WormBase-Caltech Weekly Calls
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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"