thanks for participating
Jason Stajich
Thanks again for participating in the Fungal Genome Tools session. It is
my hope we'll continue to have these types of demonstrations of what new
tools are out there. We also should work to have a focused workshop on
integrating tools. Can I ask the presenters to email a copy of your
talk or a link to the talk on your website so that I can create
information page about this session. It appears that to share documents
we can do this within Google Docs and I will see about setting up a
system for this to allow us to share and edit the information.
Please also pass along the link to the mailing list to your colleagues
that may be interested.
http://groups.google.com/group/fungal-genome-tools
and I hope we can have a chance to exchange more ideas and resources
among ourselves and the community.
One problem we all have been struggling with, is a central and single
place to obtain the latest version of the fungal genomes from all
sites. This is certainly a monumental task to curate, but seems to have
been undertaken by several groups at once. Would be possible to work
towards this goal with perhaps different groups focusing on phylogenetic
taxa or other partitions so that we can benefit from this shared
effort? Along with that is of course the meta-data about what version
of the genome and if we are also keeping the annotation and resulting
predicted proteins and coding or non-coding gene sequences. This is
minimal data that each genome-centric site has and can be represented
simply with FASTA and GFF3-compliant files. This overlaps greatly with
what NCBI and RefSeq are intended to cover but so far has been
insufficiently up-to-date and also difficult to sort out data files that
properly list LOCUS and Chromosome names in formats suitable for many
browsers. It also seems like data is being produced at a higher rate
than is able to be curated by one place so I wonder whether a
distributed approach wouldn't be helpful here too?
I will post around a link to the presentations as soon as I have them
all gathered.
Thanks,
Jason
--
Jason E Stajich, PhD
Assistant Professor
Dept of Plant Pathology & Microbiology
University of California, Riverside
951.827.2363
http://lab.stajich.org http://fungalgenomes.org twitter:stajichlab
http://plantpathology.ucr.edu http://genomics.ucr.edu
Brett Tyler
Thanks for your great effort in putting the session together and in
launching fungaldb.
I agree that a central site in which collect the latest version of
fungal genomes could be deposited and accessed would be great.
Ideally the data could be in a central resource (in the cloud?) but
accessible to distributed curators. We'd be willing to take care of
oomycetes (assuming they are allowed in ;-) ).
Cheers
Brett
--
*****************
Brett Tyler
Professor
Virginia Bioinformatics Institute
Virginia Polytechnic Institute and State University
Washington Street
Blacksburg, VA 24061-0477
Telephone: (540) 231-7318
Fax: (540) 231-2606
Email: bmt...@vt.edu
Web: https://www.vbi.vt.edu/article/articleview/141
Twitter: @BrettTylerVT
Administrative Assistant:
Maureen Lawrence-Kuether
Telephone: (540) 231-5995
Email: mlaw...@vbi.vt.edu
*****************
Mike Csukai
Again I would like to thank you for putting together the session at
Asilomar. It is a shame we were not able to get a dialog going but the
format of chapel and size is not exactly conducive to this.
I have to agree that a central site with the latest version of fungal
genomes would be great. We and other companies and institutes do this
independently for our favourite organisms and it really is a
significant duplication of effort. JGI has done a great job with the
Dothideomycetes, but this is still limiting if you want to look more
broadly. Hosting a central for fungal genomes is not a trivial task
and one that requires long term commitment and support which to my
mind means that NCBI or EBI will probably need to be involved but I
could be wrong.
As part of the EBI Elixir project Syngenta has been encouraging the
EBI to deal with more agriculturally important fungi and a little
progress in this direction has been made with a range of genomes
already hosted in Ensembl Genomes:
A number of Oomycetes: Phytophthora infestans, Phytophthora ramorum,
Phytophthora sojae, with Pythium ultimum and Hyaloperonospora
arabidopsidis at the end of April.
It also contains Fungi
Aspergillus clavatus
Aspergillus niger
Aspergillus flavus
Aspergillus oryzae
Aspergillus fumigatus A1163
Aspergillus fumigatus Af293
Aspergillus terreus
Aspergillus nidulans
Neurospora crassa
Saccharomyces cerevisiae
Schizosaccharomyces pombe
Puccinia graministritici CRL 75-36-700-3
Neosartorya fischeri
And by end April:
Gibberella zeae
Gibberella moniliformis
Fusarium oxysporum
A small number I know (but a start perhaps) but EBI would be happy to
talk to any community about their genomes and the guy to talk to is
Paul Kersey (pkersey..at..ebi.ac.uk).
Regards
Mike
Jason Stajich
Thanks for the feedback. I am hopeful the NCBI & EBI will be involved
in the future. The issue is really providing the data in a standardized
format and in whole-genome form.
I've been in contact with Paul and Ewan about this from the beginning
and Paul was part of the Burroughs Wellcome sponsored discussion last
year. I expect the Gates foundation and efforts to make better resources
for plant pathogens will probably insure Ensembl takes a plant pathogen
context while I think FungiDB will likely focus on medically relevant
ones (though I am interested in both).
I hope to have a chance for more discussion in the future about what
tools will help researchers seeking to address different questions. I
hope you'll be able to help speak up on behalf of the needs for tools
from your perspective. If you think it is critical just to have
centralized dbs of the genomes and annotations or tools for additional
data mining or interfacing with expression analyses, etc.
Hope to speak more with you about the projects and development efforts.
Best,
Jason
--
Jason Stajich
To clarify - In FungiDB, we intend to support plant, animal, and model
system Fungi, but I'm hoping to especially improve access for some of
the medically relevant Fungi with little in the way of genome tools
resources. I also think a link to Oomycetes will be important, but am
not sure whether FungiDB have resources to take this on right away or
perhaps rely on the Ensembl, VBI, JGI, and other efforts first.
I'm also gathering the presentations from our session in March (still
missing a couple) onto a single website -
http://tools.fungalgenomes.org/. I hope there can be similar sessions
at future conferences perhaps following a theme, like a discussion on
common strategies for ortholog finding and sharing, annotation,
comparative genomics, expression data integration, etc.
I would be happy to also include links to tutorials provided by
different sites and help to link the database and tools efforts. One
thing that was apparent from discussions with members of the community
is many people aren't aware of what is even available.
Thanks.
Jason
Gavin Sherlock
There is duplication of effort - AspGD has all the Aspergilli sequences available, as well as a synteny viewer, and CGD will be doing the same for the C. albicans and related species. It seems that FungiDB will do this also, as will EBI, and JGI for various overlapping sets of fungi. In our case, our main focus is on the annotation of genes and their products, and the updating of the genomes, based largely on experimental evidence, whereas in the case of these other resources, I think the goal is to be comprehensive with respect to the genomes provided, and/or provide additional search tools supporting complex Boolean logic. I'm not sure that there is a solution to this overlap in effort - it is almost impossible to have a database that is all things to all people, unless you have unlimited resources. Rather then, there are various databases, with different strengths and weaknesses (which reflect their underlying goals), which to some extent compete, and hopefully (and this is the important point) collaborate for the benefit of the communities that they serve. Given that all of us have finite resources, and probably all have long to do lists, it would be valuable if we work together to maximize what can be done for the various communities that use our offerings.
Cheers,
Gavin
________________________________________________________
Gavin Sherlock
Associate Professor
Dept. of Genetics
S201A, Grant Building,
Stanford University Medical School,
Stanford,
CA 94305-5120
Tel: 650 498 6012
Fax: 650 724 3701
http://genome-www.stanford.edu/~sherlock