Fun Facts About Fungi

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Mining a Database: Bioinformatics in Action


MICH Fungus Collection

Large specimen databases list, or catalogue, all the specimens in a collection. These large databases often contain data on hosts, habitats, collectors, and date collected. Researchers interested in the ecology and biology of fungi can "mine", or search, large databases for data. Some examples of mined data are lists of rare species, all species found in lodgepole pine forests, all species found on wood, all species collected by Alexander H. Smith, all species from Idaho, or all species from Mount Rainier National Park. The biological and geographical information contained in specimen records make databases an important resource for biodiversity studies.

Before mining data, researchers need to remember that databases are often under construction and not all specimens may be listed. Large herbaria and museums often contain millions of specimens. Typing specimen data into the computer database is slow work, and it may take years to completely catalogue a collection. The Michigan Fungus database only contains 35,000 specimen records, 12% of the 280,000 specimens in the collection. Only records that have latitude and longitude for the site where the specimen was collected can be mapped on the computer. Finally, species names often change, and the changes may not have been made in the database. Despite these problems, mining databases is often the only way to find some types of information.

Suggested Mining Trips


Species Checklist

Trip 1.

Make a checklist of all the species in the database from your state using this search form for the Fungus Collection database.

Checklist Search Form

You enter your choice of location (state, county, specific location like a town or national park, host, habitat like bog, substrate like wood, or foreign country. The search makes a list of species and their common names. The number of times a species name is repeated in the list indicates how commonly it has been collected.

To find out more about the species in the list you can do a search for general information about that species using this search form:

General Information about Species Search Form

To list all of the specimens of a species in the checklist and get associated information like images and DNA sequences you can use this search form (also used in Trip 2, below):

Specimen Data Search Form


specimen data

Trip 2.

Prepare a report on one of the milk mushrooms (Lactarius species). The report could include:

  • The common name.
  • The scientific (Latin) name.
  • A picture of the mushroom.
  • The beginning and end dates of the season for collecting the species.
  • A description of where it grows (hosts -- Pinus albicans, substrates -- soil, wood, etc., habitats -- bogs, forest, etc).
  • A technical description of the species (shape, color, spore size, etc.).
  • A general description of its geographic distribution (South, Midwest, etc.).

You can display all of the specimens in the database that match your key words by using this search form:

Specimen Data Search Form

Directions

For names, fill in the boxes at step 2. You can enter common names like morel, or milk. Common names must have an * at the beginning and end of the word(s), *milk* or *black morel* for example. Scientific names can be entered instead of common names. If you know the exact spelling use the = option, =Verpa for instance. If you do not know the exact spelling use the LIKE option, LIKE Verp*, for instance.

Step 2 also allows you to select special searches. You can display all of the pictures in the database by clicking on the IMAGES ONLY box under the blanks. DNA and conservation status data can also be found this way. If you enter a common name and click on IMAGES ONLY, you will only find records for that species which contain images. You may not find any data with this search. At this time, only a few specimen records have pictures.

Step 3 allows you to pick a location (state or county of the USA, foreign countries) and hosts or habitats (where the fungus lives). You do not enter any names in the boxes in step 2 if you want to list all the species from a location or habitat. If you enter a name in step 2, only data for that species from the location or habitat you entered will be displayed. Step 3 is a way to create a "check list" of species in the database from a state or county, or a list for a single host or habitat.

In step 4 you send items you want to find in the database by clicking on the SUBMIT QUERY button. If you want to start the search over you click the RESET button, then reenter names, state, etc.


distribution map

Trip 3.

Make a "dot" map showing the geographic distribution of American collections. You can display all the specimens and their data by clicking on one of the dots. Major roads, rivers, lakes and states and counties are also displayed.

Make a Map Search Form

You enter a keyword and then select from a list of choices to make a map. The buttons on the map display allow you to magnify or move the map.


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Last update: 20 Jan 00. © 2002. Robert Fogel, Ivins, UT 84731. Text edited by Patricia Rogers