Difference between revisions of "WormBase-Caltech Weekly Calls"

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== 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 ===
* 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 ===
* 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 ===
* 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 ===
* 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 [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 BioRXiv 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 ===
* 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,
<pre style="white-space: pre-wrap;
white-space: -moz-pre-wrap;
white-space: -pre-wrap;
white-space: -o-pre-wrap;
word-wrap: break-word">
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

Revision as of 14:01, 15 July 2019

Previous Years

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2014 Meetings

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GoToMeeting link: https://www.gotomeet.me/wormbase1

2019 Meetings







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

IWM workshop

  • Videos ready for upload
  • Wen and Raymond now have access to outreach@wormbase.org account; will upload videos

Protocol 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.