862 organizations in 94 countries
***new chart for # unique visitors
10,000
Unique Web Visitors to TreeGenes Database per month, January-December 2015

5. TreeGenes Database: Species
treegenesdb.org
1,774 species from 101 genera
At least one genetic artifact from each species
Conifers but is also inclusive of all forest trees
Full genome sequence: 13 species
Transcriptome/Expression resources: 3,920,817 sequences from 263 species
106 genetic maps from 35 species
** update #s here

6. TreeGenes Database: Data Sources
treegenesdb.org
Automated scripts
Primary databases such as NCBI
Appropriate data should be submitted to primary databases first
User submissions
For data and metadata not captured well by primary databases
We don’t hold RAW data (but link to it), we hold EST etc
Where do we get our data?
NCBI resources
User Submissions
Including Journal Accession Number
Examples of studies – Genotype, Phenotype, and Environment
Plant Ontology (standardizing our data)
What data we have & where it comes from
Overview
automated searchig & manual user submission

7. TreeGenes Database: Data Sources
treegenesdb.org
Automated scripts
NCBI
Transcripts, Protein, Unigene
Databases
Linked to literature records, etc.
Incorporated into visualization tools
Literature
Web of Science, PubMed
# papers
Where do we get our data?
NCBI resources TSA= transcriptome shotgun assembly
User Submissions
Including Journal Accession Number
Examples of studies – Genotype, Phenotype, and Environment
Plant Ontology (standardizing our data)
What data we have & where it comes from
Automated
NCBI
protein, tsa, est, unigene...
Literature?
WoS, pubmed

8. TreeGenes Database: Data Sources
treegenesdb.org
User submissions
Internal projects or collaborations (day one)
Submissions of data post-analysis at publication time
Where do we get our data?
NCBI resources TSA= transcriptome shotgun assembly
User Submissions
Including Journal Accession Number
Examples of studies – Genotype, Phenotype, and Environment
Plant Ontology (standardizing our data)
What data we have & where it comes from
Automated
NCBI
protein, tsa, est, unigene...
Literature?
WoS, pubmed

9. TreeGenes Database: Data Sources
treegenesdb.org
User submissions
Submit genetic maps, association or population study data
Population genetics including association studies (emph phenotype, genotype, environmental data (emph GPS coordinates))
-This type of information is not captured well by other databases
-Collecting ****metadata****—how you did your analysis, what your results are
NOT like dryad—we connect the information, giving it value
Most submissions from journal requirement:
Tree Genetics and Genomes

10. TreeGenes Database: Data Sources
treegenesdb.org
User submissions
Genetic maps, association or population studies
Population genetics including association studies (emph phenotype, genotype, environmental data (emph GPS coordinates))
-This type of information is not captured well by other databases
-Collecting ****metadata****—how you did your analysis, what your results are
NOT like dryad—we connect the information, giving it value

11. TreeGenes Database: Data Sources
treegenesdb.org
User submissions
Obtain TGDR accession number!
Genetic maps, association or population studies
Population genetics including association studies (emph phenotype, genotype, environmental data (emph GPS coordinates))
-This type of information is not captured well by other databases
-Collecting ****metadata****—how you did your analysis, what your results are
NOT like dryad—we connect the information, giving it value

12. TreeGenes Database: Data Sources
treegenesdb.org
User submissions
Genetic maps, association or population studies
Will be converted to Tripal module and made available to the community
Population genetics including association studies (emph phenotype, genotype, environmental data (emph GPS coordinates))
-This type of information is not captured well by other databases
-Collecting ****metadata****—how you did your analysis, what your results are
NOT like dryad—we connect the information, giving it value

13. TreeGenes Database: Data Access
treegenesdb.org
Tools
Existing viewers
Custom development
Custom Interface Development:
Combination of Existing viewers and custom development:
GMOD project –
CMAP interface (1)
Gbrowse/Web Apollo (1)
DiversiTree (2 slides)
Genetic Stock Center (2 slides) (AdapTree and Collaborative) -> Genotype and Phenotype
We contribute development towards association studies, particularly including environmental information

14. TreeGenes Database: Interfaces
treegenesdb.org
CMAP interface (1) : browser-based tool for comparing maps (genetic, sequence, etc)
Search by species, publication set, feature (name/ID), feature type
View map: individual features w/ locations, list of feature types

15. TreeGenes Database: Interfaces
treegenesdb.org
Bulk retrieval of resequencing data, genotypes, and phenotypes
SSWAP—form of web service—idea that we can push and pull things between analytical tools and visualization tools (over the web instead of over the desktop)
Type of web service we developed in collab with iplant
Acknowledge damian at end –u of a or semantic options

16. TreeGenes Database: Interfaces
treegenesdb.org
Much of our data that comes in is geo referenced.. Talk about this in user sub slide
Custom Interface Development:
History of CartograTree – Tree Biology Working Group through iPlant
CartograTree (3-4)
Providing context to geo-referenced data
Data from TreeGenes, WorldClim, Ameriflux, TRY-db

17. TreeGenes Database: Transition to Tripal
treegenesdb.org
Transition to Tripal and Chado
Challenges
Ontologies
Standardizing for the first time
25 years of custom schemas!
Expand on this?

18. TreeGenes Database: Transition to Tripal
treegenesdb.org
Transition to Tripal and Chado
Advantages
Ontologies
Save time!
Connect data with other databases (Tripal Gateway)
Improve analytical capabilities (Tripal Gateway)
Our contribution: analytical workflows
Review & clean up database
Expand on this?

19. TreeGenes Database: Transition to Tripal Outcomes
treegenesdb.org
Outcomes
Expanded datasets: access Hardwood Genomics, GDR, TreeGenes from one location
Expanded analytical, HPC resources
Improve CartograTree capabilities
New Tripal module: user submission
Expand on this?

20. TreeGenes Database: Team
treegenesdb.org
Project Leads
Jill Wegrzyn
University of Connecticut
David Neale
Development Team
Steven A Demurjian Jr P0383
Hans Vasquez-Gross
Lead Database
Administrator
Emily Grau P0322
Advising
Damian Gessler
Semantic Options
Emphasize our role in DIBBs—association genetics workflow
Along with transitioning underlying schema, we are developing association genetic workflow—work into ctree, expland HPC
Mention integrating DiversiTree
Start in Galaxy
If using a galaxy hosted instance through us, it will be kind of like diversitree—but expanded!!
@TreeGenes
TreeGenes Database