- AgBioData-LIST - Main Bioinformatics Lab

AgBioData Webinar November 2026 on AI-Assisted Literature Curation by the NLP for Biocuration WG

by MARCELA KAREY TELLO-RUIZ

*How do we move from promising AI tools to practical, scalable GGB literature curation?* Join us on *Wednesday, November 4* for a webinar with Olivia Haley (USDA), Kapeel Chougule (CSHL), and Laura Tibbs-Cortes (USDA) from the AgBioData NLP for Biocuration Working Group on the *lessons learned from working with Textpresso, plant papers and genes*. Since its formation in March 2025, the NLP for Biocuration Working Group has been evaluating AI-assisted tools and approaches to help scale literature curation across agricultural genomics databases. The group has explored tools including Textpresso, BioBERT, Elicit, and OntoGPT, developed shared benchmarking practices, and coordinated efforts toward a Textpresso proof of concept tailored to agricultural species. As part of the monthly AgBioData Webinar Series <https://www.agbiodata.org/webinars>, Olivia, Kapeel, and Laura will share lessons learned from evaluating these tools, benchmarking AI-assisted literature workflows, and building shared infrastructure to support literature curation across the agricultural genomics community. The presentation will also introduce the AgBioData implementation of Textpresso, including its graphical user interface (GUI), API, and command-line tools. Wednesday, November 4 | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Nov+202…>. Note that it will be Standard Time in the United States (no longer daylight saving time). Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 *N**LP4Biocuration: Advancing FAIR, AI-Assisted Literature Curation Across the AgBioData Consortium The AgBioData* The NLP4Biocuration Working Group was formed in March 2025 to evaluate, prototype, and coordinate the integration of natural-language-processing (NLP) and large language model (LLM) tools to support scalable, ontology-driven literature curation across agricultural genomics databases. This effort is conducted under the umbrella of the AgBioData Consortium and is supported by the *NSF Research Coordination Network award #2126334* <https://www.agbiodata.org/projects/nsf-rcn>, a shared community resource initiative that promotes interoperable informatics solutions. Over the past eight months, working group members performed a coordinated assessment of AI-assisted literature tools, developed shared benchmarking practices, and explored infrastructure options for cross-database deployment. Tools evaluated include BioBERT, Elicit, Textpresso, OntoGPT, and early agentic-AI frameworks, with attention to their utility for named entity recognition, relationship extraction, summarization, and paper prioritization for plant and crop species. Several members implemented pilot pipelines comparing AI-generated literature sets with manually curated datasets, providing practical insights into recall, precision, and model behavior within agriculture-specific contexts. To facilitate shared learning and reproducibility, the group established a structured "tool review" framework and a community repository of test cases, datasets, and documented workflows. A major milestone is the ongoing organization of a Textpresso proof-of-concept deployment tailored for agricultural species. Participating AgBioData resources, including SorghumBase, MaizeGDB, GDR, SoyBase, GrainGenes, and others, are assembling FAIR-compliant gene lists, entity vocabularies, and open-access corpora, and are coordinating with the Alliance of Genome Resources team on compute requirements for a shared AWS-based test environment. In parallel, the group distributed a survey across AgBioData member databases to capture literature volume, workflows, AI adoption, and technical barriers; survey findings are guiding both a manuscript currently in development and continued infrastructure planning. Aligned with FAIR principles, the AgBioData consortium advances sustainable informatics infrastructure. By aligning NLP4Biocuration activities with these principles, the working group is helping establish sustainable informatics infrastructure and analytics-driven methods that benefit the entire agricultural genomics community. This presentation will cover the AgBioData implementation of Textpresso, including the GUI and programmatic access by API and command line tools. See also this news blog <https://www.agbiodata.org/node/654>. Marcela -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager https://www.agbiodata.org/ Phoenix Bioinformatics

2 days, 3 hours

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Reminder Tomorrow: PlantGraph Webinar, Wed 6 October 2026 -- AgBioData

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

3 weeks, 3 days

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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

1 month, 1 week

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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

1 month, 1 week

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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, 4 weeks

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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, 4 weeks

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AgBiodata Webinar September 2026 -- Emily Clough on Single-Cell Data Submissions to NCBI-GEO

by MARCELA KAREY TELLO-RUIZ

*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

2 months

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THIS WEDNESDAY: McKenzie Mabry on Crop Wild Relatives, Herbaria, and Food Security

by MARCELA KAREY TELLO-RUIZ

Hello Everyone, Join us this *Wednesday, August 5, at 1:00 PM ET* for the next webinar in the AgBioData Webinar Series <https://www.agbiodata.org/webinars>. *McKenzie Mabry* (iDigBio), of the *Florida Museum of Natural History, University of Florida, and the New York Botanical Garden*, will present: *"Crop Wild Relatives and the Role of Herbaria in Future Food Crop Security"* This webinar will explore the important role that herbarium collections and crop wild relatives play in supporting future food security. The Zoom link and webinar abstract are included below. We hope you'll be able to join us! Best, Marcela *Wednesday, August 5th, 1PM ET* | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Aug+202…> . Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 -- Speaker:* McKenzie Mabry* (Florida Museum of Natural History, University of Florida & New York Botanical Garden; iDigBio) Title: *Crop Wild Relatives And The Role Of Herbaria In Future Food Crop Security* Abstract: Although Nikolai Vavilov recognized the potential of crop wild relatives (CWR) in the early 1900s, the advent of genome editing technologies such as CRISPR now enables scientists to more fully leverage CWRs as a source of genetic diversity for cultivated crops. As global agriculture faces escalating pressures from climate change, plant biologists are increasingly focused on sustaining crop productivity under shifting environmental conditions while meeting the demands of a growing population. CWRs represent a critical reservoir of genetic variation that can be harnessed to address these challenges. While efforts to expand germplasm collections of CWRs are ongoing, herbaria remain an underutilized resource. At the same time, the growing availability of digitized herbarium data provides new opportunities to address large-scale research questions. In this study, occurrence records for CWRs of several important crop species are obtained from repositories such as iDigBio and Global Biodiversity Information Facility. Following data cleaning, ecological niche modeling is used to estimate global habitat suitability under both current and future climate scenarios. This work highlights the increasingly important role of herbaria and digitized biodiversity data in supporting crop improvement efforts, particularly in the context of ongoing climate change. -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager https://www.agbiodata.org/ Phoenix Bioinformatics

3 months

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AgBiodata August 2026 webinar -- McKenzie Mabry (iDigBio) on Crop Wild Relatives and the Role of Herbaria in Future Food Crop Security

by MARCELA KAREY TELLO-RUIZ

*Genome editing has revived interest in crop wild relatives as a source of genetic diversity — but are we fully tapping herbaria to find them? Join us next Wednesday 5th of August to learn how digitized biodiversity records and niche modeling are mapping where climate-resilient crop relatives may be found, now and in the future.* Hello Everyone, As part of the monthly AgBioData Webinar Series <https://www.agbiodata.org/webinars>, McKenzie Mabry (iDigBio) of the Florida Museum of Natural History, University of Florida & New York Botanical Garden, will present the talk titled: “*Crop Wild Relatives And The Role Of Herbaria In Future Food Crop Security*”. Full abstract and zoom link below. We hope you can join us! Best, Marcela -- * Wednesday, August 5th, 1PM ET* | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Aug+202…> . Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 -- Speaker:* McKenzie Mabry* (Florida Museum of Natural History, University of Florida & New York Botanical Garden; iDigBio) Title: *Crop Wild Relatives And The Role Of Herbaria In Future Food Crop Security* Abstract: Although Nikolai Vavilov recognized the potential of crop wild relatives (CWR) in the early 1900s, the advent of genome editing technologies such as CRISPR now enables scientists to more fully leverage CWRs as a source of genetic diversity for cultivated crops. As global agriculture faces escalating pressures from climate change, plant biologists are increasingly focused on sustaining crop productivity under shifting environmental conditions while meeting the demands of a growing population. CWRs represent a critical reservoir of genetic variation that can be harnessed to address these challenges. While efforts to expand germplasm collections of CWRs are ongoing, herbaria remain an underutilized resource. At the same time, the growing availability of digitized herbarium data provides new opportunities to address large-scale research questions. In this study, occurrence records for CWRs of several important crop species are obtained from repositories such as iDigBio and Global Biodiversity Information Facility. Following data cleaning, ecological niche modeling is used to estimate global habitat suitability under both current and future climate scenarios. This work highlights the increasingly important role of herbaria and digitized biodiversity data in supporting crop improvement efforts, particularly in the context of ongoing climate change. -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager https://www.agbiodata.org/ Phoenix Bioinformatics

3 months

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Join the New AgBioData Education & Training Working Group!

by MARCELA KAREY TELLO-RUIZ

Dear AgBioData Community, *Passionate about teaching, training, or improving agricultural research data practices? **This one is for you!* The AgBioData Consortium is launching a new Education & Training Working Group <https://www.agbiodata.org/working_groups/edu-training>. Building on the success of the original Education Working Group—which developed the AgBioData Curriculum for teaching FAIR data practices <https://zenodo.org/records/14278084>—we are expanding our efforts to create more accessible, practical, and community-driven training resources for researchers, educators, students, and database professionals. This next phase will focus on: - Identifying AgBioData community training needs and priorities. - Updating the AgBioData curriculum for diverse audiences. - Developing a structured AgBioData certification program. - Creating online training modules on bioinformatics data management, reporting, publication, and data submission best practices. Participation requires approximately 2 hours per month for meetings, plus flexible offline contributions based on your interests and availability. By joining this working group, you will: - Help shape the future of AgBioData education and training. - Earn authorship on publications, training modules, and other community outputs. - Contribute your expertise in ways that fit your interests and schedule. - Connect with a multidisciplinary network of researchers, educators, curators, and database professionals. Interested in joining? Sign up here: https://forms.gle/CLKYAuyrDxqQtiRG7 If you have any questions, please contact Jodi at jhumann(a)wsu.edu. We hope you’ll join us in building the next generation of FAIR data education resources for the agricultural genomics community. Kind regards, Marcela On behalf of the AgBioData Steering Committee -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

4 months

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AgBioData-LIST