Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_August_2015|August]]
 
[[WormBase-Caltech_Weekly_Calls_August_2015|August]]
  
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[[WormBase-Caltech_Weekly_Calls_September_2015|September]]
  
== September 3, 2015 ==
 
  
=== Development instances at Caltech ===
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== October 1, 2015 ==
* 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) ===
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=== Topic 1 ===
* 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 ===
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=== Topic 2 ===
* 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 ==
 
 
 
=== WormBook changes [Paul S] ===
 
* What could we do with the new changes?
 
* Worm Breeder's Gazette?
 
** Jane & Todd working on streamlining process of submission
 
* GSA wants to publish higher impact chapters
 
* Egg shell chapter is too detailed (won't generate enough citations for GSA)
 
* GSA will do a methods chapter on CRISPR (hot topic)
 
* Go-ahead with incorporation of micropublications?
 
** We need a name to call it; branding
 
** Incorporation of pathway/process pages
 
* Marie-Anne Felix et al. asked for species descriptions
 
* Mark Blaxter et al. asked for genome announcements
 
* How will citations work/look?
 
* Will chapter updates still be possible under GSA? That will be up to GSA
 
 
 
=== Author first pass incorporation of community curation requests  ===
 
* We already have a developed Author-First Pass (AFP) pipeline to request data from authors
 
* We could co-opt the AFP pipeline to request community curation, specifically concise descriptions and allele-phenotype
 
* We can remake the AFP e-mail to shift focus to concise descriptions and allele-phenotype forms
 
 
 
 
 
== September 24, 2015 ==
 
 
 
=== E-mails soliciting contributions ===
 
* Can we automate the e-mails for concise descriptions?
 
* May be better to e-mail manually
 
* We want to e-mail a smaller group of people before ramping up to mass e-mails
 
 
 
=== BioCurator meeting ===
 
* Geneva, Switzerland
 
* Mary Ann proposed community curation workshop
 
* Mary Ann in communication with Pascal
 
 
 
=== WormBase ParaSite ===
 
* Had SAB meeting
 
* Want to have more integration at the search level
 
* Want to have a plan for data mining
 
 
 
=== Datomic ===
 
* Thomas had good results with a table maker for Datomic
 
* We will need a certificate (web security, SSL) to query Datomic at Hinxton
 
* Thomas wrote an ACEDB-to-Datomic converter; Juancarlos testing with a subset of data
 
* Accessibility of Datomic information online? Some tutorials and videos available
 
 
 
=== SObA (Summary of Ontology-based Annotations) ===
 
* Raymond acquired expression clusters from Wen to test the (David's) anatomy enrichment tool
 
* Many expected results, some not
 
* Considering a SObA-view of genes in a particular expression cluster, using existing annotations
 

Revision as of 21:38, 30 September 2015