Difference between revisions of "WormBase-Caltech Weekly Calls"

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*Can we map everything to the proposed hierarchy or do we need to add some more classes?
 
*Can we map everything to the proposed hierarchy or do we need to add some more classes?
  
=== Author data in Expr_pattern===
+
=== Personal communications in Expr_pattern ===
 
* 27 objects missing reference (personal communications)
 
* 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 (and other specs) must be a publication, as defined by the 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.
 
** 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 (and other specs) must be a publication, as defined by the 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.
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** 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).  
 
** 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.
 
** Daniela can go over the entire list and contact the authors for such cases.
 +
** Are personal communications used in other classes?
 +
 +
=== 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?
 +
 +
=== 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 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).

Revision as of 17:48, 10 February 2021

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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?

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 (and other specs) must be a publication, as defined by the 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?

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?

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 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).