WormBase Workshop:2015 International C. elegans Meeting

Tools & Resources• InterMine / WormMine – Chris Grove• JBrowse – Scott Cain• The WormBase Ontology Browser – Raymond Lee• ParaSite, Ensembl Genomes, and UCSC Assembly

Hub for C. elegans – Kevin Howe/Michael Paulini• Gene Ontology: annotations and enrichment

tools – Kimberly Van Auken

Community Annotation Tools• Introduction & Overview– Genetic variations annotation – Mary Ann Tuli

• Contributing & editing gene concise descriptions – Ranjana Kishore

• Micropublications – Daniela Raciti

WormBase Workshop:2015 International C. elegans Meeting

WormBase Data Mining Options

• WormMine• Flat files (click “FTP site” under “Downloads”

at bottom of WormBase homepage)• Website API• Perl interface• Bioperl interface to sequence feature

databases• And more…

WormMineThe WormBase instance of the

InterMine biological data warehouse

WormMine: An Overview

WormMine

Biological Entities WormMine Entities

Genes Proteins Lists Queries Tables

WormMine: An Overview

• Genes• Alleles• Allele-phenotypes• Genomic coordinates• CDSs, transcripts• GO annotations• Expression patterns

– Life stages, anatomy

• Expression clusters– Co-expressed genes

• Proteins– Amino acid sequences– Molecular weight– CDSs, transcripts– Motifs, domains

Biological Entities:

WormMine: An Overview

• Lists– Lists of biological

entities– Constrain queries on

lists– Compare & contrast,

intersection, union, etc.• Queries– Template and custom

queries– Constrain on biological

entities or lists

• Tables– Lists and query results– Sortable,

downloadable– Export as a

WormMine list

WormMine Entities:

Finding WormMine• Click on “WormMine” under the WormBase

homepage “Tools” menu

WormMine Homepage

WormMine Homepage

1. Brief tutorial

WormMine Homepage

2. General Search

WormMine Homepage

3. Lists

4. Queries

WormMine Homepage

WormMine Lists

WormMine Lists

WormMine Lists: Uploading a list

WormMine Lists: Browsing existing lists

WormMine Lists: Browsing existing lists

WormMine Lists: Browsing existing listsWormMine Table

AttributesAttributes

Entities

Entities

WormMine Lists: Browsing existing lists

WormMine Queries

WormMine Queries

WormMine Queries

WormMine Query Templates

WormMine Query Templates

WormMine Query Template Options

WormMine Query Template ResultsWormMine Table

WormMine QueryBuilder

WormMine QueryBuilder: Genes

WormMine QueryBuilder: Genes

WormMine QueryBuilder: Genes

WormMine QueryBuilder: Genes

WormMine QueryBuilder: Genes

WormMine QueryBuilder: Genes

WormMine QueryBuilder: Import query from XML

WormMine QueryBuilder: Import query from XML

WormMine QueryBuilder: Import query from XML

Questions?• E-mail help@wormbase.org anytime, for any

questions!Thank you!!

AcknowledgementsWormBase Web Development Team:

Todd HarrisSibyl Gao

Paulo Nuin