WormBase-Caltech Weekly Calls December 2020

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"