Manager Call 2020-06-10: Difference between revisions

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* Recent paper published in Bioinformatics: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa548/5848643
* Recent paper published in Bioinformatics: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa548/5848643
"We applied the approach to 20 commonly-studied species in two recent UniProt-GOA releases and identified 250 potential misannotations in the 2018-11-6 release, where only 25% of them were corrected in the 2019-6-3 release. Importantly, 56% of the misannotations are “Inferred from Biological aspect of Ancestor (IBA)” "  
"We applied the approach to 20 commonly-studied species in two recent UniProt-GOA releases and identified 250 potential misannotations in the 2018-11-6 release, where only 25% of them were corrected in the 2019-6-3 release. Importantly, 56% of the misannotations are “Inferred from Biological aspect of Ancestor (IBA)” "  
* http://baderlab.org/GeneSets recommends using Human_GOBP_AllPathways_no_GO_iea_{Date}_{ID}.gmt – (recommended file) contains only genesets from GO biological process excluding annotations that have evidence code IEA (inferred from electronic annotation), ND (no biological data available), and RCA (inferred from reviewed computational analysis) and all pathway resources.
*  
* GOA is most often seen as the original source of GO data (site and ftp are easier to use)
 
Note: it would have been better if the article also mentioned the percentage as this is a very low number overall.
Note: it would have been better if the article also mentioned the percentage as this is a very low number overall.


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* we need to be doing more to vet all of the different sources that provide GO
* we need to be doing more to vet all of the different sources that provide GO
* even our SAB members may sometimes do dubious things with GO - this is on us rather than them though
* even our SAB members may sometimes do dubious things with GO - this is on us rather than them though
== Proposed Organization ==
Paul & Chris presenting the proposed organization for the group, with Product Owners and Tech Leads, as well as the project main tasks/priorities


==Update on previous round of priorities==
==Update on previous round of priorities==
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Actions for next GO User meeting ? Is it a priority ? Need to improve API & API related documentation, create interactive notebooks, etc.
Actions for next GO User meeting ? Is it a priority ? Need to improve API & API related documentation, create interactive notebooks, etc.
Tech leads: update the document when tasks are done. This will be needed to set the next priorities.


== Noctua Planning Meeting ==
== Noctua Planning Meeting ==

Latest revision as of 11:37, 10 June 2020

Agenda

  • Agenda: Pascale
  • Minutes: Laurent-Philippe
  • Present:
  • Regrets:

New management structure

Action on BLM?

SGD, others participating in https://www.shutdownstem.com/ https://connect.medrxiv.org/news/2020/06/09/strike4blacklives https://blogs.cornell.edu/arxiv/2020/06/08/strike4blacklives/

Action: Suzi will send a post on twitter

'Public image' of GO data quality

"We applied the approach to 20 commonly-studied species in two recent UniProt-GOA releases and identified 250 potential misannotations in the 2018-11-6 release, where only 25% of them were corrected in the 2019-6-3 release. Importantly, 56% of the misannotations are “Inferred from Biological aspect of Ancestor (IBA)” "

Note: it would have been better if the article also mentioned the percentage as this is a very low number overall.

From Chris: Some lessons here:

  • bioinformaticians like simple formats like gmt
  • we need to be doing more to vet all of the different sources that provide GO
  • even our SAB members may sometimes do dubious things with GO - this is on us rather than them though

Proposed Organization

Paul & Chris presenting the proposed organization for the group, with Product Owners and Tech Leads, as well as the project main tasks/priorities

Update on previous round of priorities

https://docs.google.com/spreadsheets/d/1lZO0cf64_eufimUhEdcpiZMGEmvF6_7BW-GQWBXR3Mw/edit#gid=199463565

Actions for next GO User meeting ? Is it a priority ? Need to improve API & API related documentation, create interactive notebooks, etc.

Tech leads: update the document when tasks are done. This will be needed to set the next priorities.

Noctua Planning Meeting

  • Two-hour meeting planned Wednesday, June 10th 9-11AM PCT
  • Objective: discuss development options on a (relatively) high level; decide priorities for the next round of development
  • Development time frame: roughly through the end of the year (2020)
  • For grant renewal: any specific needs or objectives? (from last call: for testing in Uniprot, what would be the minimal set of species integrated in Neo ?)

Emails about job/volunteers

Recent (Monday), trickle in the past- distribute within GO or not?