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
  
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
+
=== 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_September_2020|September]]
+
=== 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_October_2020|October]]
+
=== 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_November_2020|November]]
 
  
 +
== 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
  
= 2021 Meetings =
+
=== Cleaning up bounced emails to outreach@wormbase.org ===
== January 14th, 2021 ==
+
* 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.
 +
<pre>Example: Expr_pattern : "Expr450"
 +
Gene "WBGene00000776"
 +
Protein_description "CPL-1"
  
=== PubMed LinkOut to WormBase (Kimberly) ===
+
Expr_pattern : "Expr552"
* Other databases link out from PubMed to their respective paper pages
+
Gene "WBGene00006528"
* For exampel, https://pubmed.ncbi.nlm.nih.gov/20864032/ links out to GO and MGI paper pages
+
Protein_description "Tubulin alpha"</pre>
* Would like to set this up for WormBase and ultimately for the Alliance, but this will require some developer help
 
* Work on this next month (after AFP and GO grant submissions)?
 
  
 +
** 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>
  
==Dec 3rd, 2020==
 
  
=== Hench et al paper ===
+
* Empty tags. Can remove tags from WB Expression model? Yes
* Thomas Burglin would like the data from paper 00046864 to be included in WB
+
** Cell -> 0 objects
* They want to provide APT profiles (signal intensity along the  anterior-posterior axis over time) as images and movies (time lapse reporter expression)
+
** Expressed_in -> 0 objects
* They have recorded movies for 60 homeobox genes and over 85 genes in total.
+
** Protein -> 0 objects
* If we decide to import the collection, movies, images, and description could be displayed as the collection from Murray: https://wormbase.org/species/all/expr_pattern/Expr10431#012--10
+
** Pseudogene -> 0 objects
  
=== WormBase Papers and Alliance ABC - What papers to add? ===
 
  
* PubMed keyword search 'elegans' (Approve, Reject, Remove)
+
* 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
* Legacy papers from manual concise descriptions
+
**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>
  
  
{| border=1 cell-padding=5 cell-spacing=10
+
**Tiling_array
|-
+
<pre>Example: Expr1040545 - Miller study
! PMID
+
Currently accessible via the schema
! Paper Editor Action
+
https://wormbase.org/species/all/expr_pattern/Expr1040545#0123--10</pre>
! WBPaper ID
 
! Paper Title
 
! Species (For primary papers, species are those for which experiments are reported; does not include sequence alignments)
 
! Primary/Not Primary
 
! Other Paper Editor Flags
 
! Any SVM Positives
 
! Add to ABC
 
! Comments (1)
 
! Comments (2)
 
! Comments (3)
 
|-
 
| 31761535
 
| Approve
 
| 58971
 
| The Hyaluronidase, TMEM2, Promotes ER Homeostasis and Longevity Independent of the UPR ER
 
| Homo sapiens, Caenorhabditis elegans
 
| Primary
 
| Author-Person
 
| Catalytic Activity; Genetic Interactions; Gene Regulation; New Mutant Phenotype; Overexpression Phenotype; RNAi Phenotype
 
| Yes
 
|
 
|
 
|
 
|-
 
| 31868179
 
| Approve
 
| 58999
 
| Measuring the Effects of Bacteria and Chemicals on the Intestinal Permeability of Caenorhabditis elegans
 
| Caenorhabditis elegans
 
| Primary
 
| Author-Person
 
| None
 
| Yes
 
|
 
|
 
|
 
|-
 
| 16919905
 
| Approve
 
| 28426
 
| The trifecta of aging in Caenorhabditis elegans.
 
| Caenorhabditis elegans
 
| Not-primary
 
| Author-Person
 
| N/A
 
| Yes
 
|
 
|
 
|
 
|-
 
| 28744338
 
| Approve
 
| 51561
 
| Role of Kallistatin Treatment in Aging and Cancer by Modulating miR-34a and miR-21 Expression.
 
| Caenorhabditis elegans, Homo sapiens (human, humans), Mus musculus (mice, mouse), Rattus norvegicus (rats)
 
| Not-primary
 
| Author-Person
 
| N/A
 
| Yes
 
|
 
|
 
|
 
|-
 
| 31875562
 
| Reject
 
| None
 
| Intracellular Vesicle Fusion Requires a Membrane-Destabilizing Peptide Located at the Juxtamembrane Region of the v-SNARE
 
| Mus musculus (mouse), Rattus norvegicus (rat)
 
| Primary
 
| N/A
 
| N/A
 
| Not from WormBase, but if added from another group we'd want to indicate that it doesn't have C. elegans experimental data?
 
| Paper shows partial sequence alignment including C. elegans snb-1 in Figure 1A; other species in alignment include M. musculus, H. sapiens, X. leavis, and D. melanogaster
 
| PubMed indexes proteins and their respective species shown in sequence alignments
 
|
 
|-
 
| 31569547
 
| Reject
 
| None
 
| Mapping the Biotransformation of Coumarins through Filamentous Fungi
 
| Cunninghamella elegans, Aspergillus brasiliensis
 
| Primary
 
| N/A
 
| N/A
 
| No
 
|
 
|
 
|
 
|-
 
| 10625658
 
| Entry into WB pre-dated current paper editor
 
| 12789
 
| Both PCE-1/RX and OTX/CRX interactions are necessary for photoreceptor-specific gene expression
 
| Homo sapiens (human), Mus musculus (mouse, mice, murine), Rattus norvegicus (rat, rats), Bos taurus(bovine)
 
| Primary
 
| non-nematode; Author-Person (pre-dated current Author-Person curation criteria)
 
| N/A
 
| Yes
 
| Used in legacy, manual ceh-8 gene description
 
| Used in human manual GO curation (Protein2GO)
 
| 492 non-nematode-flagged papers in WB; not systematically associated with species, but we could do that
 
|-
 
| N/A
 
| Entered into curation database via custom script
 
| 57497
 
| The ER chaperone ENPL-1 acts outside the ER to promote insulin secretion in concert with oxidized ASNA-1.
 
| Caenorhabditis elegans
 
| Not designated
 
| Author-Person
 
| N/A
 
| Yes
 
| 2019 International Worm Meeting Abstract
 
|
 
|
 
|-
 
|}
 
  
*/home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~3300 papers
 
*/home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~100 papers
 
  
*What about WormBase Parasite papers?
+
**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
  
== December 17, 2020 ==
+
===Braun Server Room===
* HGNC IDs/names/etc. in OA
+
* Manager Dave Mathog retired. Uncertain about its management or fate.
* What shows up in autocomplete? What shows up in term info?
 
* Juancarlos will need to get curator preferences for autocomplete list and term info list.
 
* Wen will update the Alliance Simplemine to provide updated info to Postgres/OA
 
** "AGR Gene ID" and "AGR Gene Name" will be changed to "Gene ID", "Gene Name", "Gene Symbol"
 

Latest revision as of 17:40, 26 February 2021

Previous Years

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2011 Meetings

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2014 Meetings

2015 Meetings

2016 Meetings

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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.