Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
= 2016 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2016|January]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_February_2016|February]]
 
  
[[WormBase-Caltech_Weekly_Calls_March_2016|March]]
 
  
[[WormBase-Caltech_Weekly_Calls_April_2016|April]]
 
  
[[WormBase-Caltech_Weekly_Calls_May_2016|May]]
+
= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_June_2016|June]]
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_July_2016|July]]
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_August_2016|August]]
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_September_2016|September]]
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
== October 6, 2016 ==
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
=== Citace upload ===
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
* Tuesday, October 25th, 2016
 
  
=== Automated descriptions ===
+
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
* Ranjana working with Juancarlos to run and update automated descriptions pipeline
 
  
=== Intellectual lineage ===
+
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
* First draft up on WormBase development site
 
  
=== Noctua ===
 
* Raymond trying to annotate axioms for anatomy function
 
* How to connect cell types in different organisms to those in C. elegans anatomy ontology?
 
* Maybe best way is to connect based on biological function, e.g. regulate osmolarity (kidney, excretory cell)
 
* Raymond attempting to use Noctua to draw relationships between anatomy terms and function
 
* There's a distinction between annotating to an instance vs. to a class
 
* Raymond worked on modeling a statement on excretory cell function from WormAtlas
 
* Question: how much redundancy might we end up with if we annotate to higher level (cell/anatomy function) and lower level (individual gene product function)? There may be, but all of this information is valuable
 
  
=== Expr_pattern model change ===
+
== October 1, 2020 ==
* Daniela proposed a CRISPR-Cas9 tag for the expression pattern class as an experiment type
 
* Would be inline with "Reporter gene", "In situ", "Antibody", etc.
 
* Probably want "Genome editing" instead of "CRISPR-Cas9" so as to be more generic
 
* Would a GFP knock-in via genome editing be distinct from "Reporter gene"?
 
* Could have a super tag "Genome_editing" and sub-tags "CRISPR-Cas9", "Zinc_fingers", "TALEN"
 
* Maybe we'll just stick with a "Genome_editing" tag
 
  
 +
=== Gene association file formats on FTP ===
 +
* For example, current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/
 +
* Our association files have format "*.wb"; is this useful or necessary?
 +
* Other than referring to GAF in the header, it isn't clear to users what the columns refer to or what the column headers should be
 +
* We could add a README file and/or convert to the new [https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md GAF 2.2 format] which would have a more expressive file header and possibly column headers(?)
 +
** File headers could possibly link to the format specification page
  
== October 13, 2016 ==
+
=== Phenotype association file idiosyncrasy ===
 +
* As we've discussed previously, there is an oddity to how the phenotype association file we provide lists, or doesn't, references
 +
* According to the GAF spec, column 6 is for reference and is required, whereas column 8 is "With (or) From" and is optional
 +
* When we have a reference, the WBPaper ID is provided in column 6 and the WBVar ID or RNAi ID is provided in column 8
 +
* However, when we have no reference (personal communication, e.g. from NBP allele submissions), the WBVar ID is instead put in column 6 (because we need something there), and column 8 is blank.
 +
** This results in (1) column 6 having a mix of paper/reference IDs (good) and WBVar IDs (not good) and (2) WBVar IDs split between column 6 and 8; thus making it tedious to parse this file
 +
* Proposed solution: Can we come up with some type of reference object ID to associate to the personal communications (or any annotations currently lacking a formal reference)?
 +
* With the proposed solution, we can always have a reference ID in column 6 (the intended purpose of the column) and WBVar IDs for alleles can always remain consistently in column 8
 +
* Proposal is to put WBPerson IDs in column 6 for personal communications. Chris & Karen will check if this will work.
  
=== Strain requests ===
+
=== Server space in Chen Building ===
* Ranjana sending strain requests to Mary Ann
+
* It looks like that we will not have a specific space for server computers.
* Mary Ann processing published strains requested by Ranjana
 
  
=== GO meeting ===
 
* Registration is now setup
 
* Sarah (Torres) could register all WB CIT participants
 
* Kimberly is helping organize
 
  
=== AGR Portal Use Case working group update ===
+
== October 8, 2020 ==
* Working on first use case, basic text search for genes, GO terms, diseases, and orthology groups
 
* Data is being collected into a "Portal Data" Google drive: https://drive.google.com/drive/u/1/folders/0B9qQtJIEUDEhRnJKWF9NTTVMVGs
 
* Some MODs providing more data than requested; That's OK, we just want to keep it simple for the first implementation
 
* We only want, for the first pass, to retrieve genes, GO terms (no GO-gene annotations), diseases (no disease-gene annotations), and orthology groups
 
* We likely already have enough data for a first pass implementation; not comprehensive data, but that is fine for now
 
* Disease data dumped from ACEDB, based on Disease Ontology; not comprehensive for OMIM disease list
 
* We'll eventually want to pull data directly from OMIM and GO
 
  
=== Extending SPELL virtual machine ===
+
=== Webinar Announcement ===
* Has a lot of data; may be contributing to SPELL downtime
+
* Here is the live registration site: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/webinar.cgi
* Could possibly move to the cloud, but we would need a machine in the cloud
+
* Caltech zoom allows 300 attendees.
* Can only install SPELL on Ubuntu 8; SGD uses RedHat; we can ask them what they're using, how it's working
 
* Possibly SGD could run a worm instance on their machine(s)
 
  
=== Transgenome ===
+
=== Descriptions from GO-CAM models ===
* Junacarlos finished parsing the transgenome data with Daniela
+
* One suggestion for the Alliance is to create a description based on a GO-CAM model
* Checking parse output numbers with the Transgenome group
+
* Could also micropublish some descriptions (semi-automated?)
* Will the expression data be dumped out in the expression GAF? Yes, should be
+
* Can make curators authors of micropublications for GO-CAM models/pathways
* Data from Transgenome are not necessarily peer-reviewed; need to make that clear in display
 
* Some Expr_pattern objects can be linked to WBPerson, if not a WBPaper
 
* Data in GAF will point to the 2012 Cell paper as a reference for the Transgenome project
 
* Raymond suspects issues with it; what if users cannot trace data back to source (by looking up the paper)?
 
* Would be best to link directly to the respective Transgenome database page when displaying their data
 
* Notes can be added to release notes that the Transgenome data has been added to the database
 
  
=== Micropublications ===
+
=== Transcription Factors in WormBase ===
* Trial with uploading Nemametrix data; aiming in putting data for the next upload (2-4 micro)
+
* WormBase has a ?Transcription_factor class that is currently underutilized
* Added micropublication type in the ?Paper class
+
* Chris spoke with Gary Williams about the status as he has done much of the work on the class
* Micropublications will acquire WBPaper IDs
+
* Because transcription factors can often be complexes, it was decided to create the ?Transcription_factor class rather than simply an extension of tags to the existing ?Gene class
* Previous micropublications were only ?Expr_pattern objects; now will be ?Paper objects
+
* The class seems reasonably complete; it's important to note that some TFs are general transcription factors, not necessarily gene-specific or sequence-specific DNA-binding TFs; it will be good to make that distinction clear to users
* Ideally micropubs. will be indexed by PubMed and enter the WB pipeline through the normal paper route
+
* Chris has compiled a [https://docs.google.com/spreadsheets/d/1KdmvybWDWHXdlJwZgfleL4xHDoyPoYR13WAUcERF82g/edit?usp=sharing Google sheet] to assess the class before Gary W. leaves WB in the next couple of weeks
* Question: create WBPaper objects as soon as accepted? That is plan for now
+
* The Google sheet has several tabs/worksheets, including one for the ACEDB data model (and notes about usage of tags), a summary table of associated genes, bound sequence features, existence of other protein-DNA binding data, etc.
* Micropubs. will first be hosted by WormBase, but may move to an independent repository (Micropublication: biology)
+
* It would be good to make TF binding info (per gene and globally) more accessibly to our users, maybe via a new widget on gene pages (e.g. list incoming, regulating TFs and, for TF genes themselves, list potential target genes)
* Will we display images/figures from micropubs. only or for all papers? We'll need to wait and see
 
* Could we accommodate any digital data to associate with the micropub.? E.g. data points, plasmid maps, etc.
 
* Micropubs. text will be marked up as much as possible; what about making all sentences OWL statements?
 
* Would this be changing the way that authors write papers? Maybe, but should be independent of core micropublication pipeline
 
* Each micropublication/data/result could be combined as modules to create a larger, more comprehensive narrative
 
* There is a notion of a "millipublication" that could be a larger narrative from collected micropublications
 
* One original idea was that micropublications would capture data that people would not otherwise want to publish
 
* Data submitted as micropublication will not be able to be submitted as another publication later but will be cited as data point
 
* Micropubs. will be considered primary research article, not just an abstract (equivalent to meeting abstract)
 
  
 +
== October 15, 2020 ==
  
== October 20, 2016 ==
+
=== BioGRID data sharing ===
 +
* Rose from BioGRID proposed that BioGRID curate high-throughput C. elegans interaction datasets, capturing confidence scores when available, and making those annotations available to WormBase for regular ingest
 +
* Will need to consider a few points:
 +
** BioGRID doesn't curate protein-DNA interactions
 +
** We don't yet know the turn-around timeline for BioGRID curation of worm datasets; WB may be able to curate them much sooner
 +
* Chris and Jae will work with Rose et al. to coordinate HTP curation
  
=== AGR search prototype ===
+
=== Enriched genes ===
* URL: http://search.alliancegenome.org/
+
* Some genes are considered "enriched" for an expression cluster data set even if the enrichment was in comparison to another cell or tissue (not whole animal)
* Searching "WNT4", then choosing category "Gene Ontology" provides facets for species
+
* We should reconsider the ?Expression_cluster model to make sure we can appropriately model and communicate enrichment or subtypes thereof
* Question is: how are these species associated to the GO terms?
 
* Associated genes could have a species prefix or indicator
 
  
=== AGR gene page ===
 
* There was resistance to creating AGR gene pages
 
* Some see it as redundant with what is already available elsewhere
 
* Although we may want to build a foundation gene page and develop from there
 
* Maybe MODs could develop their respective gene pages to look more like an AGR standard
 
* One main reason to create AGR is to have a consolidated, consistent, standard view for data, including genes
 
* Would be good to assemble a user group (or intended audience) to receive feedback from
 
* Use Case working group has put together some ideas for a gene comparison page, keyed off of orthology group:
 
** https://docs.google.com/presentation/d/1frMMh3xfepesJq5iqSXAwwLOrb45cuqe3LValEOd4bM/edit#slide=id.p
 
  
=== Citace upload ===
+
== October 22, 2020 ==
* Next Tuesday, October 25th 10am
 
  
=== Curator call next week ===
+
=== CHEBI ===
* Topic: curation styles
+
* Karen spoke to CHEBI personnel on Tuesday
* Curation by paper, by topic, etc.
+
* CHEBI only has ~2 curators to create new entities
* Curation inter-dependencies
+
* CHEBI had submitted a proposal to establish pipelines to process requests from MODs
* Daniela will present for WormBase
+
* Chemical Translation Service (CTS)
* Send ideas to Daniela for her to cover
+
* OxO = https://www.ebi.ac.uk/spot/oxo/search
* Send older slides with relevant information to Daniela
 
  
 
+
=== Training Webinar ===
== October 27, 2016 ==
+
* Scheduled for tomorrow at 1pm Pacific/4pm Eastern
 
 
=== AGR Portal Use Case working group ===
 
* Working group had call yesterday with Paul Thomas and Judy Blake
 
* Decision was made to abandon the idea of displaying "orthology groups"/"homology groups"
 
* Instead we will display a gene-centric page with comparisons of focus gene data with data from all orthologs and paralogs
 
* Paul Thomas' group had built a prototype for pulling out orthologs with GO info: http://umodtest.usc.edu/
 
* This prototype returns closest orthologs of a focus/query gene and then displays a table of all GO annotations for all genes
 
* We would want to display orthologs for a focus gene as well as paralogs
 
* This display is very similar to the gene comparison page mockup the use case working group had been envisioning, except now the focus will be a single gene, not a PANTHER subfamily
 
 
 
=== Disease-Strain curation ===
 
* Ranjana working on disease-strain associations for WormBase
 
* Disease group working on the DAF (disease association file) format
 
* Ranjana will discuss the strain curation pipeline with Mary Ann and Karen
 
* Will want a unique ID for each strain, especially for when we merge strain data with other MODs
 
** One solution is to just prefix the strain name with "WBStrain:" to indicate it came from WormBase
 
 
 
=== Kimberly visiting CA ===
 
* Kimberly will be at CIT next Wednesday
 
* Noctua developers will be around to discuss integration with Textpresso
 
* Kimberly can send around schedule for the GO meeting
 
* Would be good for curators to setup a Noctua account before the Noctua workshop (on Nov 7)
 
* Kimberly will also be at CIT on Tuesday Nov 8th
 
 
 
=== Paper editor CGI ===
 
* Michael had some issues with the paper editor
 
* Seems to be working now
 
 
 
== November 2, 2016 ==
 
 
 
=== Micropublication update ===
 
 
 
* First Nemametrix micro in for WS257
 
* One lined up for WS258
 
* Karen and Daniela in touch with e-publishing platforms ([Highwire], Collaborative knowledge foundation), to set up collaborations for the e-journal
 

Latest revision as of 18:40, 22 October 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings



2020 Meetings

January

February

March

April

May

June

July

August

September


October 1, 2020

Gene association file formats on FTP

  • For example, current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/
  • Our association files have format "*.wb"; is this useful or necessary?
  • Other than referring to GAF in the header, it isn't clear to users what the columns refer to or what the column headers should be
  • We could add a README file and/or convert to the new GAF 2.2 format which would have a more expressive file header and possibly column headers(?)
    • File headers could possibly link to the format specification page

Phenotype association file idiosyncrasy

  • As we've discussed previously, there is an oddity to how the phenotype association file we provide lists, or doesn't, references
  • According to the GAF spec, column 6 is for reference and is required, whereas column 8 is "With (or) From" and is optional
  • When we have a reference, the WBPaper ID is provided in column 6 and the WBVar ID or RNAi ID is provided in column 8
  • However, when we have no reference (personal communication, e.g. from NBP allele submissions), the WBVar ID is instead put in column 6 (because we need something there), and column 8 is blank.
    • This results in (1) column 6 having a mix of paper/reference IDs (good) and WBVar IDs (not good) and (2) WBVar IDs split between column 6 and 8; thus making it tedious to parse this file
  • Proposed solution: Can we come up with some type of reference object ID to associate to the personal communications (or any annotations currently lacking a formal reference)?
  • With the proposed solution, we can always have a reference ID in column 6 (the intended purpose of the column) and WBVar IDs for alleles can always remain consistently in column 8
  • Proposal is to put WBPerson IDs in column 6 for personal communications. Chris & Karen will check if this will work.

Server space in Chen Building

  • It looks like that we will not have a specific space for server computers.


October 8, 2020

Webinar Announcement

Descriptions from GO-CAM models

  • One suggestion for the Alliance is to create a description based on a GO-CAM model
  • Could also micropublish some descriptions (semi-automated?)
  • Can make curators authors of micropublications for GO-CAM models/pathways

Transcription Factors in WormBase

  • WormBase has a ?Transcription_factor class that is currently underutilized
  • Chris spoke with Gary Williams about the status as he has done much of the work on the class
  • Because transcription factors can often be complexes, it was decided to create the ?Transcription_factor class rather than simply an extension of tags to the existing ?Gene class
  • The class seems reasonably complete; it's important to note that some TFs are general transcription factors, not necessarily gene-specific or sequence-specific DNA-binding TFs; it will be good to make that distinction clear to users
  • Chris has compiled a Google sheet to assess the class before Gary W. leaves WB in the next couple of weeks
  • The Google sheet has several tabs/worksheets, including one for the ACEDB data model (and notes about usage of tags), a summary table of associated genes, bound sequence features, existence of other protein-DNA binding data, etc.
  • It would be good to make TF binding info (per gene and globally) more accessibly to our users, maybe via a new widget on gene pages (e.g. list incoming, regulating TFs and, for TF genes themselves, list potential target genes)

October 15, 2020

BioGRID data sharing

  • Rose from BioGRID proposed that BioGRID curate high-throughput C. elegans interaction datasets, capturing confidence scores when available, and making those annotations available to WormBase for regular ingest
  • Will need to consider a few points:
    • BioGRID doesn't curate protein-DNA interactions
    • We don't yet know the turn-around timeline for BioGRID curation of worm datasets; WB may be able to curate them much sooner
  • Chris and Jae will work with Rose et al. to coordinate HTP curation

Enriched genes

  • Some genes are considered "enriched" for an expression cluster data set even if the enrichment was in comparison to another cell or tissue (not whole animal)
  • We should reconsider the ?Expression_cluster model to make sure we can appropriately model and communicate enrichment or subtypes thereof


October 22, 2020

CHEBI

  • Karen spoke to CHEBI personnel on Tuesday
  • CHEBI only has ~2 curators to create new entities
  • CHEBI had submitted a proposal to establish pipelines to process requests from MODs
  • Chemical Translation Service (CTS)
  • OxO = https://www.ebi.ac.uk/spot/oxo/search

Training Webinar

  • Scheduled for tomorrow at 1pm Pacific/4pm Eastern