- AgBioData-LIST - Main Bioinformatics Lab

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

2 years, 5 months

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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

2 years, 6 months

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REMINDER - Monthly Webinar TOMORROW, Dec. 6th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us TOMORROW, Dec. 6th, at 12 PM Central Time for our monthly webinar. This webinar will focus on single-cell data and metadata management in livestock and plants Benjamin Cole <https://jgi.doe.gov/our-science/scientists-jgi/benjamin-cole-genomics-of-pl…> , Christopher Tuggle <https://faculty.sites.iastate.edu/cktuggle/>, and Muskan Kapoorand <https://github.com/kapoormuskan>. 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:* *Benjamin Cole (Joint Genome Institute) on "Data management considerations for plant single-cell genomics."* While plants have arrived on the single-cell scene relatively late, the number and complexity of plant single-cell datasets have exploded over the past four years. With that massive increase in data has come a pressing need to ensure accurate documentation of the experimental provenance of plant single-cell datasets, not only for reproducibility but also for reusability in meta-analyses. During this presentation, I will discuss the current state of plant single-cell research as well as the most common practices for data storage. I will also argue for the need for better standards in the field, and what that could potentially enable. *Christopher Tuggle (Iowa State University) & Muskan Kapoor (Iowa State University) on "Single-Cell genomics data incorporation into agricultural G2P research by building a FAIR data ecosystem."* We will describe a pilot-scale project to determine if our current metadata standards for livestock and crops can be used to ingest scRNAseq datasets in a manner consistent with HCA DCP standards and if established resources (e.g., Terra) can be used to analyze the ingested data. Currently, the most comprehensive data ingestion portal for high throughput sequencing datasets from plants, fungi, protists, and animals/humans is Annotare (located at EMBL-European Bioinformatics Institute). For agricultural animal datasets, another EMBL-EBI portal, the FAANG portal, has been developed. scRNAseq data/metadata can be submitted to FAANG using a semi-automated process. We have extended this tool for scRNAseq data so that files can be validated using the HCA DCP metadata and data validation service. These files are incorporated using EMBL-EBI’s HCA DCP ingestion service and transferred to Terra for further analysis. We will also describe a Shiny-based web application, implemented in R and called Shiny-PIGGI, for the single cell-level transcriptomic study of pig immune tissues and peripheral blood mononuclear cells, which will be an important resource for improved annotation of porcine immune genes and cell types ( https://shinypiggi.ansci.iastate.edu). We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem to facilitate single cell-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species. *| 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, 7 months

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Board on Agriculture and Natural Resources Winter Meeting - Tomorrow, Dec. 5

by Annarita Marrano

Hi everybody, The Board on Agriculture and Natural Resources is holding a seminar on Access to Data *tomorrow, Dec. 5, at 11 AM ET.* The meeting will explore a range of topics of interest to the food, agriculture, and natural resources communities. The open sessions of the meeting will include a presentation on research priorities of the USDA Economic Research Service, a panel on disparities in access to data and journal publications, a briefing on a new National Academies report on Accelerating Decarbonization, and a presentation from Colorado State University researchers on a National Climate Change Roadmap: A Research Framework for U.S. Agriculture, Forestry, and Working Lands. You can find more information here <https://www.nationalacademies.org/event/41526_12-2023_board-on-agriculture-…> . Best, Annarita

2 years, 7 months

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REMINDER - Monthly Webinar Next Wed, Nov 1st, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us next Wed, Dec. 6th, at 12 PM CT for our monthly webinar. This webinar will focus on single-cell data and metadata management in livestock and plants Benjamin Cole <https://jgi.doe.gov/our-science/scientists-jgi/benjamin-cole-genomics-of-pl…> , Christopher Tuggle <https://faculty.sites.iastate.edu/cktuggle/>, and Muskan Kapoorand <https://github.com/kapoormuskan>. 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:* *Benjamin Cole (Joint Genome Institute) on "Data management considerations for plant single-cell genomics."* While plants have arrived on the single-cell scene relatively late, the number and complexity of plant single-cell datasets have exploded over the past four years. With that massive increase in data has come a pressing need to ensure accurate documentation of the experimental provenance of plant single-cell datasets, not only for reproducibility but also for reusability in meta-analyses. During this presentation, I will discuss the current state of plant single-cell research as well as the most common practices for data storage. I will also argue for the need for better standards in the field, and what that could potentially enable. *Christopher Tuggle (Iowa State University) & Muskan Kapoor (Iowa State University) on "Single-Cell genomics data incorporation into agricultural G2P research by building a FAIR data ecosystem."* We will describe a pilot-scale project to determine if our current metadata standards for livestock and crops can be used to ingest scRNAseq datasets in a manner consistent with HCA DCP standards and if established resources (e.g., Terra) can be used to analyze the ingested data. Currently, the most comprehensive data ingestion portal for high throughput sequencing datasets from plants, fungi, protists, and animals/humans is Annotare (located at EMBL-European Bioinformatics Institute). For agricultural animal datasets, another EMBL-EBI portal, the FAANG portal, has been developed. scRNAseq data/metadata can be submitted to FAANG using a semi-automated process. We have extended this tool for scRNAseq data so that files can be validated using the HCA DCP metadata and data validation service. These files are incorporated using EMBL-EBI’s HCA DCP ingestion service and transferred to Terra for further analysis. We will also describe a Shiny-based web application, implemented in R and called Shiny-PIGGI, for the single cell-level transcriptomic study of pig immune tissues and peripheral blood mononuclear cells, which will be an important resource for improved annotation of porcine immune genes and cell types ( https://shinypiggi.ansci.iastate.edu). We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem to facilitate single cell-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species. *| 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, 7 months

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Sign-Up for New AgBioData Working Groups OPEN!!!

by Annarita Marrano

Hello AgBioData community, We are happy to announce that the sign-up for AgBioData working groups is now OPEN! *Please complete this form <https://forms.gle/MeZZrCeSvUywxkQo6> by November 22 at 12 p.m. ET to join one or more of our working groups.* We will have two new working groups starting from January 2023, which are the "*Phenotypic Data Standardization and Management*" and the "*scRNAseq BIOCURATION*" working groups. Two current working groups (i.e., the *DEI Recruiting* and *FAIR Scientific Literature WGs*) are also recruiting new members to join their incredible efforts. You can find more details about them in the form. *We anticipate 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 share the registration link with anybody that you think can be interested. Thanks, Annarita

2 years, 8 months

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Nomination for a new AgBioData steering committee member due to Nov. 3rd

by Annarita Marrano

Hi everybody, The AgBioData steering committee (SC) is calling for nominations for new SC members! The SC is a vibrant, collaborative, and inclusive environment that offers opportunities to expand your leadership skills, network with agricultural research community stakeholders, and help achieve a FAIR agricultural data ecosystem. *We are looking for candidates to serve as members of the AgBioData SC willing to commit a proportion of time to AgBioData activities (approximately 2 hours/week) for a term of 3 years. * *Nominate yourself or somebody you think might fit the position by this Friday, November 3rd at https://forms.gle/jVN6GZvbhS5QnJkB7 <https://forms.gle/jVN6GZvbhS5QnJkB7>.* Best, Annarita

2 years, 8 months

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REMINDER - Monthly Webinar TOMORROW, Nov. 1st, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us *TOMORROW, Nov. 1st, at 12 PM CT* for our monthly webinar. We will host Ben Rosen <https://www.ars.usda.gov/northeast-area/beltsville-md-barc/beltsville-agric…>, who will talk about telomere-to-telomere genome assemblies of ruminant species and how they will help answer important evolutionary questions. 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 :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Presenters: * Ben Rosen, USDA-ARS *Abstract:* *The Ruminant T2T Consortium* The first draft of the human genome assembly was released over twenty years ago. However, a gapless telomere-to-telomere (T2T) “complete” assembly remained elusive until last year. The highly repetitive nature of pericentromeric, subtelomeric, and duplicated gene families, such as rRNA arrays, made them impossible to assemble. It was only with advances in long-read sequencing technologies and new bioinformatic tools that these structures were resolved. Recently, we proposed the application of these new resources, tools, and knowledge in support of a “Ruminant T2T Consortium.” Our goal is to generate complete genomes for the ruminant evolutionary lineage. The ruminant Suborder comprises six Families and 66 living genera. These species are found in geographically dispersed areas and have adapted to a wide variety of environments. They have also been subjected to both natural and artificial selection. Our hypothesis is that T2T assemblies of ruminant species with relatedness varying from those capable of interbreeding to higher evolutionary distances (up to the estimated 25 million years ago last common ancestor) will inform our understanding of the underpinnings of ruminant evolution. It will also shed light on the genomic consequences of domestication and enhance our knowledge of the functional roles of heterochromatin and other repeat regions of the genome. *| 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, 8 months

1
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REMINDER - Monthly Webinar Next Wed, Nov 1st, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us next Wed, Nov. 1st, at 12 PM CT for our monthly webinar. We will host Ben Rosen <https://www.ars.usda.gov/northeast-area/beltsville-md-barc/beltsville-agric…>, who will talk about telomere-to-telomere genome assemblies of ruminant species and how they will help answer important evolutionary questions. 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 :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: *Presenters: * Ben Rosen, USDA-ARS *Abstract:* *The Ruminant T2T Consortium * The first draft of the human genome assembly was released over twenty years ago. However, a gapless telomere-to-telomere (T2T) “complete” assembly remained elusive until last year. The highly repetitive nature of pericentromeric, subtelomeric, and duplicated gene families, such as rRNA arrays, made them impossible to assemble. It was only with advances in long-read sequencing technologies and new bioinformatic tools that these structures were resolved. Recently, we proposed the application of these new resources, tools, and knowledge in support of a “Ruminant T2T Consortium.” Our goal is to generate complete genomes for the ruminant evolutionary lineage. The ruminant Suborder comprises six Families and 66 living genera. These species are found in geographically dispersed areas and have adapted to a wide variety of environments. They have also been subjected to both natural and artificial selection. Our hypothesis is that T2T assemblies of ruminant species with relatedness varying from those capable of interbreeding to higher evolutionary distances (up to the estimated 25 million years ago last common ancestor) will inform our understanding of the underpinnings of ruminant evolution. It will also shed light on the genomic consequences of domestication and enhance our knowledge of the functional roles of heterochromatin and other repeat regions of the genome. *| 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, 9 months

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INFO - Subscription to the AgBioData mailing list

by Annarita Marrano

Dear everyone, We are excited to announce that we will soon reactivate the quarterly AgBioData newsletter with past and future events and valuable resources for this community. We will use Mailchimp as a newsletter platform. *Since you already subscribe to our mailing list, we will add your contact to our newsletter list in Mailchimp. If you prefer opting out, you will find instructions on how to unsubscribe at the bottom of the Mailchimp newsletter.* Please let us know if you have any questions. Have a lovely week, Annarita

2 years, 9 months

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