Hi everybody,
This is a friendly reminder of our monthly webinar *tomorrow, Feb. 7th, at
12 PM CT*. 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 - SC bi-weekly meeting
Time: This is a recurring meeting Meet anytime
Join Zoom Meeting
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Meeting ID: 837 3146 6263
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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
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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
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
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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
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
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Meeting ID: 820 3835 6125
Passcode: 160683
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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
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
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
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Topic: AgBioData Monthly Webinar
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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
---
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