Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[go-friends] Fwd: [Pombelist] JaponicusDB official release

Valerie Wood vw253 at cam.ac.uk
Wed Sep 1 08:02:55 PDT 2021


Dear friends and colleagues,

In collaboration with Snezka Oliferenko (Crick Institute),  we have 
rapidly deployed a model organism database (MOD) and curation system for 
the emerging model species Schizosaccharomyces japonicus. JaponicusDB 
www.japonicusdb.org uses Kim Rutherford's excellent code for the PomBase 
database and website, and the his popular curation tool (Canto 
https://curation.pombase.org/).

We have performed a round of annotation to improve gene structures, add 
missing genes, improve orthology calls and GO inferences.  Future 
curation updates (gene names, products, orthologs and gene structures) 
are possible entirely by editing files stored in GitHub; which allowing 
the community to easily propose or make updates.

The japonicus community have already curated almost 70% of their 
publications in Canto (for GO, phenotypes, interactions and 
modifications) and all future literature curation will be in the hands 
of this proactive community 
https://www.japonicusdb.org/reference_list/community.

Further information about how these two fission yeast together provides 
a powerful  model system for evolutionary cell biology in the 
announcement from Snezhka Oliferenko below.


Best Wishes,


Val


https://github.com/japonicusdb
https://www.japonicusdb.org/
@japonicusdb


-------- Forwarded Message --------
Subject: 	[Pombelist] JaponicusDB official release
Date: 	Wed, 1 Sep 2021 14:00:11 +0000
From: 	Oliferenko, Snezhana via Ucam-pombelist 
<ucam-pombelist at lists.cam.ac.uk>
Reply-To: 	Oliferenko, Snezhana <snezhana.oliferenko at kcl.ac.uk>
To: 	pombelist at pombase.org <pombelist at pombase.org>
CC: 	hniki at nig.ac.jp <hniki at nig.ac.jp>, Frank Uhlmann 
<frank.uhlmann at crick.ac.uk>, omaya.dudin at epfl.ch <omaya.dudin at epfl.ch>, 
David Teis <david.teis at i-med.ac.at>, J.T.Pronk at tudelft.nl 
<J.T.Pronk at tudelft.nl>, tom_rapoport at hms.harvard.edu 
<tom_rapoport at hms.harvard.edu>, david_pellman at dfci.harvard.edu 
<david_pellman at dfci.harvard.edu>, taisuke_seike at ist.osaka-u.ac.jp 
<taisuke_seike at ist.osaka-u.ac.jp>



Dear friends and colleagues,

We are excited to announce the official release of JaponicusDB, the 
curated model organism database for the fission yeast 
/Schizosaccharomyces japonicus/ (www.japonicusdb.org 
<http://www.japonicusdb.org>).

In recent years /S. japonicus/ has emerged as a powerful system for 
studying evolutionary cell biology, via comparison to /S. pombe/. 
Although these two fission yeasts carry out conserved cell-level 
processes using similar gene complements, substantial differences in the 
mechanisms underpinning their physiology (e.g., cell cycle and division, 
cellular polarity, differentiation, membrane biology, metabolism), 
provide invaluable opportunities to study how cell biological processes 
evolve. Together, /S. pombe/ and /S. japonicus/ form a composite model 
system in which cell biological processes, gene products, and associated 
phenotypes can be compared side by side. Furthermore, /S. japonicus/ 
serves as a valuable stand-alone system to study phenomena not apparent 
or tractable in the established yeast models (e.g., nuclear envelope 
breakdown and reformation and cellular geometry scaling).

We have finished a round of gene structure revisions, distant ortholog 
detection (not detected in several previous pipelines) and improved the 
GO annotation substantially by inferences from PomBase. With the input 
from publication authors, we have curated the bulk of /S. japonicus/ 
papers. Individual gene pages in JaponicusDB are linked with PomBase in 
the ortholog section of the gene page (and reciprocally from PomBase to 
japonicus) – do look at your favourite genes for possible phenotype 
divergence, etc. Overall, JaponicusDB functionality is similar to 
PomBase – we hope you are going to have fun using them in parallel.

Now that JaponicusDB is set up, it will be entirely community-run. Let 
us know if you would like to help out. We have a number of ongoing tasks 
including fixing reported problems with gene products, orthologs, and GO 
annotations, hosting any sequence based HTP datasets and checking 
community curation sessions. Training will be provided, and the volume 
of work will be relatively small, but it will be rewarded by authorship 
on future JaponicusDB manuscripts.

If you would like to join the /S. japonicus/ community, ask /S. 
japonicus/-related questions, and see future JaponicusDB-specific 
announcementsplease join and use this mailing list 
(https://mailman.kcl.ac.uk/mailman/listinfo/japonicus-list 
<https://mailman.kcl.ac.uk/mailman/listinfo/japonicus-list>). Our 
Twitter handle is @japonicusdb, and our GitHub organization is 
https://github.com/japonicusdb

We hope that JaponicusDB will prompt many of you to start working on our 
(second) favourite organism.

Have fun!

Snezhka Oliferenko and the PomBase team (Val Wood, Kim Rutherford, 
Midori Harris)


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/go-friends/attachments/20210901/5a97b697/attachment.html>


More information about the go-friends mailing list