AgBioData-LIST September 2026

agbiodata-list@bioinfo.wsu.edu

1 participants
4 discussions

AgBioData Webinar October 2026 -- Ehsan Estaji on PlantGraph

by MARCELA KAREY TELLO-RUIZ

[image: :seedling:] *What if the answer isn’t in a database—but in the connections between databases?* Join us on *Wednesday, October 7* for a webinar with Ehsan Estaji of the Umeå Plant Science Centre, Sweden: [image: :link:] Trapped knowledge in the AI-agent era: how PlantGraph turns multi-database questions into one traversal you can check PlantGraph connects plant data across the transcriptome, epigenome, regulome, and proteome, helping researchers turn complex, multi-database questions into one connected, traceable query. As part of the monthly AgBioData Webinar Series <https://www.agbiodata.org/webinars>, Ehsan will show how this approach can help AI agents retrieve evidence more reliably—and how we can check whether AI-generated answers actually stay grounded in that evidence. Wednesday, October 7 | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Oct+202…> . Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 Title: Trapped knowledge in the AI-agent era: how PlantGraph turns multi-database questions into one traversal you can check Abstract: A real biological question is rarely a record — it is a path. “Which salt-responsive genes also carry a promoter methylation change, a transcription-factor binding site, and a known phosphosite?” has no home database: the answer exists only as a traversal across four of them. This is why so much of what we collectively know sits trapped. Not because the facts are missing — they are curated, somewhere — but because the connections between them were never stored anywhere. Researchers rebuild those connections by hand, one question at a time, and lose them the moment they close the tabs. Capable AI agents raise the cost of that fragmentation rather than resolving it. An agent handed a set of endpoints has to plan the join itself, guessing identifiers and directions at every hop, and every hop is an opportunity to improvise. In our own benchmarking, giving a strong model tools and API access over fragmented sources did not reliably fix retrieval; connecting the data first, and retrieving over it deterministically, did. PlantGraph (plantgraph.se) integrates community plant resources into one connected knowledge graph and separates two jobs that agents usually conflate: the graph retrieves the evidence, the language model only writes over it. A multi-database question becomes a single traversal — and because that traversal actually ran, every claim can be followed back to the query that produced it and the source record that curated it. I will walk through questions spanning transcriptome, epigenome, regulome and proteome resolving in one step, how we measure when the generated narration drifts from the retrieved evidence, and where the approach still fails. PlantGraph <https://plantgraph.se/> is not a replacement for the databases it draws on — it stands on them, and every resource that connects makes the rest worth more. See also this news blog <https://www.agbiodata.org/node/652>. Marcela -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager https://www.agbiodata.org/ Phoenix Bioinformatics

2 weeks, 5 days

Deadline Extended: Nominations to the AgBioData Steering Committee (Due 28 Sept)

by MARCELA KAREY TELLO-RUIZ

Dear AgBioData Consortium members, A quick announcement following our call for nominations for a new member of the AgBioData Steering Committee: *We are extending the nomination deadline by one week*. *Nominations are now due Monday, September 28, 2026.* If you are interested in serving on the Steering Committee, please complete the *nomination form* <https://forms.gle/7g6JUFJJghxauzNdA>. You may also nominate a colleague, provided you have confirmed that they are interested in serving. We encourage members to take advantage of the additional week to consider putting themselves forward or nominating someone who would bring valuable perspectives and expertise to the Steering Committee. Thank you for your continued engagement with the AgBioData Consortium! Best, Marcela K. Tello-Ruiz On behalf of the AgBioData Steering Committee -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager https://www.agbiodata.org/ Phoenix Bioinformatics

3 weeks

Call for Nominations: AgBioData Steering Committee

by MARCELA KAREY TELLO-RUIZ

*Call for Nominations to the AgBioData Steering Committee* The AgBioData Consortium is seeking nominations <https://forms.gle/7g6JUFJJghxauzNdA> for a new member of the Steering Committee. The Steering Committee is responsible for the governance of the Consortium and for managing its activities, including our NSF-funded Research Coordination Network (RCN) grant, *“Reimagining a Sustainable Data Network to Accelerate Agricultural Research and Discovery.”* *To be eligible, nominees must be:* - A member of the AgBioData Consortium; - Actively involved with agricultural biological data (e.g., curation, data management, research, software development, library services, etc.); and - An enthusiastic advocate of FAIR data principles. Each Steering Committee member serves a *three-year term* and is expected to actively participate in the following activities: - Participate in regular Steering Committee meetings and follow-up action items; - Plan monthly AgBioData webinars and discussions; - Lead consortium-wide white papers and publications; - Plan and participate in annual all-hands meetings; - Contribute to funding proposals; and - Help shape future objectives and directions for the Consortium, in collaboration with the membership. *Nominations close September 21, 2026.* To express your interest in serving on the Steering Committee, please complete the nomination form <https://forms.gle/7g6JUFJJghxauzNdA>. To nominate someone else, please provide their name and email address *after confirming that they are interested in serving*. Elections will be held in *September/October 2026*. Marcela K. Tello-Ruiz On behalf of the AgBioData Steering Committee -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager https://www.agbiodata.org/ Phoenix Bioinformatics

1 month, 1 week

Reminder: AgBiodata Webinar Sept 2 (Tomorrow) on Single-Cell Data Submissions to NCBI-GEO

by MARCELA KAREY TELLO-RUIZ

Greetings AgBioData Colleagues! A friendly reminder of the September 2nd AgBioData webinar, we look forward to seeing you and hope your schedule allows you to join us tomorrow! === *From single cells to FAIR data! * Working with single-cell data? Make your next GEO submission FAIR from the start! Join us next *Wednesday, September 2nd*, to learn best practices for submitting single-cell data to NCBI’s Gene Expression Omnibus (GEO). As part of the monthly AgBioData Webinar Series <https://www.agbiodata.org/webinars>, *Emily Clough* of the National Center for Biotechnology Information (NCBI) will present the talk titled: “*Single-cell data submissions to NCBI’s Gene Expression Omnibus (GEO)*.” Full abstract and Zoom link below. We hope you can join us! Best, Marcela -- *Wednesday, September 2nd, 1PM ET* | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Sept+20…> . Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 -- *Speaker: *Emily Clough (NCBI) *Title:* Single-cell data submissions to GEO *Abstract: *The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository that archives gene expression and epigenomics data sets generated by next-generation sequencing and microarray technologies. The GEO repository is built and maintained by the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM). For 25 years GEO has been growing and adapting to emerging new technologies and now contains over 280,000 studies. The newest revolution in transcriptomics is single-cell technology which accounts for ~30% of all public RNA-seq studies in GEO. Single-cell data are large, structurally complex, and present unique challenges for archiving and data delivery. GEO has updated submission documentation with a section dedicated to single-cell data (https://www.ncbi.nlm.nih.gov/geo/info/seq.html#singlecell) describing required data formats, sample organization, and metadata. GEO’s metadata template provides examples for single-cell RNA-seq and multi-omics studies. This webinar will focus on best practices for single-cell submissions to GEO to meet FAIR (Findable, Accessible, Interoperable, and Reuseable) data principles. -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager https://www.agbiodata.org/ Phoenix Bioinformatics

1 month, 1 week

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AgBioData-LIST September 2026