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MYCOBANK AND ASSOCIATED DATABASES AS WORKING TOOLS FOR TAXONOMISTS: OPPORTUNITIES AND CHALLENGES Vincent Robert CBS-KNAW, Utrecht, The Netherlands,

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Presentation on theme: "MYCOBANK AND ASSOCIATED DATABASES AS WORKING TOOLS FOR TAXONOMISTS: OPPORTUNITIES AND CHALLENGES Vincent Robert CBS-KNAW, Utrecht, The Netherlands,"— Presentation transcript:

1 MYCOBANK AND ASSOCIATED DATABASES AS WORKING TOOLS FOR TAXONOMISTS: OPPORTUNITIES AND CHALLENGES Vincent Robert CBS-KNAW, Utrecht, The Netherlands,

2 HISTORY & FACTS Started in P.W. Crous, W. Gams, J.A. Stalpers, V. Robert and G. Stegehuis MycoBank: an online initiative to launch mycology into the 21st century. Studies in Mycology 50: 19–22 Originally based on a CBS Firebird database (J. Stalpers and G. Stegehuis) and an old version of BioloMICS software (V. Robert) Started at CBS-KNAW but later transferred to International Mycological Association (IMA) IMA is now the owner of MycoBank Created to centralize deposit of new fungal taxa (species, genera, families, etc)

3 HISTORY & FACTS Created to know what has been published until now and provide an exhaustive and centralized list of fungal species More and more data associated with taxa have been added to MycoBank MB numbers required by a majority of journals publishing new taxa New version of MycoBank released in April 2012 with a number of new features: 1.Complete integration with BioloMICS software allows extensive developments of new features 2.Simplified basic and advanced search enginebasicadvanced 3.Simplified registration of new taxaSimplified registration of new taxa

4 HISTORY & FACTS New version of MycoBank released in April 2012 with a number of new features: 1.Complete integration with BioloMICS software allows extensive developments of new features 2.Simplified basic and advanced search enginebasicadvanced 3.Simplified registration of new taxaSimplified registration of new taxa 4.Link out to many websites: 1. DBs containing fungi: a. Catalogue of Life (CoL) b. Encyclopedia of Life (EOL) c. Global Biodiversity Information Facility (GBIF) d. Index Fungorum (IF) e. Integrated Taxonomic Information System (ITIS) 2. Bibliography links : a. Google Scholar b. PubMed c. Libri Fungorum d. Biblioteca Digital e. Biodiversity Heritage Librar 3. General links : a. Google b. Wikimedia c. Wikipedia d. Wikispecies 4. Molecular links : a. BOLD Systems b. EMBL c. NCBI 5. Specimens and strains links : a. All Russian Collection of Microorganisms (VKM) b. CBS collection c. StrainInfo d. WDCM will be made available as soon as ready

5 Stage 1 Aspergillus 341 Penicillium 430 Genbank +++ Mycosphaerella 117 Colletotrichum 452 Calonectria 160 Phytophtora 77 MLST Fusarium 1365 Phoma 309 CBS Clinical ITS 488 FunBOL 4366 BOLD Yeasts 1365 Indoor molds 1646 Pasteur CDC Ceratocystis 92 Monilinia 54 Stenocarplella 32 Russula 608 Dermatophytes 378 Phaeoacremonium 30 Medical 315 History & facts Distributed Fungal Databases

6 HISTORY & FACTS New version of MycoBank released in April 2012 with a number of new features: 1.Complete integration with BioloMICS software allows extensive developments of new features 2.Simplified basic and advanced search enginebasicadvanced 3.Simplified registration of new taxaSimplified registration of new taxa 4.Link out to many websites 5.Pairwise sequence alignments against a large number of websites including CBS and GenBank (BOLD soon as well)Pairwise sequence alignments against a large number of websites 6.Polyphasic identifications for a number of taxonomic groupsPolyphasic identifications for a number of taxonomic groups

7 HISTORY & FACTS New version of MycoBank released in April 2012 with a number of new features: 7.Multilingual: 1.English, French, Chinese, German, Arabic, Spanish, Portuguese and Dutch are available. Thai ready but not yet published. 2.Russian, Indonesian and Japanese coming soon 3.More if volunteers are ready to translate the system in their own languages

8 HISTORY & FACTS New version of MycoBank released in April 2012 with a number of new features: 7.Multilingual 8.Remote curation of MycoBank allows curators from all around the world to manage the system, will be effectively available in April 2013.Remote curation of MycoBank

9 DISCUSSION PANELS & ANNOTATIONS

10 FUNGAL REPOSITORIES SYNCHRONIZATION Index Fungorum MycoBank Fungal Names China Central facility 1.Unique number for names 2.Avoid duplication 3.Live synchronization 4.Ensure data consistency 5.Ensure minimum dataset 6.Help curation

11 Dynamic REST (SOAP soon) protocol and allows many operators and complex queries: = < > <= >= <> STARTSWITH ENDSWITH CONTAINS AND OR NOT ( ) Candida mycobankii J. Smith Species 4569 Candida Legitimate True … Candida bertreensis J. Smith Species 4569 Candida Legitimate True … FUNGAL REPOSITORIES SYNCHRONIZATION

12 Example: &limit=1000&filter=Epithet_ STARTSWITH “bitum” FUNGAL REPOSITORIES SYNCHRONIZATION 03/02/ :21: Ca ndida bituminiphila V. Robert, B. Bonjean, Karutz, Paschold, W. Peeters & Wubbolts bitumi niphila No species species

13 Web services available for: 1.Queries and data retrieval 2.Insertion of new records/names (identification needed, only for a few registered submitters (MycoBank, IF, FN, MycoKeys ?, MycoSpecies, etc ?)) 3.Update of existing records/names (identification needed, only for a few registered submitters (MycoBank, IF, FN, etc ?) and some fields) FUNGAL REPOSITORIES SYNCHRONIZATION

14 REMOTE MYCOBANK

15 Future developments Microbiome analysis, metagenomics Mix samples NGS Genome

16 Future developments Database scaling needed

17 NOSQL Bioinformaticians IT & Software developers

18 THE TEAM V. Robert D. Vu (G. Stegehuis) N. van de Wiele A. Ben Hadj AmorS. SzokeB. Jabas E. Blom O. Chouchen M. Jaidane S. Ben Daoud Utrecht, The Netherlands Sousse, Tunisia Hannut, Belgium F. Borges dos SantosLea Vaas MycoBank curation, Utrecht, The Netherlands Joost StalpersArthur de Cock

19 Conrad L. Schoch 1, Keith A. Seifert 2, Sabine Huhndorf 3, Vincent Robert 4, John L. Spouge 1, Elena Bolchacova 5, Kerstin Voigt 6, Wen Chen 2, Andrew N. Miller 7, Michael J. Wingfield 8, M. Catherine Aime 9, Kwang-Deuk An 10, Feng-Yan Bai 11, Robert W. Barreto 12, Dominik Begerow 13, Marie-Josée Bergeron 14, Meredith Blackwell 15, Teun Boekhout 4, Mesfin Bogale 16, Nattawut Boonyuen 17, Ana R. Burgaz 18, Bart Buyck 19, Lei Cai 11, G. Cardinali 20, Priscilla Chaverri 21, Brian J. Coppins 22, Ana Crespo 18, Pedro W. Crous 4, Paloma Cuibas 18, Ulrike Damm 4, Z. Wilhelm De Beer 8, G. Sybren De Hoog 4, Ruth Del-Prado 18, Bryn Dentinger 23,56, Javier Diéguez-Uribeondo 24, Pradeep K. Divakar 18, Brian Douglas 25, Margarita Dueñas 24, Duong Vu 4, Tuan A. Duong 26, Ursula Eberhardt 4, Mostafa S. Elshahed 27, Katerina Fliegerova 28, Miguel A. García 24, Zai-Wei Ge 29, Gareth W. Griffith 25, K. Griffiths 30, Johannes Z. Groenewald 4, Marizeth Groenewald 4, Martin Grube 31, Marieka Gryzenhout 32, Liang-Dong Guo 11, Ferry Hagen 4, Sarah Hambleton 2, Richard C. Hamelin 14, Karen Hansen 33, Paul Harrold 22, G. Heller 9, Kazuyuki Hirayama 34, Hsiao-Man Ho 35, Kerstin Hoffman 6, Valérie Hofstetter 36, Filip Högnabba 37, Peter M. Hollingsworth 22, Seung-Beom Hong 38, Kentaro Hosaka 39, Jos Houbraken 4, Karen Hughes 40, Seppo Huhtinen 41, Kevin D. Hyde 43,44, Timothy James 44, Peter R. Johnston 45, E.B. Gareth Jones 17, Laura J. Kelly 22,23, Paul M. Kirk 46, Dániel G. Knapp 47, Urmas Kõljalg 48, Gábor M. Kovács 47, Cletus P. Kurtzman 49, Sara Landvik 50, Steven D. Leavitt 3, André Levesque 2, Audra S. Liggenstoffer 27, Kare Liimatainen 51, Lorenzo Lombard 4, J. Jennifer Luangsa-ard 52, H. Thorsten Lumbsch 3, Harinad Maganti 53, Sajeewa S. N. Maharachchikumbura 42, María P. Martin 24, Tom W. May 30, Alistair R. McTaggert 9, Andrew S. Methven 54, Wieland Meyer 55, Jean-Marc Moncalvo 56, S. Mongkolsamrit 52, László G. Nagy 57, R. Henrik Nilsson 58, Tuula Niskanen 51, ldikó Nyilasi 57, Gen Okada 10, Izumi Okane 59, Ibai Olariaga 60, J. Otte 61, Tamás Papp 57, Duckhul Park 45, Tamás Petkovits 57, Raquel Pino-Bodas 24, C. Qing 29, Willem Quaedvlieg 4, Huzefa A. Raja 62, Dirk Redecker 63, Tara Rintoul 2, Constantino Ruibal 18, J.M. Sarmiento-Ramírez 24, Imke Schmitt 61,64, Arthur Schüßler 65, Carol Shearer 66, Kozue Sotome 67, Frank O.P. Stefani 30, Soili Stenroos 37, Herbert Stockinger 63, Satinee Suetrong 17, Sung-Oui Suh 68, Gi-Ho Sung 38, Motofumi Suzuki 10, Kazuaki Tanaka 34, Leho Tedersoo 69, M. Teresa Telleria 24, Eric Tretter 70, Wendy A. Untereiner 16, Hector Urbina 15, Csaba Vágvölgyi 57, Agathe Vialle 14, Grit Walther 4, Qi- Ming Wang 11, Bevan S. Weir 45, Michael Weiß 71, Merlin M. White 70, Jianping Xu 53, Rebecca Yahr 22, Z.-L. Yang 29, Andrey Yurkov 13, Juan-Carlos Zamora 24, Ning Zhang 72, Wen-Ying Zhuang 11 and David Schindel, Szaniszlo Szoke, Bernard Jabas, Ammar Amor, Oussema Chouchen, Samy Ben Daoud, Ahemd Dridi, Samrock, Matteo Garbelotto, David Yarrow, Joost Stalpers, Gerrit Stegehuis, Nathalie van de Wiele, Donald Hobern, Matt Branford, Frank Bisby, Peter Bonants, Harm Huttinga, Sloan Foundation, Embarc project, EU grants QBOL, FES project, NCB Project, i4Life project, CBS, My wife and kids 10 Thanks to all mycologists, developers, EU, NCB, FES, Embarc, Sloan Foundation, QBOL, q-Bank, & iBOL projects


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