GA4GH RNASeq

Minutes and Actions 2023 - 2026

These are the minutes for the RNASeq meetings,  a subgroup of the GA4GH Large Scale Genomics Work Stream. For further information, please visit the GA4GH Work Stream page.

Meeting Protocols

Agendas, Minutes and Actions

2025-05-21:

2025-04-16: Cancelled (awaiting feedback from Beacon team)

2025-03-19: Cancelled (awaiting feedback from Beacon team)

2025-01-15: Cancelled (Due to the unavailability of the leads)

2024-12-18: Cancelled

2024-11-20: Cancelled (Due to unavailability of the leads)

2024-10-16: Canceled (awaiting feedback from Beacon team)

2024-07-17: Cancelled (Due to unavailability of the leads)

2024 -06-19: Cancelled (Due to unavailability of the leads)

2024 -05-07: RNAget and Beacon

2024 -04-17: Cancelled

2024 -03-20: Report back from Beacon

2024 -02-21: Cancelled (Due to unavailability of the leads)

2024 -01-17: Cancelled (Due to unavailability of the leads)

2023-12-20: CANCELLED (Due to holidays)

2023-11-15: CANCELED

2023-10-18: Connect recap

2023-07-19: CANCELLED (Due to the unavailability of the leads)

2023-06-21: transcriptomic data

2023-05-17: Cancelled (Due to the unavailability of the leads)

2023-04-19: Canceled (Due to Connect meeting)

2023-03-15: Compliance Suite & Python RNA get library

2023-02-15: RNAget paper & Github

2023-02-01: CANCELED (due to availabilities of the leads)

2023-01-18:  V2.0 updates & Github repo

2023-MM-DD: Template

Meeting Protocols

• Please note that by participating in meetings, attendees agree to adhere to the GA4GH Standards of Professional Conduct.
• Meetings may be recorded for note-taking purposes. Recordings will be deleted within three months of the meeting taking place.
• Dates should be specified in the international format yyyy-mm-dd

Agendas, Minutes and Actions

Previous minutes available: 2017-2018 minutes, 2019 minutes 2020 minutes

2021 minutes 

2022 minutes

Also of relevance Sequence Annotation 2020

2026-09-16:

Chair: Sean Upchurch, Emilio Palumbo, Emilio Righi

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2026-09-16: Cancelled

Chair: Sean Upchurch, Emilio Palumbo, Emilio Righi

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2026-08-26: cancelled

Chair: Sean Upchurch, Emilio Palumbo, Emilio Righi

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2026-07-15: Cancelled

Chair: Sean Upchurch, Emilio Palumbo, Emilio Righi

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2026-06-17: Cancelled

Chair: Sean Upchurch, Emilio Palumbo, Emilio Righi

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2026-05-20: Cancelled ( Due to the unavailability of the leads)

Chair: Sean Upchurch, Emilio Palumbo, Emilio Righi

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2026-03-18: Cancelled

Chair: Sean Upchurch, Emilio Palumbo, Emilio Righi

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2026-02-18: Canceled

Chair: Sean Upchurch, Emilio Palumbo, Emilio Righi

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2026-01-21: Cancelled (Due to unavailability of the leads)

Chair: Sean Upchurch, Emilio Palumbo, Emilio Righi

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2025-12-17: Cancelled

Chair: Sean Upchurch, Emilio Palumbo, Emilio Righi

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2025-11-19: Cancelled

Chair: Sean Upchurch, Emilio Palumbo, Emilio Righi

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2025-10-15: Cancelled

Chair: Sean Upchurch, Emilio Palumbo, Emilio Righi

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2025-09-16: Genomic Feature model

Chair: Sean Upchurch, Emilio Palumbo, Emilio Righi

Attendees “Name (Affiliation)”: Reggan Thomas (GA4GH)

Meeting recording:

Meeting minutes:

2025-08-27: Genomic features

Chair: Sean Upchurch, Emilio Palumbo, Emilio Righi

Attendees “Name (Affiliation)”: Reggan Thomas (GA4GH)

Meeting recording:

Meeting minutes:

Sean Upchurch and colleagues discussed the integration of RNA with Beacon and the development of a genomic feature model. They debated the inclusion of ontology terms, synonyms, and aliases in the model, emphasizing the need for clear and robust attributes. The sequence ID was clarified as the first column of the GFF file, while the region name was proposed for better descriptiveness. They also considered the implications of hierarchical relationships between genomic features and the potential redundancy of storing all annotations. The team agreed to finalize the model and present it at a future Beacon meeting, pending team approval.

Actions:

• Provide an update on the RNA Beacon integration progress at the next Connect opening session, if appropriate.
• Finalize the genomic feature object design, including the decision on how to handle the sequence ID/chromosome representation.

• Coordinate with the Beacon team on the preferred approach for handling ontology terms and parent-child relationships.

Planning for GA4GH Opening Session

• Reggan asks Sean Upchurch about the GA4GH opening session and what they plan to present.
• Sean Upchurch suggests coordinating with Beacon and possibly integrating RNA under the Beacon umbrella.
• Sean Upchurch mentions the need to update on the current level of integration with Beacon.
• Reggan and Sean Upchurch discuss the possibility of Emilio or Beacon providing updates on the integration progress.

Genomic Feature Discussion

• Emilio explains the need to clarify the genomic feature class and its future-proof attributes.
• Sean Upchurch and Emilio discuss the genomic coordinates, sequence ID, and the use of seek name in GFF files
• Sean Upchurch suggests renaming the sequence ID to avoid confusion with chromosome numbers.
• Emilio proposes using a coordinate ID that maps to the seek name or accession number.

Hierarchical Relationships and Querying

• Emilio discusses the need to capture hierarchical relationships between genomic features.
• Sean Upchurch suggests making the parent and children fields optional to avoid forcing a specific hierarchy.
• Emilio and Sean Upchurch agree on using a list of strings for parent and children fields.
• Sean Upchurch emphasizes the importance of querying by ontology terms and synonyms for efficient data retrieval.

Ontology Terms and Synonyms

• Emilio and Sean Upchurch discuss the integration of ontology terms and synonyms in the genomic feature object.
• Sean Upchurch suggests using a single queryable field for ontology terms to avoid redundancy.
• Emilio agrees on grouping ontology terms and synonyms under a single field.
• Sean Upchurch proposes calling the field "ontology terms" for clarity and consistency.

Sequence ID and Region Name

• Emilio and Sean Upchurch discuss the format of the sequence ID and its consistency across different annotations.
• Sean Upchurch suggests using "region name" instead of "region ID" for better descriptiveness.
• Emilio agrees on the use of region name and provides an example of the naming conventions used by different annotation sources
• Sean Upchurch emphasizes the importance of having a human-readable and consistent naming system for genomic coordinates.

Finalizing the Genomic Feature Model

• Emilio and Sean Upchurch finalize the genomic feature model, including required fields like feature ID, matrix ID, and annotation source.
• Sean Upchurch suggests making ontology terms an optional field to allow for flexibility in implementation.
• Emilio agrees on the optional nature of ontology terms and the importance of clear documentation.
• Sean Upchurch and Speaker 2 discuss the next steps and the need for further collaboration with Beacon.

Planning for Connect Opening Session

• Reggan asks Sean Upchurch if there is anything to present at the Connect opening session.
• Emilio mentions the need to wait for the first draft of the Beacon-RNA merge before presenting anything.
• Sean Upchurch agrees that it is too early to present anything significant
• Emilio and Sean Upchurch discuss the timeline for the next Beacon meeting and the expected progress.

The meeting concludes with a plan to continue working on the genomic feature model and prepare for the next Beacon meeting.

2025-07-16:

Chair: Sean Upchurch, Emilio Palumbo, Emilio Righi

Attendees “Name (Affiliation)”: N/A

Meeting recording:

Meeting minutes:

2025-06-25: Expression Values

Chair: Sean Upchurch, Emilio Palumbo, Emilio Righi

Attendees “Name (Affiliation)”:

Meeting recording: https://us02web.zoom.us/rec/share/j8f6VwhWqem-l52pswngP4XAOs7sJX3C3RqQteLvbdJfc18mYdT-vP1mYYjpxtNU.S7PRDb7WoCpWedJb

Meeting minutes:

RNAget action points:

• Rename expression value

• Suggested name

- Feature expression value

- RNA expression value - Specific

- Genomics feature expression value

- FeatureSample Value - count might mean raw count in the RNA world

- Genomics Feature count

- Matrix cell value - General

• Define expression values model
• Review feature model

• Change to feature_ids: {label:string,id:string}[]

Feature model query

Summary:

The team discussed renaming the "expression values" in the RNA beacon framework due to its broadness. They proposed "feature expression value" as a more specific and less confusing term. Emilior highlighted the need to clarify the scope of beacon's use, whether it will be limited to RNA Seq data or include other types. They also debated the structure of the genomic feature model, emphasizing the importance of the feature ID and the potential need for a list of identifiers. The meeting concluded with plans to finalize these details and prepare for the upcoming Connect meeting in Uppsala.

Discussion on RNA Beacon and Expression Values

• Emilio R suggests sharing his screen to discuss action points regarding the RNA beacon.

  • Emilio R explains that the namespace expression values are too broad and can lead to misunderstandings.  

• Sean Upchurch and Emilior discuss the current structure of expression values and their separation from units.  

• Emilio R suggests renaming expression values to something more specific to avoid confusion within the beacon context.

Proposing New Names for Expression Values

• Sean Upchurch proposes creating a new model for beacon that better defines the expression object.  

  • Emilio R and Sean discuss the possibility of renaming expression values to "feature expression values."  

      • The team brainstorms other potential names, including "genomic feature expression value" and "feature sample count."  

      • Emilio R plans to propose these names to the beacon team and discuss them further in a pull request.

Clarifying the Scope and Usage of RNA Beacon

• Sean Upchurch inquires about the scope of beacon's use of RNA, whether it will be limited to RNA Seq data or include other types of feature expression data.  

    • Emilio mentions that the beacon team currently wants something specific to RNA Seq data.  

      • The team discusses the potential for future use of beacon for other types of data and the need for a flexible yet specific name.

        • Emilio R plans to gather more information from the beacon team to clarify their usage and scope.

Reviewing the Genomic Feature Model

• Emilio R explains the current genomic feature model, which includes attributes like biological functions, feature class, and feature ID.  

• Sean Upchurch points out the need for feature ID to be the primary identifier, as it ties back to the data set.  

      • The team discusses the possibility of using a list of identifiers for each feature to support different annotations.  

      • Emilio R suggests writing down the query scenarios to better understand how users will interact with the data.

Finalizing the Feature Expression Value Name

• The team agrees to propose "feature expression value" as the primary name for the new model.  

      • Emilio R plans to rank other suggestions, including "genomic feature count" and "feature sample count," for the beacon team's review.  

      • The team discusses the importance of making the name self-explanatory and avoiding confusion for users.  

      • Emilio R will present the proposed names and discuss them further in the next meeting.

Planning for the Connect Meeting in Uppsala

                     • Reggan reminds the team about the upcoming Connect meeting in Uppsala and the deadline for proposal submissions.  

      • Emilio R plans to complete the proposal by the second of July and present the integration at the next Connect meeting.  

      • Reggan informs the team about the open registration and survey for the Connect meeting, offering discounted rates for early registration.  

      • The team expresses interest in attending and participating in the Connect meeting.

2025-05-21: Cancelled

Chair: Sean Upchurch, Emilio Palumbo

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2025-04-16: Cancelled (awaiting feedback from Beacon team)

Chair: Sean Upchurch, Emilio Palumbo

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2025-03-19: Cancelled (awaiting feedback from Beacon team)

Chair: Sean Upchurch, Emilio Palumbo

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2025-01-15: Cancelled (Due to the unavailability of the leads)

Chair: Sean Upchurch, Emilio Palumbo

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2024-12-18: Cancelled

Chair: Sean Upchurch, Emilio Palumbo

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2024-11-20: Cancelled (Due to unavailability of the leads)

Chair: Sean Upchurch,Emilio Palumbo

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2024-10-16: Canceled (awaiting feedback from Beacon team)

Chair: Sean Upchurch,Emilio Palumbo

Attendees “Name (Affiliation)”:

2024-07-17: Cancelled (Due to unavailability of the leads)

Chair: Sean Upchurch,Emilio Palumbo

Attendees “Name (Affiliation)”:

2024 -06-19: Cancelled (Due to unavailability of the leads)

Chair: Sean Upchurch,Emilio Palumbo

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2024 -05-07: RNAget and Beacon

Chair: Sean Upchurch,Emilio Palumbo

Attendees “Name (Affiliation)”:

Meeting recording: https://us02web.zoom.us/rec/play/YyiA0w1oXbzRf0VSD6QE-ekGRvdG-pI0c4142J9bhZ7I62Q1fuKtS5RUxSYkLO0YIiVRButs7JNSO7-j.FuhCAO3ns8tgLcJV?canPlayFromShare=true&from=share_recording_detail&continueMode=true&componentName=rec-play&originRequestUrl=https%3A%2F%2Fus02web.zoom.us%2Frec%2Fshare%2FRMj37oamM-XcPthGtNZ5xw6tlmXR45Ts3GvwpMO6oHbexfOCxC2IB87QxbBGfIEb.SHtyvQLEQxbTeTVd

Meeting minutes:

Walkthrough of RNAget Beacon V2 extension model

2024 -04-17: Cancelled

Chair: Sean Upchurch,Emilio Palumbo

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2024 -03-20: Report back from Beacon

Chair: Sean Upchurch,Emilio Palumbo

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2024 -02-21: Cancelled (Due to unavailability of the leads)

Chair: Sean Upchurch,Emilio Palumbo

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2024 -01-17: Cancelled (Due to unavailability of the leads)

Chair: Sean Upchurch,Emilio Palumbo

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2023-12-20: CANCELLED (Due to holidays)

Chair: Sean Upchurch,Emilio Palumbo

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2023-11-15: CANCELED

Chair: Sean Upchurch,Emilio Palumbo

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2023-10-18: Connect recap

Chair: Sean Upchurch,Emilio Palumbo

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2023-07-19: CANCELLED (Due to the unavailability of the leads)

Chair: Sean Upchurch

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2023-06-21: transcriptomic data

Chair: Sean Upchurch

Attendees “Name (Affiliation)”: David B

Meeting recording:

Meeting minutes:

• Need to make encode and gtx aware; in beacon there is space, would like to bring things closer. Is this the same issue? Both are good but not combinable?

• You can access from each implementation but response is different
• Main problem is that both implemented api not in totally compliant way.
• Second problem is metadata and experimental sample data is different one project from another, not easy to harmonize.

• Emlio to put the list together and look at context, left too much wiggle room. Good to classify things whether they're errors in implementation, or if differences arise from lack of higher level specificity in api spec.
• Would like to test with David’s implementation (CanDIG). Opened issue in github but it wasn’t answered; would be good to test these clients with as many as possible whether it’s robust or not.
• CanDIG v1 there was a server up. Since reboot, there isn’t rnaget server that’s up and running with data accessible. It’s part of what they want to bring back but at the moment no public data accessible.
• Transcriptome project (David Bujold)

• CanDIG building infrastructure for data sharing, focusing on clinical and genetic data. Discovery for genetic data can go into different queries (eg. beacon). As far as we know, there isn’t anything ike this for transcriptomic. If I have tumours with transcriptomic profiling, we’re at step 1 of process but we’ve been tasked to build service for transcriptomic data and allow to ask question. It’s a blank page right now, what requirements and what questions should I be asking? Eg. Give me all biosamples where transcription profiling is higher than this gene?. Etc
• Many ways to store transcriptome data, it has moved quite a bit in past 5 years.
• There aren’t single files that you can serve; we want to make data discoverable by asking questions on it. First step is figuring out what these questions are.
• Way back, talked about searching rnaget expression data given expression profile, you could have set of marker gene that has certain counts, tpm, etc. Search with that and say give me your datasets that have results that match my transcriptome profile I uploaded. We were thinking of cancer. Not just ask threshold, but maybe I have a pattern.

• There’s application here for this project’s purposes

• First step is to define what questions are and once you know, then you can develop strategy for answering them. Need to collect some amount of data, some will be rna and some will be variant. Collecting evidence to answer questions will interface with various GA4GH apis. Next, is do you need extension or is this client side? Probably a bit of both.
• This week, Emilio was in meeting with Jordi, asked him how they deal with metadata in Beacon v2, discussed this as well. They are getting requests about different kinds of beacons. We could have transicriptome beacon, that was already an idea that some people wanted to have explorative queries with rnaget. We do need to first set up questions and data, but we can in parallel see if we want to extend api, make a new one that relies on rnaget, or enter discovery WS and see if there is room for an rna beacon. This project is the driver project for this. We should discuss. Good thing with using beacon v2 would be to harmonize the metadata. They use standardized metadata which could be a base where everyone using a beacon has the same metadata. It can be clinical, genomics, it will allow for federated metadata.
• Implemented beacon for phenopackets, trying to build beacon network for CINECA project. In parallel, there’s new study group trying to brush what would be the right metadata to capture experiments.
• Old docs for RNAget use cases: GA4GH Matrix Format and API: Functional Specification and Use Cases
• Beacon v2 can get number of samples with specific profiles and also metadata attached to samples in one single query. Something we can explore.
• Good to have something to present by San Francisco.

2023-05-17: Cancelled (Due to the unavailability of the leads)

Chair: Sean Upchurch

Attendees “Name (Affiliation)”:

Meeting recording:

Meeting minutes:

2023-04-19: Canceled (Due to Connect meeting)

Chair: Sean Upchurch

Attendees “Name (Affiliation)”:

2023-03-15: Compliance Suite & Python RNA get library

Chair: Sean Upchurch,Emilio Palumbo

Attendees “Name (Affiliation)”: Emilio, Kshitiz Singh,Alex Tsai,Reggan Thomas (GA4GH)

Meeting recording ;

https://us02web.zoom.us/rec/share/2IVzald7cHohCRYoJ4bj-Ia0zW5GmZ28S2Bt_7HLynouo_4Z11vsP4O6plXDqGgw.7aJIUAD-MOnDR1xJ 

Meeting minutes

Python library -

SU - should be on the roadmap for this year.

Emilior - In couple of weeks, can have it ready

Need to be aligned with compliance suite

There are not many RNAget instances that could be used

Expecting the compliance suite and library works in the same flow

Can be completed in couple of weeks

SU - try to figure out what it is that's going on with the installation and setup problems that we've been having with the compliance suite. I think that that's kind of one thing that's sort of blocking us from approving the pull requests to the new testbed infrastructure so I think if I let me try to summarize but Emilio and I have been trying to do the installation of the compliance suite using the Python setup command.

SU - The python setup command appears to be not quite setting, pulling in the requirements. And so if we're failing, getting messages of, you know, software packages not being installed that need that have requirements that are that are not that are not listed

AS - other complaints, we do manually install whatever is on there requirement dot txt, before running the Python Python install, so maybe I just need to update the documentation and see how I did that works. and if not, I'll just work through the dependencies issues on my own

SU - noticed that a large number of bot will recall requests, updating version numbers for security patches and things in the requirements.

SU - Walkthrough of RNA Seq V1.2.0

2023-02-15: RNAget paper & Github

Chair: Sean Upchurch,Emilio Palumbo

Attendees “Name (Affiliation)”: Emilio R,Reggan Thomas

Meeting recording: https://us02web.zoom.us/rec/share/5vPrMg08NQXNZDyUTKXIEJAaCF5UMHGUnG55SE5LVCvH2lvBf7PqCNFdKw8ITd0D.GOI0gynaENJx58we

Meeting minutes:

SU: RNAget paper has been accepted with minor revisions.Paper was re-submitted.

SU : ENCODE implementation was apparently one of the reviewers couldn't couldn't get to, but we try to verify with encode that it's live and accessible and everything's fine. And then there was a comment, that code examples would be good. And we have code examples that were in the testing directory of the repository. So we updated those and moved the links directly to the main readme, so that it would be easier to find and then added a line in the paper with a link to the readme file. And so that was all done and the paper was resubmitted.

Github repo -  we discussed the proposal for version 2.0 changes. And so I think it's time to do two things.

  → One is to go ahead and start the branches that we need to put the pull requests in place.    → then we can point to the other driver projects directly to it and, and get their feedback on the changes and maybe put together a quick v2 issue to actually and bullet point out the changes that have been made just to make it a lot easier immediately

ER - need to work on the individual schema

SU - when ready, put it together as an issue and guide people through the process

ER - a demo on the web interface and server with some dummy data        

2023-02-01: CANCELED (due to availabilities of the leads)

Chair: Sean Upchurch,Emilio Palumbo

Attendees “Name (Affiliation)”:

Meeting minutes:

Meeting recording:

2023-01-18:  V2.0 updates & Github repo

Chair: Sean Upchurch,Emilio Palumbo

Attendees “Name (Affiliation)”: Emilio Righi, Reggan Thomas

Meeting recording:https://us02web.zoom.us/rec/play/sHv9oFoLNtYm9Rc1XdYSEdkzVgdb5vPS_nbJwrYCjyQ1QbCe4uRVnVtSLzzGHbklnHa9lelJAYMwnMEf.Eh7tTVf6C4DZMIVJ?autoplay=true&startTime=1674053684000

Meeting minutes:

SU - Emilio is working on V2 revision or addition to the API. A couple of them are breaking changes associated with V2.

RNA paper submitted to bioinformatics that was done at the end of september

Gone out to the reviewers and status shows as pending decision

Changes - 1) we’re a retrieval AP and one part is to make potential data to downstream clients

2) Other portion is to remove project and study portion of the API since they are not directly related to the API

2023-MM-DD: Template

Chair: Sean Upchurch

Attendees “Name (Affiliation)”: