Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
= 2020 Meetings =
= 2020 Meetings =

Revision as of 16:58, 13 January 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2020 Meetings












2021 Meetings

January 14th, 2021

PubMed LinkOut to WormBase (Kimberly)

  • Other databases link out from PubMed to their respective paper pages
  • For exampel, https://pubmed.ncbi.nlm.nih.gov/20864032/ links out to GO and MGI paper pages
  • Would like to set this up for WormBase and ultimately for the Alliance, but this will require some developer help
  • Work on this next month (after AFP and GO grant submissions)?

Dec 3rd, 2020

Hench et al paper

  • Thomas Burglin would like the data from paper 00046864 to be included in WB
  • They want to provide APT profiles (signal intensity along the anterior-posterior axis over time) as images and movies (time lapse reporter expression)
  • They have recorded movies for 60 homeobox genes and over 85 genes in total.
  • If we decide to import the collection, movies, images, and description could be displayed as the collection from Murray: https://wormbase.org/species/all/expr_pattern/Expr10431#012--10

WormBase Papers and Alliance ABC - What papers to add?

  • PubMed keyword search 'elegans' (Approve, Reject, Remove)
  • Legacy papers from manual concise descriptions

PMID Paper Editor Action WBPaper ID Paper Title Species (For primary papers, species are those for which experiments are reported; does not include sequence alignments) Primary/Not Primary Other Paper Editor Flags Any SVM Positives Add to ABC Comments (1) Comments (2) Comments (3)
31761535 Approve 58971 The Hyaluronidase, TMEM2, Promotes ER Homeostasis and Longevity Independent of the UPR ER Homo sapiens, Caenorhabditis elegans Primary Author-Person Catalytic Activity; Genetic Interactions; Gene Regulation; New Mutant Phenotype; Overexpression Phenotype; RNAi Phenotype Yes
31868179 Approve 58999 Measuring the Effects of Bacteria and Chemicals on the Intestinal Permeability of Caenorhabditis elegans Caenorhabditis elegans Primary Author-Person None Yes
16919905 Approve 28426 The trifecta of aging in Caenorhabditis elegans. Caenorhabditis elegans Not-primary Author-Person N/A Yes
28744338 Approve 51561 Role of Kallistatin Treatment in Aging and Cancer by Modulating miR-34a and miR-21 Expression. Caenorhabditis elegans, Homo sapiens (human, humans), Mus musculus (mice, mouse), Rattus norvegicus (rats) Not-primary Author-Person N/A Yes
31875562 Reject None Intracellular Vesicle Fusion Requires a Membrane-Destabilizing Peptide Located at the Juxtamembrane Region of the v-SNARE Mus musculus (mouse), Rattus norvegicus (rat) Primary N/A N/A Not from WormBase, but if added from another group we'd want to indicate that it doesn't have C. elegans experimental data? Paper shows partial sequence alignment including C. elegans snb-1 in Figure 1A; other species in alignment include M. musculus, H. sapiens, X. leavis, and D. melanogaster PubMed indexes proteins and their respective species shown in sequence alignments
31569547 Reject None Mapping the Biotransformation of Coumarins through Filamentous Fungi Cunninghamella elegans, Aspergillus brasiliensis Primary N/A N/A No
10625658 Entry into WB pre-dated current paper editor 12789 Both PCE-1/RX and OTX/CRX interactions are necessary for photoreceptor-specific gene expression Homo sapiens (human), Mus musculus (mouse, mice, murine), Rattus norvegicus (rat, rats), Bos taurus(bovine) Primary non-nematode; Author-Person (pre-dated current Author-Person curation criteria) N/A Yes Used in legacy, manual ceh-8 gene description Used in human manual GO curation (Protein2GO) 492 non-nematode-flagged papers in WB; not systematically associated with species, but we could do that
N/A Entered into curation database via custom script 57497 The ER chaperone ENPL-1 acts outside the ER to promote insulin secretion in concert with oxidized ASNA-1. Caenorhabditis elegans Not designated Author-Person N/A Yes 2019 International Worm Meeting Abstract
  • /home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~3300 papers
  • /home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~100 papers
  • What about WormBase Parasite papers?

December 17, 2020

  • HGNC IDs/names/etc. in OA
  • What shows up in autocomplete? What shows up in term info?
  • Juancarlos will need to get curator preferences for autocomplete list and term info list.
  • Wen will update the Alliance Simplemine to provide updated info to Postgres/OA
    • "AGR Gene ID" and "AGR Gene Name" will be changed to "Gene ID", "Gene Name", "Gene Symbol"