Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
= 2018 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
== January 4, 2018 ==
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[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
=== WS264 Upload ===
+
= 2021 Meetings =
* Citace upload to Wen, Tuesday January 16th, by 10am PST
 
* Upload to Hinxton on Jan 19th
 
  
=== Strain data import to AGR for disease ===
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
* Will begin to consider pulling in strains into AGR
 
* Will need to think about how genotypes are built and stored at other MODs
 
* We should encourage authors to include strain IDs
 
* Diseases are annotated to genes, alleles, and strains within WB
 
  
=== Curating phenotypes and diseases to strains or genotypes ===
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
* Should we generate a ?Genotype class to capture genotypes without a known strain name? Or to capture relevant/relative genotypes thought to be responsible for a phenotype or disease?
 
* We could create un-named strain objects, that use a new unique identifier as a primary identifier and represent the entire genotype of a strain used
 
** Introduction of a new ?Strain class attribute of a unique serial identifier (like WBStrain00001) would be very costly to implement; would need to consider how crucial this is before implementing
 
** We can, instead, use new strain (public) names like "WBPaper00012345_Strain1", etc. instead of creating new unique ID attribute for un-named strains
 
* When curating phenotypes to strains, we will want to specify what is the relevant/relative genotype that is causative/correlated with the disease or phenotype observation
 
** Would be best if the specification of the relevant genotype used controlled vocabularies (when possible) and free text (when needed); would need to work out the logistics/mechanics of such curation
 
** Transgene-phenotype curation currently specifies causative gene, but would be more complicated for strains
 
* Alternatively, we could create the ?Genotype class to represent the abstract "relative"/"relevant" genotype thought to be responsible for the phenotype or disease, and annotate directly to that ?Genotype object
 
* ?Strain approach:
 
** Use strain if named (but important to know if the control strain is not simply N2)
 
*** If control strain is simply N2, causative genotype (and respective components) can be inferred from strain genotype
 
*** If control strain is not N2, causative genotype and components would need to be specified at the moment of phenotype/disease curation (by mechanism to be worked out)
 
** If no strain name provided, create "un-named" strain that contains the entire genotype provided by authors
 
*** Control strain issues above would still need to be addressed
 
* ?Genotype approach:
 
** ?Genotype class could represent individual instances of relevant/relative genotypes that are suggested to be causative for a disease or phenotype
 
** ?Genotype objects would be created with formal construction, with DB associations to each component object (e.g. alleles, transgenes, etc.) as well as free text descriptions (for components with no corresponding DB object)
 
** Such ?Genotype objects could be used repeatedly throughout a paper when applicable, but would likely not be used in any other papers (we would likely accumulate redundant objects in the DB)
 
* We may want to consider strains with same public name that have diverged
 
** Apply new strain names with prefixes/suffixes? Create new strain objects? Keep original?
 
* Need to determine how each AGR member DB curates phenotypes or diseases to genotypes: is each "genotype" a relative or absolute genotype?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
== January 11, 2018 ==
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[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
=== IWM swag ===
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[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
* Eppendorf tube openers with WormBase logo?
 
  
=== Update on AFP Form ===
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[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
*[https://docs.google.com/presentation/d/1anFOFRK9Ida1UEvrXWf2OBAJ9F4xyU4lWJGy-qr6wRU/edit#slide=id.p3 In-progress mock-up of new form]
 
*[https://docs.google.com/spreadsheets/d/1sS_uAjBJ2r5H90Lam62Ai0HunjwvfjnklkFNrDoNXeU/edit#gid=1929595460 Data type spreadsheet]
 
*[http://wiki.wormbase.org/index.php/First-pass_flagging_pipelines#Author_first-pass_form_revisions Curation forms info]
 
  
*Idea is to move from author flagging to author validation of text mining and data submission wherever possible
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[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
*Goal is to flag all data types in a paper and either curate at WB or share with a group that does curate that data
 
*SVM flags and author flags can/will be used as filters in TPC
 
*Provide examples of what we want for each type of data to help avoid confusion
 
* Recognize entities automatically and show list to author
 
** Species, strains, genes, alleles, transgenes, etc.
 
** Ask to verify or add unrecognized
 
** Could show known/existing objects with checkboxes
 
** Possibly include unrecognized pattern matching objects? Ask author to verify if these are real?
 
** For strains:
 
*** Show recorded genotype for verification; maybe ask to update/modify if needed?
 
** For transgenes:
 
*** When author submits new transgene, send them to a transgene form, or send them an email asking for details?
 
*** Form could be for both strain and transgene
 
* Mapping data: still ask for? Maybe for balancers, but no one is reporting that. Could still ask if there's interest
 
* Maybe provide option for author to save their progress and return to the form later
 
* Phenotypes
 
** Ask for allele, RNAi and overexpression phenotypes with links to Phenotype form
 
** Also ask for drug/chemical and environmental perturbations (call treatment?); store as free text for now, accommodate with new data model when available
 
* Gene site- and time-of-action, mosaic
 
** Appears to be confusion from authors about mosaics. Should we keep this?
 
** Will keep gene site-of-action and time-of-action; leave unchecked (no SVM, yet) but allow users to indicate
 
* Cell and anatomy data
 
** Cell function ("Cell ablation (laser/genetic) data, optogenetics")
 
** Ultrastructural analysis
 
* Interaction data
 
** Genetic interactions
 
** Physical interactions
 
** Functional complementation
 
* Comparative genomics
 
* Gene expression & regulation
 
  
 +
[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
  
  
== January 18, 2018 ==
+
== September 2, 2021 ==
  
=== WormBase Tutorials ===
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1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking<br>
* May be good to get (possibly anonymous) written questions or suggestions after presenting
+
Needed for
* Wen will have Skype call with Yishi Jin
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*AFP community curation
* Micropublications
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*microPublication author tracking for all species
** how do we peer-review single experiment? No supporting information to corroborate a larger story
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*stub of person Alliance model already exists made by Adam http://dev.alliancegenome.org:11223/redoc#tag/Person
** Is the greater benefit of peer-review that the whole story is assessed by reviewers
 
** Do MPs help or hurt reproducibility?
 
** Larger papers may have lots of poor experiments that don't get much attention but still pass peer review
 
** Dedicated peer review on single experiment may be more rigorous
 
** What are the criteria/minimal requirements to micropublish?
 
* Concise descriptions
 
** SimpleMine has multiple descriptions output; people asked about the different types
 
** Yishi Jin suggested that we remind users to update manually written descriptions
 
** Showing last-updated date is important
 
** Automated descriptions relies on primary data; will rely on forms and community submissions
 
** Microreviews? Would want to guide authors what data we want; provide a template?
 
* Public/community education issues
 
** Users shouldn't assume that WormBase is comprehensively up to date
 
* Wen will also present at MidWest meeting (Ann Arbor, MI) in April and Boulder, Colorado in May
 
** Will assess topic interest ahead of time
 
  
=== New Cytoscape display for interactions ===
+
Problems:
* Sibyl developed a new Cytoscape display for interactions, now live with WS262 release
+
*this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
* Simplified colors and subtypes
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*need to do this outside of Alliance
* Redraw button to clean up the graph based on what you want to see
 
* Play around and let Sibyl and/or Chris know about issues
 
  
 +
Action
 +
*Paul talks to zfin about interest in person pages
 +
*Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
 +
*Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite
  
== January 25, 2018 ==
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Will do
 +
*create biolink model based on current WB postgres/Caltech model
 +
*Adam will add tables when we have them
  
=== UCSF visit report ===
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2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.
  
Questions from the audience
+
== September 16, 2021 ==
*Is there a way in WB to pull out verified CRISPR guides?
 
*Single cell RNAseq from Waterson lab in WB? Paper is in WB, person-paper connections might be on staging, Kimberly verifying this. Gary W will put data in WS264. Comments from Gary on this paper:
 
‘The main problem is that the authors can sort the cells into groups (corresponding to tissues, I think) and sometimes sort them into single cells, but it is hard to identify the tissues or cells. I think they found 29 groups, of which about 20 appear to be single cells.
 
I think they have a website where they invite other researchers to make suggestions about how to identify cells in their data.
 
Currently I regard this data set as still undergoing analysis and I'm waiting to see if they improve the deconvolution and identification of the cells.
 
The RNASeq data from this paper will be going into the current Build (WS264) but I will not be adding it to SPELL this Build because displaying it probably requires more thought.
 
I'm not sure that tools for displaying single-cell data have been developed very much yet. There is potentially a lot of information if eventually all 959 or 1031 somatic cells are displayed!
 
  
*List of fem-3 alleles excluding natural variants in WormMine, how to do that? The template should be fixed (checkbox)
+
1. CeNGEN enriched genes per cell type data targeted for WS283.
*Is the increase of published paper due to an increased number of labs? Expansion of the field? Is there a correlation between the increased number of publications and increased number of labs
 
*One user found powerful to be able to use the Galaxy server to do analysis after exporting data from WormMine
 
*Can you do protein domain analysis with WormMine? Is the protein->motif precanned query the best option?
 
*Enrichment: how to see which genes are expressed in a tissue or cell -> pointed user to the ontology browser
 
  
=== Skype call with Yishi Jin and Sreekanth Chalasani ===
+
2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump.  Juancarlos changed the OA population script script to exclude those.
Participants: Daniela, Karen, Wen, Jin, Shrek
 
  
*Not all images available due to publisher agreement -> not clear to users, we should put a disclaimer somewhere
+
== September 23, 2021 ==
*Shrek: thinks gene expression display should improve => hard to figure out all expression patterns
 
**Shrek and Jin feel the most important info is the reagent, and that should be displayed on the gene page/expression widget other than the Expression page
 
*Images are identical -> example on the eat-4 expression page. This is normal since one image depicts multiple neurons and the association Anatomy neuron applies.
 
http://www.wormbase.org/species/c_elegans/gene/WBGene00001135#1860--10
 
**On the eat-4 expression page the problem is amplified as one picture shows 70+ neurons
 
**We should remove the image column and have links to images only on the panel above (as currently displayed)
 
**The image column should be replaced with reagent and description, if possible. Will need to talk to Sibyl and see what is duable.
 
*Shrek pointed out that the eat-4 concise description is out of date, we explained that in the near future the manual descriptions will be superseded by automatic descriptions
 
*Neuron connectivity: missing neuron connectivity pages, there is a new reconstruction of neuroanatomy from david hall, would be great to integrate
 
  
=== New Framework for paper classification ===
+
1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?
Valerio will present a new project aimed at creating new paper classifiers: https://github.com/valearna/tpclassifier
+
* Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
 +
* Update the WB page on citing WormBase
  
*A new classification pipeline will be set up and run in parallel to the current SVM pipeline to compare the results
+
2. CeNGEN data on Gene page for WS282. A short blog to highlight.
 +
 
 +
3. Server room in Braun power down for no apparent reason. Reset.

Latest revision as of 18:17, 23 September 2021

Previous Years

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2015 Meetings

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2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

January

February

March

April

May

June

July

August


September 2, 2021

1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking
Needed for

Problems:

  • this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
  • need to do this outside of Alliance

Action

  • Paul talks to zfin about interest in person pages
  • Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
  • Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite

Will do

  • create biolink model based on current WB postgres/Caltech model
  • Adam will add tables when we have them

2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.

September 16, 2021

1. CeNGEN enriched genes per cell type data targeted for WS283.

2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump. Juancarlos changed the OA population script script to exclude those.

September 23, 2021

1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?

  • Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
  • Update the WB page on citing WormBase

2. CeNGEN data on Gene page for WS282. A short blog to highlight.

3. Server room in Braun power down for no apparent reason. Reset.