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| [[WormBase-Caltech_Weekly_Calls_February_2020|February]] | | [[WormBase-Caltech_Weekly_Calls_February_2020|February]] |
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| + | [[WormBase-Caltech_Weekly_Calls_March_2020|March]] |
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− | == March 5, 2020 ==
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− | === WormBase curation === | + | == April 2, 2020 == |
− | * Tim Schedl: WB needs to do more curation for phenotype and variation
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− | * Doing community curation, but not fast enough
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− | * Would like to work on more automation; e.g. having Textpresso return all sentences mentioning an allele in papers that are predicted to have phenotype data
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− | === Alaksa ===
| + | === Community phenotype requests === |
− | * Joesph may be able to meet with Raymond
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− | * How can the tool be maintained? If it can't it needs to be pulled
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− | | |
− | === Single cell expression tool ===
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− | * Tool is here: http://de.wormcells.com/
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− | * What do we need to consider for pulling into WormBase?
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− | * Where does the data sit and how does the tool access it? Can we integrate the data more into WormBase (e.g. local curation databases)?
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− | ** Would want it to be in sync with WormBase releases
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− | ** May not need to reprocess with every release with current (small-ish) data set
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− | * Fully integrated tool versus an embedded tool?
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− | | |
− | === Name service updates ===
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− | * For now we will stick to the CGIs that Juancarlos has built for variations and strains
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− | * Juancarlos can discuss with Matt R. and Sibyl the possibility of integrating API requests to the Name service into a CGI form for the OA
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− | == March 12, 2020 ==
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− | === Cancelled meetings ===
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− | * Meetings are being cancelled, including Biocuration 2020. Ranjana will update our Wormbase meeting page with a note to users (done)
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− | * We should start doing online advertisement for micropublications with webinars
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− | | |
− | === Storing invalid/avoided WBPersons and email addresses in Postgres ===
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− | * Currently Chris has been maintaining ([https://docs.google.com/spreadsheets/d/1FHhQk_IZIBLYkOUdVf9Kfh5zx66rkHOEVFQQ6wzT2ks/edit?usp=sharing on Google sheets]) a list of papers, people, and email addresses to omit from future WormBase outreach requests
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− | * Valerio would like to add these to Postgres to keep a more central repository of them
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− | * Chris would still like to be able to readily update/edit the content of those lists
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− | | |
− | * Proposed solutions: Keep the list in a flat file and have a cron job to sync the data to postgres daily or create a simple form to create/modify entries directly in postgres
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− | | |
− | === Updates on Alaska ===
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− | Raymond and Eduardo met with Joseph and decided to have the tool running as is for now even though maintaining it can be hard
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− | The future plan is to move the platform to Google colab to reduce maintainance work.
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− | ==Nameservice discussion==
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− | *Getting a token has worked for Chris and Ranjana
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− | *Karen and Daniela need to get tokens
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− | ==Noctua GO-CAM updates==
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− | *Noctua is a production tool available for annotations right now
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− | *Create as many interconnected models and make available for curators is the ongoing goal
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− | *Reactome models are in the process of being imported
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− | *Real time validation messages as curation is being done, is being worked on
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− | *Kimberly will send out the details for logging into Noctua and make sure all curators are on the login list
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− | == March 19, 2020 ==
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− | === Citace Upload ===
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− | * Tuesday, March 31st
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− | | |
− | === Latest ACEDB ===
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− | * Getting latest ACEDB build from staging FTP (for descriptions, etc.)
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− | | |
− | === Storing email addresses/persons to omit from requests ===
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− | * Chris and Juancarlos will work on a form to submit email addresses and WBPerson IDs to Postgres
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− | | |
− | === Mailing lists ===
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− | * Let Todd know if you want to keep your caltech.edu account on the mailing lists
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− | ==March 26th==
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− | ===Community curation=== | |
− | *Do we need to publicize any data form and urge Users to contribute? The AFP and phenotype forms already send targeted e-mail
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− | * Paul S. is getting people from the lab to do phenotype curation; Chris G will run a tutorial for interested people
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− | * Blog about phenotype form to make people generally aware
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− | * Could the phenotype form be adapted for other species? Possibly but depends on:
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− | ** Whether genotypes could be loaded and recognized
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− | | |
− | === AFP for older papers ===
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− | * Discussed recently
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− | * Many (all?) Old papers have already gone through the old AFP pipeline
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− | * Need to check what has already been curated
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− | | |
− | === Omit form ===
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− | * http://tazendra.caltech.edu/~postgres/cgi-bin/omit_form.cgi
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− | * Can view, add, or edit persons, email addresses, and IP addresses to omit from email requests (and IP addresses to block)
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− | | |
− | === Problems accessing Textpresso Central ===
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− | * Ranjana had noticed that the server was acting slow
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− | * Unknown problem; hard to pin down
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− | * Definitely a Caltech network system
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− | * Issue for past couple of weeks
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− | * May be able to ask Caltech IMSS for a diagnostic analysis
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− | * Bad switch? Maybe; there is an unused switch that could be used to test
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− | ** Maybe should dedicate an ethernet socket to the server(s) (avoiding switch altogether)
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− | * Tazendra is good, mangolassi seems to have had some trouble recently as well
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− | * All on subnet 52; Raymond has been monitoring and seems to be working well; could suggest a local (e.g. computer-specific, switch-specific) issue
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− | | |
− | === Automated concise pathway descriptions? ===
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− | * Could we generate pathway descriptions based on, for example, GO-CAM models?
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− | * Might be straightforward if clear guidelines can be documented (important players/genes, important/central functions/processes)
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− | | |
− | === Genotype OA on Sandbox ===
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− | * http://mangolassi.caltech.edu/~postgres/cgi-bin/oa/ontology_annotator.cgi
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− | * Take a look and send feedback to Juancarlos and Chris
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− | | |
− | === Name Service temp submission for strain and variation to Postgres ===
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− | * Sandbox: http://mangolassi.caltech.edu/~postgres/cgi-bin/temp_objects.cgi
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− | * Adding strains or variations will create the object in the Name Service as well as add it to Postgres
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− | * Test it and make sure it works; NOTE: Creating objects on both Mangolassi AND Tazendra will create real object entries in the Name Service; if testing on the Sandbox, make sure to tell Paul Davis and Matt Russell to remove test submissions from the Name Service
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