Hi everybody,
Don't miss our monthly webinar TOMORROW, Feb. 5th, at 12 PM CDT. David
Molik and Adam Wright from the Genome Assembly and Annotation Nomenclature
working group will present their recent publication (
https://doi.org/10.1093/genetics/iyaf006) and recommendations on gene and
genome nomenclature.
I have included more details about the webinar and the Zoom link to attend
the webinar below.
I hope you will join us.
Best,
Annarita
:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:
*Abstracts:*
*Guidelines for Gene and Genome Assembly Nomenclature (GAAN)*
Clear and informative naming schemes enhance the utility of genome
assemblies and gene annotations. We present a comprehensive nomenclature
framework which incorporates species, sequencing group,
colony/breed/strain, version, and other critical metadata in a
well-structured format. This approach aligns with standards from AgBioData
discussions and ensures compatibility with major repositories such as those
in the INSDC. To facilitate adoption, we developed the Gene and Genome
Assembly Nomenclature (GAAN) tool for validating names under these
guidelines. Future iterations of GAAN will integrate external databases
like the Darwin Tree of Life Identifiers and the Vertebrate Breed Ontology
for further validation.
*| 1P ET | 12P CT | 11A MT | 10A PT |*
Find your local time here
<https://www.timeanddate.com/worldclock/fixedtime.html?msg=David+Molik+and+A…>
*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
Dear agricultural genome or phenome researcher:
This is a further announcement of the series of four “Field Days” on Single
Cell genomics in agriculture. Also, please see below for a second reminder
on travel funding for attending the AG2PI Single Cell Workshop March 29-30!
Details on the four sessions can be found at:
https://www.faang.org/bbs?s=2025_wkshop..txt
If you are interested in attending one or more of these *free* online
sessions, please register at least 2 days in advance at:
https://docs.google.com/forms/d/1W2aSNN0QEE-yzqehj2DHsGKa9N3fvCXHPMY9gAeZa7…
We will follow up with registered people to provide Zoom information one
day before the session and provide information on obtaining the sessions'
recordings once they are available.
*ALSO:*
**We still have a handful of seats available for early career researchers
to request $600 funding that will cover costs for the SC Workshop in
Orlando, Florida:
https://www.agbt.org/home/home/agbt-ag/agworkshops/#workshop3
If you are interested in this, have your advisor send confirmation you are
eligible: that you are currently in graduate school or within 5 years of
attaining your PhD.**
Thanks for your interest!
Chris Tuggle for the AG2PI Single Cell Workshop Organizing Committee
Hi everybody,
Join us for the first monthly webinar of 2025! Next Wednesday, Feb. 5th, at
12 PM CDT, David Molik and Adam Wright from the Genome Assembly and
Annotation Nomenclature working group will present their recent publication
(https://doi.org/10.1093/genetics/iyaf006) and recommendations on gene and
genome nomenclature.
I have included more details about the webinar and the Zoom link to attend
the webinar below.
I hope you will join us.
Best,
Annarita
:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:
*Abstracts:*
*Guidelines for Gene and Genome Assembly Nomenclature (GAAN)*
Clear and informative naming schemes enhance the utility of genome
assemblies and gene annotations. We present a comprehensive nomenclature
framework which incorporates species, sequencing group,
colony/breed/strain, version, and other critical metadata in a
well-structured format. This approach aligns with standards from AgBioData
discussions and ensures compatibility with major repositories such as those
in the INSDC. To facilitate adoption, we developed the Gene and Genome
Assembly Nomenclature (GAAN) tool for validating names under these
guidelines. Future iterations of GAAN will integrate external databases
like the Darwin Tree of Life Identifiers and the Vertebrate Breed Ontology
for further validation.
*| 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
Dear everyone,
AgBioData will be at PAG 32 in San Diego! If you are attending the
conference, please join us:
- For *our workshop* on *Friday, Jan. 10, at 4 PM in room Town and
Country C*. There will be presentations from the current working groups
and we will provide updates on the consortium's direction. More info on the
workshop is available here <https://www.agbiodata.org/agb-pag32>.
- At* booth #210! *We will be there with our member databases to meet
you in person and answer questions.
Looking forward to seeing you at PAG!
Best,
Annarita
Hi everybody,
Join us TOMORROW, at 12 PM CDT, for our monthly webinar with Sarah Dyer.
She will discuss Ensembl as a precious resource for annotated genomes
across the tree of life.
I have included more details about the webinar and the Zoom link to attend
the webinar below.
I hope you will join us.
Best,
Annarita
:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:
*Abstracts:*
*Plants, pollinators, and pests in Ensembl - integrating genomics data for
agriculturally relevant species*
Ensembl is an open platform integrating publicly available genomic data to
support the exploration of gene annotations, genetic variation, and
comparative genomics. Increasing numbers of genomes are available for
agriculturally relevant species, with multiple high-quality genomes now
being generated for many crops. In addition, large-scale biodiversity
projects are increasing the number of insect genomes available for pest and
pollinator species. Providing ways to explore this genomic data is key to
supporting research and breeding efforts for agricultural species. Ensembl
Metazoa and Ensembl Plants now hold more than 380 invertebrate and almost
160 plant genomes, respectively. In addition, our new Ensembl site (
https://beta.ensembl.org) already holds more than 1,500 invertebrates and
over 100 plant genomes. The new site will ultimately replace the current
suite of Ensembl component sites, bringing annotated genomes together from
across the Tree of Life. In this webinar, we will look at the species, data
types, and tools you can find in Ensembl and ways you can access these
resources.
*| 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
Hi everybody,
Join us TOMORROW, at 12 PM CDT, for our monthly webinar with Sarah Dyer.
She will discuss Ensembl as a precious resource for annotated genomes
across the tree of life.
I have included more details about the webinar and the Zoom link to attend
the webinar below.
I hope you will join us.
Best,
Annarita
:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:
*Abstracts:*
*Plants, pollinators, and pests in Ensembl - integrating genomics data for
agriculturally relevant species*
Ensembl is an open platform integrating publicly available genomic data to
support the exploration of gene annotations, genetic variation, and
comparative genomics. Increasing numbers of genomes are available for
agriculturally relevant species, with multiple high-quality genomes now
being generated for many crops. In addition, large-scale biodiversity
projects are increasing the number of insect genomes available for pest and
pollinator species. Providing ways to explore this genomic data is key to
supporting research and breeding efforts for agricultural species. Ensembl
Metazoa and Ensembl Plants now hold more than 380 invertebrate and almost
160 plant genomes, respectively. In addition, our new Ensembl site (
https://beta.ensembl.org) already holds more than 1,500 invertebrates and
over 100 plant genomes. The new site will ultimately replace the current
suite of Ensembl component sites, bringing annotated genomes together from
across the Tree of Life. In this webinar, we will look at the species, data
types, and tools you can find in Ensembl and ways you can access these
resources.
*| 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
Hi everybody,
Join us for our monthly webinar next Wednesday, Dec. 4th, at 12 PM CDT.
Sarah Dyer will discuss Ensembl as a precious resource for
annotated genomes across the tree of life.
I have included more details about the webinar and the Zoom link to attend
the webinar below.
I hope you will join us.
Best,
Annarita
:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:
*Abstracts:*
*Plants, pollinators, and pests in Ensembl - integrating genomics data for
agriculturally relevant species*
Ensembl is an open platform integrating publicly available genomic data to
support the exploration of gene annotations, genetic variation, and
comparative genomics. Increasing numbers of genomes are available for
agriculturally relevant species, with multiple high-quality genomes now
being generated for many crops. In addition, large scale biodiversity
projects are increasing the number of insect genomes available for pest and
pollinator species. Providing ways to explore this genomic data is key to
supporting research and breeding efforts for agricultural species. Ensembl
Metazoa and Ensembl Plants now hold more than 380 invertebrate and almost
160 plant genomes, respectively. In addition, our new Ensembl site (
https://beta.ensembl.org) already holds more than 1,500 invertebrate and
over 100 plant genomes. The new site will ultimately replace the current
suite of Ensembl component sites, bringing annotated genomes together from
across the tree of life. In this webinar we will look at the species, data
types and tools you can find in Ensembl and ways you can access these
resources.
*| 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
Dear all,
We invite the AgBioData community to *a
virtual roundtable on artificial intelligence* in agricultural
genomics *TOMORROW
(November 6) at 12 PM Central Time* (Zoom link
<https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09>
).
AI and natural language processing (NLP) for biocuration are becoming more
popular in the community, allowing several applications and creating new
data-related issues. *We invite the AgBioData member databases and the
larger community to provide feedback on these challenges*, help us
understand their importance for the AgBioData member databases, and define
the focus of new AgBioData working groups.
The meeting will be 1-hour long and will feature breakout room sessions on two
main topics:
- *How databases can make data ready for AI*
- *NLP for biocuration.*
Please forward this invite to anyone you think might be interested.
Best,
Annarita
:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:
*| 1P ET | 12P CT | 11A MT | 10A PT |*
Find your local time here
<https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Virtual…>
Join Zoom Meeting
https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09
Meeting ID: 820 3835 6125
Passcode: 160683
Dear all,
We invite the AgBioData community to *a virtual roundtable on
artificial intelligence* in agricultural genomics *next Wednesday (November
6) at 12 PM Central Time* (Zoom link
<https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09>
).
AI and natural language processing (NLP) for biocuration are becoming more
popular in the community, allowing several applications and creating new
data-related issues. *We invite the AgBioData member databases and the
larger community to provide feedback on these challenges*, help us
understand their importance for the AgBioData member databases, and define
the focus of new AgBioData working groups.
The meeting will be 1-hour long and will feature breakout room sessions on
two main topics:
- *How databases can make data ready for AI*
- *NLP for biocuration.*
Please forward this invite to anyone you think might be interested.
Best,
Annarita
:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:
*| 1P ET | 12P CT | 11A MT | 10A PT |*
Find your local time here
<https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Virtual…>
Join Zoom Meeting
https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09
Meeting ID: 820 3835 6125
Passcode: 160683
Join Zoom Meeting
Join Zoom Meeting
Meeting ID: 820 3835 6125
Passcode: 160683
Hi everybody,
Join us *tomorrow*, Oct. 2nd, *at 12 PM CDT*. Montana Smith will discuss
the National Microbiome Data Collaborative (NMDC) initiative and its work
on advancing microbiome science through FAIR and standardized metadata and
data.
I have included more details about the webinar and the Zoom link to attend
the webinar below.
I hope you will join us.
Best,
Annarita
:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:
*Abstracts:*
*NMDC: Advancing microbiome science through FAIR and standardized metadata
and data*
The National Microbiome Data Collaborative (NMDC)’s mission is to support a
FAIR microbiome data-sharing network through infrastructure, data
standards, and community building that addresses pressing challenges in
environmental sciences. In this webinar, we will dive into what the NMDC is
and how standardized metadata capture enables FAIR data. We will walk
through the 4 NMDC products and how they’re lowering barriers for
experimental scientists to conduct their research in a way that ensures
data re-use.
*| 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