- AgBioData-LIST - Main Bioinformatics Lab

Webinar TOMORROW at 10 AM CST "Building a FAIR data ecosystem for incorporating single-cell genomics data into agricultural G2P research"

by Annarita Marrano

Dear all, A friendly reminder of *tomorrow's appointment* with the scRNA Biocuration WG *at 8 a.m. PST / 10 a.m. CST / 11 a.m. EST / 5 p.m. CET* (Zoom link <https://us06web.zoom.us/j/85091905235?pwd=Oqhn0Pvy3iXd5jObJi0JyacJy0bgmf.1> ). Muskan Kapoor, a graduate research assistant in Tuggle's lab, will discuss the current state of developing a single-cell data portal for farm animals. There are more details on the talk at the bottom of this email. I hope you will join us. Best, Annarita ---------------------------------------------------------------------------------------------------------------- *Abstract*: *Building a FAIR data ecosystem for incorporating single-cell genomics data into agricultural G2P research* The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA-seq) data are comparatively underdeveloped. To bridge this gap, we leveraged recent advancements in human genomics infrastructure, such as the integration of the Human Cell Atlas Data Portal with Terra, a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools, and collaborate, co-developed by the Broad Institute of MIT and Harvard, Microsoft, and Verily. In parallel, the Single Cell Expression Atlas at EMBL-EBI offers a comprehensive data ingestion portal for high-throughput sequencing datasets, including plants, protists, and animals (including humans). Developing data tools connecting these resources would offer significant advantages to the agricultural genomics community. The FAANG data portal at EMBL-EBI emphasizes delivering rich metadata and highly accurate and reliable annotation of farmed animals but is not computationally linked to either of these resources. Herein, we describe a pilot-scale project that determines whether the current FAANG metadata standards for livestock can be used to ingest scRNA-seq datasets into Terra in a manner consistent with HCA Data Portal standards. Importantly, rich scRNA-seq metadata can now be brokered through the FAANG data portal using a semi-automated process, thereby avoiding the need for substantial expert curation. We have further extended the functionality of this tool so that validated and ingested SC files within the HCA Data Portal are transferred to Terra for further analysis. In addition, we verified data ingestion into Terra, hosted on Azure, and demonstrated the use of a workflow to analyze the first ingested porcine scRNA-seq dataset. Additionally, we have also developed prototype tools to visualize the output of scRNA-seq analyses on genome browsers to compare gene expression patterns across tissues and cell populations. This JBrowse tool now features distinct tracks, showcasing PBMC scRNA-seq alongside two bulk RNA-seq experiments. We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem based on Findable, Accessible, Interoperable, and Reusable (FAIR) SC principles to facilitate SC-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species. ReplyForward

10 months, 2 weeks

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RFI and Open Meeting of the Standards for Genetic Variation Working Group - July 18th (11 AM Eastern Time)

by Annarita Marrano

Dear all, The AgBioData Standards for Genetic Variation Working Group (SGV) is preparing a white paper to support the adoption of rsIDs for agriculture and seeks your valuable input and data to further our research efforts. They invite the AgBioData community to join them on* July 18 at 11:00 ET *to review the material and *discuss collaboration opportunities*. In particular, the SGV is looking for the following information: 1. Genetic Markers Linked to Traits: - A list of genetic markers associated with specific traits used by the breeding and research community across various agricultural species, including plants, animals, and insects. See an example here <https://docs.google.com/spreadsheets/d/167DaYxbdKejoL0l6UhGqMPu-GbGsW6vIok7…> . - Information on the species and traits these markers are linked to and the methodologies/platforms employed for genotyping in your community. 2. Functional Validation and Fitness Outcomes: - Examples of genetic variations that have been functionally validated, including descriptions of the phenotypic differences these variations lead to. - Case studies or data demonstrating these genetic variations have resulted in measurable fitness outcomes for the species in question. - Information on related publications and any supporting data available. - We would like to request examples from each of the different species/database providers for review at the upcoming GV working group meeting in July. 3. Standards and Data Access for Genetic & Phenotypic Variation: FAIR/ Interoperability - Standard formats for exchanging information, identifiers, formats, and controlled vocabulary on: - Germplasm - Genetic Variation - Phenotypes - Types of views and files provided for data access. - Future targets for operating, displaying, or providing access to these data types. - Usage of rsIDs and potential barriers to their adoption in your resource. - For more information on RSIDs, please look at the following document RefSNPs: Clustered Variants <https://docs.google.com/document/d/1PHXqW7M50mE5SSl4Zprd904KCr9nWzSR4L8sx3U…> 4. Collaboration Opportunities: - Barriers encountered when working with these data types. - Opportunities for collaboration or data standards, sharing, and interoperability. We really appreciate your support and look forward to your positive response to the request for information in any of the four categories. *If you are willing to participate or are interested in contributing to our initiative and would like to collaborate, please complete this form (https://forms.gle/jcjWnLibHEKuESJe6 <https://forms.gle/jcjWnLibHEKuESJe6>) by July 16. *We will follow up with you with the Zoom link and other resources. Best, The AgBioData Standards for Genetic Variation WG

10 months, 3 weeks

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Webinar on July 17th at 10 AM CST "Building a FAIR data ecosystem for incorporating single-cell genomics data into agricultural G2P research"

by Annarita Marrano

Dear all, The scRNA Biocuration WG invites you to an open meeting on *July 17th at 8 a.m. PST / 10 a.m. CST / 11 a.m. EST / 5 p.m. CET* (Zoom link <https://us06web.zoom.us/j/85091905235?pwd=Oqhn0Pvy3iXd5jObJi0JyacJy0bgmf.1> ). Muskan Kapoor, a graduate research assistant in Tuggle lab, will discuss the current state of developing a single-cell data portal for farm animals. More details on the talk at the bottom of this email. I hope you will join us. Best, Annarita ---------------------------------------------------------------------------------------------------------------- *Abstract*: *Building a FAIR data ecosystem for incorporating single-cell genomics data into agricultural G2P research* The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA-seq) data are comparatively underdeveloped. To bridge this gap, we leveraged recent advancements in human genomics infrastructure, such as the integration of the Human Cell Atlas Data Portal with Terra, a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools, and collaborate, co-developed by the Broad Institute of MIT and Harvard, Microsoft, and Verily. In parallel, the Single Cell Expression Atlas at EMBL-EBI offers a comprehensive data ingestion portal for high-throughput sequencing datasets, including plants, protists, and animals (including humans). Developing data tools connecting these resources would offer significant advantages to the agricultural genomics community. The FAANG data portal at EMBL-EBI emphasizes delivering rich metadata and highly accurate and reliable annotation of farmed animals but is not computationally linked to either of these resources. Herein, we describe a pilot-scale project that determines whether the current FAANG metadata standards for livestock can be used to ingest scRNA-seq datasets into Terra in a manner consistent with HCA Data Portal standards. Importantly, rich scRNA-seq metadata can now be brokered through the FAANG data portal using a semi-automated process, thereby avoiding the need for substantial expert curation. We have further extended the functionality of this tool so that validated and ingested SC files within the HCA Data Portal are transferred to Terra for further analysis. In addition, we verified data ingestion into Terra, hosted on Azure, and demonstrated the use of a workflow to analyze the first ingested porcine scRNA-seq dataset. Additionally, we have also developed prototype tools to visualize the output of scRNA-seq analyses on genome browsers to compare gene expression patterns across tissues and cell populations. This JBrowse tool now features distinct tracks, showcasing PBMC scRNA-seq alongside two bulk RNA-seq experiments. We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem based on Findable, Accessible, Interoperable, and Reusable (FAIR) SC principles to facilitate SC-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species.

10 months, 3 weeks

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AgBioData at the Plant Biology 2024 conference!!

by Annarita Marrano

Hello everyone, We will be in Honolulu next week for the Plant Biology 2024 Conference! If you will be there, join us for the "Plant Bioinformatics Resources for FAIR Agricultural Data Discovery and Reuse" on Saturday, June 22, at 10 AM in room 312. Some of our member databases will present their recent updates and resources (https://www.agbiodata.org/pbr-aspb-2024). We will also be in *booth #406* to meet all of you in person and talk about our work and future directions. Have a lovely week, Annarita

11 months, 2 weeks

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REMINDER: Please participate to an AgBioData survey on FAIR data management

by Annarita Marrano

Dear AgBioData members, This is a friendly reminder to participate in our *brief survey* on the impact of AgBioData activities on FAIR data management awareness if you haven't already done so. This survey is a follow-up to a similar one we ran in 2022 and will help us quantify the impact of our efforts during the three-year National Science Foundation (NSF) RCN project on increasing the awareness and implementation of FAIR practices in the AgBioData community. Your participation in this survey is crucial for our mission to enhance FAIR data in agricultural research and will provide insights that can help us define the consortium's directions and secure future funding. Click here <https://tinyurl.com/AgBioData24> to participate in this survey. We would like to emphasize that your participation in this survey is entirely voluntary and anonymous. For general questions or assistance accessing and completing the survey, please write to me or contact Dr Michael Coe at michael(a)cedarlakeresearch.com. Thanks for your contribution to AgBioData and for being part of our community! Best, Annarita

11 months, 3 weeks

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REMINDER - Monthly Webinar TOMORROW at 12 PM CT

by Annarita Marrano

Hi everybody, This is a friendly reminder of our monthly webinar tomorrow at 12 PM CDT. We have *Ethy Cannon *(USDA-ARS) talking about the *pan-genomic resources at MaizeGDB*. 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:* *Pan-genomic resources at MaizeGDB* Pan-genomes, encompassing the entirety of genetic sequences found in a collection of genome assemblies within a clade, can be more useful than single reference genomes. This is especially true for Zea mays, which has a particularly diverse and complex genome. Presenting full pan-genome data is challenging, especially for a diverse species, but valuable when pan-genomic data can be linked to extensive gene models and gene data, including classical gene information, markers, insertions, expression and proteomic data, and protein structures, as is the case at MaizeGDB. I will present the pan-gene analysis pipeline Pandagma and MaizeGDB’s pan-gene data centre, which offers a variety of browsing and visualizations, including sequence alignment visualization, gene trees and more, which enables exploration of pan-genes in Zea. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> *Join Zoom Meetinghttps://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 <https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09>* Meeting ID: 820 3835 6125 Passcode: 160683

12 months

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REMINDER - Monthly Webinar Next Wed, June 5th, at 12 PM CT

by Annarita Marrano

Hi everybody, Join us next Wed, June 5th, at 12 PM CDT for our monthly webinar. *Ethy Cannon *(USDA-ARS) will talk about the *pan-genomic resources at MaizeGDB*. 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:* *Pan-genomic resources at MaizeGDB* Pan-genomes, encompassing the entirety of genetic sequences found in a collection of genome assemblies within a clade, can be more useful than single reference genomes. This is especially true for Zea mays, which has a particularly diverse and complex genome. Presenting full pan-genome data is challenging, especially for a diverse species, but valuable when pan-genomic data can be linked to extensive gene models and gene data, including classical gene information, markers, insertions, expression and proteomic data, and protein structures, as is the case at MaizeGDB. I will present the pan-gene analysis pipeline Pandagma, and MaizeGDB’s pan-gene data centre, which offers a variety of browsing and visualizations, including sequence alignment visualization, gene trees and more, which enables exploration of pan-genes in Zea. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> *Join Zoom Meetinghttps://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 <https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09>* Meeting ID: 820 3835 6125 Passcode: 160683

1 year

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REMINDER: Please participate to an AgBioData survey on FAIR data management

by Annarita Marrano

Dear AgBioData members, This is a friendly reminder to participate in our *brief survey* on the impact of AgBioData activities on FAIR data management awareness if you haven't already done so. This survey is a follow-up to a similar one we ran in 2022 and will help us quantify the impact of our efforts during the three-year National Science Foundation (NSF) RCN project on increasing the awareness and implementation of FAIR practices in the AgBioData community. Your participation in this survey is crucial for our mission to enhance FAIR data in agricultural research and will provide insights that can help us define the consortium's directions and secure future funding. Click here <https://tinyurl.com/AgBioData24> to participate in this survey. Please submit your answers *by May 31*. We would like to emphasize that your participation in this survey is entirely voluntary and anonymous. For general questions or assistance accessing and completing the survey, please feel free to write to me or contact Dr Michael Coe at michael(a)cedarlakeresearch.com. Thanks for your contribution to AgBioData and for being part of our community! Best, Annarita

1 year

1
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Please participate to an AgBioData survey on FAIR data management

by Annarita Marrano

Dear AgBioData members, We'd like to invite you to participate *in a brief survey* to measure the impact of AgBioData activities on FAIR data management awareness. This is a follow-up survey from a similar one we ran in 2022 and will help us quantify the impact of our efforts during the three-year National Science Foundation (NSF) RCN project on increasing the awareness and implementation of FAIR practices in the AgBioData community. Your participation in this survey is crucial for our mission to enhance FAIR data in agricultural research and will provide insights that can help us define the consortium's directions and secure future funding. Click here <https://tinyurl.com/AgBioData24> to participate in this survey. Please submit your answers *by May 31*. We would like to emphasize that your participation in this survey is entirely voluntary and anonymous. For general questions or assistance accessing and completing the survey, please feel free to write to me or contact Dr Michael Coe at michael(a)cedarlakeresearch.com. Thanks for your contribution to AgBioData and for being part of our community! Best, Annarita

1 year

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Charla Lambert on the SACNAS organization, this Monday (May 6) at 11 AM ET

by Annarita Marrano

Hi everybody, The DEI Recruiting WG invites everyone to join our meeting *this Monday, May 6, at 11 AM*. Dr Charla Lambert, president of the Advancing Chicanos/Hispanics and Native Americans in Science (SACNAS) organization, will talk about SACNAS, its 50-year history diversifying science in the U.S., and how it might benefit your group's outreach, networking, and recruitment activities. Zoom link to participate: https://us06web.zoom.us/j/89060768261?pwd=TC9EOWR3UVdQS3UxNGZWQTEvWDFaZz09. I hope you will join numerous. Best, Annarita

1 year

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