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]]
 
  
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
+
== 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_July_2020|July]]
+
=== 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
  
==July 9th, 2020==
+
=== Date tag in Expr_pattern ===
===Gene names issue in SimpleMine and other mining tools===
+
* The date tag seems to be populated for objects that have authors (above) to probably capture when the submission occurred.
*Wen: Last week, Jonathan Ewbank raised the issue of gene names that may refer to multiple objects.
+
* In addition, Date is populated for a large scale submission from Ian hope (2006-03), later published.
*this can be an issue for multiple data mining tools including WormMine, BioMart, and Gene Set Enrichment.
+
* 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).
*Perhaps have a standalone approach to check if any gene name among a list may refer to multiple objects (users check their name lists before submitting them to any data mining tool).
+
** We  can get rid of date, too. And pull the fo for the ones for which authors do not match
*Jae: The public name issue has heterogeneous natures. That means there may be no single solution to solve all those problems.  
 
*Gene list curation from high-throughput studies, confusing usage of public names probably less than 2% (still cannot be ignored). See examples below--
 
**single public name is assigned to multiple WBgene ID, Wen has a list of these genes
 
**overlapped or dicistronic genes, ex. mrpl-44 and F02A9.10
 
**overlapped or dicistronic, but has a single sequence name, examples:
 
    exos-4.1 and tin-9.2 (B0564.1)
 
    eat-18 and lev-10 (Y105E8A.7)
 
    cha-1 and unc-17 (ZC416.8)
 
  
**simple confusion from authors, ex. mdh-1 and mdh-2
+
=== Proposed WormBase metrics page ===
*One of the most significant problems is a propagation to other DB and papers of  these gene name issues.
+
* Inspired by MGI's stats page:
*We can make a special note for each gene page, but the people using batch analysis could not catch that easily.
+
** http://www.informatics.jax.org/mgihome/homepages/stats/all_stats.shtml
*Conclusion: Jae and Wen will work on a tool that lets Users "sanitize" their gene lists before submission to data mining tools. They will also write a microPub explaining this issue to the community.
+
* 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
  
===Wormicloud===
 
*Please test and leave any feedback on the word cloud tool (Wormicloud), https://wormicloud.textpressolab.com/
 
*Valerio and Jae have worked on a tool that uses data in Textpresso; given a keyword, eg. "transposon", the tool generates a word cloud and word trend.
 
*Any keyword can generate a graph that plots trends of occurence across the years in publication abstracts.
 
  
===Noctua 2.0 form ready to use===
+
== Feb 18th, 2021 ==
*Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways
 
  
===Nightly names service updates to postgres===
+
=== CenGen data ===
*Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.
+
* 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.
  
==July 16th, 2020==
 
===Citing ontologies and their versions===
 
*Came up in the context of the Alliance: It would be best practice to provide users with the list of ontologies used and their versions/date.
 
*If WB ontology developers could make sure their ontology file headers (WB anatomy ontology, WB life stage, etc.) conformed to obo file header specifications, then it would be easy to pull in version and date information into the Alliance.
 
*Some useful links
 
**http://www.obofoundry.org/principles/fp-004-versioning.html
 
**http://obo-dashboard-test.ontodev.com/ (you can see that wbbt, wbls version metadata attribute is generating a warning).
 
**Note: OBO-foundry may not have been updated, but good practice to check your headers, anyway.
 
* Chris worked with Nico yesterday to update the ODK version for WBbt and WBls; versioning should be fine now (once the OBO dashboard runs again (hasn't run since February))
 
* Important point: the GitHub release version date tag (e.g. "v2020-06-30") needs to match the ODK release date (as stored in the OBO and OWL file headers)
 
** There are some existing mismatches, Chris is cataloging them now
 
  
=== Gene Name Sanitizer ===
+
== Feb 25th, 2021 ==
* Would be good to always (when possible) make users aware of name ambiguities
 
* Wen will keep the "Multiple Output" section at the bottom of SimpleMine output
 
* The gene name sanitizer will be built as a stand alone tool
 
* Important to include history of gene names
 
  
=== Tools linking to SimpleMine ===
+
===Expr_pattern clean up===
* Vennter and other tools link to SimpleMine with hard coded field/column names; we should have more dynamic/robust linking without relying on hard coded field names
+
* 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"
  
 +
Expr_pattern : "Expr552"
 +
Gene "WBGene00006528"
 +
Protein_description "Tubulin alpha"</pre>
  
== July 23rd, 2020 ==
+
** Sequence 12 objects -> Decision: Move to remarks
 +
<pre>Example: Expr_pattern : "Expr12"
 +
      Gene "WBGene00003976"
 +
      Sequence "Z28377|Z28375|Z28376"</pre>
  
=== Alliance pathway working group ===
+
** Laboratory 23 objects -> can infer via publication -> Decision: good to ignore
* Integrating pathways from GO-CAM, Reactome, Meta-cyc
+
<pre>Example: Expr_pattern : "Expr87"
* Raymond, Chris interested
+
        …
* Laurent-Philippe wants to work on user-friendly displays of GO-CAM models
+
Laboratory "ML"
 +
Gene "WBGene00003012"</pre>
  
=== Working on Alliance paralogs ===
 
* In the works
 
  
=== Summer project ===
+
* Empty tags. Can remove tags from WB Expression model? Yes
* Neuronal regulation of dauer formation
+
** Cell -> 0 objects
* Fernando has been collecting literature
+
** Expressed_in -> 0 objects
* Will work on GO-CAMs and build a relevant model(s)
+
** Protein -> 0 objects
 +
** Pseudogene -> 0 objects
  
=== Disk failures ===
 
* Brought down wobr1, wobr2, spica
 
* Raymond has upgraded OS from 8-year old OS, beefed up hardware
 
* wobr1 and wobr2 are back to full function
 
* Having trouble bringing back spica on the network
 
  
=== WormMine updates ===
+
* 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
* Paulo working on importing new classes: SO_term, disease_model_annotation, transgene, construct, molecule, wbprocess, interaction
+
**Microarray, Microarray_results
* Chris is working with Paulo to move them in; talk to Paulo and/or Chris if interested in discussing
+
<pre>example: Expr1050000 -Yanai study
* Spreadsheet to map ACEDB/XML attributes to ACEDB attributes: https://docs.google.com/spreadsheets/d/1-fpzVU3rblN3Rp38wQjd3121z3rVkxmR9_i5T0EIPNo/edit?usp=sharing
+
Currently accessible via the schema
* Still have some loader headaches
+
https://wormbase.org/species/c_briggsae/expr_pattern/Expr1050000#0123--10</pre>
* Do we know the usage stats of WormMine?
 
* BlueGenes
 
** New interface coming; in the works, not sure when it will be fully functional
 
** Lacks some useful features in the current Intermine (Intermine devs are aware and working on it)
 
** Does BlueGenes have better loading? Don't know
 
  
=== WB move to Chen building ===
+
 
* Need to sort out what will get moved over; will be more limited space
+
**Tiling_array
* How late can move happen? If all is OK, move will happen 2nd week of January 2021
+
<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

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2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

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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.