A Construction Toolkit For Online Biological Databases Lacey-Anne Sanderson

What is Tripal? What is Tripal? Features Features Highlighting those in the upcoming release: Tripal 0.4 Highlighting those in the upcoming release: Tripal 0.4 Extensions Extensions Those currently available and some under development Those currently available and some under development How you can contribute How you can contribute

Chado Drupal Tripal What is Tripal?

An open-source Biological Database that An open-source Biological Database that Is easy to set up with few requirements Is easy to set up with few requirements Lower IT Costs Lower IT Costs Reliably stores your data without much more work than Excel Sheets Reliably stores your data without much more work than Excel Sheets Upload data into chado completely through the web-interface Upload data into chado completely through the web-interface Display tables of data that are sortable, filterable and only contain the columns you care about Display tables of data that are sortable, filterable and only contain the columns you care about Facilitates sharing of data… Facilitates sharing of data… But only with the people you are ready to share it with But only with the people you are ready to share it with What is Tripal?

Widely used and supported. Widely used and supported. A flexible, expandable platform A flexible, expandable platform Start with a fully functional, professional website then simply add functionality to handle Biological Data Start with a fully functional, professional website then simply add functionality to handle Biological Data Handles User Management & Permission Control out of the box Handles User Management & Permission Control out of the box Searching Searching Taxonomy/Tags Taxonomy/Tags User Comments User Comments Contact Forms Contact Forms Forums Forums Menu’s Menu’s User Profiles User Profiles File Management File Management What is Tripal?

100’s of “modules” to extend the functionality of your website 100’s of “modules” to extend the functionality of your website Drupal Views: Custom SQL queries and tables Drupal Views: Custom SQL queries and tables CCK: Add your own content to any page CCK: Add your own content to any page Panels: Customize the layout of any page Panels: Customize the layout of any page Pathauto: Create path alias’ Pathauto: Create path alias’ Wysywyg Editors Wysywyg Editors Webforms Webforms CAPTCHA’s CAPTCHA’s What is Tripal?

Fully Theme-able with 1000’s of themes freely available Fully Theme-able with 1000’s of themes freely available Change the look-and-feel of your site with the click of a button Change the look-and-feel of your site with the click of a button What is Tripal?

Install Drupal Install Drupal Then just download Tripal and any extension modules and enable them through the Drupal site Then just download Tripal and any extension modules and enable them through the Drupal site Will be able to install a pre-configured Tripal using a Drush installation script/profile Will be able to install a pre-configured Tripal using a Drush installation script/profile Drush is the command-line functionality for Drupal Drush is the command-line functionality for Drupal What is Tripal? v 0.4

One-click Chado Installer One-click Chado Installer Details Pages for Main Chado Content Types Details Pages for Main Chado Content Types Complex listings of data Complex listings of data Searching of Chado Content Searching of Chado Content Job Management Job Management Materialized Views Support Materialized Views Support Data Loaders Data Loaders Custom Page Layouts Custom Page Layouts Developers API Developers API Tripal Features

Webpages specific to a single record in chado Webpages specific to a single record in chado Generated based on information in chado Generated based on information in chado Allow direct editing of a single record Allow direct editing of a single record Permissions determine which users are allowed to edit content Permissions determine which users are allowed to edit content Enabled for Enabled for Organisms Organisms Features Features Libraries Libraries Analysis’ Analysis’ Stocks Stocks Tripal Features

Data from Organism table in Chado Custom content added specifically to this page Optional feature summary block added by Tripal: counts feature types in Chado. Tripal Features

Shows all libraries (e.g. genomic BAC, EST, FOSMID, etc) available for a species Tripal Features

Data taken from the Chado ‘feature’ table. EST’s in the contig alignment GO terms annotated to this feature. Pulled directly from Chado. Tripal Features

Data taken from the Chado ‘stock’ table. External Database References (‘dbxref’ <= ‘stock_dbxref’) Stock Relationships (‘stock_relationship’) Properties (‘stockprop’) Tripal Features

Integration of Chado with the Drupal Views Module Integration of Chado with the Drupal Views Module Create custom SQL queries through the web- interface Create custom SQL queries through the web- interface Formatting of the results into a variety of formats including lists, tables, and RSS feeds Formatting of the results into a variety of formats including lists, tables, and RSS feeds Sorting, Filtering (admin set values, user provided values and/or variables from the path) Sorting, Filtering (admin set values, user provided values and/or variables from the path) Exporting of tables to Excel, fasta, etc. Exporting of tables to Excel, fasta, etc. Permissions handling Permissions handling Tripal Features

Create custom SQL queries through the web-interface Create custom SQL queries through the web-interface Tripal Features

And produces this table And produces this table Tripal Features

All Chado tables are integrated by default All Chado tables are integrated by default Can change field names and help text to be more specific to your site Can change field names and help text to be more specific to your site Specify custom data handlers allowing you to customize Specify custom data handlers allowing you to customize The way fields are displayed The way fields are displayed The form elements used for filters (advanced searching) The form elements used for filters (advanced searching) New sort criteria New sort criteria Tripal Features v 0.4

Full-text built-in Drupal searchFull-text built-in Drupal search Slow to index, but fast to searchSlow to index, but fast to search Available for features, libraries, analysis’ and organismsAvailable for features, libraries, analysis’ and organisms Tripal Features Download FASTA file of results

Advanced custom searches usingAdvanced custom searches using Uses Drupal Views FiltersUses Drupal Views Filters Administrators can set up their own search formsAdministrators can set up their own search forms through the web interfacethrough the web interface to search a base:to search a base: Chado tableChado table or Materialized viewor Materialized view and related tablesand related tables Tripal Features v 0.4

Advanced custom searches usingAdvanced custom searches using Example: Advanced Search for features by organism, type, and/or analysis it was generated inExample: Advanced Search for features by organism, type, and/or analysis it was generated in Tripal Features v 0.4

Can be used to greatly speed up querying of chado content by pre- joining tablesCan be used to greatly speed up querying of chado content by pre- joining tables Useful for complex listings or searchesUseful for complex listings or searches Tripal Features

Creation of custom Materialized ViewsCreation of custom Materialized Views Specify fields and a query to generateSpecify fields and a query to generate All done through the web interfaceAll done through the web interface Tripal Features

Update materialized views at the click of a buttonUpdate materialized views at the click of a button Uses the job management systemUses the job management system Tripal Features

Integrate with Drupal Views to allow for listings of data and/or advanced searchingIntegrate with Drupal Views to allow for listings of data and/or advanced searching Through the web interfaceThrough the web interface Specify field names (human-readable), help text and custom handlersSpecify field names (human-readable), help text and custom handlers Specify relationships to chado tablesSpecify relationships to chado tables Tripal Features v 0.4

Format-specific loadersFormat-specific loaders FASTA and GFF3 for loading feature dataFASTA and GFF3 for loading feature data OBO for loading ontologiesOBO for loading ontologies Tripal Features

Generic Tab-delimited LoaderGeneric Tab-delimited Loader Allows loading of any tab-delimited fileAllows loading of any tab-delimited file Can insert into multiple tables, multiple timesCan insert into multiple tables, multiple times Create a saved loading profile that can be applied to many filesCreate a saved loading profile that can be applied to many files Tripal Features v 0.4

Generic Tab-delimited LoaderGeneric Tab-delimited Loader Can specify in the loading profileCan specify in the loading profile Chado table/field to load a given column intoChado table/field to load a given column into Foreign key relationships between recordsForeign key relationships between records Constant valuesConstant values for a loading profilefor a loading profile specific to a given filespecific to a given file Regular Expressions to transform data before loadingRegular Expressions to transform data before loading Tripal Features v 0.4

Generic Tab-delimited LoaderGeneric Tab-delimited Loader For each file create a loading jobFor each file create a loading job Keeps track of progress, details, number of records insertedKeeps track of progress, details, number of records inserted Allows you to enter file-specific constantsAllows you to enter file-specific constants Tripal Features v 0.4

Expose Chado data to panels in the form of blocks Expose Chado data to panels in the form of blocks Allows tripal administrators to arrange chado content on details pages Allows tripal administrators to arrange chado content on details pages Decide if you want the Sequence Features page to only contain basic details and other details such as properties, relationships, annotation appear as tabs Decide if you want the Sequence Features page to only contain basic details and other details such as properties, relationships, annotation appear as tabs Or combine everything onto a single page Or combine everything onto a single page Panels supports custom layouts with any combination of rows and columns Panels supports custom layouts with any combination of rows and columns Tripal Features

Put content in any region you want Put content in any region you want Panels supports custom layouts with any combination of rows and columns Panels supports custom layouts with any combination of rows and columns Tripal Features

At the Tripal-core level: At the Tripal-core level: Functions to submit and update job status for the Jobs Management system Functions to submit and update job status for the Jobs Management system Functions to easily add materialized views for your extensions. Functions to easily add materialized views for your extensions. Functions for adding custom CV terms needed for modules or applications Functions for adding custom CV terms needed for modules or applications At the Chado-centric module level: At the Chado-centric module level: Generic Insert/Update/Delete for Chado tables Generic Insert/Update/Delete for Chado tables Supports ALL chado tables –not just those supported by Tripal Supports ALL chado tables –not just those supported by Tripal Pie Charts and expandable tree browser for showing features with assigned ontologies Pie Charts and expandable tree browser for showing features with assigned ontologies At the Analysis module level: At the Analysis module level: Functions for registering new analysis modules Functions for registering new analysis modules Use of Drupal hooks for integrating new analyses Use of Drupal hooks for integrating new analyses Tripal Features

tripal_core_chado_select tripal_core_chado_select array tripal_core_chado_select (string $tablename, array $columns, array $values) array tripal_core_chado_select (string $tablename, array $columns, array $values) tripal_core_chado_insert tripal_core_chado_insert array tripal_core_chado_insert (string $tablename, array $values) array tripal_core_chado_insert (string $tablename, array $values) tripal_core_chado_update tripal_core_chado_update array tripal_core_chado_update (string $tablename, array $match, array $values) array tripal_core_chado_update (string $tablename, array $match, array $values) Tripal Features

Usage: Usage: $columns = array( ‘feature_id’, ‘name’, ‘uniquename’ ); $values = array( ‘organism_id’ => array(‘genus’ => ‘Lens’), ‘type_id’ => array( ‘cv_id’ => array(‘name’ => ‘sequence’), ‘name’ => ‘gene’, ), ‘dbxref_id’ => array( ‘db_id’ => array(‘name’ => ‘NCBI’), ),); $result = tripal_core_chado_select('feature',$columns,$values); The above example, returns an array of all Lentil genes with NCBI accessions The above example, returns an array of all Lentil genes with NCBI accessions Updates and Inserts follow a similar scheme Updates and Inserts follow a similar scheme Tripal Features

Applications Analysis Modules Chado-Centric Modules Tripal Core (API) Tripal can be extended at the Application and Analysis Module layers, or where Chado-centric modules are missing. Anyone may develop Applications and Analysis modules Anyone may help with development of Chado- centric modules but in coordination with core Tripal developers. Tripal Extensions

Tripal Extensions are made available through the Tripal SourceForge Site Tripal Extensions are made available through the Tripal SourceForge Site Some extensions coming soon include: Some extensions coming soon include: Breeder’s Toolbox Application Breeder’s Toolbox Application Genotype Experiments Genotype Experiments Webservices Webservices GMOD RPC, Tripal-specific REST GMOD RPC, Tripal-specific REST GBrowse Integration GBrowse Integration Current release is for GBrowse 1.x Current release is for GBrowse 1.x Tripal Extensions

Analysis Modules: Analysis Modules: There are already modules developed for supporting the following analysis’: There are already modules developed for supporting the following analysis’: BLAST BLAST GO GO Interpro Interpro KEGG KEGG Unigene Unigene In version 0.2 these were include in core Tripal but have been moved to a separate Drupal Package In version 0.2 these were include in core Tripal but have been moved to a separate Drupal Package Tripal Extensions

Tripal is still maturing but anyone can extend it to suit their needs. Tripal is still maturing but anyone can extend it to suit their needs. These extensions can be shared with others and can be made available by on the Tripal website: These extensions can be shared with others and can be made available by on the Tripal website: If you are interested in developing an extension feel free to the mailing list: If you are interested in developing an extension feel free to the mailing list: Tripal Extensions

Main Bioinformatics Lab Stephen Ficklin (project lead) Chun-Huai Chen Taein Lee Dorrie Main, Ph.D Il-Hyung Cho, Ph.D. Sook Jung, Ph.D Clemson University Genomics Institute Meg Staton, Ph.D University of Saskatchewan Lacey-Anne Sanderson Kirstin Bett, Ph.D Ontario Institute for Cancer Research GMOD Coordinator, Scott Cain, Ph.D Emory University Previous GMOD Help Desk, Dave Clement s

Development of Tripal has been supported by components of several funded projects, including: Development of Tripal has been supported by components of several funded projects, including: Current Funding Tree Fruit GDR: Translating Genomics into Advances in Horticulture: USDA Specialty Crops Research Initiative, September 2009 – August An Integrated Web-based Relational Database for the Curation of Cacao Genetic and Genomic Data: USDA-ARS SCA, January January Developing an Online Toolbox for Tree Fruit Breeding: Washington Tree Fruit Research Commission, April 2009 – March RosBREED: Enabling Marker-assisted Breeding in Rosaceae: USDA Specialty Crops Research Initiative, September 2009 – August 2013 Genomics-Assisted Plant Breeding for Cool Season Food Legumes: University of Idaho Special Grants, USDA NIFA, May 2010 – April 2013 Loblolly Pine Genome Sequencing: USDA DOE, January 2011-January 2016 PURENET: Agriculture and Agri-Food Canada, May 2009 – March 2011 iMAP: Saskatchewan Pulse Growers Association, September 2010 – September 2013 Comparative Genomics of Environmental Stress Responses in North American Hardwoods: NSF Plant Genome Research Program, February January 2015 Past Funding Genomic Tool Development for the Fagaceae, NSF Award # Genomic Tool Development for the Fagaceae, NSF Award # Clemson University Genomics Institute (CUGI)Clemson University Genomics Institute (CUGI) Clemson’s Cyberinfrastructure and Technology Integration Group (CITI)Clemson’s Cyberinfrastructure and Technology Integration Group (CITI)

Sourceforge: Mailing Lists: GMOD Tripal Pages: