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How to Use Mushroom Observer

This page provides some short descriptions of common uses of this website followed by an overview of the basic concepts used.

Common Tasks:

  1. Keeping Up with Changes – The default page for Mushroom Observer is the ‘Activity Log’, it is also accessible through the ‘Latest Changes’ link in the left-hand panel. This page shows you the most recent changes on the site. It lists new Observations and Species Lists as well as significant changes to any already existing ones. Additions of Images and Comments are considered significant changes to the relevant observations. Changes to Names are also listed. Click the page numbers at the top and bottom of the page to browse through older changes. Observations and names created as a side effect of other changes are not listed separately.

    Note : The latest changes can be tracked using our RSS feed. See this wikipedia article for more information about RSS feeds.

  2. Searching – There are several interesting ways to search for information on the site. The simplest is to type a search string into the search box near the top of each page and click one of the buttons next to it. This will give you a list of all the Observations, Images, Names or Locations that contain fields matching the given string. If you need a little more control over the search, try clicking ‘Advanced Search’.

    You may also browse the site using the links in the left-hand panel. For example, clicking on ‘Names’ under ‘Indexes’ on the left of the page shows all the species that have observations, listed alphabetically. You can page through this list, or skip directly to the letter of a name you are interested in by clicking the appropriate page number or letter along the top or bottom of the list. Click a name from this list to see a description of the species and a list of observations of that species. If you click a genus like ‘Agaricus’, it will also show a list of species in that genus. Note, however, that in this case it will only show observations that have been identified to the genus level, not ones that have been identified as a species in that genus. On the other hand, if two names are considered synonyms, you will see observations for either name on this page. (NOTE: If you do a search on ‘Agaricus’, it will show all the observations whose name contains that string, so you get all the observations that belong to that genus.)

    Whenever you click an observation or other result on an index page, it will take you to a page showing that result. At the top of the page you will see ‘Prev’, ‘Next’, and ‘Index’ links. These let you browse forward or backward through the results or return to the index. At the top of the index page you will often see links allowing you to sort the results by different criteria, such as by date, name or user. In the same place you will sometimes find links that let you turn an index of observations into an index of names or images of those same observations. For example, if you click ‘Your Observations’, it will show you a list of observations you have posted. Click ‘Show Names’ at the top of the page to see a list of the species you have seen, or click ‘Show Locations’ to see a list of all the locations you’ve gone mushrooming in.

    Power users may also be interested in our new API providing direct access to our database back-end. This can be used to mine our database for images or species descriptions for inclusion in wikipedia or other public websites. You can also use it to upload observations and images and much more. Please contact the webmaster for more information.

  3. Getting Help with an Unknown – In order to get help with an unknown, you need to have a user account. These can be created easily by selecting ‘Create Account’ from the left-hand panel. See the discussion of Users below for more details.

    Once you are logged in, create a new Observation by selecting ‘Create Observation’ in the left-hand panel. Enter all the details you can into the resulting form. You can leave the ‘Scientific Name’ field blank call it ‘unknown’, or if you think you know the genus or family or other group, give that Name followed by ‘sp.’, e.g., ‘Russula sp.’. In the ‘Notes’ field provide information about habitat, odor, smell and anything else not clear from the photos. Once the form is as complete as you can make it, click ‘Create’.

    You should now be looking at a page showing you the information you just entered. However, if you used a name that is not currently in the database, you will be asked if you want to add the name. This also gives you a chance to catch and fix typos. In addition, if you use a name that is considered deprecated, you will be given the option of using a preferred synonym.

    Once you have created the new observation, you can upload any Images you have by selecting the ‘Add Images’ link on the right-side of the page. It is very important either that it be an image you took or that you have the explicit permission of the person who created the image to upload it to the site. If you did not take the image, please update the ‘Copyright Holder’ field to reflect the actual owner. This page also allows you to select the License you want to release the image under.

    When you add unknowns, the community will generally propose one or more names for it within 24-hours. If you find any of the suggested names compelling, you should not hesitate to revisit your observation and Vote on them. Please see the discussion below on voting, as well. Members of the community may also post feedback via Comments. By default your account is set up to deliver comments posted about your observations to you by email. If you are asked to provide more details on the collection, we prefer that you select ‘Edit Observation’ (at the top of the observation page) and add them to the ‘Notes’ field than to just post another comment.

  4. Adding Observations You Have Identified – Use the same process as Getting Help with an Unknown, except this time provide your identification in the ‘Scientific Name’ field. You are strongly encouraged to say something about how you arrived at the identification. We’ve provided a small set of checkboxes to make this easy (‘Recognized by sight’, ‘Based on microscopic features’, etc.), but you are encouraged to elaborate on them in the provided text fields (e.g., list the references you used, or enter ‘sequenced the DNA and compared it against the data in GenBank’!). Community members will often post Comments if there is some question about the collection or if they would like clarification as to why you ruled out other Names. Roy Halling has provided beautifully illustrated presentations describing macroscopic and microscopic features. More documentation on creating scientifically valuable collections is available from the MycoPortal Links Page.

  5. Proposing Names – Any member of the community can propose Names for any Observations. Click an observation (e.g., from the ‘Activity Log’ page) and scroll down below the observation notes. There should be a list of Proposed Names enclosed in a thin outlined box. Most observations will already have at least one proposed name (by the owner). From here you may either click ‘Propose Another Name’ or Vote on existing names. In either case you will have to log in before you are allowed to do so.

    When you click ‘Propose Another Name’ you will be presented with a form much like the one used to create an observation. In addition to the name, you are required to choose a confidence level. This is your Vote, and you may change it on the ‘Show Observation’ page at any time you like. As with creating an observation, you are strongly encouraged to give some explanation as to why you think your Name applies to this Observation (and why other names don’t). When you are finished, click ‘Create’. You will be given a chance to correct typos or to choose an accepted name if you entered a deprecated one.

    Users are not allowed to propose a name if someone else has already done so. The only reason to do so would be to describe alternative reasons for reaching the same conclusion. Instead use the discussion forum provided by comments to do this.

  6. Voting on Proposed Names – Click an Observation, e.g., from the ‘Activity Log’ page, and scroll down to the ‘Proposed Names’ box. Note that you must login before you can see or change any of your Votes. Once you have logged in, you should see pulldown menus next to each Proposed Name. Your vote expresses the degree of confidence or agreement you have with placing that name on that observation. Everything above ‘Doubtful’ is considered a positive vote, everything below ‘Could Be’ negative. Choose ‘No Opinion’ to tell it to delete your vote. When you’ve changed all the votes you want to, be sure to click ‘Update Votes’ to record your votes. Don’t worry, if you forget and try to navigate away without casting your votes it will complain (unless you have Javascript disabled).

    Roughly speaking, votes for a name are weighted, summed and then divided by the number of votes for that name. The name with the highest score wins, and that name will be applied to that observation throughout the site. In the case where multiple synonyms are proposed for an observation it lumps the votes together, choosing each user’s strongest vote within that group of synonyms. In the end, assuming that group of synonyms wins, the currently accepted name is used as the community consensus. If there is still debate in the scientific community about which name is appropriate for a given taxon, then it will use votes the best it can to decide between multiple accepted names. Note that the owner’s vote automatically carries a little more weight, as do the votes of users who have made a large Contribution to Mushroom Observer or who are considered experts. Click ‘Contributors’ or click a user’s name to see the contribution and expert status. (We use the log base 10 of users’ contributions.)

  7. Adding Comments – When you are looking at an Observation, if you would like to post or respond to a Comment, select the ‘Add Comment’ link near the top of the page. If you are not currently logged in to a User account, you will be asked to log in. Once you are logged in, you will be given a form asking for a summary and your comment. Note that you can do some simple formatting in the comment section. This is briefly documented below the text field with a link to detailed documentation. You can also add links within a comment using standard HTML formatting. The HTML gets automatically cleaned to avoid security problems like script injection, so try not to get too fancy.

  8. Tracking a Particular Species or Genus Through Email – Mushroom Observer allows you to request an email any time a particular Name is given to an Observation. If that name is a genus or species it will also send you an email whenever a species or subspecies is observed. To turn this feature on, go to the page for a Name you are interested in (see Searching) and click ‘Email Tracking’. You can configure it so that the person who made the observation that was given that name will be sent a customized email to let them know you are interested in their observation. If you don’t provide any instructions, they will not be sent an email. If the observer gives the name at the time the observation is created, they will be shown your message immediately through the website. You can modify or disable your request for a particular name by going back to that name and again selecting ‘Email Tracking’ and clicking the ‘Disable’ button on the page that comes up.

  9. Describing Species – Click any Name link you see throughout the site. For example, click on ‘Names’ under ‘Indexes’ on the left side of the page then click on any of the results, or search for a name in the search bar, or click the ‘About <name>…’ link at the top of any Observation page. These all take you to a page summarizing everything we know about this taxon. If you are familiar with this species and there is something you would like to add, click ‘Edit Name’ and add your notes. You are encouraged to cite references including field guides and scientific papers. Short quotes from references are fine, but please don’t make extensive quotes without obtaining permission from the original author.

  10. Projects – Projects are a way for a group of Users to work together to create a set of work that they want to keep out of the public eye until they are ready to publish it. The original purpose was to support university classes where there was a desire to keep a more controlled environment while the class was going.

    Anyone can create a new project by clicking on ‘List Projects’ in the left-hand panel and then clicking on ‘Add Project’. The person who creates the project is always a member and an administrator for that project. An administrator for a project can add new members by clicking the ‘Add Members’ link at the top of a project’s ‘Show Project’ page. Administrators can also make other users administrators for the project by going to one of the ‘Change Status’ links available on the ‘Show Project’ or ‘Add Members’ pages. Any User can send requests to the admins for a project. These requests are emailed to the admins and contain a link for changing that user’s status.

    Currently the primary focus of projects is writing Descriptions for various species. Note, however, that anyone can now create new descriptions for a species (see Describing Species) by clicking on ‘Create’ at the top of the ‘Show Name’ page. Descriptions that are created for a project are visible only to members of that project until they are published, and editable only by the owner of the description and project administrators. When a description is published it will become the official description if no official description exists yet.

  11. Working with Maps – Currently there are three types of maps available on Mushroom Observer: Occurrence Maps (e.g., Occurrence map for Craterellus cornucopioides), Location Maps (e.g., Salt Point State Park) and the Global Map.

    To see an occurrence map for a particular Name, go to the page for that name (e.g., enter the name in the search bar, select ‘Names’), and click ‘Search’, then click ‘Occurrence Map’ at the top of the page.

    Users are encouraged to add to the occurrence map for a name. The easiest way is to create a new Observation using an already defined Location. Note, however, that auto-completion for the ‘Locality’ field will list all matching locations whether they are defined or not.

    You can also explicitly choose not to have an observation show up on the occurrence map. This allows you to record observations of mushrooms in places like mushroom fairs, old photos or other places where you may not know where the mushroom was actually collected. When creating or editing an observation there is a checkbox labeled ‘Is this location where it was collected?’. By default it is checked. If you uncheck it, that observation will not appear in any occurrence maps.

  12. Defining Undefined Locations – Many Observations have been reported from undefined Locations. These observations will not appear in our occurrence maps. An excellent, easy way for Users to help out if they have a little spare time is to locate and define these undefined locations.

    When browsing through observations, defined location names will be followed by a link labeled ‘Click for map’. Undefined location names will be followed by a link labeled ‘Search’. If you click the link for an undefined location, it will show a list of observations reported for that location. The resulting page will include two links at the top of the page: ‘Define This Location’ and ‘Merge With A Defined Location’. Clicking on ‘Define This Location’ will present a form which you can use to create that location. Clicking on ‘Merge With a Defined Location’ will present you with a list of similar locations which have already been defined. Clicking on any of these locations will perform the merge.

    You can also see a list of all locations in use by clicking on ‘List Locations’ in the left-hand panel. This page lists both the defined locations (first column, sorted alphabetically) and the undefined locations (second column, sorted by the number of observations reported from that location). In some cases the same location has been given multiple names (e.g., ‘Point Reyes National Seashore’ and ‘Pt Reyes Park’). You can merge an undefined location with a defined location by clicking on ‘Merge’ next to the undefined location (see above).

    When defining a new location, the first thing to do is to review its name. Mushroom Observer tries to enforce a set of rules.

    In theory it is possible for the same location to be defined more than once (presumably by different users). If this happens, you can request a merge by editing one of the two locations and changing its name to be exactly the same as the other’s. This will not have any immediate effect, but it will display a warning message, and an email will be sent to the site administrators with the details. Merging defined locations is restricted since it can cause significant data loss.

  13. Creating Species Lists – To create a Species List, click ‘Create List’ in the left-hand panel. Fill out the various fields. In the ‘Write-In Species’ field, you should give each species a Name on a line by itself. When you go to create the list, each line is checked to see if there is a match in the database. If there is no matching name, you will be asked if you want to add the unknown names to the database. This gives you a chance to catch and fix typos as well as giving you a simple way to add missing names. Each name given in the ‘Write-In Species’ field (or loaded from a file) will be used to create a completely new Observation. The ‘Species List Notes’ are only shown when the entire species list is shown. Use ‘Notes for each new member’ to indicate text you would like to add to each new observation.

    There are several methods of collecting a set of existing observations into a new list. In the simplest method, first create an empty species list, then go to each of the observations you want to add and select ‘Manage Species Lists’. This will give you the opportunity to add that observation to any species list you own. (Note, you can add anyone’s observations to a species list you own.)

    In another method, you may select ‘Create List’ directly from any index of observations or names. For example, you may use the search bar at the top of the page or the ‘Advanced Search’ feature to request all observations from Michigan. When it shows you the first page of results, click ‘Create List’ (in the left-hand panel), and it will give you a list of all the matching names to choose from in the new species list form.

    Lastly, when you are viewing an existing species list, you may click ‘Make a Copy of This List’ or ‘Save This List for Later’ at the top of the page. ‘Make a Copy of This List’ will take you directly to a new species list form, with all the information of the existing list already filled in. ‘Save This List for Later’ will copy that species list’s names to the clipboard. The next time you click ‘Create List’, the new species list form will give you this list of names to choose from (unless you show another observation or name index in the meantime).

Concepts Glossary:

  1. Comment – Comments are the standard way to discuss an Observation or its associated Images. Each comment is owned by a particular User. A comment may only be edited or deleted by the owner or a site administrator. You can look up all comments that have been made about your observations by clicking on ‘Comments for You’ in the upper right of the page (the ‘inbox’ icon).

  2. Image – A photograph or illustration of one or more mushroom species. Images are associated with one or more Observations. A given Image is owned by a particular User who may or may not be the copyright holder. Only the owner or a site administrator can remove an image or edit the associated information. All images in the site are required to be released under one of the Creative Commons licenses or in the public domain. If you dispute the given copyright or the licensing of an image you are the copyright holder of, send mail to the webmaster.

  3. LicenseImages on Mushroom Observer are posted with an explicit license. The current options are the Creative Commons Attribution, Share Alike License, the Creative Commons Attribution, Non-Commercial, Share Alike License and Public Domain. The primary difference is whether the image can be used in any potentially commercial setting. One of the side effects of selecting the non-commercial license is that your image cannot be used on Wikipedia. The license can be set on a per image basis. The looser, Wikipedia compatible license is the default for new Users. However, you can select the non-commercial license to be your default by selecting it on your ‘Preferences’ page and clicking on ‘Save Changes’. Public domain is supported primarily for images that are already in the public domain or for images from certain government institutions that cannot claim ownership of works

  4. Location – A rectangular region enclosing a given location, as defined by the northern, southern, eastern and western boundaries. In addition to the position, locations can also include a minimum and maximum elevation along with various notes. Note that the elevations should be in meters not feet. A location is not considered to be owned by a particular User. Any user may change or define any location, but all of a user’s changes are subject to review by the community. To help with this review process, copies of the previous versions are kept.

  5. Name – A name for some group of mushrooms. Most commonly this is the name of a species, but it can be any taxon (genus, family, variety, etc.). Names can also refer to groups that are not officially recognized scientific names such as common names or functional groups like Gasteromyces. A name is not considered to be owned by a particular User. Any user may change any name, but all changes are subject to review by the community. To help with this review process, copies of previous versions are kept. Names can have an acknowledged author. The author is normally only given for scientific names. The author should follow the standard practice of listing the person who first correctly published the name. In the case of names at or below the species level, the author may also include the person who transfered the species to the current genus, e.g., (Singer) Jenkins.

  6. Observation – A record of a single mushroom species at a particular time and Location. Typically associated with one or more Names (see Proposed Name below) and some number of Images. Each observation is owned by a User, and can only be edited or deleted by that user or a site administrator. However, any user may post Comments about any observation. Observations can also be included in one or more Species Lists.

  7. Proposed Name – A Name as proposed for a given Observation. Any number of names may be proposed for a single observation by members of the community. No special treatment is given to any member’s name. Community consensus is arrived at through the process of voting. Each proposed name for an observation is owned by a single User. However, even the user who proposed the name cannot necessarily modify or delete a name once other members of the community have cast Votes for or against it. Fortunately you may always propose additional names. There is never any sort of penalty associated with proposing incorrect names.

  8. Species List – A list of Observations (not Names). Includes a date, a Location and a title for the list. A given species list is owned by a particular User. Only the owner or a site administrator can change or delete a species list. There are no strict rules for how species lists should be used. This is an area that is likely to change in the future as the community comes up with clearer ideas for how they should be used.

  9. User – An account on Mushroom Observer. You are required to provide a valid email address when you first create an account. This allows the system to stop automated programs from creating bogus accounts. It also provides a way for other users to get in touch with you. However, your email address will never be revealed unless you request an email be sent to another user and then only to that user. If you are concerned about having your email address in our database, once you have verified your account, you can go to the ‘Preferences’ page and remove your address.

  10. Vote – One User’s vote on a Proposed Name for a given Observation. Expresses a level of confidence or agreement with that name, with half the choices (“Could Be” and up) being positive and half (“Doubtful” and below) being negative. Votes are owned by that user, and can only be changed or deleted by the owner or a site administrator.