Hi everybody,
The registration for the *2025 AgBioData community workshop* is OPEN!
This two-day workshop (*May 14-15, 9:00 AM - 1:00 PM CDT*) will feature
presentations from current working groups, keynote speakers, and
discussions on relevant data-related topics, such as AI and database
sustainability. We'll share more details about the meeting agenda soon!
*Register by May 5* and contribute your valuable experience and insights on
data generation, management, and reuse. *Registration link
(https://forms.gle/rBZbEYKj73Lz9H9J8
<https://forms.gle/rBZbEYKj73Lz9H9J8>).*
I hope you will join us.
Have a lovely weekend.
Best,
Annarita
Dear everybody,
The registration for the *2025 AgBioData community workshop* is now OPEN!
This two-day workshop (*May 14-15, 9 AM - 1 PM CDT*) will feature
presentations from current working groups, keynote speakers, and
discussions on relevant data-related topics (e.g., AI, database
sustainability). We will share more details on the meeting agenda soon!
*Register by May 5* and contribute with your valuable experience and
insights on data generation, management, and reuse. *Registration link
(https://forms.gle/rBZbEYKj73Lz9H9J8
<https://forms.gle/rBZbEYKj73Lz9H9J8>).*
I hope you will join us.
Have a lovely weekend.
Best,
Annarita
Hi everybody,
Join us tomorrow, *April 2nd, at 12 PM CDT,* and meet iBeetle-Base
<https://ibeetle-base.uni-goettingen.de/>, the new AgBioData member
database. *Gregor Bucher *from the University of Gottingen will discuss
this integrated genomic and phenotypic information resource for red flour
beetle research.
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:*
*iBeetle-Base - a phenotypic database with community edition*
The red flour beetle *Tribolium castaneum* has become an important insect
model organism to study gene function and RNAi mediated pest control.
iBeetle-Base was developed to document morphological phenotypes from the
genome-wide RNAi gene-knockdown screen iBeetle and has become an integrated
resource of genomic and phenotypic information for *Tribolium
castaneum* research.
Since our last release in 2024, iBeetle-Base allows the community to
contribute RNAi phenotypes and associate Gene Ontology terms and
publications with *Tribolium* genes (“community addition”). This novel
functionality overcomes the lack of curators for databases of small
communities. Further, we improved data accessibility, via programming
interfaces alongside traditional HTML pages, which facilitates the
automatic usage of the database by scripting and third-party tools.
Importantly, this phenotypic database with its special adaptations to small
research communities could become the nucleus for other interlinked
databases in the future. iBeetle-Base is freely accessible at
https://ibeetle-base.uni-goettingen.de/
*| 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 next Wednesday, *April 2nd, at 12 PM CDT* for our monthly webinar
with *Gregor Bucher* from the University of Gottingen. He will present
iBeetle-Base <https://ibeetle-base.uni-goettingen.de/>, an integrated
genomic and phenotypic information resource for red flour beetle research
and a new AgBioData member database.
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:*
*iBeetle-Base - a phenotypic database with community edition*
The red flour beetle *Tribolium castaneum* has become an important insect
model organism to study gene function and RNAi mediated pest control.
iBeetle-Base was developed to document morphological phenotypes from the
genome-wide RNAi gene-knockdown screen iBeetle and has become an integrated
resource of genomic and phenotypic information for *Tribolium castaneum*
research. Since our last release in 2024, iBeetle-Base allows the community
to contribute RNAi phenotypes and associate Gene Ontology terms and
publications with *Tribolium* genes (“community addition”). This novel
functionality overcomes the lack of curators for databases of small
communities. Further, we improved data accessibility, via programming
interfaces alongside traditional HTML pages, which facilitates the
automatic usage of the database by scripting and third-party tools.
Importantly, this phenotypic database with its special adaptations to small
research communities could become the nucleus for other interlinked
databases in the future. iBeetle-Base is freely accessible at
https://ibeetle-base.uni-goettingen.de/
*| 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,
This is a friendly reminder of the monthly webinar TOMORROW at 12 PM CDT
with *Alenka Hafner*. Alenka will present the current recommendations and
future directions of the AgBioData Data Reuse working group, recently
published on GigaScience (https://doi.org/10.1093/gigascience/giae106).
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:*
*AgBioData's Data Reuse WG: our current guidelines and future
considerations*
The scientific community has long benefited from the opportunities provided
by data reuse. Recognizing the need to identify the challenges and
bottlenecks to reuse in the agricultural research community and propose
solutions for them, the data reuse working group was started within the
AgBioData consortium framework. Throughout two years of remote meetings and
asynchronous discussion, we identified the limitations of data standards,
metadata deficiencies, data interoperability, data ownership, data
availability, user skill level, resource availability, and equity issues,
with a specific focus on agricultural genomics research. We described these
in a white paper, out now in GigaScience (
https://doi.org/10.1093/gigascience/giae106), while proposing possible
solutions stakeholders could implement to mitigate and overcome these
challenges and providing an optimistic perspective on the future of
genomics and transcriptomics data reuse.
*| 1P ET | 12P CT | 11A MT | 10A PT |*
Find your local time here
<https://www.timeanddate.com/worldclock/fixedtime.html?msg=Alenka+Hafner+on+…>
*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 next Wed., March 5th, at 12 PM CDT for our monthly webinar with
Alenka Hafner. Alenka will present the current recommendations and future
directions of the AgBioData Data Reuse working group, recently published on
GigaScience (https://doi.org/10.1093/gigascience/giae106).
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:*
*AgBioData's Data Reuse WG: our current guidelines and future
considerations*
The scientific community has long benefited from the opportunities provided
by data reuse. Recognizing the need to identify the challenges and
bottlenecks to reuse in the agricultural research community and propose
solutions for them, the data reuse working group was started within the
AgBioData consortium framework. Throughout two years of remote meetings and
asynchronous discussion, we identified the limitations of data standards,
metadata deficiencies, data interoperability, data ownership, data
availability, user skill level, resource availability, and equity issues,
with a specific focus on agricultural genomics research. We described these
in a white paper, out now in GigaScience (
https://doi.org/10.1093/gigascience/giae106), while proposing possible
solutions stakeholders could implement to mitigate and overcome these
challenges and providing an optimistic perspective on the future of
genomics and transcriptomics data reuse.
*| 1P ET | 12P CT | 11A MT | 10A PT |*
Find your local time here
<https://www.timeanddate.com/worldclock/fixedtime.html?msg=Alenka+Hafner+on+…>
*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,
You have till Friday, Feb. 28, to nominate yourself and someone else as a
NEW AgBioData steering committee (SC) member (
https://forms.gle/1dTTbEhN8FDs6Ep5A*)*!
The SC is a vibrant, collaborative, and inclusive environment that offers
opportunities to expand 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 who are willing to commit a proportion of *their time to
AgBioData activities (approximately 2 hours/week) for 3 years. *
Please let me know if you have any questions.
Best,
Annarita
Hi everybody,
Please *see below two important opportunities*:
- The AgBioData steering committee (SC) is calling *for nominations for
new SC members*!
Do you want to take a leadership role within the AgBioData consortium?
Do you know someone who can contribute significantly to the AgBioData
steering committee? Nominate* yourself or somebody you think might fit
the position by next Friday, February 28, at *
https://forms.gle/1dTTbEhN8FDs6Ep5A
*! *The SC is a vibrant, collaborative, and inclusive environment that
offers opportunities to expand 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 who
are willing to commit a proportion of their time to AgBioData activities
(approximately 2 hours/week) for 3 years. *
- You have until Friday, February 21, to register for the new AgBioData
working group on
*Natural Language Processing for biocuration (NLP4Biocuration WG)! The
NLP4Biocuration WG will explore the application of existing NLP tools to
biocuration and identify their limitations with AgBioData-curated
content. Join it by completing this form
<https://docs.google.com/forms/d/e/1FAIpQLSe0exyHDowMCnL1_VkCBsff6T0sSPTl3pg…>
by
February 21! The commitment will generally be between 2-6 hours monthly,
including meeting attendance and offline work (e.g., literature, writing,
etc.). Please share the registration link with anybody who you think is
interested.*
Please let me know if you have any questions.
Have a lovely week!
Annarita
Dear all,
This is a friendly reminder to register for the new working group (WG)
on *Natural
Language Processing (NLP) for biocuration*!
The NLP4Biocuration WG will explore the application of existing NLP tools
to biocuration and identify their limitations with AgBioData-curated
content. *Complete this form to join the working group by February 21! *
*The commitment will generally be between 2-6 hours monthly*, 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 data archiving and management practices
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
- possibility to join the AgBioData Ambassador and Championship programs
Please share the registration link with anybody who you think is interested.
Best,
Annarita
Dear all,
Registration for the new working group (WG) on *Natural Language Processing
(NLP) for biocuration* is now OPEN!
The NLP4Biocuration WG will explore the application of existing NLP tools
to biocuration and identify their limitations with AgBioData-curated
content.
*Join the NLP4biocuration working group by completing this form
<https://docs.google.com/forms/d/e/1FAIpQLSe0exyHDowMCnL1_VkCBsff6T0sSPTl3pg…>
by February 21! *
*The commitment will generally be between 2-6 hours monthly*, 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
- possibility to participate in the AgBioData Ambassador and
Championship programs
Please share the registration link with anybody that you think can be
interested.
Best,
Annarita