Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
  
 +
= 2021 Meetings =
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
 
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
+
== Feb 4th, 2021 ==
 +
===How the "duplicate" function works in OAs with respect to object IDs (Ranjana and Juancarlos)===
 +
*A word of caution: when you duplicate a row, for those OAs with Object IDs (eg., WBGenotype00000014) note that the object ID gets duplicated as well and does not advance to the next ID like the PGID does
 +
*If you do use the "duplicate" function, remember to manually change the Object ID
 +
* We can implement checks to make sure distinct annotations/objects don't share the same ID
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
+
=== GAF Wiki and headers ===
 +
* Any more comments about the Wiki page and the proposal? https://wiki.wormbase.org/index.php/WormBase_gene_association_file
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
=== Missing references in expression GAFs ===
 +
* ~300 missing from anatomy association file and ~45 missing from development association file
 +
* Daniela looking into missing refs; many are personal communications or very old papers
 +
* Will change ?Expr_pattern model to possibly remove ?Author reference and add in a ?Person reference instead
 +
** 399 objects in WS279 reference an author; Daniela will take a look
 +
* Would be good to have some reference for those objects in the GAF file on the FTP site; could use WBPerson when ready
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
 
  
 +
== Feb 11th, 2021 ==
 +
=== Alliance Literature Paper Tags ===
 +
*What do we definitely want to transfer to the Alliance?
 +
*Alliance literature group [https://docs.google.com/spreadsheets/d/1d3Y73x1BFiARkbxrvPPX2tCh5rFeBQRoBMHOcaXmijA/edit#gid=1866989939 spreadsheet]
 +
*Current flags vs legacy flags
 +
*Can we map everything to the proposed hierarchy or do we need to add some more classes?
 +
*Kimberly will review existing tags/flags to sort out what we know we need and what is questionable
  
== June 4, 2020 ==
+
=== Personal communications in Expr_pattern ===
 +
* 27 objects missing reference (personal communications)
 +
** Even if we capture the WBPerson in the Person tag, how are we submitting these to Alliance? The evidence required by the expression JSON spec https://github.com/alliance-genome/agr_schemas/blob/master/ingest/expression/wildtypeExpressionModelAnnotation.json (and other specs) must be a publication, as defined by the publicationRef.json https://github.com/alliance-genome/agr_schemas/blob/master/ingest/publicationRef.json. If there's no PMID for a publication listed as evidence, a MOD ID will suffice for the "publicationId" but we have no WBPaperID created for such  objects.
 +
** One way to solve this: Daniela can go over the list and see if the initial personal communication resulted in  a publication later on. One example is Expr181 (expression of cpl-1 in hypodermis and pharynx), communicated  via email by Sarwar Hashmi in 2000, Expr450 (expression of cpl-1 in hypodermis, intestine) communicated by  Britton in 2001. The pattern was published in 2002 by Hashmi and Britton in 2002 (WBPaper00005099). Daniela can then associate WBPaper00005099 to Expr181 and Expr450.
 +
** The solution above still  does not work for all: An example is lad-2 personal communication from Oliver Hobert, 2002. Later published by Lishia Chen (2008). Removing Oliver’s personal communication will remove evidence of data provenance from the Hobert’s lab. Unless Oliver published this in a paper that was eluded from our flagging system (e.g. flagged SVM negative).
 +
** Daniela can go over the entire list and contact the authors for such cases.
 +
** Are personal communications used in other classes?
 +
** Action item: Daniela will add Persons in the person tag for such communications. Will request a model change to Hinxton. Will ask Magda to populate column 6 of the GAF file with Author data. Will add a request for the DQMs to allow Persons in the 'Evidence' in the JSON in addition to Papers
  
=== Citace (tentative) upload ===
+
=== Author data in Expr_pattern ===
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
+
* 399 Expression objects have the author tag populated. Most of them were submitted even prior Wen started working on Expr_pattern.
* Citace upload to Hinxton on Friday, July 10th
+
** out of 399 objects, we have 32 for which the authors partially match. One example is Expr60, which has Bauer as extra author in the .ace file. Bauer is not listed as author in the paper.
 +
** should we keep the author info and store it in the Person tag? Even if we do, how are we submitting these to Alliance? And should we at all? This is legacy data
 +
** Decision: we can remove the authors and add in the remarks the historic info
  
=== Caltech reopening ===
+
=== Date tag in Expr_pattern ===
* Paul looking to get plan approved
+
* The date tag seems to be  populated for objects that have authors (above) to probably capture when the submission occurred.
* People that want to come to campus need to watch training video
+
* In addition, Date is populated for a large scale submission from Ian hope (2006-03), later published.
* Masks available in Paul's lab
+
* We can still keep this info as is for WB (currently stored in citace minus) but what are we going to do for the Alliance submission? The tag was used last time in 2006 for the Hope study but prior to this was used in  the ‘90s (1990, 1998).
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
+
** We  can get rid of date, too. And pull the fo for the ones for which authors do not match
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
 
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
 
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
 
* Also, need to submit who you were in contact with for contact tracing
 
* Form is used all week, and hold on to it until asked to be submitted
 
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
 
  
=== Nameserver ===
+
=== Proposed WormBase metrics page ===
* Nameserver was down
+
* Inspired by MGI's stats page:
* CIT curators would still like to have a single form to interact with
+
** http://www.informatics.jax.org/mgihome/homepages/stats/all_stats.shtml
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
+
* Sibyl and Paulo working on. Prototype here: https://master.d25n59ij2csrbn.amplifyapp.com/
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
+
** Current prototype is C. elegans specific
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
+
* Chris is collecting ideas and queries here:
* Hinxton is pulling in CGC strains, how often?
+
** https://docs.google.com/spreadsheets/d/1OeZuMRSHelVD7tGRIxEkCKOyDaBPN29wrGbNU3TGxKU/edit?usp=sharing
* Caltech could possibly get a block of IDs
+
* Could eventually be used across the Alliance
  
=== Alliance SimpleMine ===
 
* Any updates? 3.1 feature freeze is tomorrow
 
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
 
  
 +
== Feb 18th, 2021 ==
  
== June 11, 2020 ==
+
=== CenGen data ===
 +
* How can we incorporate the CenGen data into WormBase pages? i.e. provide users info:
 +
** Per gene: what cells express this gene?
 +
** Per cell: what genes are expressed in this cell?
 +
** May be derived from Eduardo's data processing
 +
* CenGen has a weekly call: have invited Wen, Daniela, and Raymond
 +
** Too much for all three to join?
 +
* Good to establish healthy boundaries for responsibilities
 +
* Do they want to collaborate or no?
 +
* We can link to the main CenGen page; once gene-level data is available we can consume and make available
 +
* Eduardo's tool is one WormBase tool for processing and providing CenGen data; will make them aware
 +
* Ultimately this data (and its presentation) will need to get into the Alliance; may remain a WB-specific/portal feature for the near future
 +
* Alaska? Probably won't be maintained
  
=== Name Service ===
+
=== Cleaning up bounced emails to outreach@wormbase.org ===
* Testing site now up; linked to Mangolassi
+
* Many unread messages (~140) in inbox
* CGI from Juancarlos not accepting all characters, including double quotes like "
+
* Many of those are bounced emails from AFP pipeline and webinar announcements
* Example submission that fails via CGI
+
* If relevant people could review those bounced emails and, as appropriate, add people or email addresses to the Omit list using the Omit Form CGI (http://tazendra.caltech.edu/~postgres/cgi-bin/omit_form.cgi) that would be appreciated.
WBPaper000XXXX; genotype: blah::' " ` / < > [ ] { } ? , . ( ) * ^ & % $ # @ ! \ | &alpha; &beta; Ω ≈ µ ≤ ≥ ÷ æ … ˚ ∆ ∂ ß œ ∑ † ¥ ¨ ü i î ø π “  ‘ « • – ≠ Å ´ ∏ » ± — ‚ °
 
* Juancarlos will look into and try to fix
 
  
=== Alliance Literature group ===
 
* Textpresso vs. OntoMate vs. PubMed
 
* Still some confusion about what the different tasks can be performed in each tool
 
* Working on collecting different use cases on spreadsheet
 
* Sentence-based search is big strength of Textpresso
 
* At latest meeting performed some large searches for OntoMate and Textpresso
 
* Literature acquisition: still needs work
 
** Using SVM vs. Textpresso search to find relevant papers
 
** Species based SVM? Currently use string matching to derive different corpora
 
** Finding genes and determining which species those genes belong to?
 
  
=== Alliance priorities? ===
+
== Feb 25th, 2021 ==
* Transcription regulatory networks
 
* Interactions can focus on network viewer eventually
 
** May want different versions/flavors of interaction viewers
 
** May also want to work closely with GO and GO-CAMs
 
* Gene descriptions can focus on information poor genes, protein domains, etc.
 
  
=== Sandbox visual cues ===
+
===Expr_pattern clean up===
* Juancarlos and Daniela will discuss ways to provide visual cues that a curator is on a sandbox form (on Mangolassi) vs live form (on Tazendra)
+
* Seldom populated  tags. Can we move the associated info into remarks and get rid of the tag? This is in view of the Alliance import
* AFP and Micropub dev sites have indicators
+
** Protein_description 33 objects -> Decision: Move to remarks -> Done DR 2021/02/26. Redundant info such as CPL-1 in Protein_description and CPL-1 in gene name were omitted.
* Could play with changing the background color? Maybe too hard to look at?
+
<pre>Example: Expr_pattern : "Expr450"
* Change the color of the title of the form, e.g. the OA?
+
Gene "WBGene00000776"
* Will add red text "Development Site" at top of the OA form
+
Protein_description "CPL-1"
 +
 
 +
Expr_pattern : "Expr552"
 +
Gene "WBGene00006528"
 +
Protein_description "Tubulin alpha"</pre>
 +
 
 +
** Sequence 12 objects -> Decision: Move to remarks
 +
<pre>Example: Expr_pattern : "Expr12"
 +
      Gene "WBGene00003976"
 +
      Sequence "Z28377|Z28375|Z28376"</pre>
 +
 
 +
** Laboratory 23 objects -> can infer via publication -> Decision: good to ignore
 +
<pre>Example: Expr_pattern : "Expr87"
 +
        …
 +
Laboratory "ML"
 +
Gene "WBGene00003012"</pre>
 +
 
 +
 
 +
* Empty tags. Can remove tags from WB Expression model? Yes
 +
** Cell -> 0 objects
 +
** Expressed_in -> 0 objects
 +
** Protein -> 0 objects
 +
** Pseudogene -> 0 objects
 +
 
 +
 
 +
* Microarray, Tiling Array, RNAseq associations -> Discuss with the Expression WG how to bring in images for these and treat as image  objects liked to the high  throughput data
 +
**Microarray, Microarray_results
 +
<pre>example: Expr1050000 -Yanai study
 +
Currently accessible via the schema
 +
https://wormbase.org/species/c_briggsae/expr_pattern/Expr1050000#0123--10</pre>
 +
 
 +
 
 +
**Tiling_array
 +
<pre>Example: Expr1040545 - Miller study
 +
Currently accessible via the schema
 +
https://wormbase.org/species/all/expr_pattern/Expr1040545#0123--10</pre>
 +
 
 +
 
 +
**RNASeq
 +
<pre>Example:
 +
Expr_pattern : "Expr1142792" - Yanai study
 +
Gene "WBGene00007063"
 +
RNASeq "RNASeq_Study.SRP029448"
 +
Currently accessible  via the schema
 +
https://wormbase.org/species/all/expr_pattern/Expr1142792#0123--10</pre>
 +
 
 +
* Others
 +
** Historical_gene -> 51 objects. How are historical gene tags treated for other classes in Alliance? -> keep in Alliance and maintain the same mechanism when  curation will be  moved over
 +
** EPIC -> Ad hoc Tag for Murray, no correspondence with method ontology terms -> ok to ignore
 +
** Species -> what are we doing with non elegans annotations?
 +
** MovieURL -> 32 - Mohler -> move to  movies -> talk again with Raymond
 +
 
 +
===Braun Server Room===
 +
* Manager Dave Mathog retired. Uncertain about its management or fate.

Latest revision as of 17:40, 26 February 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings


2021 Meetings

January


Feb 4th, 2021

How the "duplicate" function works in OAs with respect to object IDs (Ranjana and Juancarlos)

  • A word of caution: when you duplicate a row, for those OAs with Object IDs (eg., WBGenotype00000014) note that the object ID gets duplicated as well and does not advance to the next ID like the PGID does
  • If you do use the "duplicate" function, remember to manually change the Object ID
  • We can implement checks to make sure distinct annotations/objects don't share the same ID

GAF Wiki and headers

Missing references in expression GAFs

  • ~300 missing from anatomy association file and ~45 missing from development association file
  • Daniela looking into missing refs; many are personal communications or very old papers
  • Will change ?Expr_pattern model to possibly remove ?Author reference and add in a ?Person reference instead
    • 399 objects in WS279 reference an author; Daniela will take a look
  • Would be good to have some reference for those objects in the GAF file on the FTP site; could use WBPerson when ready


Feb 11th, 2021

Alliance Literature Paper Tags

  • What do we definitely want to transfer to the Alliance?
  • Alliance literature group spreadsheet
  • Current flags vs legacy flags
  • Can we map everything to the proposed hierarchy or do we need to add some more classes?
  • Kimberly will review existing tags/flags to sort out what we know we need and what is questionable

Personal communications in Expr_pattern

  • 27 objects missing reference (personal communications)
    • Even if we capture the WBPerson in the Person tag, how are we submitting these to Alliance? The evidence required by the expression JSON spec https://github.com/alliance-genome/agr_schemas/blob/master/ingest/expression/wildtypeExpressionModelAnnotation.json (and other specs) must be a publication, as defined by the publicationRef.json https://github.com/alliance-genome/agr_schemas/blob/master/ingest/publicationRef.json. If there's no PMID for a publication listed as evidence, a MOD ID will suffice for the "publicationId" but we have no WBPaperID created for such objects.
    • One way to solve this: Daniela can go over the list and see if the initial personal communication resulted in a publication later on. One example is Expr181 (expression of cpl-1 in hypodermis and pharynx), communicated via email by Sarwar Hashmi in 2000, Expr450 (expression of cpl-1 in hypodermis, intestine) communicated by Britton in 2001. The pattern was published in 2002 by Hashmi and Britton in 2002 (WBPaper00005099). Daniela can then associate WBPaper00005099 to Expr181 and Expr450.
    • The solution above still does not work for all: An example is lad-2 personal communication from Oliver Hobert, 2002. Later published by Lishia Chen (2008). Removing Oliver’s personal communication will remove evidence of data provenance from the Hobert’s lab. Unless Oliver published this in a paper that was eluded from our flagging system (e.g. flagged SVM negative).
    • Daniela can go over the entire list and contact the authors for such cases.
    • Are personal communications used in other classes?
    • Action item: Daniela will add Persons in the person tag for such communications. Will request a model change to Hinxton. Will ask Magda to populate column 6 of the GAF file with Author data. Will add a request for the DQMs to allow Persons in the 'Evidence' in the JSON in addition to Papers

Author data in Expr_pattern

  • 399 Expression objects have the author tag populated. Most of them were submitted even prior Wen started working on Expr_pattern.
    • out of 399 objects, we have 32 for which the authors partially match. One example is Expr60, which has Bauer as extra author in the .ace file. Bauer is not listed as author in the paper.
    • should we keep the author info and store it in the Person tag? Even if we do, how are we submitting these to Alliance? And should we at all? This is legacy data
    • Decision: we can remove the authors and add in the remarks the historic info

Date tag in Expr_pattern

  • The date tag seems to be populated for objects that have authors (above) to probably capture when the submission occurred.
  • In addition, Date is populated for a large scale submission from Ian hope (2006-03), later published.
  • We can still keep this info as is for WB (currently stored in citace minus) but what are we going to do for the Alliance submission? The tag was used last time in 2006 for the Hope study but prior to this was used in the ‘90s (1990, 1998).
    • We can get rid of date, too. And pull the fo for the ones for which authors do not match

Proposed WormBase metrics page


Feb 18th, 2021

CenGen data

  • How can we incorporate the CenGen data into WormBase pages? i.e. provide users info:
    • Per gene: what cells express this gene?
    • Per cell: what genes are expressed in this cell?
    • May be derived from Eduardo's data processing
  • CenGen has a weekly call: have invited Wen, Daniela, and Raymond
    • Too much for all three to join?
  • Good to establish healthy boundaries for responsibilities
  • Do they want to collaborate or no?
  • We can link to the main CenGen page; once gene-level data is available we can consume and make available
  • Eduardo's tool is one WormBase tool for processing and providing CenGen data; will make them aware
  • Ultimately this data (and its presentation) will need to get into the Alliance; may remain a WB-specific/portal feature for the near future
  • Alaska? Probably won't be maintained

Cleaning up bounced emails to outreach@wormbase.org

  • Many unread messages (~140) in inbox
  • Many of those are bounced emails from AFP pipeline and webinar announcements
  • If relevant people could review those bounced emails and, as appropriate, add people or email addresses to the Omit list using the Omit Form CGI (http://tazendra.caltech.edu/~postgres/cgi-bin/omit_form.cgi) that would be appreciated.


Feb 25th, 2021

Expr_pattern clean up

  • Seldom populated tags. Can we move the associated info into remarks and get rid of the tag? This is in view of the Alliance import
    • Protein_description 33 objects -> Decision: Move to remarks -> Done DR 2021/02/26. Redundant info such as CPL-1 in Protein_description and CPL-1 in gene name were omitted.
Example: Expr_pattern : "Expr450"
	Gene	 "WBGene00000776"
	Protein_description	 "CPL-1"

	Expr_pattern : "Expr552"
	Gene	 "WBGene00006528"
	Protein_description	 "Tubulin alpha"
    • Sequence 12 objects -> Decision: Move to remarks
Example: Expr_pattern : "Expr12"
		      Gene	 "WBGene00003976"
		      Sequence	 "Z28377|Z28375|Z28376"
    • Laboratory 23 objects -> can infer via publication -> Decision: good to ignore
Example: Expr_pattern : "Expr87"
        …
	Laboratory	 "ML"
	Gene	 "WBGene00003012"


  • Empty tags. Can remove tags from WB Expression model? Yes
    • Cell -> 0 objects
    • Expressed_in -> 0 objects
    • Protein -> 0 objects
    • Pseudogene -> 0 objects


  • Microarray, Tiling Array, RNAseq associations -> Discuss with the Expression WG how to bring in images for these and treat as image objects liked to the high throughput data
    • Microarray, Microarray_results
example: Expr1050000 -Yanai study
Currently accessible via the schema
https://wormbase.org/species/c_briggsae/expr_pattern/Expr1050000#0123--10


    • Tiling_array
Example: Expr1040545 - Miller study
Currently accessible via the schema
https://wormbase.org/species/all/expr_pattern/Expr1040545#0123--10


    • RNASeq
Example: 
	Expr_pattern : "Expr1142792" - Yanai study
	Gene	 "WBGene00007063"
	RNASeq	 "RNASeq_Study.SRP029448"
Currently accessible  via the  schema
https://wormbase.org/species/all/expr_pattern/Expr1142792#0123--10
  • Others
    • Historical_gene -> 51 objects. How are historical gene tags treated for other classes in Alliance? -> keep in Alliance and maintain the same mechanism when curation will be moved over
    • EPIC -> Ad hoc Tag for Murray, no correspondence with method ontology terms -> ok to ignore
    • Species -> what are we doing with non elegans annotations?
    • MovieURL -> 32 - Mohler -> move to movies -> talk again with Raymond

Braun Server Room

  • Manager Dave Mathog retired. Uncertain about its management or fate.