- AgBioData-LIST - Main Bioinformatics Lab

AgBioData monthly webinar - Next Wed, Feb. 1st

by Annarita Marrano

Hi everybody, We will have our first webinar of the year next Wed, *February 1st. *Monica Munoz-Torres <https://tislab.org/members/monica-munoz-torres.html> from the University of Colorado School of Medicine will talk about the Monarch Initiative <https://monarchinitiative.org/>, a consortium and a set of resources that seeks to bridge the space between basic and applied and clinical research by developing tools that facilitate connecting data across a variety of scientific approaches and disciplines. 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. Monica Munoz-Torres, University of Colorado School of Medicine Host: Dr. Monica Poelchau Abstract: *The Monarch Initiative: harmonizing cross-species data for disease diagnostics and discovery.* Addressing complex scientific challenges requires weaving together data from diverse sources, organisms, contexts, formats, and granularities, and building a coherent holistic view of this data landscape to address any given problem is non-trivial – much of the relevant information is scattered and not readily accessible for searching or analysis. The Monarch Initiative is a consortium and a set of resources aiming to overcome these limitations by integrating the fragmented data landscape into the most comprehensive open collection of genotype-phenotype data available. Monarch seeks to bridge the space between basic and applied and clinical research, developing tools that facilitate connecting data across a variety of scientific approaches and disciplines including genomics, proteomics, molecular modeling, diagnosis of disease and syndromes, and the organization of patient record data. The Monarch Knowledge Graph (KG) links together clinical, biomedical, and basic science research data spanning multiple species, and it supports reasoning across a wide range of organisms, body systems, and diseases. We founded the Human Phenotype Ontology (HPO), one of the most widely used biomedical ontologies and the gold standard for describing human phenotypes, and are also creators of the Mondo unified disease ontology, the Unified Phenotype Ontology (uPheno), the cross-species anatomy ontology (Uberon), the Environmental Conditions and Treatments Ontology (ECTO), and most recently, the Vertebrate Breed Ontology (VBO), a single source for data standardization and integration of all breed names. We also created the Simple Standard for Sharing Ontology Mappings (SSSOM) to harmonize the ontologies that are used by the sources, and the only ISO-approved standard for exchanging detailed, case-level phenotype data, Phenopackets. Monarch tools and resources are publically available and are designed for both informatics users, as well as clinical and basic research use cases. By making data more interoperable, our widely-used standards for data annotation and exchange help support a wide range of data sharing and reuse by projects and organizations around the world, and reduce the effort they need to devote to data harmonization. During this presentation, we will introduce you to a few of these resources and offer you the information to find and implement the ones that best serve your scientific needs. *| 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 +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

2 years, 2 months

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AG2PI Field Day: Mitigating Methane Emissions in Dairy Cattle

by Scott, Nicole M [AGRON]

Dear AgBioData community members, The next Agricultural Genome to Phenome Initiative (AG2PI) Field Day will be "Mitigating Methane Emissions in Dairy Cattle Through Genetics and Nutrition: The Need for Improved Forages" and will be on Wednesday, February 8 from 10:30 AM to 12:00 PM (CST, UTC-6). In this field day, we will first hear from Dr. Francisco Peñagaricano regarding how omics tools can be used to mitigate enteric methane emissions from dairy cattle. Then, Dr. Ermias Kebreab will detail various strategies currently being pursued for enteric methane abatement. We invite you to register for this Zoom event at https://www.ag2pi.org/workshops-and-activities/field-day-2023-02-08/, 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. 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). 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 ***

2 years, 2 months

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AgBioData at PAG 30!

by Annarita Marrano

Hello AgBioData fellows! We will be at PAG 30! We will have a *workshop on Friday, Jan. 13* (see details below) and *a booth (#230)*. Please come to hear about our working groups' work and progress, and meet our community and genomic, genetic, and breeding resources. *Workshop description:* Title: "*The AgBioData Consortium: Challenges and Recommendations for FAIR Genetic, Genomic and Breeding Data <https://plan.core-apps.com/pag_2023/event/3cee484866e6d00c5e492240c4d27482>* " Location: Town and Country C Date: Friday, Jan 13, 4:00 PM Duration: 2 hours 10 minutes *About* AgBioData is a consortium of agricultural biological databases with the mission of consolidating standards and best practices for acquiring, displaying, and reusing genomic, genetic, and breeding (GGB) data. Our National Science Foundation Research Coordination Network (NSF-RCN) grant aims to address major issues around agricultural GGB data and databases by developing community-based recommendations and educational materials, and informing policy and decision-makers about the growing importance of scientific data curation and management to the research community. In the first year of the NSF-RCN grant, we established seven working groups (WGs) around topics important to anybody that generates, curates, and uses GGB data, specifically: Data Federation, Education, Genotype to Phenotype, Genome Nomenclature, Ontologies, Pan-Genomes, and Standards for Genetic Variation. In this workshop, we introduce the AgBioData consortium; share challenges, recommendations, and resources developed by several of these working groups; and provide preliminary insights on the long-term sustainability of the AgBioData database resources. We invite the larger community at PAG to learn about AgBioData, give us feedback on our working groups’ recommendations, and join our efforts to promote and facilitate FAIR data in agricultural research (https://www.agbiodata.org). *Workshop agenda:* *4:00 PM PT * "Data Federation in Genetics, Genomics and Breeding Databases - Current Status, Needs and Future Directions <https://plan.core-apps.com/pag_2023/event/6d1e5518daff93525372c4f032be253a>", Monica Poelchau *4:20 PM PT* "An Open Access Curriculum for Using Agricultural Biological Databases for Research and FAIR Data Sharing. <https://plan.core-apps.com/pag_2023/event/6d1e5518daff93525372c4f032be065c>", Margaret E. Staton *4:40 PM PT* "Challenges and Opportunities in Connecting Genes, Alleles, and Pan-Genes to Phenotype Data <https://plan.core-apps.com/pag_2023/event/6d1e5518daff93525372c4f032be2578>", Sushma Naitani *5:00 PM PT * "Guidelines for Standardizing Gene Model Nomenclature and Genome Assembly Quality Metrics <https://plan.core-apps.com/pag_2023/event/6d1e5518daff93525372c4f032be124b>", Kapeel Chougule *5:20 PM PT* "Towards Standards for Biocuration & Interoperability of Genetic Variation Data <https://plan.core-apps.com/pag_2023/event/6d1e5518daff93525372c4f032be173f>", Marcela Karey Tello-Ruiz *5:40 PM PT* "Sustainability Analysis of Agbiodata Databases <https://plan.core-apps.com/pag_2023/event/6d1e5518daff93525372c4f032bdffe2>", Shabari Subramaniam

2 years, 2 months

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Please complete the survey of the SGV WG!!!!

by Annarita Marrano

Dear AgBioData Community members: The Standards for Genetic Variation (SGV) Working Group aims to improve standards for the detection, annotation, and archiving of variation data. We are interested in understanding the genetic variation data you may have produced or are hosting, where it comes from, and what you plan to do with it. *If you are interested in these topics and want to stay updated, please fill in this short survey <https://docs.google.com/forms/d/e/1FAIpQLSfon9MB8XPxl4OmZjI4MhX1Cul9CViDnZo…>. *It will take less than 5 minutes! We hope to present the survey results next week at PAG 30, so please complete the survey* by 12 PM ET on Jan 12th*. Thanks much in advance, Marcela K. Tello-Ruiz, on behalf of the SVG Working Group

2 years, 2 months

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Reminder: Submit Your Comments to FFAR's Data Solutions RFI

by Annarita Marrano

Reminder: Submit Your Comments to FFAR's Data Solutions for Accelerating Climate-Smart Agriculture RFI The deadline to submit comments for the Foundation for Food & Agriculture Research's <https://urldefense.com/v3/__https://r20.rs6.net/tn.jsp?f=001GAa_LcL_8Sp6F64…> (FFAR) Request for Information <https://urldefense.com/v3/__https://r20.rs6.net/tn.jsp?f=001GAa_LcL_8Sp6F64…> (RFI) that supports advancing data solutions to accelerate climate-smart agriculture adoption is December 21, 2022. FFAR is issuing a RFI to explore investments that can increase the use of FAIR <https://urldefense.com/v3/__https://r20.rs6.net/tn.jsp?f=001GAa_LcL_8Sp6F64…> (Findable, Accessible, Interoperable, Reusable) data in agricultural research, with a specific emphasis on climate-smart mitigation and adaptation research related to the AgMission <https://urldefense.com/v3/__https://r20.rs6.net/tn.jsp?f=001GAa_LcL_8Sp6F64…>™ initiative. With sufficient volume of relevant standardized and interoperable data, agricultural sciences can apply advanced data analytics to address the challenges facing agricultural producers. FFAR encourages comments from scientists studying agricultural systems and agronomic practices, experts in agricultural data or privacy, developers of metric and digital tools to support on-farm decision-making, and developers and managers of digital data repositories with agricultural and environmental data. For more information, and to respond to this RFI, visit the Data Solutions for Accelerating Climate-Smart Agriculture Open Opportunity RFI webpage. <https://urldefense.com/v3/__https://r20.rs6.net/tn.jsp?f=001GAa_LcL_8Sp6F64…> ### Foundation for Food & Agriculture Research The Foundation for Food & Agriculture Research <https://urldefense.com/v3/__https://r20.rs6.net/tn.jsp?f=001GAa_LcL_8Sp6F64…> (FFAR) builds public-private partnerships to fund bold research addressing big food and agriculture challenges. FFAR was established in the 2014 Farm Bill to increase public agriculture research investments, fill knowledge gaps and complement USDA’s research agenda. FFAR’s model matches federal funding from Congress with private funding, delivering a powerful return on taxpayer investment. Through collaboration and partnerships, FFAR advances actionable science benefiting farmers, consumers and the environment. Connect: @FoundationFAR <https://urldefense.com/v3/__https://r20.rs6.net/tn.jsp?f=001GAa_LcL_8Sp6F64…>

2 years, 3 months

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AgBioData monthly webinar - Tomorrow!

by Annarita Marrano

Hi everybody, This is a friendly reminder of our webinar tomorrow (*December 7th).* We will have Sushma Naithani <http://naithanilab.cgrb.oregonstate.edu/> from Oregon State University talking about Plant Reactome <https://plantreactome.gramene.org/index.php?lang=en>, a platform that allows the integration of OMICs data for the biocuration of plant genes and pathways. 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. Sushma Naithani, Oregon State University Host: Dr. Monica Poelchau Abstract: *Plant Reactome: Using OMICs data for biocuration of plant genes and pathways* The major challenge in analyzing and connecting genotype to phenotype data at the organismal level is their integration and visualization for knowledge synthesis, which is required for generating OMICs data-driven predictive models for precision breeding of crops as well as accessing the needs of conservation of biodiversity and long-term sustainability. The Plant Reactome (https://plantreactome.gramene.org) is one such platform that allows integration of data from heterogeneous sources (i.e., published literature, transcriptome, proteome and metabolome data, orthology-based projections) for synthesizing in silico modeling of system-level plant pathway networks including metabolic pathways, biological processes associated with plant development and reproduction, and genetic-regulatory mechanisms that mediate plant survival under varied stress conditions. It provides a valuable framework for understanding how a gene, a group of connected genes, or genotypic differences culminate into a phenotype and supports the generation of data-driven hypotheses for understanding the intra-and -inter-species differences for basic and translational research and precision breeding. Here, we emphasize our recent efforts in using Omics data for improving gene/gene family functional annotations and biocuration of gene-gene networks. *| 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

2 years, 3 months

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LAST WEEK to JOIN the New AgBioData working groups!!

by Annarita Marrano

Hi everybody, If you haven't done yet, you are still on time to *join the new AgBioData working groups*! They will focus on and address* data-related issues and priorities* raised by the AgBioData community, such as - data federation training - data reuse - database financial sustainability - diversity, equity, and inclusion in ag research - FAIR scientific literature and biocuration - public genetic resources management Each working group 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

2 years, 3 months

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AgBioData monthly webinar - Next Wed, December 7th

by Annarita Marrano

Hi everybody, Next Wed, *December 7th*, we will have Sushma Naithani <http://naithanilab.cgrb.oregonstate.edu/> from Oregon State University talking about Plant Reactome <https://plantreactome.gramene.org/index.php?lang=en>, a platform that allows the integration of OMICs data for the biocuration of plant genes and pathways. 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. Sushma Naithani, Oregon State University Host: Dr. Annarita Marrano Abstract: *Plant Reactome: Using OMICs data for biocuration of plant genes and pathways* The major challenge in analyzing and connecting genotype to phenotype data at the organismal level is their integration and visualization for knowledge synthesis, which is required for generating OMICs data-driven predictive models for precision breeding of crops as well as accessing the needs of conservation of biodiversity and long-term sustainability. The Plant Reactome (https://plantreactome.gramene.org) is one such platform that allows integration of data from heterogeneous sources (i.e., published literature, transcriptome, proteome and metabolome data, orthology-based projections) for synthesizing in silico modeling of system-level plant pathway networks including metabolic pathways, biological processes associated with plant development and reproduction, and genetic-regulatory mechanisms that mediate plant survival under varied stress conditions. It provides a valuable framework for understanding how a gene, a group of connected genes, or genotypic differences culminate into a phenotype and supports the generation of data-driven hypotheses for understanding the intra-and -inter-species differences for basic and translational research and precision breeding. Here, we emphasize our recent efforts in using Omics data for improving gene/gene family functional annotations and biocuration of gene-gene networks. *| 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 +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

2 years, 4 months

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AG2PI upcoming events

by Scott, Nicole M [AGRON]

Hello AgBioData community members, Agricultural Genome to Phenome Initiative (AG2PI) has some upcoming events you may be interested in: AG2PI Training Workshop The next AG2PI training workshop is December 9, 11am-1pm CST (UTC-6). This workshop on "Train Your Network: simplifying computer vision application development" will demonstrate a new image classification program, "Train Your Network", designed for use by anyone, including the most novice users of AI. There will be opportunities to provide feedback on this new user interface and software, so all are encouraged to attend. Register at https://www.ag2pi.org/workshops-and-activities/workshop-2022-12-09/. Seed Grant RFP Q&A session AG2PI will hold a one hour question/answer session this Friday, December 2 (12-1pm, CST), regarding the new RFP opportunity (which we termed "coconut" grants). Meeting details are at https://www.ag2pi.org/workshops-and-activities/conference-2022-12-02/. See full RFP at https://www.ag2pi.org/seed-grants/coconut-seed-grant-2022-10-28/ AG2PI conference - save the date We are excited to announce the next AG2PI Conference: Mapping the Future of Agricultural Genome to Phenome Research, which will be held Thursday-Friday, June 15-16, 2023, in Kansas City, MO. This event will include talks by community thought leaders, stakeholder roundtables, small group discussions, and networking opportunities, all designed to map the future of AG2P research and develop recommendations concerning the research investments needed to achieve that future. These recommendations have been requested by USDA-NIFA. The conference will be open to all, but registration will be required. Registration is expected to open in February 2023. A limited number of travel stipends will be available. Additional details to follow. We are also looking for nominations of thought leaders who can present on these themes: 1) Exciting breakthroughs in AG2P research and/or 2) Needed directions in AG2P research/policies. To submit a nomination, fill out this Google Form (https://forms.gle/Fd4g6wkVMP3Jkxnp8) explaining who you are nominating and why by December 4. Thank you, 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 ***

2 years, 4 months

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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

2 years, 4 months

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AgBioData-LIST