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| | [[WormBase-Caltech_Weekly_Calls_March_2017|March]] | | [[WormBase-Caltech_Weekly_Calls_March_2017|March]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_April_2017|April]] |
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| − | == April 6, 2017 ==
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| − |
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| − | === AGR time spent ===
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| − | * Paul S asking about %time spent on AGR project
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| − | * Time spent on working groups, conference calls, AGR development
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| − | * Send estimates to Paul
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| − |
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| − | === SimpleMine ===
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| − | * Two tables added to SimpleMine for human orthology
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| − | * Now SimpleMine output has many columns (30+)
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| − | * We may want to give users the option to specify which output they want
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| − | * Users could specify groups of data (with checkboxes): gene IDs/names, phenotypes, orthology, etc.
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| − | * All checkboxes can be checked by default
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| − |
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| − | === Enrichment tools ===
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| − | * Raymond working on display for paper
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| − |
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| − | === Gene Ontology SObA graph ===
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| − | * Raymond, Juancarlos working on
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| − | * Working on paper
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| − |
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| − | === WormMine updates ===
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| − | * WS258 adding gene class
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| − | * WS259 adding more info (almost all meta data) on variations, laboratory and strains, RNAi phenotypes (hopefully)
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| − | * Expression data in WormMine is problematic
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| − | * Many genes being annotated to the same ~6 tissues or so
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| − | * Resulting in erroneous data for some genes
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| − | * Chris will send GitHub ticket to Todd
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| − | * Todd will discuss with Paulo today
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| − |
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| − | === Gene Ontology ===
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| − | * Some very complex terms becoming immediate children of root terms (e.g. "biological process")
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| − | * May be result of attempt to create logical definitions/equivalence axioms
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| − | * Raymond will discuss with Kimberly
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| − |
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| − |
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| − | == April 13, 2017 ==
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| − |
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| − | === Methods in Molecular Biology chapter ===
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| − | * Chapter draft sent out Monday night
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| − | * Will send to Martin at MiMB by late next week
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| − | * Please take a look and send comments
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| − | * Authors check their sections and send figure legends to Chris
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| − |
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| − | === Progress report ===
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| − | * If someone finds the 2016 report, send around to group
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| − | * May 1st deadline (need to verify)
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| − |
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| − | === 2017 IWM ===
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| − | * Early registration Deadline May 18th
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| − |
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| − | === Models for citace ===
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| − | * Wen will fit models to local citace, should be ready by tomorrow
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| − |
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| − | === Citace Upload ===
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| − | * Tuesday, April 25th, 10am
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| − |
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| − | === Enrichment tool ===
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| − | * Now available for gene ontology and phenotype on live site
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| − | * Paper being submitted soon
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| − | * Need to change "Tissue Enrichment Analysis" link title under WormBase Tools menu
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| − |
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| − | === SObA for Gene Ontology ===
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| − | * Data source was server on Berkeley BOP; thought it was public but were discouraged to use
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| − | * Seth Carbon said we could use it but might not always be working; now it seems to be down or dysfunctional
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| − | * SObA for GO will be broken until we install our own local server (Raymond working on)
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| − |
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| − | === Dumping data for upload, taking over for Karen ===
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| − | * Karen will take care of dumping and uploading the data for this upload
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| − | * Karen will review the molecule curation with other curators at the IWM
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| − |
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| − | === Datomic meeting ===
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| − | * Matt, Sibyl, Adam, Todd, Juancarlos, Raymond sat in
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| − | * Raymond: thought Datomic would take over from ACEDB completely, but it seems we will still use ACEDB for some time for e.g. FMap
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| − | * Seems there should be an executive meeting about Datomic to make clear what it will be used for and what it won't be used for
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| − | * Several web pages and widgets are now being served by Datomic
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| − | * There's a question about how we now handle model changes going forward
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| − | * Juancarlos will send around link for newest Datomic querying tool; may require access for specific IP addresses
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| − |
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| − |
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| − | == April 20, 2017 ==
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| − |
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| − | === Gene Ontology data for SObA ===
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| − | * Use of GO server; hasn't been reliable
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| − | * Raymond working on establishing our own server to host all GO data
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| − | * Raymond and Juancarlos will keep working on SObA representation of GO annotations
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| − |
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| − | === Progress Report ===
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| − | * WS259 can be used as the current reference
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| − | * Paul will send around last year's progress report
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| − | * What was the last release that we referenced in last year's progress report? We'll say WS254
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| − | * Wen will generate numbers for WS254 (resurrect WS254 ACEDB)
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| − | * Opportunity to specify/narrow scope of project
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| − | * Want to push community/automated curation, with curators laying foundation of data models, forms
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| − | * Promote LEGO curation; need to learn what needs to be said about plan going forward/what we want to accomplish
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| − |
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| − | === LEGO curation ===
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| − | * Phenotype curation in LEGO? Need to review phenotype-to-GO pipeline
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| − | * Want/need a mapping of phenotype terms to GO process terms; may require context-dependent mapping (e.g. "dumpy" phenotype)
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| − | * We don't make direct associations of phenotypes to LEGO models, although we do have "inferred from mutant phenotype" evidence code
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| − | * Want a mechanism to automate conversion of WB annotations into LEGO models
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| − | * Want a display mechanism that is user friendly, convert hairball into pathway
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| − | * We could focus on a particular topic/disease and collectively contribute
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| − | * Do we want to write a proposal to take existing, granular annotations (e.g. at level of mutation details) and map to LEGO model?
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| − | * Can we integrate the micropublication pipeline into LEGO model generation?
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| − | * How to assess the confidence of assertions?
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| − |
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| − | === Follow up on transgene question from user ===
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| − | * Karen will contact authors of paper
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| − |
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| − | === Citace upload ===
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| − | * Tuesday, Apr 25th, 10am
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| − |
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| − |
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| − |
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| − | == April 27, 2017 ==
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| − |
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| − | === Gene Ontology data for SObA ===
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| − | * All GO annotation data loaded at Caltech (bigGO solr database, 54GB)
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| − | * 100 species, 922296 bioentity (protein, gene product ...)
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| − | * [http://131.215.12.204/~raymond/cgi-bin/soba_biggo.cgi Testing site], try
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| − | let-23, KRas (human)
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| − | eat-4, SLC17A7 (human)
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| − | * Heavy querying may cause the server to go down; need to check why
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| − | * ~7 hours to load
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| − | * Can there be an option to specify a GO term and zoom in to that portion of the graph?
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| − | * Implement a GO-Slim browsing functionality?
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| − | * MGI has tissue=stage matrix, good for drilling down the annotations by the ontology/hierarchy:
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| − | ** http://www.informatics.jax.org/gxd/marker/MGI:88351?tab=stagegridtab#gxd=markerMgiId%3DMGI%3A88351%26theilerStage%3D%26assayType%3D%26results%3D100%26startIndex%3D0%26sort%3D%26dir%3Dasc%26tab%3Dstagegridtab
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| − | * Matrix is a nice complement to the SObA graph when the graph is very complex
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| − | * Would be nice to have a term or branch search to draw attention to relevant section of graph
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| − | * Would we want faceted search of species? Maybe, but may not be necessary for only 100 species
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| − | * Can put focus species (AGR species?) at the top, rest alphabetical
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| − | * Pie chart representation, comparative view of different species/taxa, each pie "slice" represents number of annotations from that species
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| − | * We could filter on experimental evidence codes (in addition to IEA filter)
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| − |
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| − | === AGR lexica ===
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| − | * Karen's SBIR, trying to get gene names from each AGR database
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| − | * Non-trivial, in some cases, to query out curated papers list
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| − |
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| − | === Micropublications ===
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| − | * Call for gene expression micropublications
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| − | * Blog post
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| − | * Working on micropublication booklet to distribute at IWM
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| − |
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| − | === Methods in Molecular Biology chapter ===
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| − | * Submitted last Friday
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| | | | |
| | == May 4, 2017 == | | == May 4, 2017 == |
