3. Querying

The Select Query
The Accession Query
The Taxonomy Query
The Statistics Query

Chapter 8. The Select Query

The Select option of the Main Menu is the primary way to retrieve accessions and associated data from the database. You select data based on your requirements or search criteria. You determine your search criteria through a series of options, choices, and questions and answers.

The type of data you can obtain is:

• Passport Data
• Characterization/Evaluation data
• Inventory Data (Management Version Only)

Once the data are selected, you can either Display them, Refine the search criteria using additional specifications, or Output them.

To make your query go faster, it is best to begin using no more than three of your most important criteria in Define. These will be your baseline criteria. All your Accessions must have these criteria. Then use single queries in Refine to search for additional criteria while isolating the data of interest to you.

If you use the same criteria all the time, it might be helpful to put them into a Mask, so you don’t have to type them in each time you make the same query.

Note: At any prompt within the Select option, you can press <Esc> or <Cancel> to return to the Main Menu.

Define

This is where you query the database for the accessions that you want.

Note: We suggest you use both Define and Refine to make your search go more quickly.

Using the Select Define Option

Suppose you are a wheat breeder and you want to acquire an accession of Triticum aestivum with a winter habit and resistance to Hessian Fly Biotype L. This is how you would query the system to select your accessions.

At the Main Menu:

Choose Select

A new screen appears from which you make other selections:

Define is automatically highlighted. Refine and Output are not yet an option, because you have not chosen any accessions.

Choose Define

A Define window appears:

Note the Inventory searches section near the bottom of the screen above.

There are two types of Inventory to choose from:

1. Active inventory—consists of only that Inventory from which you can obtain material.
2. All available inventory—pertains to all the data in the system, whether or not you can obtain the material.

To begin your query,

Choose the type of Inventory search you want

Type a scientific name, a common name, or a secondary identifier on the line, and choose <OK>, or

Leave the line blank and click the <Scientific Name> or <Common Name> push button to choose from a pop-up list.

In our example as a wheat breeder looking to obtain Triticum aestivum with a winter habit and resistance to Hessian Fly, Biotype L, do the following:

Leave the Active inventory only radio button on, since we want to order material.

Choose the <Scientific Name> push button.

If there are many genera in the system, you would first choose your genus. Since we have only Triticum in this sample data set, another pop-up automatically appears with a list of all the species for Triticum. See below:

Choose your species, aestivum

A new screen appears asking if you want to display the Crop Specific Descriptor List for WHEAT, as follows:

We want to see the list of descriptors, so we:

Choose <Yes>

The first screen of the Crop Specific Descriptor List for Triticum aestivum (wheat) looks like this:

The Descriptors display on successive screens and are ordered by the number you give each descriptor. If no number is assigned, the descriptors are displayed in the order in which you enter them. The number that orders them could be an IPGRI or any number you choose. The Descriptors display twice, first with their short descriptions and then in detail.

The first group of Descriptors in the list is the Characterization/Evaluation Descriptors from the Crop Specific Descriptor List, followed by the queriable Inventory Descriptors then the queriable Passport Descriptors.

At the bottom of each screen you see More? <Yes> <No> prompts which allow you to continue or stop the display. Choose <Yes> to continue the display or <No> to stop the display.

When you have seen enough of the various descriptors from the lists, at the More?: prompt:

Choose <No>, or press N

At this point, the Specify a descriptor prompt appears:

Your options vary.

1. You can type in the descriptor or your choice and choose <OK> or
2. You can type in one of the following words, or

• Help - Takes you to the explanation of the Descriptors for your Crop Descriptor List.
• Quit - returns you to the Main Menu.
• No - Takes you directly to your search.

      3. You can use the push buttons explained below:

  .

  • <OK> means type in a descriptor name, choose <OK> and you go to the Comparison Operator screen, or do not type anything and choose <OK> to complete your search.
  • <No> means you don’t want to add any further descriptors and will execute the query.
  • <Cancel> means you return to Select of the Main Menu.
  • <Char/Eval>means you see a pop-up of abbreviated Characterization/Evaluation descriptors. You then have two choices:

  Click on a descriptor to choose it, or

  Click on Exit to leave without choosing any

  • <Inv> shows you a pop-up of the abbreviated inventory descriptors. To pick one,

  Click on an item, or

  Click on Exit to leave without choosing any

  • <Passport> shows a pop-up of abbreviated passport descriptors from which you can query. To pick one,

  Click on an item, or

  Click on Exit to leave without choosing any

  • <Help> shows the crop descriptor list, followed by the inventory descriptors followed by the passport descriptors. You cannot make your choice from this list. If you choose <No> without limiting your request to any descriptors, the program will select all the accessions in the database.

  Back to our example: You are a wheat breeder interested in Triticum aestivum with a winter habit and resistance to Hessian Fly, Biotype L.

  Choose the push button <Char/Eval>

  

  When you see the descriptor you want, click on it, or arrow to it and press <Enter>. At this point, using our example:

  Choose HABIT

  After specifying the descriptor, the comparison operator screen appears, see below.

  

  The Comparison Operator screen provides a brief message at the bottom of the screen explaining the operator. For help understanding the descriptor Habit:

  Click on Help, or press H <Enter>

  The help screen then appears for HABIT, see below :

  

  When you finish with help and want to return to the Comparison Operator screen,

  Choose <OK>

  In our example of selecting wheat with a winter habit, after returning to the comparison operator list:

  

  Choose =

  The next screen displays your specified descriptor and operator, and asks the following. "Select accessions where HABIT is EQUAL to ______________________"

  

  If this descriptor contains coded values that you can choose from, you can use the <Values> push button to get the list. If there are no coded values, the <Values> button does not appear. To select for winter habit:

  Type W, or
  Choose <Values>
  Choose W
  Choose <OK>

  The next screen asks if you want another descriptor.

  

  We want to select further for Hessian fly resistance, Biotype L. To do so:

  Type HESSIANFLY
  Choose <OK>

  Because Hessian Fly is one of the descriptors that has a qualifier, a special screen for qualifiers appears, see below:

  

  Choose Biotype L

  You will then be asked for a comparison operator.

  For assistance, choose HELP

  The Help screen on Hessian Fly is below:

  

  Click <No>, when you are finished viewing, and the comparison operator screen reappears.

  We want resistance to be better than 5; to select this, follow these steps:

  Click <, or move the arrow key to highlight < and press <Enter>.

  The next screen appears, asking specific values to go with the comparison operator:

  

  Type 5 on the line.
  Choose <OK>

  The following screen shows your selection and asks if you want to include another descriptor: Habit = W, Hessian Fly, Biotype L, with resistance better than 5. See below:

  Using a Mask You can save these selection criteria to be used again in a Mask. The reason for using a Mask is to save the set of query criteria into a file that can be used repeatedly in the future. This reduces the amount of time entering the same criteria. This is especially useful when you use a query often, such as producing weekly/monthly reports. The button for saving a Mask, is labeled <Save Mask>. Let’s save this as a Mask.

  Choose <Save Mask> .

  A new screen pops up with information on how to do this. Notice that it overlays the original screen, so that you still see some of the descriptors. See below:

  

  You need to give a name to your query. Use something that will help you remember what the query is. You are limited to eight characters. For our example, we chose: WHHESL. This represents Wheat, Habit, Hessian Fly, Biotype L.Type WHHESL into the field and choose <Yes> to complete creation of the Mask. Now whenever you choose Triticum aestivum, you are asked if you want to use a Mask. If you choose to do so, the following screen would appear and asks which Mask you want to use:

  

  Choose this mask if you want to do the same query

  Modifying a Mask

  When you want to add to a Mask or change it in some way, you can overwrite the existing file with any Descriptors you want, but you cannot add (append) to a Mask that already exists. This prevents you from mistakenly adding pepper Descriptors to tomato Descriptors.You can change a Mask one of two ways:

  Begin using the Mask and add Descriptors to it. To save the new Mask, overwrite the existing file.

  Begin a new query. When you finish adding Descriptors, save the Mask using the name of the Mask you want to change and overwrite the existing file. This destroys the old file.

  Now, let’s go back to our query. The screen below is in view after the Mask operation is done:

  

  You can either add more Descriptors or conduct the search. Since we have selected all our criteria, we want to begin the search.

  Choose <No>, you do not want to specify another descriptor.

  Your search begins. A counter on the screen shows you how many Accessions match your search criteria. If you are looking for only a few Accessions and the counter shows that you have already selected some, press <Esc>.This stops the search and allows you to look at the Accessions already found. However, you can let the search continue until all the Accessions have been found. Your results look something like the following:

  

  Refine

  Once you have made a preliminary query of the database using Define, you may want to narrow your search further using Refine. The Refine option looks for accession data from the already-selected data file that fulfill the new additional criteria you select.Using Refine also helps speed up your search. When you put many criteria into Define or Refine, the search is very slow. It is best to put only a few criteria into Define and follow it up with single-criterion searches in Refine. With Refine, you choose new selection criteria without having to reenter the previous search criteria. You could also save your first set of criteria as a Mask, then bring the Mask back and add more search criteria to it. To use Refine, you must have first used Define to make a database query. To begin, return to the Select menu. Your choices now are: Define, Refine, Output, and Exit.

  Choose Refine

  The next screen asks you to Specify Another Descriptor: and shows you what has already been chosen.

  

  Suppose you, the wheat breeder, now want to find a plant that has white kernels as well. At the Specify another descriptor: prompt

  Choose <Char/Eval>

  Choose, in the list of descriptors, KERNELCOL

  You are now at the Comparison Operator screen for kernel color. For a description of kernel color:

  Choose help

  This screen appears:

  

  White kernel color is coded as number 8.

  Choose <OK> to return to the comparison operator screen.
  Choose = on the operator screen
  Type 8, and
  Choose <OK>

  You are now back at the Specify another descriptor: prompt. Since we don’t want to search for any other criteria at this time, don’t add anything more.

  Choose <No>

  You can stop the search in Refine, if you feel the counter has shown a desirable number of accessions selected, by pressing <Esc> when given the choice.You, as the wheat breeder, have now selected 10 Triticum aestivum accessions from the database, resistant to Hessian Fly Biotype L, with a winter habit and white kernels.

  Output

  The Output area allows you to see the data from your chosen accessions. To get to this area, from the Main Menu:

  Choose Select
  Choose Output

  A new pop-up appears with several choices:

  

  The upper line in the above screen, beginning with the word Display, allows you to select the format for the presentation of your data. The lower line, beginning with the word Default lets you determine the amount and kind of data you want to see.

  Type of Output

  With pcGRIN, you can manipulate your data for presentation four ways:

  • Default Data
  • Custom Data
  • All Data
  • Label Data (This is for the Management Version)
  Default Data Uses the Currently Selected Fields

  This choice provides:

  • quick results
  • only the data specified by your search criteria
  • the accession identifier(s)
  • the known taxonomy
    • family
    • genus
    • species

  Customized Data

  This choice provides:

  • all the information presented in Default Data, plus
  • the ability to modify your view of the accessions by:
    • adding descriptors
    • deleting descriptors
  • menu screens to walk you through the process

  Detailed instructions for Custom Data

  When you choose Custom, a new screen appears with the list of available descriptors that you can add or delete from your output. Addition and deletion of fields are two separate operations. You can only perform one operation at a time, and must re-enter the custom add/delete screen each time you wish to switch to the other operation.

  Note: You cannot go into the right window to Delete once you are in the left window until you exit the left window, and vice versa.

  Let’s start at the Output Selected Data screen.

  Choose Custom
  Choose <OK>

  The following screen appears:

  

  Adding a Field

  To add a field to your data, work in the left window:

  Choose <Insert> to enter the left window
  Or press the <Insert> key on your keyboard
  Or press the letter I
  Or position the cursor in the left window and press the Leftmouse button

  Once inside the left window, you can choose other available fields,

  Choose the field(s) you want to include
  When you finish adding, choose <End> or the Rightmouse button

  You are now returned to the main screen and can either add more fields or delete some fields. To do so, you must enter one of the windows by choosing <Insert> or <Delete>.

  Deleting a Field

  To delete a field from your output, you first enter the right window. To enter this window:

  Click <Delete> with the Leftmouse button to enter the right window, or
  Press the <Delete> key on your keyboard, or
  Press the letter D, or
  Position the cursor in the right window and press the <Leftmouse> button

  Once inside the right window:

  Choose the fields you want to delete
  When you finish deleting, press <End> or the <Rightmouse> button

  When you finish adding and removing fields:

  Choose <OK>, or
  Press <Ctrl><End>

  All the Data

  This choice provides:

  • A detailed view of all the key fields for your accessions
  • A way to compare your choices better by looking at all the passport, character/evaluation data that’s available

  Note: Export All does not export every field in the pcGRIN data dictionary. It contains only the fields that you see in the Custom area.

  Labels

  This choice is left over from the Management Package.  It provides you storage labels with the following information:

  • Accession identifier
  • Taxonomy
  • Cultivar name
  • Inventory number
  Your labels appear for each accession. Remember, you will only get labels for active inventory if that is what you chose on the bottom of the first Define or Refine screen. You can get labels for all your inventory if on the bottom of the Define or Refine screen you click on the radio button Use all available inventory.

  Format of Output

  If you look at the upper line of the Output Selected Data screen, there are four formats to choose from when displaying your data.

  

  With pcGRIN, you can format your data for presentation four ways:

  1. Display data
  2. Print data
  3. Export data
  4. Text data

  Display Data
  If you choose to Display your results, they appear on your monitor, and nowhere else.

  Print Data
  If you choose to Print your results, they print out for you, and they appear on your screen.

  Export Data
  You can export the results of your Define or Refine to files outside the program for use in other PC database, spreadsheet, or word processing programs. Your accessions export to the following files:

  Text files

  These files are flat ASCII files that can be used as interchange files to load into other databases. These files are in "SDF" (space delimited format). The files that are created are:

  • Passport/evaluation data (PCGRIN.EXP)
  • Inventory data (IPCGRIN.EXP)
  • Cooperator data (CPCGRIN.EXP)

  xBASE-compatible DBF files

  These files can be used by any software that can handle DBF formats for the following types of data:

  • Passport/evaluation data (PCGRIN.DBF)
  • Inventory data (IPCGRIN.DBF)
  • Cooperator data (CPCGRIN.DBF)

  Without leaving the Export area of pcGRIN, you can press V to look at the pcGRIN xBASE File that the program creates for you.

  Definition File

  These files can be used to see how the table is defined for:

  • Passport/evaluation definition data (PCGRIN.DEF)
  • Inventory data definition file (IPCGRIN.DEF)
  • Cooperator data definition file (CPCGRIN.DEF)

  Text Data

  When you create this type of output, you can give the file that you assign a name of your choice. The screen guides you:

  If you choose a name that is already in your pcGRIN directory, you are told that it is already there and asked if you want to Overwrite (wipe out what is there and replace it with this file) or Append (add this file to the end of the file with the same name).

  

  Choose O or A
  Choose <Yes>

  You are then asked if you want to see the file you just created.

  

  If you look at the file, either in pcGRIN or outside of it, you will see that it is a straight text file that you can modify in any word processing or editing package.

  .

  Chapter 9. The Accession Query

  The Accession Query option allows you to retrieve Accession information quickly using only one criterion. Accession Query is different from Select Query, because Select Query allows you to use many criteria to get your results. The Accession Query results allow you to see the same information that you would see if you had used the Select Query. Here is a list of what you might see:

  • current taxonomy
  • place of collection
  • donor information
  • cultivar and/or local name(s)
  • collector or developer details
  • pedigree
  • quarantine status
  • other identifiers
  • inventory availability
  • characterization/evaluation data

  To begin using the Accession option, at the Main Menu:

  Choose Accession

  

  The upper portion of this screen shows examples of the different types of identifiers you can put onto the line under Type an identifier:. The identifiers you can use are:

  • primary identifier, such as PI number
  • secondary identifier, such as a donor number
  • local name
  • cultivar name
  • scientific name
  Common names, such as "Carrot," in this case, cannot be used.

  The lower portion of the screen shows the actual selection area. Type your identifier into the upper, shaded line of this area. Pressing <OK> without typing anything, retrieves all the Accessions in the database.

  Note: Your search takes place in the following order:

  1. pcGRIN looks through the Accession table for a match first.
  2. pcGRIN looks through Taxonomy for a match second.
  3. pcGRIN looks through the Secondary Identifiers for a match third.

  When querying the system, a complete or partial name can be used. The name can be entered in upper case, lower case, or a combination of cases. Suppose you are a wheat breeder looking for a cultivar. You cannot remember the exact way to spell the cultivar, but you are sure that it begins with the letter P. At the Type an identifier: prompt:

  Type P

  This search will select all the Secondary Identifiers that begin with the letter P, and it will pull all the Taxonomy that begins with the letter P. We don’t have any Taxonomy that begins with the letter P, so that will not cause any extra Accessions to be selected. This screen follows:

  

  As stated in the above screen, press any key to bring up the next screen:

  

  Note: When you choose an identifier that is part of the secondary identifier area, you search all the fields in the secondary identifier (cultivar name, donor number, collector number, institute number, local name, and other number).

  Move the cursor bar to select the accessions you are interested in and:

  Click the Leftmouse button on your choice, or arrow to your choice and press <F9>

  Choose all the accessions you want. To finalize your choice and display the Accession data:

  Press the Rightmouse button or <Ctrl><End>

  We are interested in Palmira 1 and Palmira 2. The first accession displays as follows when viewed in windows format:

  

   

  Chapter 10. The Taxonomy Query

  The Taxonomy Query provides all the taxonomic information in the database about a species and its associated accession data, if any. Typical displays include:

  • family name
  • complete scientific name and authority
  • common name
  • species synonyms
  • species citations (literature references)
  • protologue (original publication of the species)
  • species distribution
  • number of accessions for this species
  • order processing deduction and amount
  Using the Taxonomy Query

  To use the Taxonomy Query, at the Main Menu:

  Choose Taxonomy

  The first screen follows:

  

  This screen allows you to either type a species identifier or lets you choose from all the names in the system. To choose from all names, leave the species identifier blank and choose <OK>.

  There are three sections to this screen.

  1. The species identifier line.
  2. The place where you specify whether the identifier is a scientific or common name.
  3. The place to choose to go ahead with your selection or to leave the Taxonomy area.

  Working with a Scientific Name

  If you are selecting a Scientific Name, the identifier must be a proper scientific name or part of one, that is:

  • a genus name
  • a binomial (genus and species name)
  • a trinomial (genus, species, and varietal name)
  • a synonym

  You must choose the Scientific Name push button when using a scientific name.

  Common Name identifiers allow you to query the system using common names to begin your search. For example you could enter the common name wheat to begin your search rather than typing in the scientific name Triticum. You must choose the Common Name push button when starting your search with a common name.

  Any of the species identifiers may be entered in upper case, lower case, or a combination of cases, plus, you have to enter only the first few letters to pull all the species that begin with those letters. Some examples of what you can enter:

  Triticum
  Triticum aestivum
  Triticum dicoccon ssp. asiaticum
  T

  If you are unsure about the spelling of your identifier, leave the Enter a species identifier: line blank, choose either a Scientific Name or Common Name query and choose <OK>.

  Suppose you are a wheat breeder and wish to view all the species in Triticum, type:

  T
  Choose Scientific Name
  Choose <OK>

  The next screen lists the species names from which you can choose:

  

  Note: Synonyms are dim in the display and their correct name is highlighted. You cannot select synonyms here.

  Select the species you are interested in. In our example, we chose T. boeoticum

  This select operation is a toggle. You can deselect a species the same way you selected it if you mistakenly choose something you do not want. When you are finished choosing names:

  Press your Rightmouse button, or <Ctrl><End>

  Your taxonomic information appears. Notice that you also see the number of accessions for each taxon in addition to other taxonomic information, in the picture below:

  

  Note:You can see the accessions for the species you just chose by going directly to the Accession area.

  To see the accessions associated with this taxonomy, go from here to the Accession area, and the taxonomy is automatically on the shaded line labeled: Type an identifier:.

  To do so, from the Main Menu:
  Choose Accession

  In the screen below, notice the taxonomy is already in the field labeled Type an identifier:

  

  At this point, all you do to see your accessions is to choose <OK>.

  Chapter 11. The Statistics Query

  Statistics reports are located inside the Other Area. It is here that you create numerical summaries of accessions based on your species and country data.To get here from the Main Menu,

  Choose Other
  Choose Statistics

  After you choose Statistics the following is the next screen that you will see:

  

  It is from this screen that you choose one of four reports of the database on the following types of requests:

  1. A list of all the Species in your database
  2. A list of all the Countries of origin in your database
  3. A list of all the Species for specified country(s) of origin
  4. A list of all the Country(s) of origin for certain species

  Each time you do a search in the Statistics area, a file of the results is automatically created in your PCGRIN directory. The file is called STATS.TXT and can be viewed or printed from DOS. The next search in the Statistics area overwrites this search or any previous search. If you want to save one of your searches, you have to go to the DOS pcGRIN directory and change the name.

  Species Report

  This option provides you with a Species report. How many accessions do you have for the Species you are interested in. When you choose Species, a new screen asks you for details:

  

  The above screen asks you to type in a complete or partial species name. If you type only the first letter of the species name, you get a listing of all of the species in the system that begin with that letter. If you leave this line blank and choose <OK>, you get a listing of all the species in the system.

  To save your results to a printer, in addition to seeing them in the monitor, in the field labeled Send output to the printer?:

  Type Y, Yes, or touch the space bar until Yes is listed

  Suppose you are a wheat breeder looking for the number of accessions in the Triticum durum species in the database. Into the field labeled Type the species or first few characters (<Enter>=ALL):

  Type Triticum d

  Your results automatically appear on the screen as seen below:

  

  There are 1,365 Triticum durum accessions in the database.

  Country of Origin Report

  The Country of Origin provides the names of countries in your database and the total number of accessions for each country you are interested in.

  

  To execute a query here, type the complete or partial country name in the space provided. If you want to search for information on all the countries in the database, leave the space blank and choose <Enter>. That is what we will do.On the line that says Type the country or first few characters (<Enter>=ALL):,

  Press <Enter>

  The first screen of your results looks like the following:

  

   

  Species for Country of Origin Report

  This report lets you see how many species you have for each country, and the number of accessions for each of those species. When you choose this option, you are asked two questions.

  Type the country or first few characters (<Enter>=ALL): ______________
  Type the species or first few characters (<Enter>=ALL): ______________

  Suppose you are a wheat breeder and want to know how many Triticum accessions you have from Ethiopia.

  On the first line type Ethiopia
  On the second line type Triticum

  Your results look like the following:

  

   

  Country of Origin for Species Report

  This report lets you determine the number of countries of origin you have for a certain species and how many accessions you have for each species.

  Suppose you want to know how many countries Triticum aestivum accessions are from and how many accessions are from each country. When you are asked your two questions:

  Type the species or first few characters (<Enter>=ALL):
  Type the country or first few characters (<Enter>=ALL):

  On the first line type Triticum aestivum
  Leave the second line blank

  Your results would be the following screen:

  

  Triticum aestivum came from at least 80 countries for a total of 6,880 accessions.