2. Concepts

Data Concepts
Software Concepts

Chapter 6. Data Concepts

Among the different groups of data that can be linked to each accession in pcGRIN, five of them—Descriptors, Taxonomy, Geography—have concepts that are explained in detail in this chapter.

Descriptors

Descriptors are used throughout the pcGRIN system to provide information on the accessions. Some descriptors are a permanent part of the system and cannot be changed, and some of them can be created and modified by you.

The various descriptors in the system can be organized into three groups:

• Passport Descriptors
• Characterization/Evaluation Descriptors
• Inventory Descriptors (Standard and Additional Inventory Descriptors)

Passport Descriptors

All accessions in the pcGRIN database are described by the same set of Passport descriptors. These descriptors don’t depend on crop information. They usually include the information received with the accession at the time it’s added to the plant collection, such as:

• Accession identifier (Primary identifier)
• Taxonomy Secondary identifiers
• Cultivar name
• Donor or collector or developer information
• Source information
• Pedigree

An explanation of these identifiers and their format is given below.

Accession identifier (Primary identifier)

The Accession identifier is the main identifier for the accession. It is also known as the primary identifier. It is assigned to the plant material (accession) when it first enters a genebank. It must be a unique identifier that consists of at least two parts, a prefix and a number. It may consist of three parts, a prefix, a number, and a suffix. The type and number of characters for the three parts are:

1. a prefix (up to 4 characters)
2. a number (up to 7 digits)
3. a suffix (up to 4 characters)

At least one space separates each Accession identifier part.

When you are querying pcGRIN, you can enter the prefix in upper or lower case. If you know only the number and not the prefix, you can still find your accession. However, if you know only the prefix, you cannot find your accession. Some examples of Accession identifiers are:

PI 500000
CIav 9401

Taxonomic name

The taxonomic name is the scientific name of the material. It consists of one of the following:

Cultivar name

This is the name of the cultivated variety. It does not have to be unique within the system.

Inventory identifier

The Inventory identifier can indicate the type of material that is stored and is closely tied to the accession. Inventory can be for either seed or clonal material.

Seed Inventory

In seed material, the Inventory identifier is the Regeneration Date. You can have more than one inventory sample for each accession, each identified by its own Regeneration Date. The same Regeneration Date can be used for different Accessions, since each one is tied to the accession identifier. It is easy to determine which accession each sample belongs to.

Clonal Inventory

In clonal material, the identifier for the sample is composed of 10 characters or less.

Secondary identifier

The secondary identifier is a term used to consolidate all identifiers except for the primary identifier, the inventory identifier, and the taxonomic identifier. It contains a string of letters and/or numbers that can be up to 30 characters long. These identifiers are typically:

• collector numbers
• donor numbers
• local names
• cultivar names
• crop registry numbers
• other institute's identifiers

List of Passport Descriptors

Certain Passport Descriptors can be searched for in pcGRIN. They are grouped together for ease of use into the topic Passport Descriptors on the search screens. A complete set of searchable descriptors is given below and is also seen when you click on the button labeled <Passport Descriptors> in the Select area screens:

Passport Descriptor and its Short Definition

• ACELLO means Elevation
• ACNO means ID Number
• ACP means ID Prefix
• ACS means ID Suffix
• ACYCOL means Year Collected
• COLLSRC means Source of collected material
• COLL_NUM means Collector Number
• CULTIVAR means Cultivar Name
• EVQNAM means Environment Name
• GEOCTY means Country Name
• GEOSTA means State/Province Name
• LAT means Latitude (decimal notation)
• LNAME means Last name of a cooperator
• LOCAL_NAME means Local Name
• LON means Longitude (decimal notation)
• ORG means Institute or organization of a cooperator
• RYPIA means Year PI number assigned
• RYRECD means Year received
• SAMPSTAT means Status of accession
• SIDID means Secondary ID

Characterization/Evaluation Descriptors (Crop Descriptors)

These descriptors refer to physiological or morphological traits that are evaluated for a specific crop. Descriptors consist of a name, sometimes an identifying number, a definition, and a descriptor state or values (sometimes a range of values). If you use a number, such as an IPGRI number, the Descriptors will sort, in ascending order, according to this number.

Both Characterization and Evaluation Descriptors are grouped into one area in pcGRIN.

Characterization Descriptors are inherited and do not change with the environment. In general, these Descriptors are easily seen with your eye. Some examples of these descriptors are:

• Leaf shape
• Flower color
• Plant habit
• Seed color
• Chromosome number

Evaluation Descriptors are those descriptors that vary with environmental conditions. They change from one location to another. Some examples of these descriptors are:

• Plant height
• Days to maturity
• Protein percent
• Disease resistanceYield

Descriptor Qualifiers

Occasionally one of the Descriptors is further differentiated by a qualifier. These qualifiers are used mainly to distinguish between different reactions to races or biotypes of a pathogen or pest to which the descriptor applies. An example of a Descriptor Qualifier is given for the wheat descriptor Hessian Fly, as this screen shows:

Crop Descriptor Lists

A Crop Descriptor List is a grouping of Characterization/Evaluation Descriptors by crop or group of related species. Each Descriptor List contains one or more Crop Descriptor(s). Some examples of Crop Descriptor Lists are Wheat, Peppers, Maize. IPGRI has its own lists of crop descriptors. Each species should be part of only one Descriptor List.

Inventory Descriptors

These descriptors define your inventory. Certain Inventory Descriptors are a permanent part of the inventory descriptor list and are defined below:

• ACTIVE means part of the Seed/Clonal inventory distributable sample
• CLONE_ID means this is a Clonal inventory identifier
• HARV_YEAR means the Seed inventory regeneration date
• LAST_GERM means the Seed inventory date of last germination
• LOCATION means the Inventory location
• NUMREGEN means the regeneration number for the inventory sample
• ONHAND mean how much seed inventory quantity available
• UNITS means the Units for grass, seeds, buds, etc.

  Taxonomy

  The Taxonomy area provides all the taxonomic information about a species and its associated Accession data, if any. This includes data that is consistent for the species as a whole. Typical displays include of the taxonomy include:

  • Family name
  • Complete scientific name and authority
  • Common name
  • Species citations
  • Species synonyms
  • Literature references
  • Species distribution (in the query only version)

  In addition to the nomenclature information above, pcGRIN taxonomy also includes the following:

  • Number of accessions for this species
  • Crop descriptor list
  • Order processing deduction and amount

    Geography

    The Geography area contains the country and state/provinces used in pcGRIN for the origin of an accession, for a cooperator’s address, etc. Country names are from the International Organization for Standardization (ISO). There are also some historical country names preserved in for country name changes.

    Sorts

    Before we can discuss sorts, you need to know that pcGRIN stores data four ways:

  1. Numeric - with only numbers allowed
  2. Characters - with alphanumeric characters
  3. Date - with year month and day in numeric digits
  4. Coded - with alphanumeric characters.

There are two types of sorts in pcGRIN based on the data type.

Numeric and Date Field Sorts: When you do a search on a numeric field, the answers sort based on the first unit of each piece of data, then on the first and second units, and so on in the following way: 1, 2, 3, 12, 14, 24, 100.

Character and Coded Field Sorts: These types of fields sort on the first unit, then on the second unit, then on the third unit, etc. When you do a sort in one of these fields, the same numbers as above, appear in this order: 1, 12, 14, 100, 2, 24, 3.

This explanation is provided to make you aware that coded data is often represented with numerical values (for example, 1 = sweet, 9 = hot). These numeric values sort based on character data type and, therefore, may not appear as you expect.

Chapter 7. Software Concepts

Comparison Operators

When you query pcGRIN for descriptor traits with multiple values, a comparison operator screen appears. This screen allows you to select only those traits that interest you.

List of Comparison Operators

The Comparison Operator screen helps select options when you query the system. The screen looks like the following:

In this example, the first comparison operator, =, is highlighted and its definition appears at the bottom of this screen. When you move the cursor bar to other comparison operators, an explanation for them is also seen at the bottom of the screen. A complete set of the operators and their descriptions are given below:

• "=" means to select information EQUAL to a specified value
• "=+" means to display and select information equal to multiple values selected from a table that shows the number of accessions for each value
• "<>" means to select information NOT EQUAL to a specified value
• "<" means to select information LESS THAN a specified value
• "<=" means to select information LESS THAN or EQUAL to a specified value
• ">" means to select information GREATER THAN a specified value
• ">=" means to select information GREATER THAN or EQUAL to a specified value
• "ALL" means to select ALL information associated with the descriptor
• "CN" means to select information CONTAINING a specified value (works only in non-numeric fields)
• "BT" means to select information falling BETWEEN two specified values
• "HELP" means to display a help screen with information or available codes

The =+ Explanation

This is a special comparison operator that provides more detailed information and choices than the other operators, such as:

• The option to choose more than one specific value
• A total number of accessions in the system that have these values.

Example

Suppose we are looking for wheat with winter habit and spring habit. Look at the descriptor called HABIT, and

Choose the operator =+, and the following screen appears:

You see that winter habit has 3561 accessions, and that spring habit has 2797 accessions. You can choose both of these by arrowing to each and pressing the <Enter> key or the Leftmouse button on each one. <Ctrl><End> or the Rightmouse button completes your selection.

The Eval Values section of the screen cannot always show all the codes at once. You may have to scroll to see all your options.

Masks

A Mask allows you to create—and save for future use—a subset of Descriptors selected out of the entire group of descriptors. This saves the time it would take to select these criteria again.

Query Masks

When you make a Query in the Select area, you define the values you wish to be included in your search. If you then create a Mask based on these search criteria, they’re saved to a file. When you recall this Mask file, the saved set of values can then be used to make a new Query with your predetermined criteria. Using the Query Mask you can create and save as many Mask files as you would like. Specific instructions for using Query Masks are located in Chapter 9, The Select Query.

Dates

The date format can be set at either:

    dd/mm/yyyy or mm/dd/yyyy

Make your choice in the Preferences area.