Difference between revisions of "Manager Call 2020-05-20"

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m (Strategy for moving forward)
m (Consortium Meeting Recap)
 
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* Agenda: Huaiyu  
 
* Agenda: Huaiyu  
 
* Minutes: Suzi
 
* Minutes: Suzi
* Present: Chris, David, Huaiyu, Judy, Kimberly, Laurent-Philippe, Pascale, Paul T., Seth
+
* Present: Chris, David, Huaiyu, Judy, Kimberly, Laurent-Philippe, Pascale, Paul T., Seth, Suzi
 
* Regrets:
 
* Regrets:
  
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*Possibly also be pro-active about what to include in a users meeting by soliciting input via the go-announcments list? other lists?
 
*Possibly also be pro-active about what to include in a users meeting by soliciting input via the go-announcments list? other lists?
 
*We need to consider what resources we have to support different types of meetings, frequency of meetings, etc.
 
*We need to consider what resources we have to support different types of meetings, frequency of meetings, etc.
 +
*Also, solicit questions before the meeting.
  
 
==Consortium Meeting Recap==
 
==Consortium Meeting Recap==
 +
*Laurent-Philippe generated a summary for Paul S.
 +
*Need to clarify with Paul S. about the intended use for this meeting summary; progress report?
  
  
  
 +
Proposal of recap :
  
 +
During the last six months, the GO consortium has steadily increased the number of annotated publications and more than 10 000 additional PAINT annotations have been added to our knowledgebase. The consortium is also continuing its efforts to help the MODs in their transition to a new curation framework, Noctua, which include basic and advanced UIs to create both standard GO annotations and GO-CAMs. In parallel of those efforts, the translation of Reactome pathways to GO-CAMs is underway and an article should soon be published. A number of tools and statistics have also been integrated to the pipeline to improve QC and ensure the quality of each release in a more timely mannered. To help in global efforts on COVID-19, GO has also created a dedicated page to gather annotations and models on how the virus infects human cells and what human functions/processes seem to be impaired based on a recent PPI network provided by Gordon et al.
 +
 +
In the next phase, aside from its general activity of producing and reviewing annotations, the GO consortium will continue its efforts toward the transition to the Noctua Curation Framework, reinforce its APIs and libraries to further help our users. The virtual GO User Meeting was a success with 90+ researchers and developers attending; more virtual targeted meetings should be organized later in the year
 +
 +
 +
*Overall, the sentiment is that the virtual meeting was very successful.
 +
 +
*Going forward, we should think about three meeting tracks and their frequency:
 +
**Consortium-wide meetings
 +
**User meetings
 +
**Small, focused working meetings
 +
 +
==COVID-19 and the ISCB==
 +
*ISCB has released a COVID-19 page to consolidate information from different groups
 +
*Judy will submit the work that GO is doing to the ISCB site
 +
*https://www.iscb.org/covid19
  
  

Latest revision as of 09:04, 20 May 2020

Agenda

  • Agenda: Huaiyu
  • Minutes: Suzi
  • Present: Chris, David, Huaiyu, Judy, Kimberly, Laurent-Philippe, Pascale, Paul T., Seth, Suzi
  • Regrets:

Results of user meeting survey

  • https://docs.google.com/forms/d/11BSWAs8G5vSEBOKubSNRIXNXyD3CYT586M2uX26FTc4/edit#responses
  • Most attendees filled out the survey relatively quickly after the meeting
  • 50% PhD student and post-docs; others were mostly staff scientists and PIs
  • Most people were working in bioinformatics, some bench scientists
  • Gene function and enrichment analyses were most common uses of GO
  • More targeted meetings about enrichment, data access and integration, APIs, curation would be helpful
  • 50% of users work with human data; others mice, rat, all organisms

Discussion points from survey

  • Judy: bench scientists increasingly need to have skills in data analysis; we need to serve this community as well
  • David: should we have more than one type of users meeting depending upon who we're targeting/training?
  • Huaiyu: it would also be interesting to know what the distribution of bench scientists vs bioinformaticians is at the Pasteur Institute
  • Paul T: we need to know what questions people are trying to ask and answer by using GO
  • Paul T: what obstacles do people find when trying to use GO
  • Laurent-Philippe: can we recommend specific tools for people to use, could be ours, could be other groups' tools
  • Chris/Paul T: maybe we should re-visit the tool registry idea but define the standards for inclusion
  • Laurent-Philippe: update/provide new ten simple rules/tips for using and/or developing tools for GO
  • Chris: we will increasingly need to answer questions about the differences among GO-CAM, Reactome, KEGG, etc.
  • L-P and Chris: we also need to improve documentation on when to use enrichment vs subsets
    • Paul T: Dustin can make the PANTHER slim available

Strategy for moving forward

  • Virtual meeting seemed to work quite well
  • More frequent virtual meetings, along with some on-site meetings when we have GOC meetings, would be good
  • AI: Contact Michelle to get her input on how best to arrange a users meeting.
  • Possibly also be pro-active about what to include in a users meeting by soliciting input via the go-announcments list? other lists?
  • We need to consider what resources we have to support different types of meetings, frequency of meetings, etc.
  • Also, solicit questions before the meeting.

Consortium Meeting Recap

  • Laurent-Philippe generated a summary for Paul S.
  • Need to clarify with Paul S. about the intended use for this meeting summary; progress report?


Proposal of recap :

During the last six months, the GO consortium has steadily increased the number of annotated publications and more than 10 000 additional PAINT annotations have been added to our knowledgebase. The consortium is also continuing its efforts to help the MODs in their transition to a new curation framework, Noctua, which include basic and advanced UIs to create both standard GO annotations and GO-CAMs. In parallel of those efforts, the translation of Reactome pathways to GO-CAMs is underway and an article should soon be published. A number of tools and statistics have also been integrated to the pipeline to improve QC and ensure the quality of each release in a more timely mannered. To help in global efforts on COVID-19, GO has also created a dedicated page to gather annotations and models on how the virus infects human cells and what human functions/processes seem to be impaired based on a recent PPI network provided by Gordon et al.

In the next phase, aside from its general activity of producing and reviewing annotations, the GO consortium will continue its efforts toward the transition to the Noctua Curation Framework, reinforce its APIs and libraries to further help our users. The virtual GO User Meeting was a success with 90+ researchers and developers attending; more virtual targeted meetings should be organized later in the year


  • Overall, the sentiment is that the virtual meeting was very successful.
  • Going forward, we should think about three meeting tracks and their frequency:
    • Consortium-wide meetings
    • User meetings
    • Small, focused working meetings

COVID-19 and the ISCB

  • ISCB has released a COVID-19 page to consolidate information from different groups
  • Judy will submit the work that GO is doing to the ISCB site
  • https://www.iscb.org/covid19