Hi everybody,
Join us next Wed, April 3rd, at 12 PM CDT for our monthly webinar. Zachary
Miller <https://www.maizegenetics.net/zackmiller> from Cornell University
will talk about Practical Haplotype Graph (PHG), a streamlined and simple
pangenome system.
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:*
*The Practical Haplotype Graph Version 2: A Streamlined and Simple
Pangenome System*
The Practical Haplotype Graph (PHG) is a powerful tool for representing
diverse plant pangenomes and imputing new sample genotypes for breeding
programs and other purposes. Low-coverage sequencing data from various
technologies (DaRT, GBS, etc.) is sufficient to identify paths through the
graph, which can be stored efficiently within the PHG database or used to
call variants and create custom genomes for alignment. PHGv2 refines and
streamlines the original PHGv1 platform.
*| 1P ET | 12P CT | 11A MT | 10A PT |*
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Dear everyone,
This is a friendly reminder to register for the *2024 AgBioData community
workshop *(April 29-30; May 2)!
This year's community workshop will be completely *VIRTUAL* and feature WG
presentations, breakout room sessions, and more from 9-11 AM CDT daily. We
are working on finalizing the workshop's agenda and will send it soon with
other useful information.
*Please register for the community workshop by completing this
form (https://forms.gle/MjLhMcw75YS3dWmcA
<https://forms.gle/MjLhMcw75YS3dWmcA>) **by April 15*.
I hope you will be able to join us!
Please let me know if you have any questions.
Have a lovely week.
Annarita
Dear AgBioData community members,
The next Agricultural Genome to Phenome Initiative (AG2PI) Field Day will be "Phenomic Prediction & Bioinformatic Workflows - AG2PI "Coconut" Grant Outcomes" and will be on Wednesday, March 20 from 10:30 AM to 12:00 PM (CDT, UTC-5). In this field day, we will first hear from Dr. Daniel Runcie regarding how phenomic prediction can be used as a tool for plant breeding. Then, Dr. Fiona McCarthy will review new bioinformatic workflows her team has developed to support genomic analyses. Both of these presentations are outcomes from AG2PI "coconut" (large seed) grants.
We invite you to register for this Zoom event at https://www.ag2pi.org/workshops-and-activities/field-day-2024-03-20/, 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 ***
Hi everybody,
Join us tomorrow, March. 6th, at 12 PM CDT, for our monthly webinar. Cyril
Pommier <https://orcid.org/0000-0002-9040-8733> will talk about FAIR plant
phenomics data management tools and guidelines from the ELIXIR and Emphasis
European infrastructures.
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:*
*FAIR Plant Phenomics Data Management Tools and Guidelines from ELIXIR and
Emphasis European Infrastructures*
Plant phenomics data has been greatly facilitated over the past ten years
at several levels: data standards to organize and describe data, databases
for the management of the experiments, data repositories to ensure
long-term accessibility supplemented by data portals to maximise
findability and finally, guidelines to ease their usage. We will review the
recent advances from joint initiatives involving two European
infrastructures: ELIXIR (Life science data) and EMPHASIS (Plant phenomics).
First, we will update the current status of MIAPPE (www.miappe.org), a data
standard interoperable with the Breeding API that enables not only
phenotyping experiment formalisation but also their linking with
genotyping. We will also give an overview of its usage in generic data
repositories such as Dataverse or Zenodo and their relation with
experimental databases such as PHIS. Finding the right documentation to use
those tools and standards is not always straightforward. The RDMKit (
https://rdmkit.elixir-europe.org/) is a guidelines portal that has been
built to help researchers find the information subset they need. Through a
dedicated section, such as the plant domain page (
https://rdmkit.elixir-europe.org/), it shows the complementarity between
standards and tools and provides the guidance needed for data management.
Finally, we will also update the status of FAIDARE (
https://urgi.versailles.inrae.fr/faidare/), a global data portal that
indexes 30 databases using either BrAPI or a generic minimal format.
*| 1P ET | 12P CT | 11A MT | 10A PT |*
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Meeting ID: 820 3835 6125
Passcode: 160683
Dear everyone,
We are happy to announce that the registration for the *2024 AgBioData
community workshop *(April 29-30; May 2) is now *OPEN*!
This year's community workshop will be completely *VIRTUAL* and feature WG
presentations and breakout room sessions from 9-11 AM CDT daily. We will
soon share more details on the workshop agenda and other helpful
information.
*Please register for the community workshop by completing this
form (https://forms.gle/MjLhMcw75YS3dWmcA
<https://forms.gle/MjLhMcw75YS3dWmcA>) **by April 15*.
I hope you will be able to join us!
Please let me know if you have any questions.
Have a lovely week.
Annarita
Hi everybody,
Please see below for details about a position as "Genomic Data Engineer" in
the Plant Comparative Analysis Group at the Joint Genome Institute:
*http://phxc1b.rfer.us/LBLbNj9kY <http://phxc1b.rfer.us/LBLbNj9kY>*
Best,
Annarita
Hi everybody,
Join us next Wed, March. 6th, at 12 PM CDT, for our monthly webinar. Cyril
Pommier <https://orcid.org/0000-0002-9040-8733> will talk about FAIR plant
phenomics data management tools and guidelines from the ELIXIR and Emphasis
European infrastructures.
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:*
*FAIR Plant Phenomics Data Management Tools and Guidelines from ELIXIR and
Emphasis European Infrastructures*
Plant phenomics data has been greatly facilitated over the past ten years
at several levels: data standards to organize and describe data, databases
for the management of the experiments, data repositories to ensure
long-term accessibility supplemented by data portals to maximise
findability and finally, guidelines to ease their usage. We will review the
recent advances from joint initiatives involving two European
infrastructures: ELIXIR (Life science data) and EMPHASIS (Plant phenomics).
First, we will update the current status of MIAPPE (www.miappe.org), a data
standard interoperable with the Breeding API that enables not only
phenotyping experiment formalisation but also their linking with
genotyping. We will also give an overview of its usage in generic data
repositories such as Dataverse or Zenodo and their relation with
experimental databases such as PHIS. Finding the right documentation to use
those tools and standards is not always straightforward. The RDMKit (
https://rdmkit.elixir-europe.org/) is a guidelines portal that has been
built to help researchers find the information subset they need. Through a
dedicated section, such as the plant domain page (
https://rdmkit.elixir-europe.org/), it shows the complementarity between
standards and tools and provides the guidance needed for data management.
Finally, we will also update the status of FAIDARE (
https://urgi.versailles.inrae.fr/faidare/), a global data portal that
indexes 30 databases using either BrAPI or a generic minimal format.
*| 1P ET | 12P CT | 11A MT | 10A PT |*
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Meeting ID: 820 3835 6125
Passcode: 160683
Forwarding this announcement from Timothy P.L. Smith (USDA-ARS, Meat Animal
Research Center):
-------------------------------------------------------------------------
We are pleased to announce that Drs. Arang Rhie and Sergey Koren, from the
Center for Genomics and
Data Science Research at the National Institutes of Health, have agreed to
conduct an in-person hands-
on workshop on inspecting and resolving genome assembly graphs in
conjunction with the Advances in
Genome Biology and Technology Agriculture conference (AGBT-Ag) in Phoenix
on Sunday, April 14, 7-9
pm (following the RCN workshop). The workshop will be organized by Drs.
Brenda Murdoch and Ben
Rosen, and requires registration for the conference at www.agbt.org.
Resolving assembly graphs is an important component of generating full
haplotype separated diploid or
polyploid assemblies in animals or plants, and particularly important in
the context of “complete”
telomere-to-telomere (T2T) assembly. The Ruminant T2T project aims to
generate T2T assemblies of
cetartiodactyla species and other species that can generate the appropriate
data types but the graph
resolution step is a manual process and additional trained personnel would
be beneficial to speed
progress and accelerate other T2T efforts.
The training will cover evaluating assembly graphs in bandage, resolving
tangles that are amenable to
manual resolution, and generating assemblies with resolved sequence. Some
easy and difficult graphs
will be examined during the two hour workshop. We are very grateful that
Arang and Sergey are willing
to develop this tutorial and provide their expertise.
Please email Kelsey McClure at kelsey.mcclure(a)usda.gov if you want to
attend the workshop by March
5, so that we can make sure we can accommodate the number of interested
participants. If you hope to
attend but do not know if you will be able to by that deadline, please go
ahead and email with a
statement to that effect.
Dear AgBioData members,
We, Agricultural Genome to Phenome Initiative (AG2PI), have three announcements to share:
1. AG2PI virtual field days are back! The next field day will be held February 21, 10:30 AM to 12:00 PM (CST, UTC-6) and will highlight the "coconut" (large seed) grant projects led by Dr. Pankaj Jaiswal on plant stress ontology and by Dr. Seth Murray on building a more connected unmanned aerial systems (UAS) community. For more information and to register, visit https://www.ag2pi.org/workshops-and-activities/field-day-2024-02-21/.
1. Reminder: AG2PI is offering student conference travel grants up to $1500 to any* undergraduate and graduate students attending an institution in the US. Details and instructions to apply can be found on the AG2PI website (https://www.ag2pi.org/seed-grants/student-conference-travel-awards-2023-11-…). These will be awarded on a rolling basis until all funds are committed, so apply soon! Application portal will close by June 1, 2024 and all travel must be completed by August 1, 2024. (*students must be engaged in AG2PI-related research, broadly, to apply)
1. A Request for Proposals has been released by USDA NIFA for FY2024 regarding the AG2PI program. There will be a NIFA Technical Assistance Webinar for the RFP on March 21, 2024. Registration details can be found here: https://www.nifa.usda.gov/events/technical-assistance-webinar-agricultural-….
Please share this message with anyone you think might be interested in either of these opportunities.
Have a wonderful week,
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 ***
Hi everybody,
Join us today* at 12 PM CT *for our monthly webinar. We will have Alex
Ignatchenko and Paul Thomas talking about TreeGrafter, a method of
predicting Gene Ontology annotations, and other tools implemented in
InterProScan.
*Zoom link:
https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09
<https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09>.*
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 |*
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