wormbase workshop: 2015 international c. elegans meeting tools & resources intermine / wormmine...
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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 [email protected] anytime, for any
questions!Thank you!!
AcknowledgementsWormBase Web Development Team:
Todd HarrisSibyl Gao
Paulo Nuin