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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]] |
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− | == September 3, 2015 ==
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− | === Development instances at Caltech === | + | == 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.
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− | === GObA (Graph of Ontology-based Annotations) === | + | === Topic 1 === |
− | * Added a couple new graph types
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− | * Working out details before sending out to Beta testers
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− | * Example pages:
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− | ** For daf-2: http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryGraph&focusTermId=WBGene00000898
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− | ** For daf-3: http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryGraph&focusTermId=WBGene00000899
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− | === Anatomy enrichment tool === | + | === Topic 2 === |
− | * Enter list of genes, get a list of anatomy terms
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− | * Developed originally by David Angeles
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− | * Being incorporated and worked on by Raymond
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− | | |
− | === Community allele-phenotype annotations ===
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− | * Outreach: sending out e-mails to relevant people
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− | ** Not done yet
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− | * May be good to travel out to labs to give instructions, outreach
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− | * We'll gather a list of labs that publish phenotypes and contact them
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− | * We can also push the micropublication process
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− | | |
− | === Logical Extensions of Gene Ontology (LEGO) ===
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− | * Further developments being made on Noctua and other LEGO software
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− | * Lots of discussion on LEGO modeling, how to best do it
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− | * Testing is scheduled
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− | * Protein complexes in cellular component ontology?
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− | ** GO will collaborate with Protein Ontology group to work out how to capture that info
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− | * Molecular function ontology annotation approach is being refactored
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− | * Noctua being used for phenotype annotations, would be good to see how
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− | | |
− | === Phentoype-association file: Attributing phenotypes to genes via genetic interaction ===
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− | * Can we (and how do we) capture genes as involved in a process, for example, SynMuv genes in vulva development
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− | * The phenotype association file currently only on direct phenotype annotations, not interaction-based phenotypes
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− | * Gene Ontology captures these events (associations to a process, for example) with the evidence code, Inferred from Genetic Interaction
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− | == September 10, 2015 ==
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− | === E-mail "blitz" for community forms ===
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− | * Ranjana & Kimberly are composing e-mail to PIs for concise description
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− | * Chris is going to e-mail first authors for allele-phenotype contributions
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− | | |
− | === SObA (Summary of Ontology-based Annotations) ===
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− | * E.g. daf-2: http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryGraph&focusTermId=WBGene00000898
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− | * Daniela asking for a zoom option to see names of smaller nodes in "weighted" graph
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− | ** We cannot do this currently
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− | * It may be possible to develop this; will need to test
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− | === Anatomy/Tissue enrichment tool ===
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− | * Counting genes annotated to a term, selecting terms with 100+ annotations
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− | * Reason parent-child, ancestor-descendant relationships; keep most granular terms (remove ancestors)
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− | * Create table of genes (~4,000) annotated to these terms (genes in rows, anatomy terms in columns)
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− | * Take ?Expression_clusers/studies based on anatomy terms, take genes from that set as a test query (positive control)
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− | * Using HSN neuron expression set, were able to retrieve HSNL and HSNR, as well as another terms
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− | * Need to be aware of ?Expression_clusters that represent depletion rather than enrichment
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− | | |
− | === EQ-PATO-style annotations ===
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− | * Phenotype and RNAi OA's have been updated on the sandbox
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− | * Data models have been proposed
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− | * Awaiting model approval to move ahead
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− | === Yeast-One Hybrid data from Walhout lab ===
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− | * We will be getting data from Marian Walhout in the next couple of weeks
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− | * We hope to be up-to-date on all the Y1H data from her lab soon
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− | === WormBook chapter reviews ===
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− | * Some reviews have come in
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− | * Most we are still waiting on
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− | | |
− | === modSeek & SPELL ===
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− | * Klaus Richter has been using SPELL to annotate a list of 200-300 genes
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− | * SPELL was periodically frozen; problems from Yahoo web-indexing
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− | * Klaus wanted a standard file listing the most correlated genes for each gene in WormBase
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− | * Cannot use SPELL for this, but we can use Seek
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− | * Would be great to see expression correlation incorporated into the Cytoscape network viewer
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− | * Will try to establish a pair-wise correlation table of all protein-coding genes (~20,000x~20,000)
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− | * Maybe web can read off of such file
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− | | |
− | == September 17, 2015 ==
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− | === WormBook changes [Paul S] ===
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− | * What could we do with the new changes?
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− | * Worm Breeder's Gazette?
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− | ** Jane & Todd working on streamlining process of submission
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− | * GSA wants to publish higher impact chapters
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− | * Egg shell chapter is too detailed (won't generate enough citations for GSA)
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− | * GSA will do a methods chapter on CRISPR (hot topic)
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− | * Go-ahead with incorporation of micropublications?
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− | ** We need a name to call it; branding
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− | ** Incorporation of pathway/process pages
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− | * Marie-Anne Felix et al. asked for species descriptions
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− | * Mark Blaxter et al. asked for genome announcements
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− | * How will citations work/look?
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− | * Will chapter updates still be possible under GSA? That will be up to GSA
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− | === Author first pass incorporation of community curation requests ===
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− | * We already have a developed Author-First Pass (AFP) pipeline to request data from authors
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− | * We could co-opt the AFP pipeline to request community curation, specifically concise descriptions and allele-phenotype
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− | * We can remake the AFP e-mail to shift focus to concise descriptions and allele-phenotype forms
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− | == September 24, 2015 ==
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− | === E-mails soliciting contributions ===
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− | * Can we automate the e-mails for concise descriptions?
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− | * May be better to e-mail manually
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− | * We want to e-mail a smaller group of people before ramping up to mass e-mails
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− | | |
− | === BioCurator meeting ===
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− | * Geneva, Switzerland
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− | * Mary Ann proposed community curation workshop
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− | * Mary Ann in communication with Pascal
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− | | |
− | === WormBase ParaSite ===
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− | * Had SAB meeting
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− | * Want to have more integration at the search level
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− | * Want to have a plan for data mining
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− | === Datomic ===
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− | * Thomas had good results with a table maker for Datomic
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− | * We will need a certificate (web security, SSL) to query Datomic at Hinxton
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− | * Thomas wrote an ACEDB-to-Datomic converter; Juancarlos testing with a subset of data
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− | * Accessibility of Datomic information online? Some tutorials and videos available
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− | === SObA (Summary of Ontology-based Annotations) ===
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− | * Raymond acquired expression clusters from Wen to test the (David's) anatomy enrichment tool
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− | * Many expected results, some not
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− | * Considering a SObA-view of genes in a particular expression cluster, using existing annotations
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