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| | = 2015 Meetings = | | = 2015 Meetings = |
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| − | = January 2015 =
| + | [[WormBase-Caltech_Weekly_Calls_January_2015|January]] |
| | | | |
| − | == January 8, 2015 ==
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| | | | |
| − | === Community annotation=== | + | = February 2015 = |
| − | * author participation
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| − | **Cecilia: still lots of work, need to manually process data submitted by authors
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| − | ** old data kept for history and for comparison
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| − | ** people mess up institution names - institution field on submission form being changed to a controlled vocabulary
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| − | ** campus addresses also not standardized - will organize/create address fields, e.g., street address, mail-code, etc.,
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| − | ** add example address
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| − | ** ~10 author submissions a week
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| − | ** most curation involves extracting people information from papers (~800 week), as automated as possible right now - people and affiliation are extracted from xml, but information still needs to be parsed
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| − | ** can we mine author data from other sources (institution, laboratory); important to get laboratory address for sending strains; two sets of data- (1) easy- people associated with a laboratory, (2) difficult- people not in a registered lab
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| | | | |
| − | ===Cross-product development=== | + | == February 5, 2015 == |
| − | Raymond
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| − | * embarking on cross-product generation- ex., male tail, versus hermaphrodite tail - better to have one 'tail' and add modifiers
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| − | * wants to move to OWL now; comment is that obo relationships are not directly translatable into OWL
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| − | * Uberon has elegans anatomy
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| | | | |
| − | Gary
| + | === Topic 1 === |
| − | * starting to work with Chris and Karen on developing cross-products, still in exploration phase
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| − | * not looking at OWL yet
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| − | * will get relationships from Raymond
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| | | | |
| − | ===Sequence feature curation=== | + | === Topic 2 === |
| − | Daniela, Gary, Xiaodong, Mary Ann are validating papers as positive/negative in curation status form. As soon as ready, Mary Ann/Gary will start curating
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| − | | |
| − | ===Rose alleles===
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| − | * 150,000 new alleles, Mary Ann done just all bar 12 of them in time for WS247
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| − | * phenotypes were only reported for a small fraction
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| − | | |
| − | ===CGC strains===
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| − | Mary Ann received latest update, CGC very busy with strains generated through new gene engineering techniques
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| − | | |
| − | === WB WBook chapters ===
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| − | Main outline [https://docs.google.com/a/wormbase.org/document/d/1l6pExlCMI88pi_-djk8jt7IzNsMDV-nIEY9Z1gBNh-A/edit here]- note this document cannot be edited, people can create their own shared docs for their respective papers
| |
| − | *Gene Function and Interaction google docs (Chris, Gary S., Karen, Kimberly)
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| − | [https://docs.google.com/a/wormbase.org/document/d/1mAxrqVIhxDNpkTUBmtu12sAo58pEG763tgASlzy-3JU/ here]
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| − | *Pathways and Processes (Karen) [https://docs.google.com/a/wormbase.org/document/d/1maTRPoIdmbZqfnd-8jZ5dCYPGM2fF6ihk9ZMhjcVL1Y/edit?usp=drive_web here]
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| − | * Expression (Daniela)
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| − | | |
| − | ===Micropublication===
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| − | * Hobert- micropublication for expression = small facts, which are data that will never be published (Daniela working with Hobert on these)
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| − | * Community annotation not linked to a publication
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| − | * a couple models for WB dealing with the micropubs
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| − | ** WB captures all submissions blind and posts them
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| − | ** WB reviews submission - curators decide which micropubs have value
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| − | * need to establish microattributions to increase the value of submissions
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| − | * involve semi-peer review through automated fact review requests to scientists who've worked on the gene, cell, entity, etc.
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| − | * need to set up a pilot, to get a feel for the amount of participation/work this tool will be
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| − | | |
| − | === Picture curation ===
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| − | *for topic curation
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| − | **want to annotate figures with genes - involves model change
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| − | **want dynamic display with slide show, different highlighted figures - need to work with webteam
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| − | * community voting - crowdsourcing - need to work with webteam
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| − | * WB-blessed image represented through wikipathways
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| − | | |
| − | ===Kimberly===
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| − | Continuing work on the new GO model
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| − | | |
| − | ===Juancarlos===
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| − | * management of automated descriptions with Ranjana
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| − | * phenotype requests through RNAi and allele phenotype done in december
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| − | | |
| − | ===Automated descriptions===
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| − | * playing with pulling out useful data to add to description automation (James and Ranjana)
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| − | | |
| − | | |
| − | == January 15, 2015 ==
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| − | | |
| − | === New expression objects and pictures ===
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| − | * Cross-species comparison of developmental gene expression
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| − | * Have life stage annotation
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| − | * Microarray experiments
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| − | * Do we have data on significant differences from C. elegans? Can we get the analysis or algorithm?
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| − | | |
| − | === Neuro anatomy ===
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| − | * 3 ways to access neuro-connectivity data
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| − | * ACEDB, Kris Gunsalus' server at NYU (defunct), Nikhil Bhatla's connectivity browser
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| − | * We would like to adopt Nikhil's browser (for neural connectivity AND the cell lineage browser); we need to act before it disappears
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| − | | |
| − | === FPKM RNA-Seq data display ===
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| − | * Should we suggest splitting the data display by tissue, life stage, treatment, etc.?
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| − | * Gary Williams is responsible; need to talk to him
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| − | | |
| − | === Heavy metal toxicity/response ===
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| − | * New topic, all papers have been checked
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| − | * Need to send list of relevant genes to Hinxton
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| − | * Curators can now flag figures relevant as topic diagrams
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| − | | |
| − | === Phenotype picture curation ===
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| − | * We will begin to collect pictures for phenotypes
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| − | * Will require model changes
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| − | | |
| − | === Phenotype OA Strain fields ===
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| − | * "Parental strain" autocomplete field added to TAB 2 of Phenotype OA
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| − | * Plan is to put parental strains in the Phenotype_info hash
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| − | * Natural isolate strains can be directly annotated with phenotype?
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| − | | |
| − | === BioCuration meeting in April ===
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| − | * Xiaodong is writing up an abstract, will send around before submission
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| − | * Xiaodong will run a curation tutorial for Chinese speakers
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| − | | |
| − | | |
| − | ==Jan 22, 2014==
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| − | === ad hoc curation of tier III species (Mary Ann)===
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| − | WBPaper00046176 describes Ctr- genes and alleles (fig 3). Although we do not curate this (and other tier III) species, should we place this information somewhere, on an ad hoc basis?
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| − | http://tazendra.caltech.edu/~acedb/daniel/00046176_Wei14_temp.pdf
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| − | | |
| − | Mins: Curate as much as existing models allow and hopefully expand at later date. The volume of this sort of data will increase as we encourage Community Curation.
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| − | Don't seek out papers, but add data as they come along.
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| − | Talk to Hinxton about adding gene models.
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| − | | |
| − | === Complex Gene Loci (Mary Ann) ===
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| − | e.g. lin-15A/lin-15B
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| − | | |
| − | unc-17/cha-1
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| − | | |
| − | We should use existing Gene_cluster model and add new Type tag to differentiate between e.g. rrn Gene cluster and e.g. lin-15A lin-15B complex loci.
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| − | | |
| − | nb. Maybe hard to discuss w/o Paul Davies.
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| − | | |
| − | Mins: The above was agreed. Need to agree on Types and make model proposal. Detailed curation (e.g. of alleles) will not be done within the Gene_cluster but within the allele as appropriate.
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| − | | |
| − | ===micropublication===
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| − | *Daniela starting to work on author submission forms for expression patterns where people can submit images
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| − | *Requirements? Paul says needs sequence - minimal important stuff, sequence, expression pattern, construct, reporter gene
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| − | *define minimal standards (minimal amount to reproduce experiment)
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| − | *genome coordinates are ok for elegans, but not for other species whose genomes
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| − | *making a micropublication - identifier, research object identifier(?)
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| − | *put them in paper class? no
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| − | *look research gate, academia U, mendeley etc - social media/science community person catalog.
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| − | *ultimate goal to convince NIH to capture and catalog these bits of information
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| − | *review function - how to build this in? how many reviewers do you need, how and who to get to participate
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| − | *continue work on submission form
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| − | | |
| − | | |
| − | == January 29, 2015 ==
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| − | | |
| − | === WormBase WormBook chapter ===
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| − | * Screenshots of WormBase.org website?
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| − | * Yes, the WormBook chapter should be updatable
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| − | * We can focus the discussion on general principles and underlying logic, more so than specific user tutorials
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| − | * First draft deadline: February 28, 2015
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| − | | |
| − | | |
| − | === SPELL ===
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| − | * Not going to be maintained?
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| − | * We don't know if/when it is going to die
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| − | * ModSeek is a potential replacement: http://seek.princeton.edu/modSeek/
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| − | * Data is stable, interface is not
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| − | | |
| − | | |
| − | === Workshops at international meeting ===
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| − | * Should we have a ~30 minute open discussion at the end of the 90-minute workshop?
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| − | * Maybe, but we should take a survey before to assess what people are interested
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| − | * Survey could be part of the registration process for the workshop
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| − | ** What kind of survey do we want? What have we done in the past? Does Todd know?
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| − | ** Should be simple, maybe ranking importance
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| − | ** What tools do people use that they would like to see incorporated into WormBase?
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| − | ** GO-enrichment analysis tools, etc.
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| − | * Plan is still to have 4-6 talks
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| − | * When/how do we want to handle/discuss user concerns and criticisms?
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| − | * Do we have a plenary session? We should, maybe Kevin was going to apply for one?
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| − | ** A plenary talk would likely be short (~3 min?) and would be mostly to advertise our presence at the meeting/workshop
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| − | * We could discuss which resources we provide/link to that are third party and possibly out of our control
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| − | * Review FTP site and what data is there
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| − | * Community Annotation
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| − | ** Automated concise description corrections/updates
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| − | ** Data submission pipelines, author first pass forms, RNAi data submission table
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| − | ** Need to be specific, not vaguely discussing community contribution
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| − | ** Discuss making data submission part of the publication process
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| − | *** Mention existing data submission pipelines used by publishers
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| − | *** Want to make things easy for users
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| − | *** Emphasize expedited data incorporation
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| − | ** Competition to curate alleles?
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| − | *** WBPerson T-shirts for winning lab
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| − | ** We can discuss micropublications
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| − | * Soliciting developer efforts?
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| − | * Incorporation of community developed tools
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| − | | |
| − | === WormBase IWM souvenirs ===
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| − | * We could have prizes for community annotators
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| − | * We could make bags again
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| − | | |
| − | | |
| − | === Optogenetics as new data type ===
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| − | * Raymond adding as new data type
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| − | * Will add to curation status form, author first pass form, etc.
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| − | * Potential subcategories exist
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| − | * Curators can let Raymond know about important subtypes to recognize/include
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| − | | |
| − | | |
| − | === Linux machines updated ===
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| − | * Vulnerability has been plugged for all non-Textpresso Linux machines (Raymond)
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| − | * Machines have been set up to automatically install security updates
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| − | * Eventually would be good to handle with a server administration tool
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