Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[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]]
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[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
 
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[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
 
−
 
 
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[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 
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[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 
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[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
 
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[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
 
−
 
 
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[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
 
  
−
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
−
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
 +
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
−
== October 3, 2019 ==
 
  
−
=== SObA comparison graphs ===
 
−
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
 
−
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
 
−
** [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1 Example comparison between lin-3 and let-23]
 
−
* [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 2]
 
−
** [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1) Example comparison between lin-3 and let-23]
 
−
* What information does a user most care about?
 
−
# What terms (nodes) are annotated to gene 1 and what terms to gene 2
 
−
# For a given term, what is the relative number of annotations between gene 1 and gene 2.
 
−
# For a given node, what is the relative number of annotations each gene has to the total annotations of that gene.
 
−
* # 3 is actually what we applied to size the nodes in the single-gene version of SObA. Thus, not surprisingly, I think it is important.
 
−
* Generally people like Prototype 2 as a default view; we could possibly have a toggle to see the other view
 
−
* In either case users need a good legend and/or documentation
 
−
* Jae, it would be good if a user could specifically highlight nodes specific to each gene and gray-out or de-emphasize the common nodes
 
  
−
=== Germ line discussion ===
+
== May 7, 2020 ==
−
* Currently, the anatomy ontology has "germ line" as a type of "Cell" and a type of "Tissue", and "germ cell" as a type of "germ line"
 
−
* Chris would like to (1) remove "germ line" from under "Cell" and leave it under "Tissue" and (2) move "germ cell" out from under "germ line" and place directly under "Cell"
 
−
** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request]
 
−
* Chris will update pull request to include a change to move "germline precursor cell" out from under "germ line" and place it under "Cell" (done)
 
  
−
=== Script to remove blank entries from Postgres ===
+
=== Alliance COVID Page ===
−
* Chris stumbled across several entries in the OA that were blank (empty strings) or consisted of only whitespace, some of which were causing errors upon upload to ACEDB
+
* Available on stage
−
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
+
* Textpresso for Coronavirus up for testing
−
* Does anyone object to removing these entries throughout Postgres?
 
−
* Juancarlos will remove all the empty fields identified by his script
 
  
 +
=== SimpleMine at Alliance ===
 +
* Still some confusion about what it is
 +
* Will try to help clarify on PI meeting on Friday
  
−
== October 10, 2019 ==
+
=== Development environment for Alliance work ===
 +
* Raymond and Juancarlos have been working on
 +
* Existing hardware is strained; set up virtual machine
 +
* Still some technical issues
  
−
=== Biocuration 2020 ===
+
=== Open Publishing Festival ===
−
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
+
* Later this month
−
* Dates: Sunday May 17th to Wednesday May 20th, 2020
+
* Micropublications involved
−
* Will have 3rd POTATO workshop
+
* Organized by the Collaborative Knowledge Foundation
−
* [https://www.jax.org/education-and-learning/education-calendar/2020/05-may/biocuration-2020-conference Meeting website]
+
* Will involve publishers of books, journals, etc.
−
* Key Dates
+
* Will have a MOD-focused event, would be good to have WB curators participate/attend
−
** October 31, 2019 - Paper Submission Deadline
+
* Open to all
−
** January 24, 2020 - Abstract  and Workshop Submission Deadline
 
−
** March 6, 2020 - Notification of Acceptance
 
−
** April 6, 2020 - Early Bird Registration Ends
 
−
** May 8, 2020 - Registration Deadline
 
−
* Academic ISB Member, early bird registration fee is $250
 
−
* Author First Pass form paper, submitting to Database, biocuration issue (managed by biocuration group); authors have an opportunity to present at Biocuration conference
 
  
−
=== ICBO 2020 ===
+
=== Genotype class ===
−
* International Conference on Biomedical Ontologies
+
* Ranjana finished populating the Genotype OA with genotypes needed for disease curation
−
* [https://icbo2020.inf.unibz.it/ Meeting website]
+
* Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
−
* Held in Bozen-Bolzano, Italy
+
* There could end up being a discrepancy between an original or published name of a genotype and the components that are inferred by WormBase
−
* 16 - 19 September 2020
+
* Would be good to be clear/transparent about which components were automatically inferred
  
−
=== SObA comparison tool ===
+
=== WS277/278 ===
−
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
+
* Pipelines are pushed back by about 14 days/2 weeks
  
−
=== Textpresso derived paper connections ===
 
−
* For example for strains and constructs, maybe anatomy terms?
 
−
* May want to flag Textpresso predictions (as opposed to manually connected)
 
−
* Couple of options:
 
−
** 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
 
−
** 2) Not part of database build, but make associations live (using RESTful API to link out to Textpresso and submit search with URL) using Textpresso with links to Textpresso and Textpresso results, giving users chance to see context of matches in sentences at the Textpresso site
 
−
*** A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
 
−
*** Do a diff so that Textpresso pulls up only additional papers (not already associated)?
 
−
** 3) Could populate WB page with connections made through a Textpresso API call (could cache results? maybe, but might as well choose 1st option?)
 
−
* Transgene pipeline:
 
−
** Arun wrote script, matching transgene names (using regex; Is and Si transgenes) to papers, automatically populate OA
 
−
** Another script, captures Ex transgenes as well, automatically connects to construct objects
 
−
** WB only displays verified papers; unverified (predicted) associations are not dumped
 
−
* Could integrate author verification as part of AFP pipeline, even for older papers? Would we want to re-request AFP results for authors that have already replied in the past? Probably not
 
−
* Could embed AFP predictions in WB display with link to AFP form for authors (and others?) to verify, via logged-in users? Or via a validation token sent via email?
 
−
* Chris will make GitHub ticket to ask WB web team to add a link to Textpresso search from References widget on respective page; will require a Textpresso URL constructor
 
−
* Can apply to: genes, transgenes, constructs, strains, alleles, AFP-vetted entities
 
  
 +
==May 13, 2020==
  
−
== October 17, 2019 ==
+
=== SURF students ===
 +
* Welcome Fernando!
 +
* Will work on neuron function with respect to dauer formation
  
−
=== Alliance All Hands Face-to-Face ===
+
=== Progress Report ===
−
* Flights: has everyone already booked? No, not yet
+
* Review Google Doc from Paul to make sure you're latest updates are there
−
* Any coordination of flights from Pasadena/LA?  
+
* Doc here: https://docs.google.com/document/d/1f3ettnkvwoKKiaAA4TSrpSQPEF7FmVVn6u2UdflA_So/edit?usp=sharing
−
** Ranjana and Valerio got a direct flight from Burbank to Boston on Sunday for premeetings
 
  
−
=== SObA Comparison Tool ===
+
===Genotype class===
−
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
+
*Have 27 genotypes in the genotype OA, dumper and test .ace file ready
−
* Prototype discussed last week, updated with feedback from prior discussions
+
*Will test ace file in citace as soon as we get the new models file, can also send to Paul D., in advance to test
−
* Would this be a stand-alone tool discoverable under the Tools menu?
+
*Disease OA annotations now converted to the newly created genotypes where needed
−
** Possibly; could be a gene page widget, but may be out of place
+
*Need to work on disease dumper changes next
−
** Stand-alone tool probably makes more sense
 
−
* Life stage graph doesn't specify expression pattern vs. expression cluster; pretty much only expression patterns (no clusters)
 
  
−
=== SObA ===
+
=== What genes should be linked to genotypes? ===
−
* Raymond intending to share progress on SObA at December Alliance All-Hands Face-to-Face
+
* We have a "Gene" tag in the ?Genotype model for capturing relevant genes
−
* For example, share GO SObA graph for other species
+
* What should we consider a "relevant gene"?
−
* Will need to be dependent on a SOLR server with all species data
+
* We plan to populate the "Gene" tag with genes identified by the variation-to-gene mapping pipeline
−
** Raymond has run into problems trying to setup his own SOLR server
+
* For transgenes, what genes should be extracted as "relevant"? Genes whose promoters are cloned? Genes that are expressed? Genes whose 3'UTR's are cloned? Wild type rescue genes used as a marker/selection tool, e.g. "unc-119(+)"?
−
** Raymond asked Seth Carbon if we could us GO server, but he prefers not
+
* For rearrangements, consider relevant any genes "inside" the rearrangement?
−
** Appear to be software versioning issues, possible memory issues
+
* For now, we will omit any genes from transgenes or rearrangements from being dumped into the "Gene" tag
 +
* In the future, we may want to consider genes that have been specifically annotated as having some functional consequence and informs that the gene is of functional relevance to the genotype
  
−
=== GO meeting ===
+
=== Volunteer Community Curators ===
−
* Kimberly can give update on recent updates to GO from the recent GO meeting
+
* Have had an additional 13 people volunteer
−
* Slides are shared online
+
* Single one-on-one tutorial for someone in Hong Kong this past Monday
 +
* Chris will hold a tutorial today and tomorrow for everyone else
 +
* Have received many new community annotations from volunteers (and authors), validation still pending
  
−
=== "all stages Ce" life stage ===
+
=== Open Publishing Festival ===
−
* Currently used to annotate that RNA was collected from, or a gene was observed to be expressed during, all C. elegans life stages
+
* Ranjana will join as a panelist
−
* "all stages Ce" is currently the root node of the C. elegans branch, but needs to change to generic "C. elegans life stage"
+
* Other MOD curators will also join
−
* Should we:
+
* Festival calendar: https://openpublishingfest.org/calendar.html
−
** 1) Create a "C. elegans life span" or "C. elegans life cycle" term to represent the entire life span and annotate to that?
 
−
*** Does this mean that, for example, a gene is expressed at some point during the life cycle or consistently throughout the entire life span?
 
−
** 2) Annotate instead to, for example, "embryo Ce", "larva Ce", and "adult Ce" individually
 
−
* Note: authors are often vague in their descriptions simply saying "during all stages" possibly stating a beginning and end of the range
 
−
* Wen: not comfortable making a decision right now; want to discuss with Gary Williams and with other MOD members about how to handle large scale expression data
 
−
* Daniela: will look through existing (old and new) expression pattern annotations made to "all stages Ce" to see if it would be reasonable to annotate each case individually to "embryo Ce", "larva Ce", and "adult Ce" individually
 
  
−
=== Gene class missing description ===
+
=== Move to Chen building ===
−
* The gene class "aatf" has no description, so in the aatf-1 gene page Overview widget, the gene has empty parentheses next to the gene name where there should be a description of what "aatf" stands for (coming from the ?Gene_class description)
+
* Scheduled for late January 2021
−
* Jae or Ranjana will create a ticket and assign it to someone at Hinxton
 
  
 +
=== First completely virtual GO meeting ===
 +
* Kimberly: went really well
 +
* Only met 4 hours per day, due to time zone differences
 +
* Had breakout sessions for focus groups
  
−
== October 24, 2019 ==
+
=== Alliance Literature Acquisition working group ===
 +
* Plan to come up with use cases for OntoMate and Textpresso
 +
**Ontomate link https://rgd.mcw.edu/QueryBuilder/
  
−
=== Textpresso links from WB page References widgets ===
+
* Kimberly plans to draw up most common use cases for Textpresso
−
* Discussed with Sibyl and Adam on last week's Textpresso call
+
* Google doc for test cases: https://rgd.mcw.edu/QueryBuilder/getResult/?qFieldConditions%5B0%5D.fieldName=ontology&qFieldConditions%5B0%5D.fieldValue=Coronavirus%20infectious%20disease
−
* Sibyl working on mockups for including Textpresso derived paper associations in the References widget
 
−
* Had originally considered for the following classes
 
−
** Strain
 
−
** Gene
 
−
** Variation
 
−
** Transgene
 
−
** Construct
 
−
** Anatomy_term
 
−
* Sibyl asks: could we put this link in all References widgets in WB?
 
−
** Classes with References widgets include:
 
−
*** Antibody
 
−
*** Clone
 
−
*** Construct
 
−
*** Expression cluster
 
−
*** Expression pattern
 
−
*** Gene
 
−
*** Interaction
 
−
*** Life stage
 
−
*** Rearrangement
 
−
*** RNAi
 
−
*** Strain
 
−
*** Transgene
 
−
*** Variation
 
−
*** Analysis
 
−
*** Molecule
 
−
*** Process
 
−
** Any Textpresso search on internal WB identifiers, like WBInteraction000###### or WBRNAi00######, or on long complicated names is certainly meaningless, so the following classes are probably ruled out:
 
−
*** Antibody
 
−
*** Expression cluster
 
−
*** Expression pattern
 
−
*** Interaction
 
−
*** RNAi
 
−
*** Analysis
 
−
** Otherwise it could probably be beneficial to include the additional classes, searching on public name:
 
−
*** Clone
 
−
*** Life stage
 
−
*** Rearrangement
 
−
*** Molecule
 
−
*** Process
 
−
* Created Google Doc summary [https://docs.google.com/document/d/19y5wNIHLmBRm4z7Rz6NG-NQYlZbtobXuQcH6dz0s8Rg/edit?usp=sharing here]
 
−
* So the current list of candidate classes is:
 
−
** Strain
 
−
** Gene
 
−
** Variation
 
−
** Transgene
 
−
** Construct
 
−
** Anatomy_term (no References widget currently)
 
−
** Clone
 
−
** Life stage
 
−
** Rearrangement
 
−
** Molecule
 
−
** Process
 
−
* Eventually, we may want to incorporate papers found by Textpresso directly into the References widget
 
−
** We would want predicted associations to be made explicitly so
 
−
** We could populate the database, but there are reservations about doing this
 
  
  
−
=== Updates from GOC Meeting, Berkeley ===
+
== May 21, 2020 ==
−
* Status of MOD Imports into Noctua
 
−
** Starting with WormBase and MGI GO annotations into GO-CAM
 
−
** GPAD/GPI is standard import format
 
−
* GO-CAM Specifications and Validation
 
−
* Noctua Form
 
−
* Pathways2GO
 
−
* Priorities for next 6 months:
 
−
** Create gene-centric Noctua views
 
−
** Create pathway-centric Noctua views
 
  
 +
=== Volunteer curators ===
 +
* Received surge of annotations earlier this week
 +
* All tutorials done for now; all but 3 recorded
 +
* Each tutorial is ~1 hour in length
  
−
== October 31, 2019 ==
+
=== AFP tutorial ===
 +
* AFP group working on tutorial/webinar
 +
* Had someone on phenotype curation tutorial specifically asking about it (Kimberly responded)
  
−
=== Alliance 2.3 release ===
+
=== Open Publishing Festival ===
−
* Are variants listed on gene pages? Yes, in Alleles and Variants table
+
* Had micropublication session yesterday, went well
−
* Should we be listing strains as models if they don't have phenotype or disease data?
+
* Had ~50 participants
 +
* Saved Zoom chats? Can get public ones, maybe not private ones
  
−
=== New SObA tools ===
 
−
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Gene comparison tool]
 
−
** Select a data/ontology type, type in two genes, and graph will be generated/displayed
 
−
** Nodes colored red and blue respective to annotations from each gene
 
−
*** Absolute count slices - shows percentage of annotations to that node coming from each gene
 
−
*** Relative count slices - shows percentage of annotations to that node compared to all annotations for that gene
 
−
*** Percentage slices rendered after binning/rounding; will update to not round (be more precise) so that 80% doesn't fill the node portion
 
−
** Amigo/Solr now using MD5 Checksums instead of text strings; loss of data, may request rollback or some feature that can restore data; SObA now "frozen" at an older release of Amigo because of this
 
−
** Clicking on a node gives a total count of annotations to that node (direct and inferred); can we make an easy way for users to see all those annotations? Maybe provide a pop-up table that can be viewed and downloaded/exported?
 
−
** Node pop-ups for "Relative count slices" view says, for example, "75% of gene total". This is confusing; might be better to say "75% of total annotations to gene" or something.
 
−
** User interface updates
 
−
*** Right now, graph is automatically rendered after entering second gene; genes with no data do not show up in autocomplete
 
−
*** Will implement a "Submit" button so that user can make selections in various orders and then confirm
 
−
*** Problematic to allow a lookup on all possible genes because the tool is indexing the Solr database; if no data for a gene (for a data type) the gene does not appear to exist; Will change lookup to look at Postgres on Tazendra (or some other complete source)
 
−
*** We eventually want a gene name lookup service/API for the Alliance to provide all gene names for all species
 
−
*** It would be better to either:
 
−
**** (A) provide clear text that explains that a gene will not appear in the autocomplete if it has no data for the selected data type
 
−
**** OR (B) allow a user to type in their gene, but if it doesn't have data indicate so in the autocomplete (will need to consider when genes are entered but then user switches data type; will it then perform another lookup and indicate presence of data or not?)
 
−
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Terms+to+SObA+Graph Enriched term list tool]
 
  
 +
== May 28, 2020 ==
  
−
== November 7, 2019 ==
+
=== Wormicloud ===
 +
* Introducing a new tool for a graphical summary of queried papers, Please take a look and leave any comments on it. (http://textpressocentral.org:5010/)
  
−
=== ?Genotype class ===
+
=== Genes to Physical Map ===
−
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
+
* https://colab.research.google.com/drive/1e83jv94-eO_VQ7kKdJ36TgDDb4WRkFhM?usp=sharing
−
* Several classes have a "Genotype" tag with text entry
+
To run: Runtime->Run All. Change the list of gene names and run again.
−
** Strain
 
−
** 2_point_data
 
−
** Pos_neg_data
 
−
** Multi_pt_data
 
−
** RNAi
 
−
** Phenotype_info
 
−
** Mass_spec_experiment (no data as of WS273)
 
−
** Condition
 
−
* Collecting all genotype text entries yields ~33,000 unique entries, with many different forms:
 
−
** Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae"
 
−
** Strain entries, like "BA17[fem-1(hc-17)]" or "BB21" or "BL1[pK08F4.7::K08F4.7::GFP; rol-6(+)]"
 
−
** Anonymous transgenes, like "BEC-1::GFP" or "CAM-1-GFP" or "Ex[Pnpr-9::unc-103(gf)]"
 
−
** Complex constructs, like "C56C10.9(gk5253[loxP + Pmyo-2::GFP::unc-54 3' UTR + Prps-27::neoR::unc-54 3' UTR + loxP]) II"
 
−
** Text descriptions, like "Control" or "WT" or "Control worms fed on HT115 containing the L4440 vector without insert" or "N.A."
 
−
** Bacterial genotypes, like "E. coli [argA, lysA, mcrA, mcrB, IN(rrnD-rrnE)1, lambda-, rcn14::Tn10(DE3 lysogen::lavUV5 promoter -T7 polymerase]"
 
−
** Including balancers, like "F26H9.8(ok2510) I/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III)"
 
−
** Reference to parent strain, like "Parent strain is AG359"
 
−
** Referring to RNAi, like "Pglr-1::wrm-1(RNAi)" or "Phsp-6::gfp; phb-1(RNAi)"
 
−
** Referring to apparent null or loss of function alleles, like "Phsp-4::GFP(zcIs4); daf-2(-)" or "ced-10(lf)"
 

Revision as of 18:15, 28 May 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings


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

2020 Meetings

January

February

March

April


May 7, 2020

Alliance COVID Page

  • Available on stage
  • Textpresso for Coronavirus up for testing

SimpleMine at Alliance

  • Still some confusion about what it is
  • Will try to help clarify on PI meeting on Friday

Development environment for Alliance work

  • Raymond and Juancarlos have been working on
  • Existing hardware is strained; set up virtual machine
  • Still some technical issues

Open Publishing Festival

  • Later this month
  • Micropublications involved
  • Organized by the Collaborative Knowledge Foundation
  • Will involve publishers of books, journals, etc.
  • Will have a MOD-focused event, would be good to have WB curators participate/attend
  • Open to all

Genotype class

  • Ranjana finished populating the Genotype OA with genotypes needed for disease curation
  • Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
  • There could end up being a discrepancy between an original or published name of a genotype and the components that are inferred by WormBase
  • Would be good to be clear/transparent about which components were automatically inferred

WS277/278

  • Pipelines are pushed back by about 14 days/2 weeks


May 13, 2020

SURF students

  • Welcome Fernando!
  • Will work on neuron function with respect to dauer formation

Progress Report

Genotype class

  • Have 27 genotypes in the genotype OA, dumper and test .ace file ready
  • Will test ace file in citace as soon as we get the new models file, can also send to Paul D., in advance to test
  • Disease OA annotations now converted to the newly created genotypes where needed
  • Need to work on disease dumper changes next

What genes should be linked to genotypes?

  • We have a "Gene" tag in the ?Genotype model for capturing relevant genes
  • What should we consider a "relevant gene"?
  • We plan to populate the "Gene" tag with genes identified by the variation-to-gene mapping pipeline
  • For transgenes, what genes should be extracted as "relevant"? Genes whose promoters are cloned? Genes that are expressed? Genes whose 3'UTR's are cloned? Wild type rescue genes used as a marker/selection tool, e.g. "unc-119(+)"?
  • For rearrangements, consider relevant any genes "inside" the rearrangement?
  • For now, we will omit any genes from transgenes or rearrangements from being dumped into the "Gene" tag
  • In the future, we may want to consider genes that have been specifically annotated as having some functional consequence and informs that the gene is of functional relevance to the genotype

Volunteer Community Curators

  • Have had an additional 13 people volunteer
  • Single one-on-one tutorial for someone in Hong Kong this past Monday
  • Chris will hold a tutorial today and tomorrow for everyone else
  • Have received many new community annotations from volunteers (and authors), validation still pending

Open Publishing Festival

Move to Chen building

  • Scheduled for late January 2021

First completely virtual GO meeting

  • Kimberly: went really well
  • Only met 4 hours per day, due to time zone differences
  • Had breakout sessions for focus groups

Alliance Literature Acquisition working group


May 21, 2020

Volunteer curators

  • Received surge of annotations earlier this week
  • All tutorials done for now; all but 3 recorded
  • Each tutorial is ~1 hour in length

AFP tutorial

  • AFP group working on tutorial/webinar
  • Had someone on phenotype curation tutorial specifically asking about it (Kimberly responded)

Open Publishing Festival

  • Had micropublication session yesterday, went well
  • Had ~50 participants
  • Saved Zoom chats? Can get public ones, maybe not private ones


May 28, 2020

Wormicloud

Genes to Physical Map

To run: Runtime->Run All. Change the list of gene names and run again.

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