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| [[WormBase-Caltech_Weekly_Calls_September_2020|September]] | | [[WormBase-Caltech_Weekly_Calls_September_2020|September]] |
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| + | [[WormBase-Caltech_Weekly_Calls_October_2020|October]] |
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− | == October 1, 2020 ==
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− | === Gene association file formats on FTP ===
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− | * For example, current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/
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− | * Our association files have format "*.wb"; is this useful or necessary?
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− | * Other than referring to GAF in the header, it isn't clear to users what the columns refer to or what the column headers should be
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− | * We could add a README file and/or convert to the new [https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md GAF 2.2 format] which would have a more expressive file header and possibly column headers(?)
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− | ** File headers could possibly link to the format specification page
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− |
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− | === Phenotype association file idiosyncrasy ===
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− | * As we've discussed previously, there is an oddity to how the phenotype association file we provide lists, or doesn't, references
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− | * According to the GAF spec, column 6 is for reference and is required, whereas column 8 is "With (or) From" and is optional
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− | * When we have a reference, the WBPaper ID is provided in column 6 and the WBVar ID or RNAi ID is provided in column 8
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− | * However, when we have no reference (personal communication, e.g. from NBP allele submissions), the WBVar ID is instead put in column 6 (because we need something there), and column 8 is blank.
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− | ** This results in (1) column 6 having a mix of paper/reference IDs (good) and WBVar IDs (not good) and (2) WBVar IDs split between column 6 and 8; thus making it tedious to parse this file
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− | * Proposed solution: Can we come up with some type of reference object ID to associate to the personal communications (or any annotations currently lacking a formal reference)?
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− | * With the proposed solution, we can always have a reference ID in column 6 (the intended purpose of the column) and WBVar IDs for alleles can always remain consistently in column 8
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− | * Proposal is to put WBPerson IDs in column 6 for personal communications. Chris & Karen will check if this will work.
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− |
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− | === Server space in Chen Building ===
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− | * It looks like that we will not have a specific space for server computers.
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| + | ==Nov 5th, 2020== |
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− | == October 8, 2020 ==
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− |
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− | === Webinar Announcement ===
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− | * Here is the live registration site: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/webinar.cgi
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− | * Caltech zoom allows 300 attendees.
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− |
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− | === Descriptions from GO-CAM models ===
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− | * One suggestion for the Alliance is to create a description based on a GO-CAM model
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− | * Could also micropublish some descriptions (semi-automated?)
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− | * Can make curators authors of micropublications for GO-CAM models/pathways
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− |
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− | === Transcription Factors in WormBase ===
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− | * WormBase has a ?Transcription_factor class that is currently underutilized
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− | * Chris spoke with Gary Williams about the status as he has done much of the work on the class
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− | * Because transcription factors can often be complexes, it was decided to create the ?Transcription_factor class rather than simply an extension of tags to the existing ?Gene class
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− | * The class seems reasonably complete; it's important to note that some TFs are general transcription factors, not necessarily gene-specific or sequence-specific DNA-binding TFs; it will be good to make that distinction clear to users
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− | * Chris has compiled a [https://docs.google.com/spreadsheets/d/1KdmvybWDWHXdlJwZgfleL4xHDoyPoYR13WAUcERF82g/edit?usp=sharing Google sheet] to assess the class before Gary W. leaves WB in the next couple of weeks
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− | * The Google sheet has several tabs/worksheets, including one for the ACEDB data model (and notes about usage of tags), a summary table of associated genes, bound sequence features, existence of other protein-DNA binding data, etc.
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− | * It would be good to make TF binding info (per gene and globally) more accessibly to our users, maybe via a new widget on gene pages (e.g. list incoming, regulating TFs and, for TF genes themselves, list potential target genes)
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− | == October 15, 2020 ==
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− |
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− | === BioGRID data sharing ===
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− | * Rose from BioGRID proposed that BioGRID curate high-throughput C. elegans interaction datasets, capturing confidence scores when available, and making those annotations available to WormBase for regular ingest
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− | * Will need to consider a few points:
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− | ** BioGRID doesn't curate protein-DNA interactions
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− | ** We don't yet know the turn-around timeline for BioGRID curation of worm datasets; WB may be able to curate them much sooner
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− | * Chris and Jae will work with Rose et al. to coordinate HTP curation
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− |
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− | === Enriched genes ===
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− | * Some genes are considered "enriched" for an expression cluster data set even if the enrichment was in comparison to another cell or tissue (not whole animal)
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− | * We should reconsider the ?Expression_cluster model to make sure we can appropriately model and communicate enrichment or subtypes thereof
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− | == October 22, 2020 ==
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− |
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− | === CHEBI ===
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− | * Karen spoke to CHEBI personnel on Tuesday
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− | * CHEBI only has ~2 curators to create new entities
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− | * CHEBI had submitted a proposal to establish pipelines to process requests from MODs
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− | * Chemical Translation Service (CTS)
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− | * OxO = https://www.ebi.ac.uk/spot/oxo/search
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− |
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− | === Training Webinar ===
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− | * Scheduled for tomorrow at 1pm Pacific/4pm Eastern
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− | == October 29, 2020 ==
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− |
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− | === Overview Webinar debriefing ===
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− | * What's Good
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− | * What needs improvement
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− | * Participant requests:
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− | A place to look for Worm methods (a public {moderated} wiki page?)
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− |
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− |
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− | === New alleles extraction pipeline ===
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− | * current pipeline (on textpresso-dev) is sending data to Sanger RT system, which is being retired
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− | * the plan is to build a new pipeline to send AFP-like alerts with new entities
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− | * current pipeline reads alleles data from GSA and gene lists from Sanger, but I (Valerio) would need help from curators to understand how to get these data
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− | ==Nov 5th, 2020==
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| ===WS279 GAF 2.0 and disease files=== | | ===WS279 GAF 2.0 and disease files=== |
| *Valerio and Ranjana still working with the GAF 2.0 files to generate gene descriptions | | *Valerio and Ranjana still working with the GAF 2.0 files to generate gene descriptions |