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]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
= 2018 Meetings =
+
= 2021 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
+
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
== May 3, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
  
=== SimpleMine output ===
 
* Wen was working on simplification of SimpleMine output
 
* Considering removing general terms in an ontology when more specific terms exist
 
* Concern that we would be removing information; will keep terms
 
  
=== SPELL topics ===
+
== July 1, 2021 ==
* Topics in SPELL need some organization, possibly trimming
 
* We could create a graph (SObA) display of topics (based on GO process)
 
  
=== SPELL problem with WS265 ===
+
=== Importing genes for tm alleles from GeneACE ===
* Wen had to debug; SPELL has limit of how many genes can be processed per data set (46,340)
+
* https://github.com/WormBase/website/issues/8262
* Wen trying to accommodate, deleting some genes from data set that had no expression (kludge)
+
* Nightly dump currently excludes tm allele genes
* Wen will write to Matt Hibbs to ask how to deal with
+
* Most tm (Mitani) alleles are not being manually connected to specific genes in GeneACE
* Will Alliance work together on a system to analyze large scale expression data?
+
* Should pull the data from WS release (into Postgres) after the build has mapped the alleles to genes
 +
* ~100,000 alleles in Postgres; ~70,000 don't have a gene connection
 +
* Would Hinxton be willing to take WS-mapped allele-to-gene associations and populate GeneACE with associations not already in there?
  
=== Curator candidate ===
+
=== Citace upload ===
* Will arrive at 10am
+
* Curators upload files to Spica for citace upload on Tuesday (July 6)
* Skype calls with remote curators
 
* Curators will send group Skype handle and requested time to talk
 
  
 +
=== Chen B1 kitchen Usage Considerations ===
 +
* Clean up after oneself.
 +
* Mark food storage with name and date.
 +
* Mark storage drawers
 +
* Consumables
  
== May 10, 2018 ==
 
  
=== ECO terms for genome editing ===
+
== July 8, 2021 ==
* Asking group's feedback on ECO terms for genome editing (Daniela)
 
* What would be used for fly-enhancer trap experiment?
 
* Genomically encoded GFP, for example
 
* ECO: GFP localization
 
* ECO term, example: Fluorescent protein transcript localization evidence
 
* Single copy transgene? Endogenous locus?
 
* Whether it is CRISPR or not may not be relevant
 
* May request ECO terms that capture distinct types of transgenes evidence
 
* Will use generic term for now
 
* Do other MODs use ECO?
 
* May want to capture endogenous/non-endogenous, multi-copy/single-copy distinctions
 
* Many of these features are captured in the transgene and construct objects already; specific ECO code redundant?
 
  
=== ZFIN SAB ===
+
=== Alliance work ===
* Significant involvement in Alliance
+
* Orange team presenting initial plans at Alliance PI meeting tomorrow
* Interest in micropublications; will push a pilot
+
* What working groups are still meeting? What are their responsibilities?
* June 19, moving from older DB to Postgres
+
** Expression
* Investigating automation for some curation processes
+
** Variants
* Students review which papers to include; acquire PDF
+
** Disease & Phenotype
* Curate paper-by-paper
+
** Technical working groups
 +
*** Technical call
 +
*** Data quartermasters
 +
*** DevOps
 +
* Expression working group working on LinkML model with Gil (FB)
 +
** Includes work on antibody class, image class, movie class
 +
** Are species-specific anatomy ontologies being utilized for expression annotations or still just Uberon?
 +
* Creating a curation interface/tool:
 +
** Will require loading auxiliary data types in addition to primary data types (e.g. if we are focused on disease annotation curation, we will need to load genes, alleles, strains, etc. in addition to the disease annotations themselves) to be available to make connections to
 +
** One requirement already expressed by curators is the need to generate new entities, like alleles, and have them quickly (immediately?) available for use in curation
 +
** Maybe this could be handled by an Alliance central name server that mints new IDs (Alliance IDs and maybe also MOD IDs?) for the objects to make them available (also with a mechanism for these new objects/IDs to make their way back to the MODs as well)
 +
** Micropublication curation forms have tackled a lot of issues of collecting lexica and entity names and IDs; should consider work already done with Micropubs
  
=== Alliance ===
+
== July 15, 2021 ==
* Supplement request for year 3, due soon (May 15)
 
* Formal report from NHGRI, 18-month plan looks good
 
* Further future plans (from NHGRI perspective) aren't quite clear
 
* Software infrastructure?
 
* Central- vs. MOD-control of resources questions
 
* Likely will have to write a NIH proposal in Fall or Winter
 
* How much is Alliance going to handle human variants?
 
* NHGRI interested in metabolomics; Alliance plans?
 
  
=== Genome-wide screens ===
+
=== hlh-34 expression ===
* Had help desk question about phenotypic screens in organisms other than worms, flies, yeast, bacteria
+
* Rebecca Mcwhirter (Miller lab) contacted WB saying that the annotations to AVJ for hlh-34 are incorrect. 4 evidences list AVJ -> the authors of the first paper that describes hlh-34 expression (Cunningham et al, 2012 : http://dx.doi.org/10.1016/j.cmet.2012.05.014) had to pick one neuron per reviewer's request. The neuron should instead be AVH.
* There have been human cell line phenotypic screens (e.g. siRNA/shRNA); who curates these, if anyone?
+
* Oliver is putting together a micropub to clarify the issue
* Also, induced pluripotent stem cell experiments
+
* How to deal with existing  annotations? Add a comment in the remarks that points to the microPub? remove AVJ from the anatomy association list?
 +
* Should we also add public comments to the relevant papers?
  
=== Nameserver issues ===
+
== July 22, 2021 ==
* Issue came up about assigning unique WBStrain IDs
 
* Can use a nightly nameserver dump from Hinxton to populate Postgres/OA
 
* Will need to clean up existing strains in Postgres
 
* Also, considering unique IDs for genotypes
 
* Mechanics of naming and managing naming of objects
 
** Nightly syncing (cronjob) to nameserver
 
** Ideally, we would have instant updates; Hinxton firewall prevents direct access; Matt working on establishing a separate nameserver location to gain direct access
 
** Strain names (at least historically) have been updated quarterly from CGC file
 
** Curators need mechanism to create and use strain (and variation) names right away
 
** Current system requires manual denormalization step; has worked so far
 
  
 +
=== Copying data from textpresso-dev to tazendra ===
 +
* Michael has been asking curators to retrieve any data they might still want on textpresso-dev before the machine dies
 +
* Can we copy files to tazendra?
 +
* If so, do we need to have a more general approach/strategy other than creating new folders in the individual curator directories?
 +
* Are there any size considerations for what we copy over?  There are 1.1T free in /home2 which is not backed up
  
== May 17, 2018 ==
+
== July 29, 2021 ==
  
=== Strains ===
+
=== Textpresso Dev machine retiring ===
* Create a strain OA? Central curation tool for strain data?
+
* Need to work out when and how to move things off the machine before retiring for good
* Would need to maintain synchrony with CGC and Hinxton
 
* Postgres/Tazendra variation adding CGI: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
 
* Will add similar link for Strains, adding info to obo_name_strain and obo_data_strain as well as a tempfile, which will those objects in postgres when the nightly_geneace.pl updates the OA strain info
 
  
=== SAB 2018 ===
+
=== Proxies for Caltech-hosted tools broken ===
* Who will present? Present what?
+
* Several Caltech CGI tools using a proxy on WormBase site are broken (throwing 504 Gateway Time-out or Server Error)
* We can generate a central document with stats to give to SAB
+
* Affected tools:
* Ask SAB for opinions and guidance?
+
** https://wormbase.org/tools/soba/soba.cgi?action=Gene+Pair+to+SObA+Graph
* Would be good to assess current efforts and priorities, ask if we should stay the course or make modifications to our approach
+
** https://wormbase.org/tools/soba/soba.cgi?action=Terms+to+SObA+Graph
 +
** https://wormbase.org/tools/rnaseq/expression_dataset_locator.cgi
 +
** https://wormbase.org/tools/rnaseq/fpkmmine.cgi
 +
** https://wormbase.org/tools/ontology_browser
  
 
+
=== 2021 Genetics paper ===
== May 24th, 2018 ==
+
* Paul D has asked for contributions (~200 words each)
 
+
* Paul's preliminary suggested sections:
=== Helpdesk ===
+
** CeNGen (CalTech)
*[https://github.com/WormBase/website/issues/6423 Not sure if this falls under content....]
+
** Expression & Transcription (Wen)
* User asked about phenotype information being incorporated into the gene description
+
*** Spell (Wen)
* Chris directed him to phenotype submission form; he has since submitted the phenotypes
+
** SimpleMine (CalTech Wen)
* Phenotype data hasn't yet been incorporated into the automated descriptions pipeline
+
** WormiCloud - (Jae/Valerio Caltech)
* We can direct him to the gene description submission form
+
** Vennter (Jae/Caltech)
* Ranjana will respond to user email
+
** Gene Name Sanitizer (Wen/Raymond/Caltech?)
* Will likely swap out older WB automated description pipeline with newer Alliance automated description pipeline
+
** VFP (Valerio)
 
+
** Author first pass (Daniela)
=== Relations Ontology ===
+
** Human disease (Ranjana)
*Working on new model for importing RO terms into WormBase
+
** Molecular and genetic interactions (You/Chris)
*Question: Do we need to import all of RO?
+
** Pathways and Processes (Karen)
**For example, RO also has terms from other ontologies:
+
** Anatomy and Cell (Raymond)
    [Term]
+
* Now have 'Community Curation' for AFP and other community curation
    id: GO:0003674
+
* Also, gene descriptions section
    name: molecular_function
 
    is_a: BFO:0000015 ! process
 
    property_value: IAO:0000589 "molecular process" xsd:string
 
*Question: How much term information do we want and/or need?
 
**For example:
 
    [Typedef]
 
    id: BFO:0000050
 
    name: part of
 
    def: "a core relation that holds between a part and its whole" []
 
    property_value: IAO:0000111 "is part of" xsd:string
 
    property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string
 
    property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string
 
    property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string
 
    property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string
 
    property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at
 
    certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
 
    property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an
 
    independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically
 
    dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A
 
    material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent
 
    continuant: use 'bearer of'." xsd:string
 
    property_value: IAO:0000118 "part_of" xsd:string
 
    property_value: RO:0001900 RO:0001901
 
    property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
 
    property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
 
    property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string
 
    is_transitive: true
 
    is_a: RO:0002131 ! overlaps
 
    inverse_of: BFO:0000051 ! has part
 
 
 
*For curation, we could import only the BFO and RO ID spaces of RO, but include all of the tag-value pairs (the usage examples might be helpful)
 
*For WB, though, we could injest only the BFO and RO ID spaces of RO, and only include in the model: id, name, def, is_a, domain, range, and inverse_of tags
 
**We can always link out from WB to pages with more detail on RO terms
 
 
 
*Will use RO ids in ?GO_annotation model in the Annotation_relation part (model will need an update)
 
**The ?GO_annotation model also refers to relations used in annotation extensions.  Unfortunately, though, not all annotation extension relations are in RO, so we can't yet use RO in this part of the model.
 
**We can either import these other GO relations as a separate class, or import them if/when they get included in RO (there is a PRO/RO meeting scheduled for late October with some preliminary phone conferences prior).
 
**The Alliance Gene Expression group is also dealing with this issue.
 
*Where can we use RO terms in other curation models?
 
* Kimberly will add to the agenda for the next WB site-wide conference call
 
 
 
=== Methods in Molecular Biology book ===
 
* Eukaryotic Genome Databases, has WormBase chapter
 
* Book arrived at Caltech
 
* Chris will ask publishers about getting PDFs without watermarks
 
 
 
=== ICBO 2018 meeting ===
 
* International Conference on Biological Ontology (2018)
 
* Raymond considering submitting abstract
 
* Not clear if it needs to be a full paper; can we resubmit Biocuration meeting abstract?
 
* Can the content be published elsewhere once submitted to the meeting?
 
 
 
== May 31th, 2018 ==
 
 
 
=== Feedbacks from Front Range Worm Meeting ===
 
* Is it possible to collect old theses online and load them into Textpresso?
 
* Shall we suggest authors put "elegans" in titles and abstracts? Min Han said some of his papers do not have this keyword.
 
* Community curation. Erin Osborne Nishimura mentioned camps and courses for undergraduate research. Can they do allele and phenotype curation for WormBase? Who will follow up with her?
 
* Shall we send the AFP form to some users for feedback?
 
 
 
=== Updates about SPELL ===
 
* SGD moved their SPELL to AWS. WormBase needs to set up our own AWS and SGD can give us their code. Will Raymond be able to help set up the AWS? Once installing the AWS SPELL following SGD's code, Wen can load WormBase SPELL data to it.
 

Latest revision as of 18:30, 29 July 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

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2020 Meetings

2021 Meetings

January

February

March

April

May

June


July 1, 2021

Importing genes for tm alleles from GeneACE

  • https://github.com/WormBase/website/issues/8262
  • Nightly dump currently excludes tm allele genes
  • Most tm (Mitani) alleles are not being manually connected to specific genes in GeneACE
  • Should pull the data from WS release (into Postgres) after the build has mapped the alleles to genes
  • ~100,000 alleles in Postgres; ~70,000 don't have a gene connection
  • Would Hinxton be willing to take WS-mapped allele-to-gene associations and populate GeneACE with associations not already in there?

Citace upload

  • Curators upload files to Spica for citace upload on Tuesday (July 6)

Chen B1 kitchen Usage Considerations

  • Clean up after oneself.
  • Mark food storage with name and date.
  • Mark storage drawers
  • Consumables


July 8, 2021

Alliance work

  • Orange team presenting initial plans at Alliance PI meeting tomorrow
  • What working groups are still meeting? What are their responsibilities?
    • Expression
    • Variants
    • Disease & Phenotype
    • Technical working groups
      • Technical call
      • Data quartermasters
      • DevOps
  • Expression working group working on LinkML model with Gil (FB)
    • Includes work on antibody class, image class, movie class
    • Are species-specific anatomy ontologies being utilized for expression annotations or still just Uberon?
  • Creating a curation interface/tool:
    • Will require loading auxiliary data types in addition to primary data types (e.g. if we are focused on disease annotation curation, we will need to load genes, alleles, strains, etc. in addition to the disease annotations themselves) to be available to make connections to
    • One requirement already expressed by curators is the need to generate new entities, like alleles, and have them quickly (immediately?) available for use in curation
    • Maybe this could be handled by an Alliance central name server that mints new IDs (Alliance IDs and maybe also MOD IDs?) for the objects to make them available (also with a mechanism for these new objects/IDs to make their way back to the MODs as well)
    • Micropublication curation forms have tackled a lot of issues of collecting lexica and entity names and IDs; should consider work already done with Micropubs

July 15, 2021

hlh-34 expression

  • Rebecca Mcwhirter (Miller lab) contacted WB saying that the annotations to AVJ for hlh-34 are incorrect. 4 evidences list AVJ -> the authors of the first paper that describes hlh-34 expression (Cunningham et al, 2012 : http://dx.doi.org/10.1016/j.cmet.2012.05.014) had to pick one neuron per reviewer's request. The neuron should instead be AVH.
  • Oliver is putting together a micropub to clarify the issue
  • How to deal with existing annotations? Add a comment in the remarks that points to the microPub? remove AVJ from the anatomy association list?
  • Should we also add public comments to the relevant papers?

July 22, 2021

Copying data from textpresso-dev to tazendra

  • Michael has been asking curators to retrieve any data they might still want on textpresso-dev before the machine dies
  • Can we copy files to tazendra?
  • If so, do we need to have a more general approach/strategy other than creating new folders in the individual curator directories?
  • Are there any size considerations for what we copy over? There are 1.1T free in /home2 which is not backed up

July 29, 2021

Textpresso Dev machine retiring

  • Need to work out when and how to move things off the machine before retiring for good

Proxies for Caltech-hosted tools broken

2021 Genetics paper

  • Paul D has asked for contributions (~200 words each)
  • Paul's preliminary suggested sections:
    • CeNGen (CalTech)
    • Expression & Transcription (Wen)
      • Spell (Wen)
    • SimpleMine (CalTech Wen)
    • WormiCloud - (Jae/Valerio Caltech)
    • Vennter (Jae/Caltech)
    • Gene Name Sanitizer (Wen/Raymond/Caltech?)
    • VFP (Valerio)
    • Author first pass (Daniela)
    • Human disease (Ranjana)
    • Molecular and genetic interactions (You/Chris)
    • Pathways and Processes (Karen)
    • Anatomy and Cell (Raymond)
  • Now have 'Community Curation' for AFP and other community curation
  • Also, gene descriptions section