Manager Call 2019-09-11
Items from last week
ACTION ITEM: [Kimberly]: Open a ticket to see how we'll handle the Gramene/Planteome data
ACTION ITEM: [To discuss later] Make sure that the Types are used correctly - right now for example C. elegans provides genes and PAINT uses proteins for the same type of identifier. This is misleading for users. July suggests widening the definition of protein to include gene and protein.
ACTION ITEM: [Seth to open a ticket] Date on the ontology is different from the release date: http://skyhook.berkeleybop.org/release/ontology/go-basic.obo - in the go-basic.obo the date is Aug 31, the release is from Sept 1st.
- Agenda: Laurent-Philippe
- Minutes: Kimberly
GO Meeting general
Agenda first draft (by Pascale) https://docs.google.com/document/d/16ZCV1vyTHSEf20z_PO4F8S-uqD2ZvnyExV0McMWnFI0/edit
GO meeting (Paris May 2020)
Laurent-Philippe will discuss the current status.
Contacts at Pasteur: Claudine Mayer, Natalia Pietrosemoli, Michael Nilges Bioinformatics hub led by Olivier Gascuel
Stats for all releases Discuss stats page ?
Need for a IT/Cloud strategy
While not yet critical / urgent, it is important to have a IT/Cloud strategy for the project to ease the sharing of resources, virtual machines, protocols, loggings etc. Laurent-Philippe created a document for the USC AWS account in April. It could serve as a basis for discussion. Example of ticket affected by the lack of IT/Cloud strategy: https://github.com/geneontology/operations/issues/30
Problem to solve: GO servers and resources are scattered across multiple IT and multiple AWS accounts which are neither listed nor shared. Aside from inconsistency, lack of transparency, being cost ineffective and problems to maintain the architecture in the long term, sharing resources both for development and production is complicated and susceptible to create non standard applications and pipelines. A shared IT/Cloud strategy would also allow developers to quickly share and launch any GO tool for deep and quick iterative testing.
Proposal: allocate some time for the next period (October-May 2020) to:
1. list all currently used IT & cloud resources (servers, storage, DNS, cloud accounts, etc)
2. define together a group strategy and SOP for those IT & cloud resources
3. define and share base images and docker containers to launch all GO tools for deep testing and rapid development
Examples of what this SOP could define:
- how many on-site servers and AWS accounts we have and how they are organized to share resources, security permissions and costs (e.g. maybe we still want 1 LBNL and 1 USC account, but then both should be linked to a parent GO account giving permissions to each organization)
- who are the current admins of these servers and AWS accounts
- who to ask to access more restricted resources (e.g. Seth is the only one to know where the geneontology.org DNS is hosted and to have permission to alter any URL *.geneontology.org ; same thing for release.geneontology.org)
- where and how is administered email@example.com ?
- how to create new AWS accounts for GO developers (e.g. Laurent-Philippe, Ben and Anushya had to use their own accounts, hence not sharing any standard, resource, images or security permissions)
- what default security permissions are granted to GO developers (e.g. ability to launch a test server, to write in some locations, etc)
- list all images and docker containers to launch and test in a standard and reproducible way any given GO tool (e.g. Noctua stack, GOLr, NEO, GO API, etc)
- Huaiyu, Judy, Kimberly, Laurent-Philippe, Paul T., Seth, Suzi A.
Other Annotation Groups
- Kimberly will contact Pankaj about making GR annotations internal to GOA
- Pascale will contact Fiona (AgBase) to set a deadline for dealing with their annotations
Annotation Entity Type
- Groups need to be compliant with current GAF specs
- QC will need to reflect the GAF spec
- The 'annotated entities' will be used to construct annotation stats, but this won't be publicly available until we're all on the same page
- Seth created a ticket to fix the date on the ontology release file
GOC Meeting Agenda
- Everyone should review and make comments, suggestions
- We will discuss next week
- Judy and Paul T. have suggestions for additional presenters for the users meeting
- They should get in touch with Chris about updating the agenda
Spring 2020 Meeting in Paris
- May 11th -15th room booked at the Pasteur (50-70 attendees)
- Paul T: - auditorium for a day for a workshop?
- We can use the room booked for whatever purposes we need
- Laurent-Philippe can inquire about a larger auditorium-type room for a workshop
- We need to write a proposal for workshops and let local informatics groups provide feedback on what they'd like to attend
- We can point them to the October meeting agenda to give them some idea of what we might discuss
- Can check GO stats for all Zenodo releases
- These will be used to QC releases and report stats on the GO website
- We can discuss display in more detail next week
- Seth: Is there an architectural document for this?
- Paul T.: we should definitely include this as a project
- There's been ongoing discussion about this issue
- We need Chris for this discussion, though, so did not discuss in detail on this call
- There is a strategy, although perhaps it's not as formally or centrally documented as desired