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| [[WormBase-Caltech_Weekly_Calls_September_2016|September]] | | [[WormBase-Caltech_Weekly_Calls_September_2016|September]] |
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| + | [[WormBase-Caltech_Weekly_Calls_October_2016|October]] |
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− | == October 6, 2016 ==
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− | === Citace upload ===
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− | * Tuesday, October 25th, 2016
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− |
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− | === Automated descriptions ===
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− | * Ranjana working with Juancarlos to run and update automated descriptions pipeline
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− |
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− | === Intellectual lineage ===
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− | * First draft up on WormBase development site
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− |
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− | === Noctua ===
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− | * Raymond trying to annotate axioms for anatomy function
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− | * How to connect cell types in different organisms to those in C. elegans anatomy ontology?
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− | * Maybe best way is to connect based on biological function, e.g. regulate osmolarity (kidney, excretory cell)
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− | * Raymond attempting to use Noctua to draw relationships between anatomy terms and function
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− | * There's a distinction between annotating to an instance vs. to a class
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− | * Raymond worked on modeling a statement on excretory cell function from WormAtlas
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− | * Question: how much redundancy might we end up with if we annotate to higher level (cell/anatomy function) and lower level (individual gene product function)? There may be, but all of this information is valuable
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− |
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− | === Expr_pattern model change ===
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− | * Daniela proposed a CRISPR-Cas9 tag for the expression pattern class as an experiment type
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− | * Would be inline with "Reporter gene", "In situ", "Antibody", etc.
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− | * Probably want "Genome editing" instead of "CRISPR-Cas9" so as to be more generic
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− | * Would a GFP knock-in via genome editing be distinct from "Reporter gene"?
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− | * Could have a super tag "Genome_editing" and sub-tags "CRISPR-Cas9", "Zinc_fingers", "TALEN"
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− | * Maybe we'll just stick with a "Genome_editing" tag
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− | == October 13, 2016 ==
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− |
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− | === Strain requests ===
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− | * Ranjana sending strain requests to Mary Ann
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− | * Mary Ann processing published strains requested by Ranjana
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− |
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− | === GO meeting ===
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− | * Registration is now setup
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− | * Sarah (Torres) could register all WB CIT participants
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− | * Kimberly is helping organize
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− |
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− | === AGR Portal Use Case working group update ===
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− | * Working on first use case, basic text search for genes, GO terms, diseases, and orthology groups
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− | * Data is being collected into a "Portal Data" Google drive: https://drive.google.com/drive/u/1/folders/0B9qQtJIEUDEhRnJKWF9NTTVMVGs
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− | * Some MODs providing more data than requested; That's OK, we just want to keep it simple for the first implementation
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− | * We only want, for the first pass, to retrieve genes, GO terms (no GO-gene annotations), diseases (no disease-gene annotations), and orthology groups
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− | * We likely already have enough data for a first pass implementation; not comprehensive data, but that is fine for now
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− | * Disease data dumped from ACEDB, based on Disease Ontology; not comprehensive for OMIM disease list
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− | * We'll eventually want to pull data directly from OMIM and GO
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− |
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− | === Extending SPELL virtual machine ===
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− | * Has a lot of data; may be contributing to SPELL downtime
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− | * Could possibly move to the cloud, but we would need a machine in the cloud
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− | * Can only install SPELL on Ubuntu 8; SGD uses RedHat; we can ask them what they're using, how it's working
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− | * Possibly SGD could run a worm instance on their machine(s)
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− |
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− | === Transgenome ===
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− | * Junacarlos finished parsing the transgenome data with Daniela
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− | * Checking parse output numbers with the Transgenome group
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− | * Will the expression data be dumped out in the expression GAF? Yes, should be
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− | * Data from Transgenome are not necessarily peer-reviewed; need to make that clear in display
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− | * Some Expr_pattern objects can be linked to WBPerson, if not a WBPaper
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− | * Data in GAF will point to the 2012 Cell paper as a reference for the Transgenome project
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− | * Raymond suspects issues with it; what if users cannot trace data back to source (by looking up the paper)?
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− | * Would be best to link directly to the respective Transgenome database page when displaying their data
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− | * Notes can be added to release notes that the Transgenome data has been added to the database
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− |
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− | === Micropublications ===
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− | * Trial with uploading Nemametrix data; aiming in putting data for the next upload (2-4 micro)
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− | * Added micropublication type in the ?Paper class
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− | * Micropublications will acquire WBPaper IDs
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− | * Previous micropublications were only ?Expr_pattern objects; now will be ?Paper objects
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− | * Ideally micropubs. will be indexed by PubMed and enter the WB pipeline through the normal paper route
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− | * Question: create WBPaper objects as soon as accepted? That is plan for now
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− | * Micropubs. will first be hosted by WormBase, but may move to an independent repository (Micropublication: biology)
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− | * Will we display images/figures from micropubs. only or for all papers? We'll need to wait and see
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− | * Could we accommodate any digital data to associate with the micropub.? E.g. data points, plasmid maps, etc.
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− | * Micropubs. text will be marked up as much as possible; what about making all sentences OWL statements?
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− | * Would this be changing the way that authors write papers? Maybe, but should be independent of core micropublication pipeline
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− | * Each micropublication/data/result could be combined as modules to create a larger, more comprehensive narrative
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− | * There is a notion of a "millipublication" that could be a larger narrative from collected micropublications
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− | * One original idea was that micropublications would capture data that people would not otherwise want to publish
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− | * Data submitted as micropublication will not be able to be submitted as another publication later but will be cited as data point
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− | * Micropubs. will be considered primary research article, not just an abstract (equivalent to meeting abstract)
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− | == October 20, 2016 ==
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− | === AGR search prototype ===
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− | * URL: http://search.alliancegenome.org/
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− | * Searching "WNT4", then choosing category "Gene Ontology" provides facets for species
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− | * Question is: how are these species associated to the GO terms?
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− | * Associated genes could have a species prefix or indicator
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− |
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− | === AGR gene page ===
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− | * There was resistance to creating AGR gene pages
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− | * Some see it as redundant with what is already available elsewhere
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− | * Although we may want to build a foundation gene page and develop from there
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− | * Maybe MODs could develop their respective gene pages to look more like an AGR standard
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− | * One main reason to create AGR is to have a consolidated, consistent, standard view for data, including genes
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− | * Would be good to assemble a user group (or intended audience) to receive feedback from
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− | * Use Case working group has put together some ideas for a gene comparison page, keyed off of orthology group:
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− | ** https://docs.google.com/presentation/d/1frMMh3xfepesJq5iqSXAwwLOrb45cuqe3LValEOd4bM/edit#slide=id.p
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− |
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− | === Citace upload ===
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− | * Next Tuesday, October 25th 10am
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− |
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− | === Curator call next week ===
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− | * Topic: curation styles
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− | * Curation by paper, by topic, etc.
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− | * Curation inter-dependencies
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− | * Daniela will present for WormBase
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− | * Send ideas to Daniela for her to cover
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− | * Send older slides with relevant information to Daniela
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− | == October 27, 2016 ==
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− | === AGR Portal Use Case working group ===
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− | * Working group had call yesterday with Paul Thomas and Judy Blake
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− | * Decision was made to abandon the idea of displaying "orthology groups"/"homology groups"
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− | * Instead we will display a gene-centric page with comparisons of focus gene data with data from all orthologs and paralogs
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− | * Paul Thomas' group had built a prototype for pulling out orthologs with GO info: http://umodtest.usc.edu/
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− | * This prototype returns closest orthologs of a focus/query gene and then displays a table of all GO annotations for all genes
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− | * We would want to display orthologs for a focus gene as well as paralogs
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− | * This display is very similar to the gene comparison page mockup the use case working group had been envisioning, except now the focus will be a single gene, not a PANTHER subfamily
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− |
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− | === Disease-Strain curation ===
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− | * Ranjana working on disease-strain associations for WormBase
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− | * Disease group working on the DAF (disease association file) format
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− | * Ranjana will discuss the strain curation pipeline with Mary Ann and Karen
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− | * Will want a unique ID for each strain, especially for when we merge strain data with other MODs
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− | ** One solution is to just prefix the strain name with "WBStrain:" to indicate it came from WormBase
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− |
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− | === Kimberly visiting CA ===
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− | * Kimberly will be at CIT next Wednesday
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− | * Noctua developers will be around to discuss integration with Textpresso
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− | * Kimberly can send around schedule for the GO meeting
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− | * Would be good for curators to setup a Noctua account before the Noctua workshop (on Nov 7)
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− | * Kimberly will also be at CIT on Tuesday Nov 8th
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− |
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− | === Paper editor CGI ===
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− | * Michael had some issues with the paper editor
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− | * Seems to be working now
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| == November 3, 2016 == | | == November 3, 2016 == |