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September 3, 2015

Development instances at Caltech

• Caltech wants to provide a Beta testing environment for curators/users. we'll have to rely on juancarlos.wormbase.org as cost/benefit analysis is unfavourable to consider other options.

GObA (Graph of Ontology-based Annotations)

• Added a couple new graph types
• Working out details before sending out to Beta testers
• Example pages:
  • For daf-2: http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryGraph&focusTermId=WBGene00000898
  • For daf-3: http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryGraph&focusTermId=WBGene00000899

Anatomy enrichment tool

• Enter list of genes, get a list of anatomy terms
• Developed originally by David Angeles
• Being incorporated and worked on by Raymond

Community allele-phenotype annotations

• Outreach: sending out e-mails to relevant people
  • Not done yet
• May be good to travel out to labs to give instructions, outreach
• We'll gather a list of labs that publish phenotypes and contact them
• We can also push the micropublication process

Logical Extensions of Gene Ontology (LEGO)

• Further developments being made on Noctua and other LEGO software
• Lots of discussion on LEGO modeling, how to best do it
• Testing is scheduled
• Protein complexes in cellular component ontology?
  • GO will collaborate with Protein Ontology group to work out how to capture that info
• Molecular function ontology annotation approach is being refactored
• Noctua being used for phenotype annotations, would be good to see how

Phentoype-association file: Attributing phenotypes to genes via genetic interaction

• Can we (and how do we) capture genes as involved in a process, for example, SynMuv genes in vulva development
• The phenotype association file currently only on direct phenotype annotations, not interaction-based phenotypes
• Gene Ontology captures these events (associations to a process, for example) with the evidence code, Inferred from Genetic Interaction

September 10, 2015

E-mail "blitz" for community forms

• Ranjana & Kimberly are composing e-mail to PIs for concise description
• Chris is going to e-mail first authors for allele-phenotype contributions

SObA (Summary of Ontology-based Annotations)

• E.g. daf-2: http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryGraph&focusTermId=WBGene00000898
• Daniela asking for a zoom option to see names of smaller nodes in "weighted" graph
  • We cannot do this currently
• It may be possible to develop this; will need to test

Anatomy/Tissue enrichment tool

• Counting genes annotated to a term, selecting terms with 100+ annotations
• Reason parent-child, ancestor-descendant relationships; keep most granular terms (remove ancestors)
• Create table of genes (~4,000) annotated to these terms (genes in rows, anatomy terms in columns)
• Take ?Expression_clusers/studies based on anatomy terms, take genes from that set as a test query (positive control)
• Using HSN neuron expression set, were able to retrieve HSNL and HSNR, as well as another terms
• Need to be aware of ?Expression_clusters that represent depletion rather than enrichment

EQ-PATO-style annotations

• Phenotype and RNAi OA's have been updated on the sandbox
• Data models have been proposed
• Awaiting model approval to move ahead

Yeast-One Hybrid data from Walhout lab

• We will be getting data from Marian Walhout in the next couple of weeks
• We hope to be up-to-date on all the Y1H data from her lab soon

WormBook chapter reviews

• Some reviews have come in
• Most we are still waiting on

modSeek & SPELL

• Klaus Richter has been using SPELL to annotate a list of 200-300 genes
• SPELL was periodically frozen; problems from Yahoo web-indexing
• Klaus wanted a standard file listing the most correlated genes for each gene in WormBase
• Cannot use SPELL for this, but we can use Seek
• Would be great to see expression correlation incorporated into the Cytoscape network viewer
• Will try to establish a pair-wise correlation table of all protein-coding genes (~20,000x~20,000)
• Maybe web can read off of such file

September 17, 2015

agenda item: WormBook changes