|
|
(389 intermediate revisions by 12 users not shown) |
Line 18: |
Line 18: |
| | | |
| [[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]] | | [[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]] |
| + | |
| + | [[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]] |
| | | |
| | | |
| GoToMeeting link: https://www.gotomeet.me/wormbase1 | | GoToMeeting link: https://www.gotomeet.me/wormbase1 |
| | | |
| + | = 2020 Meetings = |
| | | |
− | = 2019 Meetings =
| + | [[WormBase-Caltech_Weekly_Calls_January_2020|January]] |
− | | |
− | [[WormBase-Caltech_Weekly_Calls_January_2019|January]] | |
− | | |
− | [[WormBase-Caltech_Weekly_Calls_February_2019|February]]
| |
− | | |
− | [[WormBase-Caltech_Weekly_Calls_March_2019|March]]
| |
− | | |
− | [[WormBase-Caltech_Weekly_Calls_April_2019|April]]
| |
− | | |
− | [[WormBase-Caltech_Weekly_Calls_May_2019|May]]
| |
− | | |
− | | |
− | == June 6, 2019 ==
| |
− | | |
− | === New SObA graphs ===
| |
− | * May put graphs within existing widgets, but don't need to rush to get that ready for IWM
| |
− | | |
− | === Phenotype association file format ===
| |
− | * May be best to leave the format as is
| |
− | * There are problems; paper IDs keep switching columns
| |
− | * Would need to revisit the reasoning for why we do it that way
| |
− | * When will the Alliance produce a similar/replacement file? Not sure
| |
− | | |
− | === Phenotype requests ===
| |
− | * Sent out 1140 emails on May 30
| |
− | * Since have received 374 annotations from 54 papers (42 requested, 12 additional)
| |
− | * 21 papers flagged as not having phenotypes
| |
− | * Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week
| |
− | | |
− | | |
− | == June 13, 2019 ==
| |
| | | |
− | === IWM ===
| + | [[WormBase-Caltech_Weekly_Calls_February_2020|February]] |
− | * Coordinating transportation of swag boxes to Pauley Pavilion
| |
− | * Workshop on Saturday June 22, from 1pm to 2:30pm
| |
− | * Saturday morning micropublication breakfast 7:30 - 8:30am
| |
− | * Workshop
| |
− | ** Presenters: it may be best to present as use cases rather than a research project
| |
− | ** Chris will cover SimpleMine for Wen
| |
− | ** Chris: won't do live demo; only screenshots, maybe some video
| |
− | * Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
| |
− | * Paul's talk
| |
− | ** Cover Alliance
| |
− | ** New features
| |
− | *** SObA (for new data)
| |
− | *** Complete for protein-protein interactions
| |
− | *** RNASeq tools
| |
− | *** Updated automated gene concise descriptions?
| |
− | ** Phenotype community curation
| |
− | *** Chris will send Paul numbers on: top community curators, overall stats (number of annotations, papers, curators)
| |
− | ** Author First Pass
| |
− | ** Micropublication
| |
| | | |
− | === SGD SAB ===
| + | [[WormBase-Caltech_Weekly_Calls_March_2020|March]] |
− | * Paul attended
| |
− | * Alliance publicity was discussed
| |
− | * SAB likes the Alliance orthology features
| |
− | * Working on topics: displaying papers and data
| |
− | * Pathways: discussion about best approach
| |
− | * Metabolic engineering
| |
− | * Meta data about RNASeq data
| |
− | ** SPELL tool, basically only tool of its kind available; need new tools
| |
− | * Species-specific proteins: how best to find them? HMMs (Jackhammer)?
| |
| | | |
− | === Concise descriptions ===
| + | [[WormBase-Caltech_Weekly_Calls_April_2020|April]] |
− | * Progress being made within the Alliance to update the automated concise gene descriptions
| |
− | * We will still accept manually written descriptions and display them in parallel with automated descriptions
| |
| | | |
− | === Micropublications ===
| + | [[WormBase-Caltech_Weekly_Calls_May_2020|May]] |
− | * If people are requesting manually written gene descriptions, they could submit a microreview
| |
− | * Concern was expressed about how to handle a really high throughput of submissions:
| |
− | ** Daniela: Working towards automating as much of the processing pipeline as possible
| |
− | ** Raymond: The throughput will be handled appropriately depending on demand; priority scheme will help
| |
− | ** Not getting lots of submissions yet, probably won't be inundated in the near future
| |
− | ** Karen: tools are still being developed; the platform is not being advertised as much as it could be; will ramp up outreach and communication once tools are in place to handle more submissions
| |
− | * Karen: Micropublications team will reach out to curators to help build submission forms for respective data types
| |
| | | |
− | === Undiagnosed Disease Network data ===
| |
− | * Andy Golden will meet with Ranjana and Chris at IWM to discuss
| |
− | * Andy asked about protocol pages at WormBase?
| |
− | * Paul: Bioprotocols and Protocols IO
| |
− | * Maybe we could interface with those existing resources to link to relevant protocols from WormBase (and WormBook)
| |
| | | |
| + | == June 4, 2020 == |
| | | |
− | ==June 27th, 2019== | + | === Citace (tentative) upload === |
− | ===IWM 2019: Feedback from Users===
| + | * CIT curators upload to citace on Tuesday, July 7th, 10am Pacific |
− | * Anatomy term synonym search | + | * Citace upload to Hinxton on Friday, July 10th |
− | ** User pointed out that "RnB" search returns 0 results; GitHub ticket made to index anatomy synonyms
| |
− | * Ciliated neurons
| |
− | ** User pointed out that male ciliated neurons are missing as a subclass of term "ciliated neuron"; GitHub ticket made, easy fix
| |
− | * Import of 22G and 26G RNAs
| |
− | ** Spoke to Julie Claycomb
| |
− | ** These are short RNAs transcribed by RNA-dependent RNA Polymerase (RdRP) off of mRNA molecules
| |
− | ** Should these be instantiated as gene objects in WormBase? Julie argues that these are not genes
| |
− | *** Should these just be transcript objects? Would they be linked to a gene? Or maybe also to any transcripts from which they could be derived?
| |
− | ** Many map uniquely to the genome, but some map in multiple locations
| |
− | ** Associated data for now would likely just be protein-RNA interactions (Argonaute-RNA interactions)
| |
− | *** May eventually include phenotype and/or gene ontology (biological process) annotations
| |
− | * Ranjana & Chris spoke with Andy Golden
| |
− | ** Andy and his lab will submit phenotype and disease data as they become available (likely pre-publication); we will likely point to a consortium as source until paper is published
| |
− | ** There is still a strong need for cross-species variant mapping/visualization
| |
− | * miRNA binding sites
| |
− | ** User asked at workshop and at booth; can we show miRNA binding sites in JBrowse? We would need to collect the data
| |
− | ** There are many sources of miRNA-target interactions, some experimental, most predicted
| |
− | *** Chris compiled [https://docs.google.com/spreadsheets/d/19-txXrGi-ROFuByyLnQYvWbKl3o12KZON56qto3MN6g/edit?usp=sharing list of interaction databases] for Alliance interactions working group
| |
− | * Ontology aware diffs of annotations (gene1 expression vs. gene2 expression)
| |
− | * Promoter sequence in experimental constructs
| |
− | * Workshop went well
| |
− | ** Next time, maybe have people bring laptops and follow along; be more interactive
| |
− | ** We could do webinars, for WormMine for example, allow people to work along with the presentation | |
− | *** Do other MODs/groups do webinars? How have they been? Useful?
| |
− | ** Competing with other workshops during the IWM
| |
− | ** Can focus on new, less-used features for webinars, tutorial videos
| |
− | * Hawaiian genome in JBrowse
| |
− | * Had internet stability issues at UCLA; can we get a local, dedicated WiFi?
| |
− | * Next meeting (2021) will likely be in Europe (Cambridge UK?)
| |
− | * User at cGal workshop asked about tissue-specific promoters/transgenes
| |
− | ** Have ~30 drivers and ~30 effectors; will WB take them in unpublished? Could make BioRChiv preprint (quick, before peer-review) and/or micropublication (after peer-review)
| |
− | * Protocols
| |
− | ** Would be good to establish (for Alliance/WB) framework for serving protocols maintained by community
| |
| | | |
− | === TAGC meeting === | + | === Caltech reopening === |
− | * Next April (2020) | + | * Paul looking to get plan approved |
− | * Alliance representation needed | + | * People that want to come to campus need to watch training video |
| + | * Masks available in Paul's lab |
| + | * Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room |
| + | ** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart |
| + | * Need to coordinate, maybe make a Google calendar to do so (also Slack) |
| + | * Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form |
| + | * Also, need to submit who you were in contact with for contact tracing |
| + | * Form is used all week, and hold on to it until asked to be submitted |
| + | * If someone goes in to the office, they could print several forms for people to pick up in WB offices |
| | | |
− | ===Giving disease model annotations a stable identifier=== | + | === Nameserver === |
− | *Currently disease model annotations get a temporary ID at the time of dump, | + | * Nameserver was down |
− | <pre style="white-space: pre-wrap;
| + | * CIT curators would still like to have a single form to interact with |
− | white-space: -moz-pre-wrap;
| + | * Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea |
− | white-space: -pre-wrap;
| + | * Still putting genotype and all info for a strain in the reason/why field in the nameserver |
− | white-space: -o-pre-wrap;
| + | * We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out |
− | word-wrap: break-word">
| + | * Hinxton is pulling in CGC strains, how often? |
− | Disease_model_annotation : "00000004"
| + | * Caltech could possibly get a block of IDs |
− | Disease_term "DOID:0050833"
| |
− | Disease_of_species "Homo sapiens"
| |
− | Variation "WBVar00275555"
| |
− | Disease_relevant_gene "WBGene00011559"
| |
− | Inferred_gene "WBGene00011559"
| |
− | Association_type "is_implicated_in"
| |
− | Evidence_code "IMP"
| |
− | Genetic_sex "hermaphrodite"
| |
− | Paper_evidence "WBPaper00035924"
| |
− | Database "OMIM" "gene" "613891 "
| |
− | Database "OMIM" "disease" "258900"
| |
− | Curator_confirmed "WBPerson324"
| |
− | Date_last_updated "2017-04-24"
| |
− | </pre>
| |
− | *Would like to institute stable identifiers across releases, so the plan is to call these objects, 'WBDisease_annotation:<number>', so then the above identifier would become 'WBDisease_annotation:00000004', or 'WBDiseaseannot:00000004' or 'WBDiseaseAnnot:00000004' | |
− | *ID convention--is underscore allowed?
| |
− | *Is 'WBDisease_annotation:00000004' too long for acedb? | |
− | * Need to ask Kevin, Hinxton; what are the other implications for maintaining and generating persistent, unique IDs | |
| | | |
− | === Anatomy ontology issues === | + | === Alliance SimpleMine === |
− | * Currently, "intestinal muscle" is considered "part of" intestine | + | * Any updates? 3.1 feature freeze is tomorrow |
− | ** User asked for intestinally expressed genes; using WOBr would also retrieve genes in intestinal muscle | + | * Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call |
− | ** David Hall confirmed that instestinal muscle cells are not part of intestine
| |
− | ** Maybe we can change to: "intestinal muscle" part_of "alimentary system"
| |
− | * Currently, "amphid process" is considered "part of" each type of amphid neuron like AWC, AFD, etc.
| |
− | ** Problem is that users looking in WOBr for AWC-expressed genes will be given genes expressed in ANY amphid process regardless of which cell
| |
− | ** Propose to change to: "amphid process" part_of "amphid neuron" only
| |