- AgBioData-LIST - Main Bioinformatics Lab

REMINDER - Monthly Webinar Next Wed, Sept 6th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us next Wed, *Sept 6th, *at 12 PM CT for our monthly webinar. We will have* Harry Caufield <https://github.com/caufieldjh>,* Lawrence Berkeley National Laboratory, talking about how *SPIRES* implements Large Language Models (LLMs) to extract structured knowledge in agricultural science and beyond. I have included below more details about the webinar and the Zoom link to attend the webinar. I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: Presenters: Harry Caufield <https://github.com/caufieldjh>, Lawrence Berkeley National Laboratory Abstract: *Staying grounded: assembling structured biological knowledge with help from large language models* Developing comprehensive knowledge bases and ontologies demands meticulous curation. The emergence of highly flexible, artificial intelligence-driven approaches to natural language processing offers novel ways to expedite this process. Current methods often rely on extensive training data, however, and struggle with complex, nested knowledge structures. In this talk, I will describe a new approach, Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES). This method for information extraction leverages the capability of Large Language Models (LLMs) to perform zero-shot learning (ZSL) with a variety of natural-language prompts. SPIRES operates with predefined data schemas, enabling information extraction that adheres to these structures. It also grounds concepts with well-established ontologies and vocabularies, avoiding the "hallucinations" common to text generated by LLMs. Within OntoGPT, an LLM-querying framework we have developed, SPIRES supports rapid application to summarization and modeling across plant science and biology. Notably, this approach allows customization for new tasks and topics without a need for new training data. We have found that OntoGPT and SPIRES are capable of extracting structured knowledge from large literature collections and constructing knowledge graphs from the resulting relationships. Through harnessing the language comprehension capabilities of LLMs, SPIRES streamlines knowledge acquisition from across agricultural science and beyond. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=September+AgBioDa…> Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 --- One tap mobile +15642172000,,82038356125#,,,,*160683# US +16469313860,,82038356125#,,,,*160683# US --- Dial by your location • +1 564 217 2000 US • +1 646 931 3860 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US • +1 929 205 6099 US (New York) • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

7 months, 4 weeks

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REMINDER - TOMORROW (12 PM CT) Virtual Round-table on phenotypic data management!!!

by Annarita Marrano

Hi everybody, Join us tomorrow, *August 2nd, *at 12 PM CT for a *virtual round-table discussion on phenotypic data management issues*! In Year 2 of our current NSF RCN grant, the AgBioData database community indicated sharing and managing phenotypic data as one of the primary data issues to address. We have surveyed our member databases, and many of them agreed that curating phenotypic data is challenging due to *their diversity in terms of data types* (e.g., images vs. spreadsheets) *and data sources* (e.g., breeding program, experimental trials, or literature), *as well as the lack of standardization*. We are inviting the AgBioData member databases and the larger community to discuss these challenges to understand their importance for AgBioData member databases and if they can be addressed entirely or partially in a new AgBioData working group. As usual, the meeting will be 1-hour long and will feature breakout room sessions! *Zoom link to attend the event at the bottom of this email.* I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=Round-Table+discu…> Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 --- One tap mobile +19292056099,,82038356125#,,,,*160683# US (New York) +13017158592,,82038356125#,,,,*160683# US (Washington DC) --- Dial by your location • +1 929 205 6099 US (New York) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 646 931 3860 US • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US • +1 564 217 2000 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

8 months, 4 weeks

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REMINDER - Monthly Webinar Next Wed, July 12th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us next Wed, *August 2nd, *at 12 PM CT for a *virtual round-table discussion on phenotypic data management issues*! In Year 2 of our current NSF RCN grant, the AgBioData database community indicated sharing and managing phenotypic data as one of the primary data issues to address. We have surveyed our member databases, and many of them agreed that curating phenotypic data is challenging due to *their diversity in terms of data types* (e.g., images vs. spreadsheets) *and data sources* (e.g., breeding program, experimental trials, or literature), *as well as the lack of standardization*. We are inviting the AgBioData member databases and the larger community to discuss these challenges to understand their importance for AgBioData member databases and if they can be addressed entirely or partially in a new AgBioData working group. As usual, the meeting will be 1-hour long and will feature breakout room sessions! *Zoom link to attend the event at the bottom of this email.* I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=Round-Table+discu…> Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 --- One tap mobile +19292056099,,82038356125#,,,,*160683# US (New York) +13017158592,,82038356125#,,,,*160683# US (Washington DC) --- Dial by your location • +1 929 205 6099 US (New York) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 646 931 3860 US • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US • +1 564 217 2000 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

9 months

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AG2PI training workshop: Virtual fence technology and applications

by Scott, Nicole M [AGRON]

Dear AgBioData community member, The next AG2PI training workshop, "Virtual Fence Technology: From Raw Data Messages to Animal Energetics Models", will be held August 7, from 2 PM to 4 PM (CDT; UTC -5). In this workshop, Drs. Jameson Brennan and Hector Menendez, along with Andrew Antaya, will demonstrate how to generate, analyze and utilize precision livestock data collected via GPS. You can access registration information for the workshop through the AG2PI website: https://www.ag2pi.org/workshops-and-activities/workshop-2023-08-07/. A GitHub link will be made available prior to the event to facilitate participation. A recording will be made available on the AG2PI workshop webpage soon after the conclusion of the event. You do not need to register in order to access the recording or GitHub- it will be publicly available at the link above. *This workshop is an outcome of an AG2PI seed grant<https://www.ag2pi.org/resources/ag2pi-funded-seed-grants/#round-3>. Please share the attached, digitally accessible flyer with your colleagues or students and encourage them to attend. Kind regards, Nicole ------------------------ Nicole Scott, PhD Program Specialist Agricultural Genome to Phenome Initiative Iowa State University 1111 WOI Rd Ames, IA 50011 office: 1077 Roy J. Carver Co-Lab phone: 515-294-3945 ag2pi.org<https://www.ag2pi.org/> *** If you no longer wish to receive messages from AG2PI, then please visit https://www.ag2pi.org/join-ag2pi/unsubscribe/ to unsubscribe *** Please note, you cannot unsubscribe if you are receiving this message through a third party ***

9 months

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TODAY webinar: Rose Marks on inequalities in plant science literature

by Annarita Marrano

Hi everybody, This is a friendly reminder of *TODAY* DEIR webinar *at 3 PM ET* with Dr. Rose Marks from Michigan State University. Rose will present her recent publication in PNAS <https://doi.org/10.1073/pnas.2217564120> about inequalities in plant science literature. Below you can find more information about her talk and the Zoom link. I hope you will join us! Best, Annarita *Speaker: *Rose Marks, Ph.D., Michigan State University *Global disparities in plant science: a legacy of colonialism, patriarchy, and exclusion* The field of plant science has grown dramatically in the past two decades, but global disparities and systemic inequalities persist. We analyzed ~300,000 papers published over the past two decades to quantify global, gender, and taxonomic disparities in plant science. Our analyses reveal striking geographical biases that are correlated with national affluence. Gender imbalances were also evident, with far more papers led by authors with masculine names than those by authors with feminine names. Lastly, we identified substantial taxonomic sampling gaps. The vast majority of surveyed studies focused on major crop and model species, and the remaining biodiversity accounted for only a fraction of publications. Taken together, our analyses reveal a problematic system of publication, with persistent imbalances that poorly capture the global wealth of scientific knowledge and biological diversity. We conclude by highlighting disparities that can be addressed immediately and offer suggestions for long-term solutions to improve equity in the plant sciences. Zoom link: https://us06web.zoom.us/j/89060768261?pwd=TC9EOWR3UVdQS3UxNGZWQTEvWDFaZz09 <https://us06web.zoom.us/j/89060768261?pwd=TC9EOWR3UVdQS3UxNGZWQTEvWDFaZz09>

9 months

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"Inequalities in plant science literature", Rose Marks at the DEI Recruiting WG open meeting series

by Annarita Marrano

Hi everybody, The AgBioData DEI Recruiting working group (WG) will feature a series of open meetings on subjects and resources related to disparity and inclusion in STEM science. The first event of this series will be *next Monday (July 24) at 3 PM ET* with Dr. Rose Marks from Michigan State University. Rose will present her recent publication in PNAS <https://doi.org/10.1073/pnas.2217564120> about inequalities in plant science literature. Below you can find more information about her talk and the Zoom link. I hope you will join us! Best, Annarita *Speaker: *Rose Marks, Ph.D., Michigan State University *Global disparities in plant science: a legacy of colonialism, patriarchy, and exclusion* The field of plant science has grown dramatically in the past two decades, but global disparities and systemic inequalities persist. We analyzed ~300,000 papers published over the past two decades to quantify global, gender, and taxonomic disparities in plant science. Our analyses reveal striking geographical biases that are correlated with national affluence. Gender imbalances were also evident, with far more papers led by authors with masculine names than those by authors with feminine names. Lastly, we identified substantial taxonomic sampling gaps. The vast majority of surveyed studies focused on major crop and model species, and the remaining biodiversity accounted for only a fraction of publications. Taken together, our analyses reveal a problematic system of publication, with persistent imbalances that poorly capture the global wealth of scientific knowledge and biological diversity. We conclude by highlighting disparities that can be addressed immediately and offer suggestions for long-term solutions to improve equity in the plant sciences. Zoom link: https://us06web.zoom.us/j/89060768261?pwd=TC9EOWR3UVdQS3UxNGZWQTEvWDFaZz09 <https://us06web.zoom.us/j/89060768261?pwd=TC9EOWR3UVdQS3UxNGZWQTEvWDFaZz09>

9 months, 1 week

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REMINDER - tomorrow's AgBioData webinar at 12 PM CT!!

by Annarita Marrano

Hi everybody, This is a friendly reminder of our monthly webinar tomorrow, *July 12th*, at *12 PM CET*. We will have *Sarah Lippincott *from *DRYAD* talking about how to integrate generalist and specialist repositories to promote agricultural data sharing and reuse. I have included below more details about the webinar and the Zoom link to attend the webinar. I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: Presenters: Sarah Lippincott, Dryad <https://datadryad.org/stash> Abstract: *Companion planting: How generalist and specialist repositories can work together to promote agricultural data sharing and reuse.* This conversation explores strategies for enhancing open sharing and reuse of agricultural data through collaboration between disciplinary and generalist repositories, specifically Dryad, an open data publishing platform and community. Generalist and specialist repositories bring distinct strengths to data sharing and reuse. Generalist repositories offer a home for a wide range of data types and support serendipitous discovery, while discipline-specific repositories offer granular metadata, specialized tools, and deep understanding of community needs. Agricultural data creators, and future data re-users, can benefit from collaboration between these different solutions, including building connections with complementary datasets stored in multiple repositories; consistency in metadata standards; and federated discovery systems. In this conversation, Dryad’s Head of Community Engagement, Sarah Lippincott, will describe Dryad’s stewardship of agricultural data and engage attendees in an exploration of how Dryad’s can work with the agricultural research community to improve data sharing, discovery, and reuse. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+monthly…> Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 --- One tap mobile +19292056099,,82038356125#,,,,*160683# US (New York) +13017158592,,82038356125#,,,,*160683# US (Washington DC) --- Dial by your location • +1 929 205 6099 US (New York) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 646 931 3860 US • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US • +1 564 217 2000 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

9 months, 2 weeks

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AG2PI upcoming virtual events: Training Workshop + Field Day + other opportunities

by Scott, Nicole M [AGRON]

Hello AgBioData community members, Friendly reminder that AG2PI will be hosting two virtual events next week: 1. Reminder: the next AG2PI virtual Training Workshop, "CartograPlant Workshop: Integrating, Visualizing and Analyzing Genotype, Phenotype, and Environmental Data from Geo-Referenced Plants" is July 12 from 10 AM to 12:30 PM m CDT (UTC-5). In this workshop, Dr. This event is an outcome of an AG2PI seed grant award to Dr. Cobo. For additional details and to register for this virtual event go to https://www.ag2pi.org/workshops-and-activities/workshop-2023-07-12/. 2. The next AG2PI virtual Field Day, "Public-Private Partnerships in Education and Commercialization" will be July 19, 10:30 AM to 12 PM (CDT, UTC-5). In this field day, Drs. Addie Thompson (Michigan State University) and Nadilia Gomez (Iowa State University) will describe their endeavors in public-private partnerships with regards to opportunities in incorporating these into educational modules and commercialization of research outcomes. For additional details and to register for this virtual event go to https://www.ag2pi.org/workshops-and-activities/field-day-2023-07-19/. 3. Recordings from the AG2PI Conference, "Mapping the Future of Agricultural Genome to Phenome Research", cohosted with USDA NIFA can be found at https://www.ag2pi.org/workshops-and-activities/conference-2023-06-15/#agenda. Each recording link is embedded within the agenda, next to its respective session. 4. An opportunity from University of Florida and ARC Centre of Excellence for Plant Success in Nature and Agriculture. This is a symposium to share understanding and approaches to predict crop performance, accounting for Genotype by Environment by Management(GxExM) Interactions: Considering Breeder, Agronomist and Farmer Perspectives. Please direct any questions to Charlie Messina (cmessina(a)ufl.edu<mailto:cmessina@ufl.edu>). See attached GxExM flyer attached. Please share with your colleagues and students. We look forward to seeing you at a future event! ------------------------ Nicole Scott, PhD Program Specialist Agricultural Genome to Phenome Initiative Iowa State University 1111 WOI Rd Ames, IA 50011 office: 1077 Roy J. Carver Co-Lab phone: 515-294-3945 ag2pi.org<https://www.ag2pi.org/> *** If you no longer wish to receive messages from AG2PI, then please visit https://www.ag2pi.org/join-ag2pi/unsubscribe/ to unsubscribe *** Please note, you cannot unsubscribe if you are receiving this message through a third party ***

9 months, 2 weeks

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AgBioData monthly webinar - Next Wed, July 12th

by Annarita Marrano

Hi everybody, Join us next Wed, *July 12th, *at 12 PM CT for our monthly webinar. We will have *Sarah Lippincott *from *DRYAD* talking about how to integrate generalist and specialist repositories to promote agricultural data sharing and reuse. I have included below more details about the webinar and the Zoom link to attend the webinar. I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: Presenters: Sarah Lippincott, Dryad <https://datadryad.org/stash> Abstract: *Companion planting: How generalist and specialist repositories can work together to promote agricultural data sharing and reuse.* This conversation explores strategies for enhancing open sharing and reuse of agricultural data through collaboration between disciplinary and generalist repositories, specifically Dryad, an open data publishing platform and community. Generalist and specialist repositories bring distinct strengths to data sharing and reuse. Generalist repositories offer a home for a wide range of data types and support serendipitous discovery, while discipline-specific repositories offer granular metadata, specialized tools, and deep understanding of community needs. Agricultural data creators, and future data re-users, can benefit from collaboration between these different solutions, including building connections with complementary datasets stored in multiple repositories; consistency in metadata standards; and federated discovery systems. In this conversation, Dryad’s Head of Community Engagement, Sarah Lippincott, will describe Dryad’s stewardship of agricultural data and engage attendees in an exploration of how Dryad’s can work with the agricultural research community to improve data sharing, discovery, and reuse. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+monthly…> Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 --- One tap mobile +19292056099,,82038356125#,,,,*160683# US (New York) +13017158592,,82038356125#,,,,*160683# US (Washington DC) --- Dial by your location • +1 929 205 6099 US (New York) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 646 931 3860 US • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US • +1 564 217 2000 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

9 months, 3 weeks

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AgBioData monthly webinar - TOMORROW!!

by Annarita Marrano

Hi everybody, This is a friendly reminder of our monthly webinar tomorrow, *June 7th, *at 12 PM CT. We will have *Peter Selby *from Cornell University talking about the *BrAPI project and its applications in plant breeding*. I have included below more details about the webinar and the Zoom link to attend the webinar. I hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: Presenters: Dr. Peter Selby, Cornell University Abstract: *Applications and impacts of the BrAPI project on plant breeding* Modern genomic breeding methods rely heavily on very large amounts of phenotypic and genotypic data, presenting new challenges in effective data management and integration. The datasets are often large and complex, and the data is often stored on multiple systems, sometimes separated by country and organization. As the common analysis methods increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. This webinar will be an introduction to The Breeding API (BrAPI) Project. The BrAPI Project began in 2014 when a small group of plant breeding and technology experts came together to try to standardize their data. Since then, BrAPI has become internationally accepted as one of the primary data exchange standards in the plant breeding domain. This webinar will give an overview of what BrAPI is, how it works, what it is capable of, and the impact the project has had so far on the community. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 --- One tap mobile +19292056099,,82038356125#,,,,*160683# US (New York) +13017158592,,82038356125#,,,,*160683# US (Washington DC) --- Dial by your location • +1 929 205 6099 US (New York) • +1 301 715 8592 US (Washington DC) • +1 305 224 1968 US • +1 309 205 3325 US • +1 312 626 6799 US (Chicago) • +1 646 931 3860 US • +1 253 205 0468 US • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 360 209 5623 US • +1 386 347 5053 US • +1 507 473 4847 US • +1 564 217 2000 US • +1 669 444 9171 US • +1 669 900 6833 US (San Jose) • +1 689 278 1000 US • +1 719 359 4580 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

10 months, 3 weeks

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AgBioData-LIST