- AgBioData-LIST - Main Bioinformatics Lab

AG2PI survey: Priorities for future funding opportunities in G2P

by Scott, Nicole M [AGRON]

Dear AgBioData member, Tell us where future research and development funds should be directed! In this survey, you will tell us which areas of agricultural genomes-to-phenomes (G2P) research you think are most critical for future investment, which are easiest to accomplish and in what areas might cross-kingdom collaborations be most successful. Summarized responses will be shared with USDA NIFA and on the AG2PI Community Survey<https://www.ag2pi.org/community-surveys/> webpage. The below URL is anonymous and does not collect identifying information. We ask that you finish the survey in one session, which should take 10-15 minutes. Follow this link to the Survey: https://iastate.qualtrics.com/jfe/form/SV_6rlzERMQZcxsLmm This survey will close July 1, 2022. Please note: If you have joined an AG2PI mailing list then you will receive a direct email from this project asking you to fill out the survey. You should only fill out the survey once. As a thank you for participating in the survey, we'd like to offer you the opportunity to enter into a random drawing for one of two (2) $50 gift cards and one of eight (8) AG2PI 20 oz aluminum water bottles. A link to a Google Form can be found at the end of the survey for you to enter the drawing. This opportunity is only open to individuals currently living in the U.S. and who are 18 years or older. As a reminder, the focus of the AG2PI project is to build cross-kingdom research communities to address the challenges of genome to phenome (G2P) research and find opportunities to work together to identify shared critical research gaps. AG2PI is not, itself, a research producing project. Importantly, this survey is an opportunity for the community to share with the USDA a vision that may be used to guide future requests for proposals in this space as Congress continues to appropriate money for the general AG2PI program authorized in the 2018 Farm Bill. We appreciate your input on how the AG2PI project can be used to better your own agricultural endeavors and inform USDA of your needs. Kind regards, Nicole Scott ------------------------ 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 ***

4 years, 1 month

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AG2PI field day next week + upcoming workshops

by Scott, Nicole M [AGRON]

Dear AgBioData community members, We wanted to share some upcoming events with you: AG2PI Field Day #19 The next AG2PI Field Day is on Wednesday, June 15 from 10:30 AM to 12:00 PM (Central Time, UTC-5). In this field day, we'll hear from Lingzhao Fang, University of Edinburgh, and Justin Walley, Iowa State University, about what is being done with quantitative multi-omics to unravel genomes-to-phenomes in crops and livestock. This discussion will hit themes that are relevant to both animal and plant sciences, so we hope you join us for an engaging conversation! We invite you to register for this Zoom event at https://tinyurl.com/AG2PI-FD19, where you will also find additional information. Upon registration, you will receive a confirmation email with information about joining the meeting. If you are unable to attend the live session, then you will be able to find a recording at ag2pi.org/<https://www.ag2pi.org/>, at a later date. Please note: you do not need to register to view the recording; it is readily available on the AG2PI website soon after the close of the event (generally within 24 hours). Feel free to share this message and attached flyer with colleagues at your institution. Upcoming workshops Community workshop: AI in Agriculture - Ethics and Responsibility Workshop 2022 (google.com)<https://docs.google.com/document/u/3/d/e/2PACX-1vQo6JwPGwEPittHg4vPI3aZ2Zyo…> - this workshop is not affiliated with AG2PI AG2PI Training Workshop: * June 23, 10am-12pm (CDT): Crop Modeling as a Tool for Understanding the Genotype X Environment Interaction (presenter: Gerrit Hoogenboom) * July 12, 1-3 pm (CDT): Bison-Fly: a UAV pipeline applied to plant breeding programs (presenter: Filipe Matias) mark your calendars, registration not yet open * July 26, 12-2pm (CDT): Omics-enabled genetic prediction (presenters: Jinliang Yang & Hao Cheng) mark your calendars, registration not yet open 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 ***

4 years, 1 month

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TOMORROW AgBiodata webinar!

by Annarita Marrano

Hi everybody, This a gentle reminder of our webinar *tomorrow*, *June 1st*, at 12 PM CT. We will have *Camille Rustenholz *from the University of Strasbourg (France) talking about the INTEGRAPE <https://integrape.eu/>project and how they defined data integration standards to maximize the power of omics in grapevine. 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. Camille Rustenholz, University of Strasbourg (France). INTEGRAPE <https://integrape.eu/> Host: Annarita Marrano Abstract: *COST ACTION INTEGRAPE: Data integration to maximise the power of omics in grapevine improvement and beyond.* The European network INTEGRAPE seeks the establishment of an open, international, and representative network, insuring that omics and phenotyping data generated in the grapevine research community are being produced in a secure and standardized format, following the F.A.I.R. principles of findability, accessibility, interoperability, and reusability. Amongst the most significant deliverables of INTEGRAPE: - the elaboration of Guideline ‘cookbooks’ and Dictionary of unified grape-sample ontologies; - the release of the PN40024 fourth genome assembly and its annotation; - the creation of the Gene Reference Catalogue; - the enlisting of Online repositories and tools for omics data exploration and visualization, which to date are not yet interoperable among them. To tackle this last challenge, we applied for a COST Innovative Grant with the GRAPEDIA project (Grapevine Encyclopedia of genes and omics), which goal is to provide the community with a single open-access database, allowing data exploration and visualization of all grapevine resources, with tools for comparative analysis and customized services. In the GRAPEDIA database, we aim at centralizing, interconnecting, and showcasing these dispersed resources, and integrating them with those genomic efforts generated by the worldwide community. The target group is the entire scientific community working on the grapevine or using grapevine as their model plant for an “orphan” plant species, and also the private sector working on R&D in vitiviniculture. *| 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) +1 312 626 6799 US (Chicago) +1 669 900 6833 US (San Jose) +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

4 years, 1 month

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AgBiodata monthly webinar - Next Wed, June 1st!

by Annarita Marrano

Hi everybody, Next Wed, *June 1st*, we will have *Camille Rustenholz *from the University of Strasbourg (France) talking about the INTEGRAPE project and how they defined data integration standards to maximize the power of omics in grapevine. 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. Camille Rustenholz, University of Strasbourg (France). INTEGRAPE <https://integrape.eu/> Host: Annarita Marrano Abstract: *COST ACTION INTEGRAPE: Data integration to maximise the power of omics in grapevine improvement and beyond.* The European network INTEGRAPE seeks the establishment of an open, international, and representative network, insuring that omics and phenotyping data generated in the grapevine research community are being produced in a secure and standardized format, following the F.A.I.R. principles of findability, accessibility, interoperability, and reusability. Amongst the most significant deliverables of INTEGRAPE: - the elaboration of Guideline ‘cookbooks’ and Dictionary of unified grape-sample ontologies; - the release of the PN40024 fourth genome assembly and its annotation; - the creation of the Gene Reference Catalogue; - the enlisting of Online repositories and tools for omics data exploration and visualization, which to date are not yet interoperable among them. To tackle this last challenge, we applied for a COST Innovative Grant with the GRAPEDIA project (Grapevine Encyclopedia of genes and omics), which goal is to provide the community with a single open-access database, allowing data exploration and visualization of all grapevine resources, with tools for comparative analysis and customized services. In the GRAPEDIA database, we aim at centralizing, interconnecting, and showcasing these dispersed resources, and integrating them with those genomic efforts generated by the worldwide community. The target group is the entire scientific community working on the grapevine or using grapevine as their model plant for an “orphan” plant species, and also the private sector working on R&D in vitiviniculture. *| 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) +1 312 626 6799 US (Chicago) +1 669 900 6833 US (San Jose) +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

4 years, 1 month

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[Register Today] Making FAIR'S Interoperability and Reusability Data Goals Possible

by Daureen Nesdill

Thought this group would be interested is this 2 hour event - Daureen Nesdill Reserve your spot to join the discussion<https://www.chorusaccess.org/events/making-fairs-interoperability-and-reusa…> Join CHORUS at a forum on Making FAIR'S Interoperability and Reusability Data Goals Possible Friday, June 17, 2022 from 11:00am - 1:00pm EST This AGU / CHORUS Forum brings together government, funder, academic institution, and scientific society stakeholders, who will outline why I & R are proving to be challenging. This two-part session also showcases some of the partial solutions being put into practice, and participants are invited to comment on at least one new promising solution. Register today!<https://www.chorusaccess.org/events/making-fairs-interoperability-and-reusa…> Session 1: The problem of actually doing Interoperability and Reusability and why it's important Speakers * Chris Marcum, Assistant Director for Open Science and Data Policy, US Office of Science & Technology Policy * Ingrid Dillo, Deputy Director, DANS: Dutch National Centre of Expertise and Repository for Research Data; Co-chair of Council Research Data Alliance Additional speakers to follow Session 2: Existing partial solutions Speakers * Corinna Gries, Principal Investigator, Environmental Data Initiative * Jens Klump, Geoscience Analytics Team Leader in the Mineral Resources, Commonwealth Scientific and Industrial Research Organisation (CSIRO) * Jane Wyngaard, Lecturer, Department of Electrical Engineering, University of Cape Town Sara Rotjan Assistant Marketing Director Pronouns: she/her/hers On behalf of CHORUS AIP Publishing 1305 Walt Whitman Road │ Suite 110 | Melville NY 11747-4300 │ USA t +1.516.576.2237 | m +1.917.309.1183 srotjan(a)aip.org<mailto:srotjan@aip.org> | publishing.aip.org Follow us: Facebook<https://www.facebook.com/AIPPublishing> │ Twitter<https://twitter.com/AIP_Publishing> │ LinkedIn<https://www.linkedin.com/company/aip-publishing>

4 years, 1 month

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AG2PI Field Day: International Centers & Partnerships: Genetic Improvement Resources and Opportunities

by Scott, Nicole M [AGRON]

Dear AgBioData community members, The next AG2PI Field Day is on Wednesday, May 18 from 10:30 AM to 12:00 PM (Central Time, UTC-5). In this field day, we'll hear about the research, community building and impact of two international research centers: Centre for Tropical Livestock Genetics and Health (CTLGH) and International Maize and Wheat Improvement Centre (CIMMYT). Appolinaire Djikeng and Kellie Watson of CTLGH will focus on their partnerships and farmer-facing programs, while Sarah Hearne of CIMMYT will discuss partnership building as part of One CGIAR. This discussion will hit themes that are relevant to both animal and plant sciences, so we hope you join us for an engaging conversation! We invite you to register for this Zoom event at https://tinyurl.com/AG2PI-FD18, where you will also find additional information. Upon registration, you will receive a confirmation email with information about joining the meeting. If you are unable to attend the live session, then you will be able to find a recording at ag2pi.org/<https://www.ag2pi.org/>, at a later date. Please note: you do not need to register to view the recording; it is readily available on the AG2PI website soon after the close of the event (generally within 24 hours). Feel free to share this message and attached flyer with colleagues at your institution and members of your listservs. 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 ***

4 years, 2 months

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AgBiodata monthly webinar - TOMORROW, May 4th

by Annarita Marrano

Hi everybody, This email is a gentle reminder of *tomorrow's webinar* with Karon Yook and Daniela Raciti from microPublication Biology <https://www.micropublication.org/>. We will start at *12 PM CT* as usual (find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…>) using the zoom link that you can see below. We also want to invite you to *vote for two new members of the AgBioData steering committee.* The steering committee members are the driving force of the AgBioData consortium, and your opinion can help us shape our future direction. As a member of AgBioData, you should have received an email from Election Runners with the link to vote. *Please vote by May 15!* I hope you'll be able to join us tomorrow. Regards, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: Presenters: Dr. Karen Yook and Dr. Daniela Raciti, California Institute of Technology, Wormbase <https://wormbase.org/#012-34-5>. Host: Leonore Reiser Abstract: *Bridging the gap between data production and database curation through microPublications* To solve a long-standing problem in data loss and accessibility, we developed a publishing platform, microPublication Biology, to bridge data publishing and database curation. Our journal accepts single experiment articles (microPublications) and embeds curation within the article submission/publishing workflow. microPublication Biology is an online, peer-reviewed, open-access journal published by the Caltech Library and discoverable in PubMed. Starting with articles focused on nematode biology, we continually expand to more organism communities, including Arabidopsis and most recently Dictyostelium, Maize, and Cotton. Our system is set up so that upon publication, atomized data is delivered directly to authoritative databases for each community (e.g., WormBase, Flybase, PomBase, TAIR), ensuring timely delivery to biological databases for deep data integration. We will give an overview of our journal and its integrated curation workflow and present our latest publishing metrics. *| 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 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) +1 312 626 6799 US (Chicago) +1 669 900 6833 US (San Jose) +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

4 years, 2 months

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AgBiodata monthly webinar May 4th

by Annarita Marrano

Hi everybody, After a break in April, we are back with our monthly webinar! Next Wed, *May 4th*, we will have *Karen Yook* and *Daniela Raciti* from Wormbase talking about how to bridge data generation and database curation through microPublications. 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. Karen Yook and Dr. Daniela Raciti, California Institute of Technology, Wormbase <https://wormbase.org/#012-34-5>. Host: Leonore Reiser Abstract: *Bridging the gap between data production and database curation through microPublications* To solve a long-standing problem in data loss and accessibility, we developed a publishing platform, microPublication Biology, to bridge data publishing and database curation. Our journal accepts single experiment articles (microPublications) and embeds curation within the article submission/publishing workflow. microPublication Biology is an online, peer-reviewed, open-access journal published by the Caltech Library and discoverable in PubMed. Starting with articles focused on nematode biology, we continually expand to more organism communities, including Arabidopsis and most recently Dictyostelium, Maize, and Cotton. Our system is set up so that upon publication, atomized data is delivered directly to authoritative databases for each community (e.g., WormBase, Flybase, PomBase, TAIR), ensuring timely delivery to biological databases for deep data integration. We will give an overview of our journal and its integrated curation workflow and present our latest publishing metrics. *| 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 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) +1 312 626 6799 US (Chicago) +1 669 900 6833 US (San Jose) +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

4 years, 2 months

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AgBioData 2022 Survey of Genomic, Genetic, and Breeding (GGB) Database Stakeholders

by Annarita Marrano

Dear AgBioData members, We are asking you to participate in a survey about standardized data curation principles and their implementation in data repositories for agricultural research and breeding programs. This survey was developed by the AgBioData consortium (https://www.agbiodata.org) in collaboration with Washington State University. Please disregard this email if you already received this survey and submitted your answers. The survey is anonymous, and your answers will be used to shape AgBioData's future goals and solutions for standardized data management in agriculture. If you are willing to participate, please submit your answers here <https://ncsu.qualtrics.com/jfe/form/SV_9Zv0sSXJhdz2bYO> by May 9th, 2022. Your opinion is valuable to us and can help AgBioData define better genomic, genetic, and breeding data curation practices. Best regards, Annarita Marrano On behalf of the AgBioData Steering Committee

4 years, 3 months

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Refresh AgBioData group of ontologies in AgroPortal

by Clement Jonquet

Dear AgBioData, A few years ago, after a review in the AgBioData community (at large, not only the ontology/metadata WG) we had produced a list of ontologies actively used by our databases. To my memory, except maybe CheBI we had them all in AgroPortal. So we created a « group » in AgroPortal for AgBioData. These ontologies can be visualized in AgroPortal here by filtering by group: http://agroportal.lirmm.fr/ontologies <http://agroportal.lirmm.fr/ontologies> We also setup a slice (i.e., a subset of the whole AgroPortal where all the UI and services are « restricted » to the AGBIODATA group): http://agbiodata.agroportal.lirmm.fr/ontologies <http://agbiodata.agroportal.lirmm.fr/ontologies> The meeting last week remind me that we should refresh/complete this list (looking at other ontologies available in AgroPortal or in other resources (BioPortal, OLS, ...). Also, at the same time I registered the « projects » using the ontologies… here : http://agroportal.lirmm.fr/projects <http://agroportal.lirmm.fr/projects> This page looks a bit « unattractive » (the UI will be refactored soon) but in fact this is the only place where the relation between a project and and ontology is formally (and machine actionably) represented e.g., http://data.agroportal.lirmm.fr/ontologies/PO/projects <http://data.agroportal.lirmm.fr/ontologies/PO/projects> (Add ?&apikey=528c4e4a-5c3e-4798-a2e2-11d96761b8ce at the end of the call in your Browser) This information allow us, for instance, to show « ontology in used » in the landscape page: So if you an take a minute to reply to this email with ONE sentence : I am XX, my database or project, YY, (still) uses ontologies/semantic resources ZZ, RR, TT, etc. I will then compile the data in AgroPortal. Bye Thanks Clement ------------------------------------------------------------------------------------------- Dr. Clement JONQUET – PhD in Informatics Senior Researcher – INRAE (MISTEA) Associate Researcher – University of Montpellier (LIRMM) Coordinator of the SIFR, AgroPortal and D2KAB projects clement.jonquet(a)inrae.fr or jonquet(a)lirmm.fr http://www.lirmm.fr/~jonquet @MISTEA (L,M,M,J): +33/0 4 99 61 22 77 @LIRMM (V): +33/0 4 67 14 97 43 -------------------------------------------------------------------------------------------

4 years, 3 months

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AgBioData-LIST