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| | [[WormBase-Caltech_Weekly_Calls_April_2014|April]] | | [[WormBase-Caltech_Weekly_Calls_April_2014|April]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_May_2014|May]] |
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| − | == May 1, 2014 ==
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| − | | |
| − | === Progress report ===
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| − | * Curation status freezes have been collected (daily?)
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| − | * These can be used for report
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| − | * Review grant proposal: milestones, quarterly updates, etc.
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| − | | |
| − | === LEGO - Paul Thomas' visit ===
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| − | * We want to work on/think about importing WB GO annotations into LEGO format
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| − | * Is .OWL format the final destination of LEGO data for us? Yes, probably
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| − | * Will we be able to automate the process and eventually port to WikiPathways or other pathway visualizer?
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| − | * Extended evidence codes? For capturing methods?
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| − | * We need some trial LEGO curation to start working out the process
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| − | * There is a communal desire to achieve a common format for pathways, whether it be SBML, SBGN, LEGO, etc. or some hybrid
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| − | * We would like to play around with how to import/interpret/export .OWL files for our data
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| − | | |
| − | === Pathway curation ===
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| − | * Topic curation: a single (or pair of) curator(s) focusing on pulling together and drawing a pathway for a topic
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| − | * Labs adopting a pathway? Outreach, community annotation
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| − | * Reaching out to experts to confirm or proof read our pathways
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| − | | |
| − | === WormBase Ontology Browser (WOBr) ===
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| − | * http://juancarlos.wormbase.org/tools/ontology_browser
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| − | * Getting closer to completion
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| − | * Working out how to handle different relationships, e.g. "part_of", "has_part"
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| − | | |
| − | | |
| − | | |
| − | == May 8, 2014 ==
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| − | | |
| − | === BioTapestry ===
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| − | * We may be able to use BioTapestry (from Davidson group) to visualize gene regulatory interactions
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| − | * Xiaodong testing out
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| − | | |
| − | === Li et al 2004 Interactome ===
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| − | * Mostly sorted out now
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| − | * Missing gene references have been filled in
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| − | * "Noncore" interactions will be omitted from website
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| − | * Almost perfect correspondence between the published dataset and WB dataset
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| − | | |
| − | === WOBr ===
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| − | * Still making progress
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| − | * Incorporating life stage and disease annotations
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| − | * There appeared to be missing gene-phenotype annotations; Raymond contacted Kevin Howe
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| − | * Raymond will try to work on from Taiwan
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| − | | |
| − | === Models ===
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| − | * Paul Davis deposited the most recent models revision (1.404) in the models CVS repository
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| − | * Curators should test their model changes
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| − | * ?Variation and ?Construct models still need work; data needs to be conformed to fit new models
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| − | * Questionable whether all the changes for ?Construct and ?Variation models and data can be made by the next upload (May 27th)
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| − | * ?Expr_pattern model being modified soon to accommodate annotation of specific conditions; working to be compatible with LEGO
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| − | | |
| − | === Curation Progress Report ===
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| − | * Each curator can use the Curation Status Form to generate numbers for their datatype(s)
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| − | * Wen can install relevant versions of ACEDB (WS238 - WS243?) to pull annotation numbers
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| − | | |
| − | | |
| − | == May 15, 2014 ==
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| − | | |
| − | === Progress Report ===
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| − | * Paul will send around format during or after the call
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| − | * Whole contribution from Caltech (bio-curation) should be about a page
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| − | * A few sentences on each curation topic
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| − | * Some mention of models, WOBr, topic curation
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| − | * Next Thursday (May 22nd) local deadline (official deadline June 1)
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| − | * WS238 - WS243, March 2013 (beginning curation) to March 2014 (end of curation) 12 months/1 year
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| − | * Curation Status Form has stats from Aug 1 2013, we can look at numbers from Aug 1 2013 to May 1 2014, 9 months, can be extrapolated to a year
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| − | | |
| − | === BioTapestry ===
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| − | * Xiaodong sent around some sample gene regulatory network diagrams based on WB data
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| − | * How do we want to use this?
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| − | * To what extent do we need time and place (spatio-temporal) information for a transcriptional regulation to use BioTapestry?
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| − | * Can we generate spatial-agnostic/temporal-agnostic diagrams?
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| − | * Xiaodong will look into curation numbers for annotations that include spatial info, temporal info, or both
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| − | | |
| − | === GO Meeting at Caltech ===
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| − | * Need to reserve a room for next Tuesday/Wednesday, 10-15 people, all day (if possible)
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| − | * Tech-oriented discussions of LEGO, GO, Textpresso
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| − | | |
| − | | |
| − | | |
| − | == May 22, 2014 ==
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| − | | |
| − | === Agenda ===
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| − | * Orion/LEGO/Textpresso meeting
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| − | * Progress Report
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| − | | |
| − | === GO/LEGO ===
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| − | * GO curation will eventually morph into LEGO curation
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| − | * Can we incoporate other WormBase data into LEGO? Hopefully, we'll have to see
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| − | * Would be good to have OA (e.g. Interaction OA) feed directly into LEGO/Orion/Noctua
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| − | * We are building pathways with various tools; long term curation goal not clear yet
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| − | * How could we represent other data in LEGO? Phenotype annotations? Expression patterns? Genetic interactions?
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| − | * Connecting tools like PAINT, OA, Textpresso, etc. to LEGO
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| − | * LEGO team worked with Juancarlos to get some LEGO tools/infrastucture (Noctua, Barista, Amigo) running at Caltech
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| − | * Mechanisms to seed LEGO diagrams is a priority
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| − | * LEGO team working with Michael to interface with Capella (Textpresso tool)
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| − | | |
| − | === Progress Report ===
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| − | * Curators should send their blurbs to Chris (in any format)
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| − | * Chris will send plain text to Paul S.
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| − | | |
| − | === Monarch Initiative ===
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| − | * http://monarchinitiative.org/
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| − | * Human diseases connected to phenotypes via genetic variants in various model organisms
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| − | | |
| − | === Athena is crashing ===
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| − | * Wen having trouble with Athena; difficult to reboot
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| − | * Data is backed up; Wen and Raymond will work on replacing Athena
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| − | | |
| − | === WS244 Upload ===
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| − | * Citace upload to Wen by Tuesday morning
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| − | | |
| − | === BioGrid data ===
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| − | * Still waiting on curator timestamps and a dump of partially curated papers from BioGrid
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| − | * Will still need to compare genetic interaction datasets
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| − | * For large scale genetic interaction datasets in both databases, we will favor the WB version, import others (best mapping of terms possible)
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| − | | |
| − | === 2004 Vidal Interactome Yeast-Two Hybrid Data ===
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| − | * Chris has nearly finished sorting out official interactions from those removed
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| − | * Once done, we can import from later interactome datasets
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| − | | |
| − | | |
| − | | |
| − | == May 29, 2014 ==
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| − | | |
| − | === Agenda ===
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| − | * Progress Report
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| − | * SAB
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| − | * Citace upload
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| − | | |
| − | === LEGO ===
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| − | * LEGO connected to OA/Postgres -- Oh, is _that_ what we're talking about ? I thought it was about writing an interface that looked like the OA that worked on their data, not on postgres at all -- J
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| − | ** Can we link curation in the OA to LEGO model?
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| − | ** Still needs to be worked out
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| − | | |
| − | === Progress report ===
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| − | * Paul putting together report
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| − | * We need to discuss priorities
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| − | | |
| − | === Citace upload ===
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| − | * Wen received new phenotypes file
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| − | * Upload to Hinxton will proceed as usual tomorrow
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| − | * Wen will send around a new upload summary today
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| − | | |
| − | === Cis-regulation interactions visualization ===
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| − | * Now that we have broken out cis-regulation events into binary interactions, we can tell Abby to display in Cytoscape on the website
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| − | * We will use Cytoscape now, maybe consider BioTapestry later
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| − | | |
| − | === Scientific Advisory Board meeting ===
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| − | * Hinxton, UK, October 5-7, 2014
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| − | * Need to consider what types of numbers and coverage we want to cover
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| − | * e.g. Exppression patterns are caught up, behind on concise descriptions but we have a plan...
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| − | * We would like to acquire better coverage of allele-phenotype/RNAi-phenotype annotations
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| − | * Percent coverage, change in coverage percentage (are we keeping up? are we caught up?)
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| − | * LEGO curation approach: WB data modeling to capture LEGO type curation
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| − | * Biological Topics, WikiPathways, Reactome
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| − | * WormBase Ontology Browser
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| − | * Proportion of papers covered, # objects curated
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| − | * Text mining support to fill in missing information
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| − | | |
| − | === (Semi-) Automated Concise Descriptions ===
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| − | * Primarily for genes with very little existing information (e.g. no papers)
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| − | * Proposed tool could pull up basic info on gene: orthology, expression clusters, RNAseq data
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| − | * Expression cluster info could provide info under what conditions a gene is up- or down-regulated
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| − | * Is degree of confidence a concern? Are there confidence weights that we should apply? Thresholds for making some statements?
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| − | | |
| − | === WormBase Ontology Browser (WOBr) ===
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| − | * Currently we are still trying to adapt AMIGO 2 to WormBase data
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| − | * Amigo is Gene Ontology centric; to what extent does it work for us?
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| − | * How do we best merge Amigo GitHub code with WormBase code for further WB-specific development?
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| − | * Expandable trees (that we are using) only work for transitive relationships; anatomy ontology has other relationship types
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| − | * GO team does want Amigo to apply to other ontologies; how can we best coordinate with Amigo development?
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| − | * Interface with a GO-annotation verifier?
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| − | **AmiGO verification manager
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| − | **http://amigo2.berkeleybop.org/cgi-bin/amigo2/matrix
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| − | **https://sourceforge.net/apps/trac/pombase/wiki/MatrixProject
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| − | **http://build.berkeleybop.org/job/check-shared-annotations/lastBuild/console
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| − | | |
| − | === CHEBI update ===
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| − | * Karen sent 280 molecules to CHEBI that we have curated with but don't yet have a CHEBI ID
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| − | * Updating can happen weekly
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