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| [[WormBase-Caltech_Weekly_Calls_May_2019|May]] | | [[WormBase-Caltech_Weekly_Calls_May_2019|May]] |
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| + | [[WormBase-Caltech_Weekly_Calls_June_2019|June]] |
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− | == June 6, 2019 ==
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− | === New SObA graphs === | + | == July 11th, 2019 == |
− | * May put graphs within existing widgets, but don't need to rush to get that ready for IWM
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− | === Phenotype association file format === | + | === Alliance all hands meeting === |
− | * May be best to leave the format as is | + | * Raymond: would be interested in discussing ontologies and their usage in the Alliance |
− | * There are problems; paper IDs keep switching columns | + | ** Phenotype, anatomy ontologies, GO, etc. |
− | * Would need to revisit the reasoning for why we do it that way | + | ** Ontology browsers, SObA |
− | * When will the Alliance produce a similar/replacement file? Not sure | |
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− | === Phenotype requests === | + | === IWM workshop === |
− | * Sent out 1140 emails on May 30 | + | * Videos ready for upload |
− | * Since have received 374 annotations from 54 papers (42 requested, 12 additional) | + | * Wen and Raymond now have access to outreach@wormbase.org account; will upload videos |
− | * 21 papers flagged as not having phenotypes
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− | * 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
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− | | + | === Protocol videos === |
− | == June 13, 2019 ==
| + | * Wen met Craig Mello at the IWM; he is interested in putting up microinjection videos online; linkable from WormBase? |
− | | + | * Can make each video a Video Weblog so people can make comments, etc. |
− | === IWM ===
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− | * Coordinating transportation of swag boxes to Pauley Pavilion
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− | * Workshop on Saturday June 22, from 1pm to 2:30pm
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− | * Saturday morning micropublication breakfast 7:30 - 8:30am
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− | * Workshop
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− | ** Presenters: it may be best to present as use cases rather than a research project | |
− | ** Chris will cover SimpleMine for Wen
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− | ** Chris: won't do live demo; only screenshots, maybe some video
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− | * Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
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− | * Paul's talk
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− | ** Cover Alliance
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− | ** New features
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− | *** SObA (for new data)
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− | *** Complete for protein-protein interactions
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− | *** RNASeq tools
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− | *** Updated automated gene concise descriptions?
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− | ** Phenotype community curation
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− | *** Chris will send Paul numbers on: top community curators, overall stats (number of annotations, papers, curators)
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− | ** Author First Pass
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− | ** Micropublication
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− | | |
− | === SGD SAB ===
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− | * Paul attended
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− | * Alliance publicity was discussed
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− | * SAB likes the Alliance orthology features
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− | * Working on topics: displaying papers and data
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− | * Pathways: discussion about best approach
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− | * Metabolic engineering
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− | * Meta data about RNASeq data
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− | ** SPELL tool, basically only tool of its kind available; need new tools
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− | * Species-specific proteins: how best to find them? HMMs (Jackhammer)?
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− | === Concise descriptions ===
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− | * Progress being made within the Alliance to update the automated concise gene descriptions
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− | * We will still accept manually written descriptions and display them in parallel with automated descriptions
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− | === Micropublications ===
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− | * If people are requesting manually written gene descriptions, they could submit a microreview
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− | * Concern was expressed about how to handle a really high throughput of submissions:
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− | ** Daniela: Working towards automating as much of the processing pipeline as possible
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− | ** Raymond: The throughput will be handled appropriately depending on demand; priority scheme will help
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− | ** Not getting lots of submissions yet, probably won't be inundated in the near future
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− | ** 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
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− | * Karen: Micropublications team will reach out to curators to help build submission forms for respective data types
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− | === Undiagnosed Disease Network data ===
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− | * Andy Golden will meet with Ranjana and Chris at IWM to discuss
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− | * Andy asked about protocol pages at WormBase?
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− | * Paul: Bioprotocols and Protocols IO
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− | * Maybe we could interface with those existing resources to link to relevant protocols from WormBase (and WormBook)
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− | ==June 27th, 2019==
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− | ===IWM 2019: Feedback from Users===
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− | * Anatomy term synonym search
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− | ** User pointed out that "RnB" search returns 0 results; GitHub ticket made to index anatomy synonyms
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− | * Ciliated neurons
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− | ** User pointed out that male ciliated neurons are missing as a subclass of term "ciliated neuron"; GitHub ticket made, easy fix
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− | * Import of 22G and 26G RNAs
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− | ** Spoke to Julie Claycomb
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− | ** These are short RNAs transcribed by RNA-dependent RNA Polymerase (RdRP) off of mRNA molecules
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− | ** Should these be instantiated as gene objects in WormBase? Julie argues that these are not genes
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− | *** 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?
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− | ** Many map uniquely to the genome, but some map in multiple locations
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− | ** Associated data for now would likely just be protein-RNA interactions (Argonaute-RNA interactions)
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− | *** May eventually include phenotype and/or gene ontology (biological process) annotations
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− | * Ranjana & Chris spoke with Andy Golden
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− | ** 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
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− | ** There is still a strong need for cross-species variant mapping/visualization
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− | * miRNA binding sites
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− | ** User asked at workshop and at booth; can we show miRNA binding sites in JBrowse? We would need to collect the data
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− | ** There are many sources of miRNA-target interactions, some experimental, most predicted
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− | *** Chris compiled [https://docs.google.com/spreadsheets/d/19-txXrGi-ROFuByyLnQYvWbKl3o12KZON56qto3MN6g/edit?usp=sharing list of interaction databases] for Alliance interactions working group
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− | * Ontology aware diffs of annotations (gene1 expression vs. gene2 expression)
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− | * Promoter sequence in experimental constructs
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− | * Workshop went well
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− | ** Next time, maybe have people bring laptops and follow along; be more interactive
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− | ** We could do webinars, for WormMine for example, allow people to work along with the presentation
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− | *** Do other MODs/groups do webinars? How have they been? Useful?
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− | ** Competing with other workshops during the IWM
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− | ** Can focus on new, less-used features for webinars, tutorial videos
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− | * Hawaiian genome in JBrowse
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− | * Had internet stability issues at UCLA; can we get a local, dedicated WiFi?
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− | * Next meeting (2021) will likely be in Europe (Cambridge UK?)
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− | * User at cGal workshop asked about tissue-specific promoters/transgenes
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− | ** 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)
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− | | |
− | === TAGC meeting ===
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− | * Next April (2020)
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− | * Alliance representation needed
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− | ===Giving disease model annotations a stable identifier===
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− | *Currently disease model annotations get a temporary ID at the time of dump,
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− | <pre style="white-space: pre-wrap;
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− | white-space: -moz-pre-wrap;
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− | white-space: -pre-wrap;
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− | white-space: -o-pre-wrap;
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− | word-wrap: break-word">
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− | Disease_model_annotation : "00000004"
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− | Disease_term "DOID:0050833"
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− | Disease_of_species "Homo sapiens"
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− | Variation "WBVar00275555"
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− | Disease_relevant_gene "WBGene00011559"
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− | Inferred_gene "WBGene00011559"
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− | Association_type "is_implicated_in"
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− | Evidence_code "IMP"
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− | Genetic_sex "hermaphrodite"
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− | Paper_evidence "WBPaper00035924"
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− | Database "OMIM" "gene" "613891 "
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− | Database "OMIM" "disease" "258900"
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− | Curator_confirmed "WBPerson324"
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− | Date_last_updated "2017-04-24"
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− | </pre>
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− | *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'
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− | *ID convention--is underscore allowed?
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− | *Is 'WBDisease_annotation:00000004' too long for acedb?
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− | * Need to ask Kevin, Hinxton; what are the other implications for maintaining and generating persistent, unique IDs
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− | === Anatomy ontology issues ===
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− | * Currently, "intestinal muscle" is considered "part of" intestine
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− | ** User asked for intestinally expressed genes; using WOBr would also retrieve genes in intestinal muscle
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− | ** David Hall confirmed that instestinal muscle cells are not part of intestine
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− | ** Maybe we can change to: "intestinal muscle" part_of "alimentary system"
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− | * Currently, "amphid process" is considered "part of" each type of amphid neuron like AWC, AFD, etc.
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− | ** Problem is that users looking in WOBr for AWC-expressed genes will be given genes expressed in ANY amphid process regardless of which cell
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− | ** Propose to change to: "amphid process" part_of "amphid neuron" only
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