WormBase-Caltech Weekly Calls
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- 1 Previous Years
- 2 2019 Meetings
- 2.1 June 6, 2019
- 2.2 June 13, 2019
- 2.3 June 27th, 2019
- 2.4 July 11th, 2019
GoToMeeting link: https://www.gotomeet.me/wormbase1
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
- 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
- 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
- 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
- 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)?
- 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
- 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 27th, 2019
IWM 2019: Feedback from Users
- Anatomy term synonym search
- 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 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 BioRXiv preprint (quick, before peer-review) and/or micropublication (after peer-review)
- Would be good to establish (for Alliance/WB) framework for serving protocols maintained by community
- Next April (2020)
- Alliance representation needed
Giving disease model annotations a stable identifier
- Currently disease model annotations get a temporary ID at the time of dump,
Disease_model_annotation : "00000004" 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"
- 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
- Currently, "intestinal muscle" is considered "part of" intestine
- User asked for intestinally expressed genes; using WOBr would also retrieve genes in intestinal muscle
- 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
July 11th, 2019
Alliance all hands meeting
- Raymond: would be interested in discussing ontologies and their usage in the Alliance
- Phenotype, anatomy ontologies, GO, etc.
- Ontology browsers, SObA
- Videos ready for upload
- Wen and Raymond now have access to firstname.lastname@example.org account; will upload videos
- 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.