- AgBioData-LIST - Main Bioinformatics Lab

Survey about Genome Assembly and Gene Model identifiers for AgBioData species.

by Annarita Marrano

Hi everybody, The Genome Assembly and Annotation Nomenclature Working Group has put together *a survey* to gather community feedback regarding *Genome Assembly and Gene Model identifiers for AgBioData species*. This survey aims to *understand community preferences regarding naming conventions and the use of genome quality metrics, *supporting the development of recommendations for our community. Your input will be greatly appreciated! Please complete this survey no later than *Dec 5th* Click HERE <https://forms.gle/yN3eRphjZD9532xDA> to access the survey, or copy the link below into your web browser. Survey link: https://forms.gle/yN3eRphjZD9532xDA Yours sincerely, Kapeel Chougule, Sarah Dyer, Ethy Cannon & Patrice Salomé, on behalf of the The Genome Assembly and Annotation Nomenclature Working Group

3 years, 7 months

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Biocurating genetic variation data meeting

by Annarita Marrano

Dear AgBioData Member and/or DB Representative: The AgBioData Standards for Genetic Variation Working Group (SGV WG) will host *a virtual meeting* next Thursday, *December 8**th,* at *10 am ET* to discuss *potential targets for biocuration* in preparation for the AgBioData Workshop at PAG 2023. On behalf of the Working Group, we would like to invite you or a member of your Team to give a brief presentation (5 minutes) on the genetic variation datasets your resource handles and that could be a target for biocuration. To confirm your participation, we ask you to please enter your name and resource in the spreadsheet below: Biocurating Genetic Variation Data, Dec 8, 10 am ET <https://docs.google.com/spreadsheets/d/1gEYXSwqdXBgaOfCK0_9XxzJ588jPxQpLgo8…> To standardize the format and speed up the lightning presentations, we suggest that you use the attached template <https://docs.google.com/presentation/d/19fgox_y3u57sxMUgMIbSqgL-iMHv76pz-lj…> as a guide. A representative of the WG might follow up with you directly on this matter. We look forward to you joining us on the 8th! https://us06web.zoom.us/j/85083512863?pwd=ZHZGd1owbHNwU3VsNTYveVloYzcwZz09 Marcela On behalf of the SGV WG

3 years, 7 months

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JOIN the New AgBioData working groups

by Annarita Marrano

Hi everybody, We just started Year 2 of our NSF RCN grant of FAIR data in agricultural research and are initiating *six new working groups around data-related issues and priorities* raised by the AgBioData community. Each working group currently has a set of achievable goals and deliverables and has a *6-12 month duration* (except for the *Sustainability*, *FAIR Scientific Literature*, and *DEI Recruiting* working groups, which will have a 2-year mandate with the possibility for their members to rotate off after a year). We anticipate that the commitment will generally be *between 2-6 hours per month*, including meeting attendance and offline work (e.g., literature, writing, etc.). This is your opportunity to shape the future of our research community by contributing to developing best practices of data archiving and management that can benefit you and all the other stakeholders. Participating in the AgBioData working groups will also offer you opportunities for - *professional networking* - *leadership skill development* - *authorship in impactful manuscripts* Please join one or more of our working groups here <https://forms.gle/ue662FBGLXaVyY1eA>, or share with anybody that can be interested! Best regards, Annarita

3 years, 7 months

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AG2PI: November field day + workshop

by Scott, Nicole M [AGRON]

Hello AgBioData community members, We wanted to share some upcoming events with you: AG2PI Field Day The next AG2PI Field Day is November 16 from 10:30 am to noon CDT (UTC-6). This virtual event will consist of a panel of industry stakeholder representatives who will answer a few questions from moderator David Ertl (chair, AG2PI Stakeholder Organizations) on what they see as challenges in ag G2P research and applications before taking questions from the audience. See flyer attached. Register for this virtual event at https://www.ag2pi.org/workshops-and-activities/field-day-2022-11-16/. AG2PI Training Workshop The AG2PI training workshop, "Sharing UAS Based High Throughput Plant Phenotyping Data Via Public Clouds" will be November 18 from 12pm to 2pm CST (UTC-6). The main goal of this workshop is to help research scientists share Unoccupied Aircraft System (UAS) High Throughput Plant Phenotyping (HTPP) data using Oracle Cloud Infrastructure. See flyer attached. Register for this virtual event at https://www.ag2pi.org/workshops-and-activities/workshop-2022-11-18/. 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 ***

3 years, 8 months

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AG2PI seed grant RFP released!

by Scott, Nicole M [AGRON]

Dear AgBioData community members, USDA NIFA recently awarded Agricultural Genome to Phenome Initiative (AG2PI<https://ag2pi.org/>) additional money to continue our seed grant program. We will be funding 6-8 proposals that address challenges in genome-to-phenome research and promise to move the science and community forward. These awards are larger than previous AG2PI seed grants (up to $250,000), which we term "coconut seed grants" in recognition of their scaled-up size, and are intended to support new or "next step" research as well as community-focused endeavors. High-risk/high-reward proposals will be considered. Applications will be due by 11:59pm CST (UTC-6) on Friday, January 6th. The anticipated start date for funded projects is March 1, 2023 and each project may be up to 12 months in duration. Further details regarding the request for proposals, application and review process can be found on the AG2PI website (https://www.ag2pi.org/seed-grants/coconut-seed-grant-2022-10-28/). Note: Lead proposer(s) must be primarily affiliated with an institution or organization that is eligible for a USDA award. Available resources: * Previously funded seed grants (narratives & deliverables): https://www.ag2pi.org/resources/ag2pi-funded-seed-grants/ * Lightning talks on previously funded projects: https://www.ag2pi.org/workshops-and-activities/field-day-2022-09-21/ * Mini-conferences on previous seed grant RFPs (note: not all information provided in these mini-conferences is applicable to the current RFP): https://www.ag2pi.org/workshops-and-activities/conference-2022-01-19/ or https://www.ag2pi.org/workshops-and-activities/conference-2021-08-12/ Feel free to share this message and opportunity with colleagues at your institution. If you have any questions, please direct them to Nicole Scott at nmscott(a)iastate.edu<mailto:nmscott@iastate.edu>. Kind regards, AG2PI Executive Board ------------------------ 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 ***

3 years, 8 months

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REMINDER: AgBioData monthly webinar - Tomorrow, November 2nd!

by Annarita Marrano

Hi everybody, This is a gentle reminder of tomorrow's webinar with *Jennifer Cross <https://www.drjenicross.com/>* from Colorado State University. She will present the "*Science of Team Science*" and how team evaluation and coaching can help interdisciplinary teams advance science and overcome institutional and infrastructural challenges and barriers Below you can find more details about the webinar and the zoom link to attend the webinar. We hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: Presenters: Dr. Jennifer Cross, Colorado State University Host: Prof. John McNamara Abstract: *Science of Team Science: Using Developmental Evaluation to Advance Transdisciplinary Teams and Evolve Science.* For the past 20 years or more, science has been evolving to answer more complex questions, which require more complex teams. While scientists are eager to engage with diverse colleagues, academic institutions are slow to change and present a variety of barriers to advancing science. I will explore how the field “science of team science” has been growing and how team assessment, evaluation, and coaching can help teams become more effective. Case studies of interdisciplinary teams will be shared to illustrate how developmental evaluation and assessment can help accelerate team growth, and overcome institutional and infrastructural challenges and barriers. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> Annarita Marrano is inviting you to a scheduled Zoom meeting. 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 +13017158592,,82038356125#,,,,*160683# US (Washington DC) +13092053325,,82038356125#,,,,*160683# US Dial by your location +1 301 715 8592 US (Washington DC) +1 309 205 3325 US +1 312 626 6799 US (Chicago) +1 646 931 3860 US +1 929 205 6099 US (New York) +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 +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 Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

3 years, 8 months

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AgBioData monthly webinar - Next Wed, November 2nd

by Annarita Marrano

Hi everybody, Next Wed, *November 2nd*, we will have *Jennifer Cross <https://www.drjenicross.com/>* from Colorado State University talking about the "*Science of Team Science*" and how team evaluation and coaching can help interdisciplinary teams advance science and overcome institutional and infrastructural challenges and barriers Below you can find more details about the webinar and the zoom link to attend the webinar. We hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: Presenters: Dr. Chris Mungall, Lawrence Berkeley National Laboratory Host: Prof. John McNamara Abstract: *Science of Team Science: Using Developmental Evaluation to Advance Transdisciplinary Teams and Evolve Science.* For the past 20 years or more, science has been evolving to answer more complex questions, which require more complex teams. While scientists are eager to engage with diverse colleagues, academic institutions are slow to change and present a variety of barriers to advancing science. I will explore how the field “science of team science” has been growing and how team assessment, evaluation, and coaching can help teams become more effective. Case studies of interdisciplinary teams will be shared to illustrate how developmental evaluation and assessment can help accelerate team growth, and overcome institutional and infrastructural challenges and barriers. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> Annarita Marrano is inviting you to a scheduled Zoom meeting. 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 +13017158592,,82038356125#,,,,*160683# US (Washington DC) +13092053325,,82038356125#,,,,*160683# US Dial by your location +1 301 715 8592 US (Washington DC) +1 309 205 3325 US +1 312 626 6799 US (Chicago) +1 646 931 3860 US +1 929 205 6099 US (New York) +1 386 347 5053 US +1 564 217 2000 US +1 669 444 9171 US +1 669 900 6833 US (San Jose) +1 719 359 4580 US +1 253 215 8782 US (Tacoma) +1 346 248 7799 US (Houston) +1 360 209 5623 US Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

3 years, 8 months

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Reminder:CALL for IDEAS for new AgBioData working groups!!!!!

by Annarita Marrano

Dear AgBioData community, You are still on time to suggest *new working groups for **Year 2 *of our NSF Research Coordination Network <http://agbiodata.org/node/487> grant about defining community-based data sharing and management standards and promoting an equitable and sustainable data ecosystem in agriculture. As the technologies and approaches for generating, analyzing, and curating data keep evolving, new issues and priorities related to data sharing arise. *We would like to know from you what these priorities are and how we can address them in new AgBioData working groups*. Please share your feedback and suggestions through *this Google form <https://forms.gle/nnGdXhfoTR64z3Ru9>* by *October 28th*! After we have received your working group ideas, the steering committee will 1) decide on the working group roster for year 2 and 2) launch the participant sign-up for the working groups of Year 2. We anticipate that the new working groups will start on January 11th, 2023. Thank you for contributing to AgBioData's mission of making agricultural data FAIR! Best regards, Annarita Marrano On behalf of the AgBioData Steering Committee

3 years, 9 months

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CALL for IDEAS for new AgBioData working groups!!!!!

by Annarita Marrano

Dear AgBioData community, *We are soliciting ideas for new working groups for **Year 2 *of our NSF Research Coordination Network <http://agbiodata.org/node/487> grant about defining community-based standards of data sharing and management, and promoting an equitable and sustainable data ecosystem in agriculture. As the technologies and approaches for generating, analyzing, and curating data keep evolving, new issues and priorities related to data sharing arise. *We would like to know from you what these priorities are and how we can address them in new AgBioData working groups*. Please share your feedback and suggestions through *this Google form <https://forms.gle/nnGdXhfoTR64z3Ru9>* by *October 28th*! After we have received your working group ideas, the steering committee will 1) decide on the working group roster for year 2, and 2) launch the participant sign up for the working groups of Year 2. We anticipate that the new working groups will start January 11th, 2023. Thank you for contributing to AgBioData mission of making agricultural data FAIR! Best regards, Annarita Marrano On Behalf of the AgBioData Steering Committee

3 years, 9 months

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AgBioData monthly webinar - TOMORROW, October 5th

by Annarita Marrano

Hi everybody, This is a gentle reminder of tomorrow's webinar with *Chris Mungall <https://bids.berkeley.edu/people/chris-mungall>* from the Lawrence Berkeley National Laboratory. He will provide a practical guide on Gene Ontology <http://geneontology.org/> and how to use it for functional annotation in plants and animals. Below you can find more details about the webinar and the zoom link to attend the webinar. We hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: Presenters: Dr. Chris Mungall, Lawrence Berkeley National Laboratory Host: Dr. Tanya Berardini Abstract: *The Gene Ontology: Making functional annotation of plants and animals FAIR.* The Gene Ontology is one of the most widely used databases in the biosciences, covering functional annotation of genes and gene products across a wide range of species. The GO is ubiquitously used to analyse a variety of types of high-throughput experimental data. Originally created to unify functional annotation across a handful of model organism databases, the GO has grown to encompass more species, and the structure of the GO has been extended to integrate with other ontologies such as CHEBI and the Plant Ontology. The structure of annotations has also evolved, and the GO now includes more expressive pathway-oriented annotations in the form of GO-CAMs (Causal Activity Models). In this talk I will give a practical guide to the structure of GO, how to find and request terms, how to search and create annotations, and how to use GO tools. I will also talk about how the broader AgBioData can contribute to the GO consortium to help seed functional annotation efforts in a more diverse range of organisms, and in particular with agriculturally relevant species. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+webinar…> 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 +13017158592,,82038356125#,,,,*160683# US (Washington DC) +13092053325,,82038356125#,,,,*160683# US Dial by your location +1 301 715 8592 US (Washington DC) +1 309 205 3325 US +1 312 626 6799 US (Chicago) +1 646 931 3860 US +1 929 205 6099 US (New York) +1 386 347 5053 US +1 564 217 2000 US +1 669 444 9171 US +1 669 900 6833 US (San Jose) +1 719 359 4580 US +1 253 215 8782 US (Tacoma) +1 346 248 7799 US (Houston) Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

3 years, 9 months

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AgBioData-LIST