AgBioData-LIST January 2024

agbiodata-list@bioinfo.wsu.edu

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2 discussions

REMINDER - Monthly Webinar Next Wed, Feb. 7th, at 12 PM CT

by Annarita Marrano

Hi everybody, After the holiday break and PAG 31, we are ready to restart our monthly webinar series! Join us next Wed, Feb. 7th, at 12 PM CT for our monthly webinar. Alex Ignatchenko and Paul Thomas will talk about TreeGrafter, a method of predicting Gene Ontology annotations, and other tools implemented in InterProScan. 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 :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Abstracts:* *Alex Ignatchenko (EMBL-EBI):* Gene Ontology (GO) Annotation (GOA) project at EMBL-EBI aims to provide high-quality GO annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. Currently, the GOA database hosts 5 million manually curated GO annotations from over 70 research groups. This set is used as a foundation for 15 automatic GO annotation pipelines. The output data re-generated ever 2 month and commonly referred to as Inferred from Electronic Annotation (IEA). The IEA pipelines use range of statistical, rule-based and machine learning algorithms to enrich existing GO annotation coverage. The generated IEA set of over 1.1 billion GO annotations is subject to over 130 checks, constraints and filters to ensure the quality of predicted GO annotations. The GOA data is publicly available from GOA ftp and the GO annotation browser QuickGO. The GOA team is constantly looking for ways to improve the quality of GO annotations and gene product coverage. The TreeGrafter is a method of prediction of GO annotations based on PANTHER family/subfamily and the InterPro signatures. The project is a collaboration between PANTHER and the InterPro team at EMBL-EBI. The algorithm was published in 2019, and it was incorporated into the InterPro in the second half of 2023. The TreeGrafter mappings were processed and added to the GOA database for testing shortly after. This implementation resulted in about 301 million GO annotations after the GOA pipeline checks and filters. More importantly, the final set has over 200 million GO annotations, which is not predicted by any other IEA methods. The GOA team plans to intergrade TreeGrafter GO annotation pipeline into the GOA database and release it to public in a first half of 2024. *Paul D. Thomas (University of Southern California and Gene Ontology Consortium)Accurate annotation of protein sequences at large scale, using evolutionary modeling* Inferring (aka “annotating” or “predicting”) the functions of the vast numbers of known protein sequences has been a longstanding challenge in genomics. Over the last decade, a comprehensive system has been developed for addressing this challenge based on constructing and applying models of function evolution in protein families. The main components of the system– including PANTHER phylogenetic trees, Gene Ontology phylogenetic annotations and TreeGrafter software (now implemented in InterProScan)– work together in an integrated software and data suite that is now beginning to be broadly used to annotate the functions of protein-coding genes. I will describe each of these components, as well as how the tool can be easily used to annotate any set of protein-coding genes and how users can give feedback to help improve the annotations. *| 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 +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

9 months, 3 weeks

Where can you find AgBioData at PAG 31!!!

by Annarita Marrano

Hello everyone, AgBioData will be at PAG 31 in San Diego on Jan. 12-17! Here are some information on when and where you can find us at PAG: - Join us for *our workshop *"*The AgBioData Consortium: Challenges and Recommendations for FAIR Genetic, Genomic and Breeding Data*" on *Friday, Jan. 12, at 4 PM* in room Town and Country C. Some of our working groups and two talented early-career AgBioData members will present their works. More details are available here <https://www.agbiodata.org/agb-pag31>. - *Join us at booth #422* and meet our member database resources. We will be there during exhibit hours to discuss our mission and answer your questions. - AgBioData will have two posters on Monday, Jan. 15, from 3-4.40. - *PO0727* - *PO0643 * - Our steering committee member, *Leonore Reiser*, will present about AgBioData and our NSF RCN grant during the workshop "*Beyond the National Plant Genome Initiative: New Frontiers and Grand Challenges in Plant Genomics*." Her talk <https://plan.core-apps.com/pag_2024/event/2562157f06c9714c1a4dcc7037839c83> is scheduled for *Sunday, Jan. 14, at 2:10 PM.* In addition, Ag2PI organized the workshop "*Supporting Agricultural Genomics Through Bioinformatics*" on Tuesday, Jan. 16, at 6.20 PM in room Palm 8. During the workshop, there will be a roundtable discussion about how bioinformaticians can support the agricultural genomics community in analyzing genomics data. This discussion will be led by plant and animal researchers with a mixture of bioinformatics expertise and topics include: - current barriers to doing reproducible genomic analyses - how bioinformatics experts can more effectively support agricultural researchers - how to ensure students have the bioinformatics skills they will need - commonalities for genomic analyses across plant, animal and microbial data sets Best regards, Annarita

10 months, 2 weeks

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AgBioData-LIST January 2024