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Online mycological resources
Lei Cai （cail@im.ac.cn）
Institute of Microbiology, CAS
Searching and Discovering
The Publishing World is Changing
e-literature
Changing Patterns of Research
The research process is no longer
likely to begin with a face-to-face
consultation with a librarian,
a visit to the library’s special
collections service points, or a
search of the online library catalogue
Faculty most often turn to
network-level services, including
both general purpose search engines
and services targeted specifically to
academia
From: Ithaka S&R Faculty Survey 2009:
Key Strategic Insights for Libraries, Publishers, and Societies. p 5.
Value of the Electronic Journal
Utilization of digital resources in mycology
Contents
1
Index fungorum
i-bol
Cybertruffle
USDA data base
Mycobank
NCBI
Q-bank
Specific database
.
2
Cyberliber
StrainInfor
CBS
Index herbariorum
3
Genome
Microbiome
Transcriptome
……
How to find type cultures and herbariums
Fungal omics databaseDigital Literature
1. Digital Literature
Index Fungoruman international database to index all formal names (scientific names) in the Fungi Kingdom.
International Barcode of life (i-bol)
NCBI-Taxonomy
NCBI-Taxonomy
NCBI-Taxonomy
NCBI-Taxonomy
Q-Bank, quick identification of common/important pathogens
Organisms included
Polyphasic identification in Q-Bank
Polyphasic identification in Q-Bank
Fusarium database
Phytophthora database
Aspergillus/Penicillium database
Some specific databases
Fusarium DatabaseFusarium database
Phytophthora Database
Phylogenetic tree was built using sequences
at seven loci (approximately 8700 nucleotides).
Aspergillus/Penicillium database
Cybertruffle
Cybernome
Cyberliber: a digital library for mycological references to nearly 60,000 individual
mycological publications, and access to more than 198,000 scanned images of pages of
mycological works
(http://nt.ars-grin.gov/fungaldatabases/index.cfm)
USDA fungal database
Mycobank
CULTURE COLLECTIONS AND
HERBARIUMS
Important culture collections ATCChttp://www.atcc.org/ATCCAdvancedCatalogSearch/tabid/112/Default.aspx NBRC Biological Resource Center, NITE
http://www.nbrc.nite.go.jp/NBRC2/NBRCDispSearchServlet?lang=en CABI
http://cabi.bio-aware.com/Biolomics.aspx?Table=GRC%20catalogue CBS Fungal Biodiversity centerhttp://www.cbs.knaw.nl/fungi/BioloMICS.aspx DSMZhttp://www.dsmz.de/microorganisms/html/strains/strain.dsm001151.html ICMP
http://nzfungi.landcareresearch.co.nz/html/mycology.asp NIAS (MAFF numbers)http://www.gene.affrc.go.jp/databases-micro_search_en.php
2. How to find the type cultures or herbariums?
* From Cyberliber
StrainInfo help you to find the type strains
eg.1.
Didymella rabiei (Kovatsch.) Arx, Beitr. Kryptogamenfl. Schweiz 11: 364.
1962.
Websites of Herbaria
3. Fungi omics databases
Genome
Microbiome
Transcriptome
Proteome
… …
Fungal Genomes
2008-75 fungal genomes project
2003-44 fungal genomes project
2002- 15 fungal genomes project
1996- Saccharomyces cerevisiae
Add Your Text
Add Your TextAdd Your Text
2012- 1000 fungal genomes project
GOLD database
NCBI-RefSeq
Microbiome
Microbiome research
by ecosystem
Microbiome database
Summary
Looking for: list of species name
list of synonyms
species description
Type specimens
Type strains
Fungus host relationship
Old literatures
Regional checklist
World herbaria
Fungal Valhalla
World culture collections
some important groups
quick identification of pathogen
Genome
Microbiome
Index fungorum
Index fungorum/Mycobank/Species fungorum
Mycobank /cyberliber
Index fungorum / Mycobank
Strain info /Mycobank /cyberliber
USDA database
Cyberliber
Cybertruffles’ Robigalia
Index herbariorum
Cybertruffles’ Fungal Valhalla
Culture collection in the world
Specialized databases
Q-Bank
JGI/Broad institute/NCBI/ENA
GOLD/IMG/MG-RAST/UNITE/…
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