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| | [[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]] | | [[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]] |
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| − | = 2020 Meetings =
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| − | [[WormBase-Caltech_Weekly_Calls_January_2020|January]]
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| − | [[WormBase-Caltech_Weekly_Calls_February_2020|February]]
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| − | [[WormBase-Caltech_Weekly_Calls_March_2020|March]]
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| − | [[WormBase-Caltech_Weekly_Calls_April_2020|April]]
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| − | [[WormBase-Caltech_Weekly_Calls_May_2020|May]]
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| − | [[WormBase-Caltech_Weekly_Calls_June_2020|June]]
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| − | [[WormBase-Caltech_Weekly_Calls_July_2020|July]]
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| − | [[WormBase-Caltech_Weekly_Calls_August_2020|August]]
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| − | [[WormBase-Caltech_Weekly_Calls_September_2020|September]]
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| − | [[WormBase-Caltech_Weekly_Calls_October_2020|October]]
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| − | [[WormBase-Caltech_Weekly_Calls_November_2020|November]]
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| | * Would like to set this up for WormBase and ultimately for the Alliance, but this will require some developer help | | * 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)? | | * Work on this next month (after AFP and GO grant submissions)? |
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| − | ==Dec 3rd, 2020==
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| − | === Hench et al paper ===
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| − | * Thomas Burglin would like the data from paper 00046864 to be included in WB
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| − | * They want to provide APT profiles (signal intensity along the anterior-posterior axis over time) as images and movies (time lapse reporter expression)
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| − | * They have recorded movies for 60 homeobox genes and over 85 genes in total.
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| − | * 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
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| − |
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| − | === WormBase Papers and Alliance ABC - What papers to add? ===
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| − |
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| − | * PubMed keyword search 'elegans' (Approve, Reject, Remove)
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| − | * Legacy papers from manual concise descriptions
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| − |
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| − |
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| − | {| border=1 cell-padding=5 cell-spacing=10
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| − | |-
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| − | ! PMID
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| − | ! Paper Editor Action
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| − | ! WBPaper ID
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| − | ! Paper Title
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| − | ! Species (For primary papers, species are those for which experiments are reported; does not include sequence alignments)
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| − | ! Primary/Not Primary
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| − | ! Other Paper Editor Flags
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| − | ! Any SVM Positives
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| − | ! Add to ABC
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| − | ! Comments (1)
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| − | ! Comments (2)
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| − | ! Comments (3)
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| − | |-
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| − | | 31761535
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| − | | Approve
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| − | | 58971
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| − | | The Hyaluronidase, TMEM2, Promotes ER Homeostasis and Longevity Independent of the UPR ER
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| − | | Homo sapiens, Caenorhabditis elegans
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| − | | Primary
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| − | | Author-Person
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| − | | Catalytic Activity; Genetic Interactions; Gene Regulation; New Mutant Phenotype; Overexpression Phenotype; RNAi Phenotype
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| − | | Yes
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| − | |
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| − | |
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| − | |
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| − | |-
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| − | | 31868179
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| − | | Approve
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| − | | 58999
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| − | | Measuring the Effects of Bacteria and Chemicals on the Intestinal Permeability of Caenorhabditis elegans
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| − | | Caenorhabditis elegans
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| − | | Primary
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| − | | Author-Person
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| − | | None
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| − | | Yes
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| − | |
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| − | |
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| − | |
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| − | |-
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| − | | 16919905
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| − | | Approve
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| − | | 28426
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| − | | The trifecta of aging in Caenorhabditis elegans.
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| − | | Caenorhabditis elegans
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| − | | Not-primary
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| − | | Author-Person
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| − | | N/A
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| − | | Yes
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| − | |
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| − | |
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| − | |
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| − | |-
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| − | | 28744338
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| − | | Approve
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| − | | 51561
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| − | | Role of Kallistatin Treatment in Aging and Cancer by Modulating miR-34a and miR-21 Expression.
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| − | | Caenorhabditis elegans, Homo sapiens (human, humans), Mus musculus (mice, mouse), Rattus norvegicus (rats)
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| − | | Not-primary
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| − | | Author-Person
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| − | | N/A
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| − | | Yes
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| − | |
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| − | |
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| − | |
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| − | |-
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| − | | 31875562
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| − | | Reject
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| − | | None
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| − | | Intracellular Vesicle Fusion Requires a Membrane-Destabilizing Peptide Located at the Juxtamembrane Region of the v-SNARE
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| − | | Mus musculus (mouse), Rattus norvegicus (rat)
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| − | | Primary
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| − | | N/A
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| − | | N/A
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| − | | Not from WormBase, but if added from another group we'd want to indicate that it doesn't have C. elegans experimental data?
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| − | | 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
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| − | | PubMed indexes proteins and their respective species shown in sequence alignments
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| − | |
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| − | |-
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| − | | 31569547
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| − | | Reject
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| − | | None
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| − | | Mapping the Biotransformation of Coumarins through Filamentous Fungi
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| − | | Cunninghamella elegans, Aspergillus brasiliensis
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| − | | Primary
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| − | | N/A
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| − | | N/A
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| − | | No
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| − | |
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| − | |
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| − | |
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| − | |-
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| − | | 10625658
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| − | | Entry into WB pre-dated current paper editor
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| − | | 12789
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| − | | Both PCE-1/RX and OTX/CRX interactions are necessary for photoreceptor-specific gene expression
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| − | | Homo sapiens (human), Mus musculus (mouse, mice, murine), Rattus norvegicus (rat, rats), Bos taurus(bovine)
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| − | | Primary
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| − | | non-nematode; Author-Person (pre-dated current Author-Person curation criteria)
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| − | | N/A
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| − | | Yes
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| − | | Used in legacy, manual ceh-8 gene description
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| − | | Used in human manual GO curation (Protein2GO)
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| − | | 492 non-nematode-flagged papers in WB; not systematically associated with species, but we could do that
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| − | |-
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| − | | N/A
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| − | | Entered into curation database via custom script
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| − | | 57497
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| − | | The ER chaperone ENPL-1 acts outside the ER to promote insulin secretion in concert with oxidized ASNA-1.
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| − | | Caenorhabditis elegans
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| − | | Not designated
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| − | | Author-Person
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| − | | N/A
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| − | | Yes
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| − | | 2019 International Worm Meeting Abstract
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| − | |
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| − | |
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| − | |-
| |
| − | |}
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| − |
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| − | */home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~3300 papers
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| − | */home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~100 papers
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| − |
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| − | *What about WormBase Parasite papers?
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| − |
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| − |
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| − | == December 17, 2020 ==
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| − | * HGNC IDs/names/etc. in OA
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| − | * What shows up in autocomplete? What shows up in term info?
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| − | * Juancarlos will need to get curator preferences for autocomplete list and term info list.
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| − | * Wen will update the Alliance Simplemine to provide updated info to Postgres/OA
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| − | ** "AGR Gene ID" and "AGR Gene Name" will be changed to "Gene ID", "Gene Name", "Gene Symbol"
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