Fungal Databases, Nomenclature & Species Banks
How to search MycoBank? Why and how should I be registered on MycoBank? How to register a new name/taxon and associated data to MycoBank? I have a new species belonging to a new genus. Which one should I register first? I have a new genus to be deposited on MycoBank but I don't know the family. What should I use as higher rank? How to perform a pairwise DNA sequence alignment using MycoBank and associated databases? What is polyphasic identification and how to do it? How to stay up to date with new releases on MycoBank? Link your website to MycoBank How to become a curator of MycoBank? How to find and export all species of multiple families? How to find all the genera belonging to an order published after a certain date? How to get data from MycoBank? Do you have some webservices?
For the moment 6 search engines are available from the MycoBank website: 1. The first is called Simple search and permits to search for fungal names (at a few rank levels). This query system is super simple and fast but is not allowing any queries on other fields than the taxon name 2. The second is called Basic search and permits to search for fungal names (at any rank level), the authority or the MycoBank unique number. 3. The third is called Advanced search and permits to search for fungal names (at any rank level), the authority or the MycoBank unique number, the year of publication, the associated bibliography, the status of the name, the epithet or the type name (basionym, combination, nomen novum). In this case, one can use several criteria at the same time. If the Match on option is set to All conditions, then all criteria asked will have to be present. If the Any conditions is selected then only one condition will be sufficient to select the wanted record(s). Complex queries can also be made. Click on the movie icon below to see how to do it. Advanced search option (click on Switch to: Advanced Search), one will be able to combine criteria using AND, OR and NOT operators. 4. The fourth one is dedicated to type specimens queries . 5. The fifth one is dedicated to bibliographic queries related to fungal name's publications. 6. The sixth one is dedicated to queries on the thesaurus database of fungal terms .
MycoBank users willing to deposit their data will have to register. We need to be able to contact the depositor for specific information (e.g. MycoBank number, possible points of attention regarding the name, actual publication, etc), and we also want to avoid fake entries. To search MycoBank, there is not need to be registered. To register for the first time follow the steps below (click on the movie icon below): 1. Click on the Login menu, go to the Create free account section create or click here 2. Enter your email address, click on the Create account button to receive a provisional password by email (this is to make sure that the provided email is real and that you are the person that can open the given email). 3. Read your email and go to the Registration form. 4. Enter your email and password (obtained by email). 5. Click on the Login button and access the registration profile form where personal information will have to be entered. 6. Change the password and personalize it. Click on the Save button. 7. You will then be registered and ready to add new fungal names and related data to MycoBank.
The registration of a new name to MycoBank is performed in a few steps, depending on the items to be submitted. This procedure has been simplified recently allowing for faster and easier deposit of data. Prepare all your data before starting the registration process. This includes type strain information (strain #, origin, substrate, sequences, ...), species related data like Latin description, anamorph-teleomorph connections, synonymy, bibliographic information, PDF or MS-Word original manuscript, ... The steps are: 1. Introduction of the new name, the hierarchy and the authority 2. Selection of the basionym (optional) 3. Definition of the morphic status and anamorph-teleomorph connections (optional) 4. Status of the name and synonymy (optional) 5. Bibliographic information related to the original publication of the new name 6. Description in Latin and other languages (preferably english) 7. Type strain/specimen information 8. Scientific data and other information links can be defined. Original manuscript can be uploaded (optional) 9. Review of the newly deposited name by the MycoBank curators and sending of the unique MycoBank number to the depositor. The new name will be available from the MycoBank website as soon as the original paper has been accepted for publication. Please contact us as soon as published to release the new name.
To keep updated with all the newly released taxa on MycoBank, got to the News section. This section can be easily queried.
In MyocBank the higher rank (family for a genus for example) must always be provided. So, when a new species belonging to a new genus must be deposited, the highest level rank should be deposited first. In this case, deposit the genus name first, then the species. If more levels have to be deposited, the general rule is to deposit the highest rank first and the lower ones after. In the last step of the registration, there is a Remark field that can be used to indicate to MycoBank curators, which species of the newly described genus is the type species.
If the next highest rank remains unkown, so in the case of a new family, if one doesn't know the order to which it belongs to, two options are possible: 1. use the next higher known rank (class, subdivision, etc) 2. use Incertae sedis as next higher rank
With the new version of MycoBank using BioloMICS software, it is now possible to perform online pairwise DNA alignments. We call this tool MycoID. Identifcations can be done by comparing a single unknown sequence against one or several reference database(s) at the same time. A number of parameters are available and can be changed dynamically by the end-user in order to obtain the best possible results. We have recently made a movie that shows how to make such an identification.
With pairwise sequence alignments, only one sequence (i.e. character) can be accounted at the same time. With polyphasic identifications, several characters can be accounted at the same time to compare an unknown profile against a list of reference taxa or strains. For example, morphological, physiological and/or molecular features can be used to compute a global similarity coefficient using the different characters or criteria at the same time. Identifications are therefore based on several features. This is potentially very powerful if the criteria used to identify are well weighted, reliable and compared using adequate algorithms. A number of databases allow to perform the so-called polyphasic identifications using the BioloMICS software. A few are listed here. A movie that shows how to make such an identification can be watched by clicking on the movie icon below.
Two easily accessible links have been implemented: 1. Using the taxon name: www.MycoBank.org/name/complete taxon name, for example www.MycoBank.org/name/Verticilliodochium tubercularioides 2. Using the MycoBank number: www.MycoBank.org/MB/MycoBank number, for example www.MycoBank.org/MB/227372
MycoBank is owned by the International Mycological Association (IMA). It is curated by a number of mycologists mainly specialized in nomenclature. Since current curators cannot know and understand the classification of all fungal clades, it is important to welcome new specialists to help with the curation of MycoBank. If you feel like helping the International Mycological Association with your extended expertise, please contact us. Remote curation of MycoBank is now possible using Citrix XenApp. Click here to see a movie illustrating how easy it is to access the system.
Click on the movie below to see how to retrieve all the species of given families in 1 go: 1. Perform an advanced search. 2. Enter the family names, separated by semi-colon (;) in the classification search box. 3. To retrieve only the species, set the rank as Sp. 4. Add full results to the list to be able to export the results to Microsoft Excel.
Click on the movie below to see how to find all the genera belonging to an order published after a certain date: 1. From the main menu of MycoBank, select “Search” and then “Advanced search on names”
We have implemented a few webservices that are briefly described at http://www.mycobank.org/Services/Generic/Help.aspx?s=searchservice. These services allow to retrieve data using the XML format. If you need different webservices, please do not hesitate to contact us.
1. Vincent Robert, Duong Vu, Ammar Ben Hadj Amor, Nathalie van de Wiele, Carlo Brouwer, Bernard Jabas, Szaniszlo Szoke, Ahmed Dridi, Maher Triki, Samy ben Daoud, Oussema Chouchen, Lea Vaas, Arthur de Cock, Joost A. Stalpers, Dora Stalpers, Gerard J.M. Verkley, Marizeth Groenewald, Felipe Borges dos Santos, Gerrit Stegehuis, Wei Li, Linhuan Wu, Run Zhang, Juncai Ma, Miaomiao Zhou, Sergio Pérez Gorjón, Lily Eurwilaichitr, Supawadee Ingsriswang, Karen Hansen, Conrad Schoch, Barbara Robbertse, Laszlo Irinyi, Wieland Meyer, Gianluigi Cardinali, David L. Hawksworth, John W. Taylor, and Pedro W. Crous. 2013. MycoBank gearing up for new horizons. IMA Fungus · volume 4 · no 2: 371–379 2. P.W. Crous, W. Gams, J.A. Stalpers, V. Robert and G. Stegehuis. 2004. MycoBank: an online initiative to launch mycology into the 21st century. Studies in Mycology 50: 19–22 3. V. Robert, G. Stegehuis and J. Stalpers. 2005. The MycoBank engine and related databases. http://www.MycoBank.org