Difference between revisions of "WormBase-Caltech Weekly Calls"

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= Previous Years =
 +
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
Line 5: Line 7:
 
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
 +
 +
 +
= 2021 Meetings =
 +
 +
[[WormBase-Caltech_Weekly_Calls_January_2021|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 ===
 +
* Any more comments about the Wiki page and the proposal? https://wiki.wormbase.org/index.php/WormBase_gene_association_file
  
2013 Meetings
+
=== 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_January_2013|January]]
+
== 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
  
[[WormBase-Caltech_Weekly_Calls_February_2013|February]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_March_2013|March]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_April_2013|April]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_May_2013|May]]
+
=== Proposed WormBase metrics page ===
 +
* Inspired by MGI's stats page:
 +
** http://www.informatics.jax.org/mgihome/homepages/stats/all_stats.shtml
 +
* Sibyl and Paulo working on. Prototype here: https://master.d25n59ij2csrbn.amplifyapp.com/
 +
** Current prototype is C. elegans specific
 +
* Chris is collecting ideas and queries here:
 +
** https://docs.google.com/spreadsheets/d/1OeZuMRSHelVD7tGRIxEkCKOyDaBPN29wrGbNU3TGxKU/edit?usp=sharing
 +
* Could eventually be used across the Alliance
  
[[WormBase-Caltech_Weekly_Calls_June_2013|June]]
 
  
[[WormBase-Caltech_Weekly_Calls_July_2013|July]]
+
== 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
  
= August 1, 2013 =
+
=== 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.
  
Quarterly Progress Reports
 
*Capturing curation stats from the Curation Status form
 
*What data types do we want to capture curation stats for that we are not currently?
 
*We have frequent database dumps that can be read for stats
 
*We can capture the stats table statically on a regular basis (daily)
 
** form at http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi
 
** cronjob to get data from "Curation Statistics Page" button at
 
** /home/acedb/cron/curation_stats/get_daily_curation_stats.pl
 
** deposits files every day at 5am to :
 
** /home/acedb/cron/curation_stats/files/
 
  
RNA-Seq and Tiling Array data
+
== Feb 25th, 2021 ==
*Data in SPELL
 
*Wen found a lot more non modENCODE data sets
 
*May use SVM for expression cluster data
 
*Gene IDs can be found from original paper or data set
 
*Up-to-date mapping to genes is not currently done
 
  
 +
===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.
 +
<pre>Example: Expr_pattern : "Expr450"
 +
Gene "WBGene00000776"
 +
Protein_description "CPL-1"
  
AMIGO2 (Wormbase Ontology Browser)
+
Expr_pattern : "Expr552"
*Raymond and Juancarlos have taken AMIGO2 infrastructure to make an ontology browser for integration into WormBase
+
Gene "WBGene00006528"
*GO Term [http://mangolassi.caltech.edu/~azurebrd/cgi-bin/testing/amigo/wobr/amigo.cgi focus page demo]
+
Protein_description "Tubulin alpha"</pre>
*Graph view shows path to root (DAG view)
 
*Inferred tree view shows:
 
**Ancestor terms, no annotation numbers
 
**Main term and children, with annotation numbers (inferred, term and descendant annotations)
 
**Annotation numbers link to list of genes
 
**Will not show "direct" annotations, only inferred
 
*Sibling term displays: list parents with option to expand to see siblings of the main term
 
*Separate [http://mangolassi.caltech.edu/~azurebrd/cgi-bin/testing/amigo/wobr/treeExpand.cgi expandable/collapsible tree] of ontology ("Browse entire ontology")
 
*Widget can be coded to integrate the ontology browser
 
  
 +
** Sequence 12 objects -> Decision: Move to remarks
 +
<pre>Example: Expr_pattern : "Expr12"
 +
      Gene "WBGene00003976"
 +
      Sequence "Z28377|Z28375|Z28376"</pre>
  
Paper Categorization
+
** Laboratory 23 objects -> can infer via publication -> Decision: good to ignore
*Word frequency
+
<pre>Example: Expr_pattern : "Expr87"
**We chose papers from the Author First Pass (AFP) list with 'stress'
+
        …
**About 40 papers in list, varied topics ('stress' is a broad term)
+
Laboratory "ML"
**Curation essentially now complete for most data types
+
Gene "WBGene00003012"</pre>
**Expanding beyond AFP?
 
*Chris will draw up preliminary tree of topics and send around
 
**We can discuss, edit, and expand as a group
 
**We want to 1) Collect positive and negative training papers and 2) Manually generate a list of key words to use for training
 
*Todd proposes for paper pages on WormBase:
 
**Show a table of flagged data types for a paper?
 
**Give users a sense of where paper is in the curation pipeline
 
  
  
 +
* Empty tags. Can remove tags from WB Expression model? Yes
 +
** Cell -> 0 objects
 +
** Expressed_in -> 0 objects
 +
** Protein -> 0 objects
 +
** Pseudogene -> 0 objects
  
= August 8, 2013 =
 
  
New Spica now has a closed (private) 'citace' account
+
* 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
*citpub account is accessible to everyone with password
+
**Microarray, Microarray_results
*People can create their own spica accounts
+
<pre>example: Expr1050000 -Yanai study
*Personal accounts are encouraged so as to avoid saving changes to citpub database
+
Currently accessible via the schema
 +
https://wormbase.org/species/c_briggsae/expr_pattern/Expr1050000#0123--10</pre>
  
  
Worm Ontology Browser
+
**Tiling_array
*Raymond has set up a server
+
<pre>Example: Expr1040545 - Miller study
*Browsing should be faster now
+
Currently accessible via the schema
*Should be transferable to the Amazon cloud
+
https://wormbase.org/species/all/expr_pattern/Expr1040545#0123--10</pre>
*Raymond will establish a WormBase development environment
 
  
  
Curation priorities
+
**RNASeq
*Paper categorization
+
<pre>Example:
*Depth vs breadth of topics (number of papers?)
+
Expr_pattern : "Expr1142792" - Yanai study
**'Stress' has been a pilot topic, but is a very broad topic
+
Gene "WBGene00007063"
**Will work on generating subcategories of 'Stress' on the [http://wiki.wormbase.org/index.php/WormBase_Paper_Categorization Paper Categorization Wiki] page
+
RNASeq "RNASeq_Study.SRP029448"
**Curators can analyze the Author First Pass list of 'Stress' papers as well as entire backlog/corpus
+
Currently accessible  via the schema
*Goals of 'covering' a topic?
+
https://wormbase.org/species/all/expr_pattern/Expr1142792#0123--10</pre>
**'Complete' and vetted process page, Wikipathway
 
**Promote 'featured processes' on WormBase for a given release
 
*We should collect positive and negative papers (for a given topic) for SVM training
 
  
 +
* 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
  
Curator's should check CGIs
+
===Braun Server Room===
*Submission forms and other CGIs may have been altered
+
* 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.