AgBioData-LIST September 2022

agbiodata-list@bioinfo.wsu.edu

2 participants
3 discussions

AgBioData monthly webinar - Next Wed, October 5th

by Annarita Marrano

Hi everybody, Next Wed, *October 5th*, we will have *Chris Mungall <https://bids.berkeley.edu/people/chris-mungall>* from the Lawrence Berkeley National Laboratory talking about Gene Ontology <http://geneontology.org/> and how to use it for functional annotation of 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

2 years, 2 months

AG2PI Field Day: Seed Grant Project Lightning Talks

by Scott, Nicole M [AGRON]

Dear AgBioData community members, The next Agricultural Genome to Phenome Initiative (AG2PI) Field Day is on Wednesday, September 21 from 10:30 AM to 12:00 PM (Central Time, UTC-5). In this field day, we will hear from a selection of seed grant recipients regarding the work they are doing to further develop the AG2PI community and advance AG2P science and technology. Talks have been pre-recorded and are in a three-minute thesis format so we can hear from eight project principal investigators in total. Each talk will be played and followed by an open Q&A session. Please note: these talks were recorded during the AG2PI "Thinking Big: Visualizing the Future of AG2PI" conference, which was co-hosted by USDA NIFA. Other recordings from this event are available on the AG2PI website at https://www.ag2pi.org/workshops-and-activities/conference-2022-09-09/. We invite you to register for this Zoom event at https://www.ag2pi.org/workshops-and-activities/field-day-2022-09-21/, 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). 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, 3 months

Nick Provart @ AgBioData webinar - TOMORROW!

by Annarita Marrano

Hi everybody, This is a gentle reminder of *tomorrow's *webinar (*Sept. 7th*) with *Nicholas J. Provart* from the University of Toronto. He will talk about the visual analytic tools for transcriptomic and genomics data (e.g., *ePlant*) developed by his lab and available at the Bio-Analytic <http://bar.utoronto.ca/> Resource <http://bar.utoronto.ca/>. 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. Nicholas J. Provart, the University of Toronto Host: Dr. Sunita Kumari Abstract: *Raising the BAR for Hypothesis Generation in Plant Biology Using Open Big Data.* We have developed tools, available as part of the Bio-Analytic Resource at http://bar.utoronto.ca, for exploring large data sets from plants, to allow deeper insights into biological questions. My lab’s three visual analytic tools for transcriptomic data (eFP Browser, ePlant, and eFP-Seq Browser) allow for rapid access to comprehensive gene expression compendia we have curated for identifying tissues, cell-types, or perturbations in which a gene is active or alternatively spliced. Interactions, be they protein-protein or regulatory, create networks. We have developed new tools for exploring such data, either from large collections of experimentally-supported protein-protein or protein-DNA interactions or from predicted interactions, including protein-protein interactions inferred from molecular docking studies. We are currently working on integrating large-scale phenotype data from field trials monitored by drone-based sensors into ePlants we have developed for several agronomically-important species to improve understanding of links between genotype and phenotype. *| 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) 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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AgBioData-LIST September 2022