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
---
One tap mobile
+15642172000,,82038356125#,,,,*160683# US
+16469313860,,82038356125#,,,,*160683# US
---
Dial by your location
• +1 564 217 2000 US
• +1 646 931 3860 US
• +1 669 444 9171 US
• +1 669 900 6833 US (San Jose)
• +1 689 278 1000 US
• +1 719 359 4580 US
• +1 929 205 6099 US (New York)
• +1 253 205 0468 US
• +1 253 215 8782 US (Tacoma)
• +1 301 715 8592 US (Washington DC)
• +1 305 224 1968 US
• +1 309 205 3325 US
• +1 312 626 6799 US (Chicago)
• +1 346 248 7799 US (Houston)
• +1 360 209 5623 US
• +1 386 347 5053 US
• +1 507 473 4847 US
Meeting ID: 820 3835 6125
Passcode: 160683
Find your local number: https://us06web.zoom.us/u/kF3akiFg7
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
