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…
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:
Questions?• E-mail [email protected] anytime, for any
questions!Thank you!!
AcknowledgementsWormBase Web Development Team:
Todd HarrisSibyl Gao
Paulo Nuin