Brazilian Agricultural Research Corporation
Ministry of Agriculture, Livestock and Food Supply

United States Department of Agriculture
Agricultural Research Service
National Laboratory for Genetic Resources Preservation  

Animal GRIN Database User Manual for the
Management of Genetic Resources

Carrie S. Wilson

Samuel Rezende Paiva

Patrícia Ianella

Theodore J. Manahan

Eduardo Vaz de Mello Cajueiro

Arthur da Silva Mariante

Harvey Blackburn

Embrapa
Brasília, DF
2016

Copies are available at:

Brazilian Agricultural Research Corporation

Parque Estação Biológica (PqEB)

Av. W3 Norte (final), CEP 70770-901 Brasília, DF, Brazil

Phone: +55 (61) 3448-4433 | Fax: +55 (61) 3448-4890

www.embrapa.br | www.embrapa.br/fale-conosco/sac

United States Department of Agriculture

Agricultural Research Service

National Laboratory for Genetic Resources Preservation

1111 South Mason Street,

Fort Collins, Colorado 80521, USA

Embrapa Technological Information

Parque Estação Biológica (PqEB)

Av. W3 Norte (final)

70770-901 Brasília, DF, Brazil

Phone: + 55 (61) 3448-4236 | Fax: + 55 (61) 3448-2494

www.embrapa.br/livraria | livraria@embrapa.br

Institutions responsible for the content

Brazilian Agricultural Research Corporation (Embrapa)

Agricultural Research Service

Unity responsible for editing

Embrapa Technological Information

Editorial coordination: Selma Lúcia Lira Beltrão, Lucilene Maria de Andrade, Nilda Maria da Cunha Sette

Editorial supervision: Wyviane Carlos Lima Vidal

E-book proofreading: Maria Cristina Ramos Jubé

Graphic design and desktop publishing: Alexandre Abrantes Cotta de Mello

Cover image: Samuel Rezende Paiva, Carrie Wilson (word cloud generate by wordle available at http://www.wordle.net/)

Cover: Alexandre Abrantes Cotta de Mello

1st edition

E-book (2016)

Use of commercial and trade names does not imply approval or constitute endorsement by U.S. Department of Agriculture (USDA). 

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Any unauthorized reproduction of this publication, in whole or in part, constitutes copyright infringement (Law n. 9,610).

International Cataloging in Publication (CIP)

Embrapa Technological Information

Animal GRIN database user manual for the management of genetic resources / Carrie S. Wilson … [et al.]. – Brasília, DF : Embrapa, 2016.

E-book in ePub format.

ISBN 978-85-7035-593-5

1. Genetic resource management. 2. Animal genetic resources. 3. Food security. 4. Economic growth. I. Wilson, Carrie S. II. Genetic Resources Information Network.

CDD 636.0821

© Embrapa 2016

Authors

Carrie S. Wilson

Animal Scientist, M.S. in Animal Science, Support Scientist at USDA-ARS National Animal Germplasm Program, Fort Collins, Colorado, USA

Samuel Rezende Paiva

Biological Scientist, PhD in Genetics and Animal Breeding, researcher at Embrapa Labex USA

Patrícia Ianella

Biological scientist, PhD in Molecular Biology, researcher at Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil

Theodore J. Manahan

Information Technology specialist, M.S. in Computer Engineering and Forest Sciences, Colorado State University, Fort Collins, Colorado, USA

Eduardo Vaz de Mello Cajueiro

Information Technology Specialist, M.S. in System Engineering and Computing, analyst at Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil

Arthur da Silva Mariante

Agricultural scientist, PhD in Animal Science, researcher at Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil

Harvey Blackburn

Animal scientist, PhD in Animal Genetics, researcher at USDA-ARS National Animal Germplasm Program, Fort Collins, Colorado, USA

Foreword

This User’s guide to Animal GRIN (Alelo Animal in Portuguese) is intended to contribute to solving one of today’s most critical animal agriculture dilemmas: how to better manage animal genetic resources to insure food security and economic growth of livestock sectors. The User’s guide and the Internet based information system it represents are a unique collaboration between the Agricultural Research Service (ARS) of the United States Department of Agriculture (USDA) and the Brazilian Agricultural Research Corporation (Embrapa), linked to the Ministry of Agriculture, Livestock and Food Supply (MAPA). It symbolizes 10 years of interaction between the two countries’ national programs for genetic resource management and utilization. Beyond enriching the experiences and expertise of both countries’ programs, it serves as a global example of successful collaboration encouraged by the Interlaken Declaration on Animal Genetic Resources in 2007.

This User’s guide and the Internet based Animal GRIN provide great opportunity to deepen the understanding of genetic resources and how it may be organized to meet the needs of humankind. We believe that the tool described herein will not only attend the purposes of the two countries, but will also enable other countries to better understand the conservation and use of their animal genetic resources.

Ibrahim Shaqir
Director Office of International Research Programs (USDA-ARS)
José Manoel Cabral de Sousa Dias
Director Embrapa Genetic Resources & Biotechnology

Steven Kappes
Office of International Research Programs (USDA-ARS)
Ladislau Martin Neto
Executive Director of Research & Development Embrapa

Introduction to Animal GRIN

As animal genebanks are initiated, they all have the common need to manage information about their country’s genetic resources. The Agricultural Research Service (ARS), research Agency of United States Department of Agriculture (USDA) had developed a first version of such a database, called Animal GRIN (Genetic Resources Information Network) in 2001 and it became apparent there were needs for improvement. In 2006, as the result of close collaborations already in place with Brazil (Embrapa – Brazilian Agricultural Research Corporation), Canada (Agri Food Canada), and the American Livestock Breeds Conservancy (now The Livestock Conservancy), it was decided to initiate a joint venture to develop the next version of the database. This is the first time three countries have become partners to build a common database for animal genetic resources (AnGR). We believe the platform will also have utility for other countries that want to better manage their AnGR. This platform will keep their name in English as Animal GRIN v.2 and it will be reconized as “Alelo Animal” in Brazil.

It is important to mention that the system is being developed in a customized way, to meet each country’s needs. For example, the U.S. program (National Animal Germplasm Program, NAGP) does not include in situ conservation; hence, a live animal database was not part of the initial version of the database. This was included in version 2 in order to allow Brazil (Embrapa) to document the animal genetic resources being kept in their Research Centers.

The database can be viewed via public reports, providing real-time access. Those reports allow anyone to view the collection within each of the three countries and throughout the world. The reports are point and click, with no prior knowledge of the database required. AnGR management tools allow us to evaluate the genetic diversity collected and assess what needs to be added to the collection, compare countries’ collections of the same breed and understand how they may be genetically similar or dissimilar, and develop tools that assist with in-situ conservation activities.

In conclusion, this database would most certainly not be ready for use today if it were not for the partnership and cooperation of these three countries and the collective database team.

Information System

An information System is made up of software, hardware, data, people, and procedures. A graphical view of how Animal GRIN is managed is shown below (Figure 1).

Figure 1. Graphical representation of Animal GRIN information system.

The User Manual

This manual serves as a reference tool for database users. This guide details how to go from an empty database to a populated database. For an existing database, it provides instructions to users about each form as well as the steps to create an incoming shipment, fulfill an outgoing request, or generate a report.

The manual is meant to be referenced as you navigate the database; it is not intended to be read from cover to cover. The figure below provides a logical flow for super users and users to use the manual to navigate through the database. Super user status is usually limited to the data manager(s) and includes the additional responsibilities of managing codes, taxonomies, location structure, and users. User status includes creating, updating, and deleting any other data in the database within your location.

Once you have used the user manual to assist you to log in and navigate through the menus, enter a shipment, enter a request, and pull reports, you will have had exposure to the majority of the database. Then, for reference, each form is listed in the Form Descriptions (modules 3 and 4). For each form, the purpose, underlying tables, related forms, and a description of each field are provided.

A description of each module in the user manual is provided in the Figure 2 and Table 1. The next topics in this chapter we will try to introduce basic concepts to understand the organization of Animal GRIN database.

Figure 2. Flow chart for using the Animal GRIN user manual for all users (blue) and super users (purple).

Table 1. Animal GRIN user manual module description.

Relational Database

The Animal GRIN database is a web-accessible relational database, which is made up of 56 tables that are linked together via IDs called keys. Tables have both primary (required) and foreign (required or optional) keys. Having the tables linked together allows the database to efficiently store, retrieve, and assemble information. The database tables consist of columns (fields or attributes) and rows (records). Then, structured query language (SQL) is used to link the tables together using their IDs to extract the information in a form that the user can use. Data entry pages referred to as forms are provided to allow the user to enter the data in a more user-friendly format that can populate more than one table at a time.

The underlying database is MySQL, and the web component is built using the programming language Ruby on Rails. Both MySQL (https://www.mysql.com/) and Ruby on Rails (http://rubyonrails.org/) are freely available, open source software packages.

The advantage of a relational database over a flat data storage format (Excel) is that redundant data is eliminated. For example, an animal stored in Excel might look like:

The equivalent data in a relational database would be:

Animal Table

Animal ID | Gender | Date of Birth | Breeder ID
1 | M | 9/17/2000 | 1
2 | M | 5/4/2009 | 2
3 | M | 12/31/2004 | 3
4 | M | 1/1/2008 | 1

Identifications Table

ID | Animal ID | ID Type | Identification
1 | 1 | 1 | 123456
2 | 1 | 2 | Bob
3 | 2 | 1 | 34567
4 | 2 | 2 | Jim
5 | 2 | 3 | 343
6 | 3 | 1 | 654908
7 | 4 | 3 | 456
8 | 1 | 1 | 876543
9 | 4 | 2 | Tom
10 | 4 | 3 | 654

Identifications Type Table

Identifications ID | Identifications Type
1 | Registration Number
2 | Name
3 | Number

Breeder Table

Breeder ID | Breeder
1 | Joe Jones
2 | Jim Black
3 | Jack Smith

Although the tables look like they contain more information than the spreadsheet, they are storing the same data. However, the tables are more efficient. If ‘Joe Jones’ needs to be changed to ‘Joe and Anna Jones’, the update would occur in one place in the database instead of searching and replacing throughout a spreadsheet. If an animal had more than one identification within a category (registration number, for example), the spreadsheet could only accommodate this by adding another column for every animal in the spreadsheet. The database does not have this issue and can accommodate multiple identifications within a category.

Entity-Relationship Diagram

An overall entity-relationship (ER) diagram of the database tables is shown in Figure 3 below. Although the table details are too small to see, the purpose of showing the relationship among all the tables is to show the complexity of the database in its entirety.

Figure 3. Overall entity relationship diagram for Animal GRIN.

Parent-Child Relationship

Several areas of the database are based on a parent-child relationship structure. The most obvious one to Super Users (users with the second most hight access) is with the taxonomy structure. In a parent-child relationship, in database terms, a child has 0 or 1 parents, but a parent can have many children. As depicted below (Figure 4), the Family Bovidae is a parent to genera Ovis and Bos. For sheep, Ovis is the parent to the species Ovis aries, which, in turn, is the parent to the breeds Suffolk and Tunis. A similar path can be traced for Bovidae Bos taurus and Bovidae Bos indicus. Understanding how this relationship works will be helpful when creating taxonomy records.

Figure 4. Example of a parent-child relationship data structure in the Animal GRIN taxonomy Table.

Navigating the Database

This module provides an overview of how to access the database and use the menus to move between forms in the database.

Accessing the Database

The database is optimized for use with Mozilla Firefox and this manual describes the database using this web browser. The latest version can be downloaded from: http://www.mozilla.org/en-US/firefox/new/. The database can be accessed at: http://nrrc.ars.usda.gov/A-GRIN.

Tip: Add this location to your web browser Favorites for future access.

The initial screen you will see is:

Click on Member Access area.

Enter your User ID (usually firstname.lastname) and password.

Contact your Database Administrator if you do not have a login and password.

This takes you to the Main Menu screen.

On the left side of the screen, you can see who is logged into the database and the country the records will be recorded for.

You can click on Edit Profile to change your password, update your email address, or control the number of search results you would like to see on a screen.

From the Main Menu left side of the screen, you can use the Signout link to exit the database.

Main Menu Navigation

The Main Menu groups forms based on how they will be used.

The Administration Area is visible only to Super Users and Administrators.

These forms relate to the creation of agreements, rules, codes, and users.

The Animal Area is a grouping of forms about individual animals, including Animal, Image, Observation, and Coefficient of Relationship.

The Full Menu link lists all forms alphabetically.

The Incoming Order area shows the forms associated with a shipment that was received into the repository.

The Loader link displays forms that can be used to load data files into the database without manual data entry.

Current loader forms available include Animal Observation, Inventory Observation (CASA), Coefficient of Relationship, and Pedigree.

The Public Area provides a link to the publicly available web pages, which can also be accessed from: http://nrrc.ars.usda.gov/A-GRIN/database_collaboration_page

Tip: You might want to Bookmark this one, too.

Reports are broken down into Manager Reports and User Reports.

Any report can be accessed by different user types (Administrator, User, etc.).

Manager Reports are designed to provide some overall picture of the collection at a point in time whereas the User Reports are designed to help the user find information to help with the data entry process.

The Request Area links to forms relating to shipments of material from the repository.

Left Side Bar Navigation

Each form has a left side bar designed to help the user access other needed forms without the need to return to the Main Menu.

Each left side bar also provides an option to return to the Main Menu and a link to Page Help.

The forms accessible from the left side bar are dependent upon the current form you are in. Below is an example from the Animal Search form:

Setting Up the Database (Super Users)

This module provides information to help the Database Administrator move from an empty database to one that is ready for data entry.

Create Users

Log in and go to the Main Menu as described in Module 1.

Under the Administration Area, select Users.

You will see an unpopulated Users Search form.

An empty search does not apply any search criteria, therefore, returning all records. This is an easy way to see all of the user records.

You can do an empty search to see the users with access to the database. You do an empty search by leaving the search criteria field empty and clicking on the search button.

You can click on the Record Source column to sort by country. This will show you the users that have access to your database. Users from other countries do not have access to your data.

The Inactive column shows you if the existing users have been inactivated.

To create a new user, either click on the Create New Animal-Germplasm User link at the bottom of the form, or select Create DB User from the Quick Picks list.

Provide the username and password to the users and encourage them to change the password the first time they logon. They can use the Update Profile link in the upper left corner of the Main Menu to change their password.

Populate the fields. The standard naming convention for user name is firstname.lastname, but it can be whatever your organization has agreed upon.

Set the User grp field using the following definitions as a guideline:

Administrator: has the ability to add new users for other countries (this should be limited to 2 people in the entire system).

Super User: can create, update, delete, and view all records, including creating and updating users for their country, adding new database codes, creating new country and country subdivision records, and adding descriptors and descriptor codes (this should be limited to 1 or 2 people per country).

Users in Brazil are limited to records within their location and assigned taxonomy(ies).

User: can create, update, delete, and view all records, excluding creating and updating users for their country, the creation of new database codes, and adding descriptors and descriptor codes (this should be the majority of database users).

If you select the Inactive flag, the user will not be able to login. This flag is to keep the user associated with the records they created or modified after they are no longer users of the system.

Click on the Create button to save the record.

Click on Create DB User in the Quick Picks list to create the next user.

Click on Return to Main Menu once all users have been created.

Create Taxonomy Structure

From the Main Menu, select Full Menu, then Taxonomy located under the Super User Menu.

Start at the highest taxonomic level by creating a Family.

In the Category field (circled above), select Family.

To the right, enter the Taxonomy Name

At the Family level, that is probably the only field to enter; you could enter the Target Core Quantity, Common Name, and Purpose, if appropriate.

Click on Save and you will see a message at the top of the form stating the record was saved (circled below).

In the Enter Parent Taxonomy Structure section, select the Family that you created.

In the Taxonomy Level Information section, select Genus in the Category field.

To the right, enter the Taxonomy Name.

As with Family, this is probably the only field to enter; you could enter the Target Core Quantity, Common Name, and Purpose, if appropriate.

Click on Save and you will see a message at the top of the form stating the record was saved.

In the Enter Parent Taxonomy Structure section, select the Family in the first box and the Genus in the second box.

In the Taxonomy Level Information section, select Species in the Category field.

To the right, enter the Taxonomy Name.

Optionally, select the Web Classification for the species; this is used to categorize animals for the public web pages.

If there is a specific or standard format for identifications for the species, it can be added to the Sample Identification field. This field exists to help with consistency of formatting identifications during the data entry process.

If there is an abbreviation for the species that is written or printed on straws or vials, it can be entered in the Taxonomy Label Abbr field.

If there is a target amount of material to be placed into Core at the species level, it can be entered into the Target Core Qty field.

A description of the species can optionally be entered in the Description field.

One or more common names can be added to the Common Names area. The Add link allows for more than one common name and the DEL link allows the name to be deleted.

The purpose of the species can be selected from the drop down list in the Purpose section. For more than one purpose, click on the Add button and select an additional purpose or purposes. The DEL button can be used to delete the purpose. Purposes are automatically ranked in the order they are entered. You can rerank them by changing the number in the Rank field; the other purposes will automatically rerank.

Additional purposes can be added by Super Users from the Main Menu, Administration Area, Taxonomy Purpose form.

The taxonomy structure is not rigid; once the Family, Genus, and Species are entered, the remaining categories can be applied as appropriate for the species being entered.

Click on Save and you will see a message at the top of the In the Enter Parent Taxonomy Structure section, select the Family, Genus, and Species.

In the Taxonomy Level Information section, select the next taxonomy level in the Category field. The level is Breed in the example.

To the right, enter the Taxonomy Name.

The Web Classification is required at the Breed level, so the field is peach colored instead of the white optional fields.

The other fields can be filled in as described for the species level.

Click on Save and you will see a message at the top of the form stating the record was saved.

Additional taxonomic levels can be added (line, strain, etc.) as needed; follow the same steps as described above.

If you want to enter multiple breeds (or lines, varieties, etc.) with the same parent taxonomy, click on the NEW CHILD - press here to Copy the saved Taxonomy Structure link and the Enter Parent Taxonomy Structure will be populated with the last taxonomy structure that was used.

Continue to add taxonomy records as needed.

Set Up Location Structure

Before setting up the location structure, you want to make sure the location codes you want to use have already been created.

From the Main Menu, select Administration Area, then DB Codes.

In the Search Criteria field, enter the name of the location structure you want to create (ex.: Room or Tank or Pie), then click Search or hit Enter on your keyboard.

If the code exists, enter the next code and repeat the process.

If a code you want does not exist, click on the Create New button or select New DB Code form from the Quick Picks.

Use the DB Object drop down list to select locations.loc_level.

The list at the bottom of the form shows the existing codes; if your code is not there, enter it in the Code Name field with an optional Code Definition; click on Save.

The new code will be added to the list at the bottom of the form.

In the Quick Picks, select New DB Code form.

Use the DB Object drop down list to select locations.container_type.

The container type is the name of your location structure; one strategy is to give it the name of the lowest level you are going to create (ex.: Cane).

The list at the bottom of the form shows the existing codes; if your code is not there, enter it in the Code Name field with an optional Code Definition; click on Save.

The new code will be added to the list at the bottom of the form.

Once you have all of your location structure codes created, click on Return to Main Menu.

From the Main Menu, select Administration Area, then Location Structure Reference.

Select the Create New button at the bottom of the form or Create New Location Structure Ref from the Quick Picks list.

Select the Container Type from the drop down list.

Use the Level title drop down list to select the highest level of the location structure.

The Capacity field is optional and is where you can enter the maximum quantity of units that can be held at that level (ex: 10 units on a cane).

Leave the Parent loc structure field empty for the top level.

If this level is required, select the Required flag check box.

If there will be lower levels associated with the location structure, select the Sublevel flag check box.

Select the Create button to save the record.

Click on the Create New Location Structure Ref link from the Quick Picks.

Select the same Container Type.

In the Level title field, select the next highest level of the location structure (ex: if Building was highest, Tank might be next).

The Capacity field is optional as described above.

Use the drop down list for the Parent loc structure to select the higher location level (ex: Building).

Required flag and Sublevel flag are the same as described above.

Select Create to save the record.

Repeat the steps until you reach the lowest level of the location structure.

For the lowest level of the location structure, do not select the Sublevel flag.

Create as many location structure types as you need for the material you have in the repository. More can be added at any time, but only by Super Users and Administrators.

Descriptors

Since descriptor records are shared between countries, but taxonomy records are not, the descriptors you want to use need to be attached to the taxonomy records they apply to.

From the Main Menu, select Administration Area, then Descriptor Search.

There may be descriptors that you do not want to use; if you don’t attach taxonomy records to them, they won’t show up when you are entering observations.

Some descriptors appear multiple times. Looking at the descriptor definition and the minimum and maximum value will help you decide which taxonomies the descriptor applies to. For example, there are several Birth Weight descriptors, one for pigs, cattle, and small ruminants.

Select the highest level taxonomy that applies to the descriptor. For example, the same birth weight descriptor can be used across all cattle, so it can be attached to the Bovidae Bos level. A descriptor that is breed specific should be attached at the breed level so it doesn’t show up for observations that it doesn’t apply to.

You can go through the descriptor list and attach taxonomies using any strategy that makes sense to you, not necessarily the one presented here.

In the Descriptor Search, search for ANM in the Search Criteria to get a list of all animal descriptors. Then, click on the Descriptor Name heading to sort the results.

Click on UPD for the first descriptor, which is 21-day litter weight in this example.

At the bottom of the form, for Full Taxonomy Name, click on Add.

Click on the search pop-up popup button.

In the pop-up, enter sus scrofa in the Search Criteria (if the Sus scrofa taxonomy hasn’t been created yet, do that first).

Click on the Search button; select Suidae Sus scrofa from the Results section.

Click on OK and the pop-up will close and return to the Descriptor form.

If you have additional taxonomies to add, click on the Add button below the Full Taxonomy Name.

Click on the Update button to save the changes.

Click on Return to Search Results in the Quick Picks.

Continue for all Animal Descriptors, then repeat the process for Taxonomy Descriptors (search for TAX) and for Entity Descriptors (search for ENT).

Tip: For a descriptor that applies across cattle, sheep, and goats, such as Horn Status, you can select the Family Bovidae as the Full Taxonomy Name.

Data Consistency

As you are setting up the database for use, it is important to consider how to standardize the data entry process and how to relay that to all users.

The way the data is entered in the database will affect how the data is displayed on the public web pages.

For example, a list of Angus bulls where some have the name in all CAPS and some have an Initial Cap looks unprofessional.

The format of identifications will affect searching features and also matching of animals in the pedigree area.

For example, Holstein cattle registration numbers in the U.S. can be reported as HOUSA123456789, H123456789, HOUSA00000123456789, or 123456789. If a single identification strategy isn’t decided upon, the pedigree link between H123456789 and HOUSA00000123456789 will not be made, although it is referring to the same animal.

A database is not a place for every person to develop their own personal style; consistency is crucial.

Developing a formatting guide and distributing to all users before they begin entering data is a useful way to document ways to keep the data entry process consistent.

Form Descriptions (All Users)

This module provides information about each form in the database and how the forms relate to the database tables.

General Notes – All Forms

All forms have a Created By field, which is autopopulated by the database with the username of the person creating the record.

All forms have a Date Created field, which is autopopulated with the date the record was created.

All forms have a Record Source field, which is autopopulated with the country the user is logged in to.

All forms have a Modified By field, which is autopopulated only when an existing record is updated; only shows the username of the most recent modification.

All forms have a Date Modified field, which is autopopulated only when an existing record is updated; only shows the date of the most recent modification.

Agreement

Purpose: To document the details of a legal agreement between the repository and a contributor.

Tables populated by this form: agreement, allocation_rules, agr_notifications.

Other forms accessed from this form: entity search pop-up.

Fields

Entity Name – Required, use the search button to open the entity search pop-up and select the entity the agreement is with.

Agreement ID – automatically filled in by database.

Established Date – Required, can use calendar pop-up to select date or manually type in mm/dd/yyyy; this is the date an agreement started.

Amended Date – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy; this can be used to track the date an agreement was modified or renewed.

Termination Date – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy; this is the date the agreement ends. This date triggers the Agreement Notifications to let Super Users know the Agreement is about to expire so it can either be renewed or any restrictions on the material will expire.

Details – Required, text field to describe the agreement, limited to 2000 characters.

Document Number – Optional, text field to enter the agreement reference number, limited to 30 characters.

Document URL – Optional, text field to enter the web address of the agreement document, limited to 100 characters.

Repository Name – Required, automatically populated with the repository the user is associated with, but the entity search pop-up can be used to select another repository.

Save – Commits the data to the database.

Cancel – Exits the form without saving the data.

Once an agreement is saved, the new record is listed at the bottom of the form; clicking on update (UPD) in the Action column allows you to enter Allocation Rules associated with the agreement.

Fields.

The form automatically populates the Agreement ID and Germplasm Owner fields with the data from the agreement.

Although the Germplasm Owner is populated on the form, Incoming Order ID, Animal, or Taxonomy could be selected instead, if that is appropriate for the agreement.

Rule ID – Automatically populated by the database.

Effective Date – Required, can use calendar pop-up to select date or manually type in mm/dd/yyyy; indicates the date the rule goes into effect, can be past, present, or future.

Duration – Optional, enter in years as a decimal (ex: 5.5).

Termination Date – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy; indicates the date the rule expires.

Priority – Required, automatically set by the database, but can be changed. Look at the list of current rules to decide if the rule you are creating should be higher or lower than existing rules.

Value Type – Required; use the drop down list to select either percent or units.

Alloc. Value – Required, if the value type is percent, this is the percentage of material that should be allocated (enter a number without a % sign). If the value type is units, this is the number of units that should be allocated.

Alloc. Category – Required, use the drop down list to select the category you are allocating material into, either Core, Evaluation, Restricted, or Working.

Germplasm Type – Required, use the drop down list to select the type of material the rule applies to (ex: semen, purified DNA).

Comments – Optional, text field to add notes about the allocation rule, limited to 100 characters.

Apply Retroactively – Check box allowing you to apply a rule in the past; this will retroactively apply to inventory if it already exists; a pop-up message will confirm this when you save the record.

Save – Commits the data to the database.

After saving the record, the form clears out and you can enter another rule, update or delete the rule you just created, or exit the form.

Agreement Search

Purpose: Allow searching for existing agreements.

Tables populated by this form: none.

Other forms accessed from this form: agreement.

The Maximum Results per Page can also be permanently set in your profile (accessed from the Main Menu left bar).

Fields.

Search Criteria - Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the ID, Established Date, Document Number, Entity Name, Person Name, and Details fields from the Agreement form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New button at the bottom of the form.

Results can be sorted by clicking on any of the Results column headers.

Allocation overview

Purpose: To view and make changes to the allocation for animals within a taxonomy.

Tables populated by this form: inventories.

Other forms accessed by this form: none.

Fields.

Full Taxonomy Name – Required, use the drop down list to select a the taxonomy you want to see allocation records for.

Search – Displays the selected taxonomy name and associated child taxonomies in the box labeled Taxonomies Included in Overview.

If there are child taxonomies in the Taxonomies Included in Overview box that you do not want to see displayed, uncheck the box next to the taxonomy name and click on the Search button again.

The Total Allocations area shows the breakdown of inventory in the allocation categories.

The Animals section lists each animal in the taxonomy; you can click on the ± button to see the Incoming Order(s) the animal is associated with. You can change the quantity in any of the catogories.

If you enter a quantity greater than the total quantity available, the form will give you an error message and won’t save the changes. If you enter a number less than the total quantity available, the form will put the remaining quantity in the Unallocated category when you save the record.

Fields.

Core – Allocation category for units used for repopulation purposes.

Evaluation – Allocation category for units to be used for determining the viability of the material.

Restricted – Allocation category for material that cannot be used because of an agreement in place with a cooperator.

Working – Allocation category for material that is available for requests.

Unallocated – Any material that is not in Core, Evaluation, Restricted, or Working is placed here.

Total Qty – Sum of all units in the allocation categories.

Update Allocations – Use this to commit changes to the database.

Cancel – Use this button to cancel changes you have made to the allocations.

Allocation Rule

Purpose: To allow the user to place inventory into allocation categories based on incoming order, germplasm owner, animal, or taxonomy.

Tables populated by this form: inventories, allocation_rules, allocation_rule_inventories.

Other forms accessed by this form: incoming order search pop-up, entity search pop-up, animal search pop-up, agreement search pop-up.

Fields.

Incoming Order ID – Select the radio button and use the incoming order search pop-up to select an incoming order to apply the allocation rule to an incoming order.

Germplasm Owner – Select the radio button and use the entity search pop-up to select a germplasm owner to apply the allocation rule to all shipments sent by a germplasm owner.

Animal – Select the radio button and use the animal search pop-up to select an animal to apply an allocation rule to all inventory for an animal.

Taxonomy – Select the radio button and use the drop down list to select a taxonomy to apply an allocation rule to all animals within a taxonomy.

Rule ID – Automatically populated by the database.

Effective Date – Required, can use calendar pop-up to select date or manually type in mm/dd/yyyy; indicates the date the rule goes into effect, can be past, present, or future.

Duration – Optional, enter in years as a decimal (ex: 5.5).

Termination Date – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy; indicates the date the rule expires.

Priority – Required, automatically set by the database, but can be changed. Look at the list of current rules to decide if the rule you are creating should be higher or lower than existing rules.

Value Type – Required; use the drop down list to select either percent or units.

Alloc. Value – Required, if the value type is percent, this is the percentage of material that should be allocated (enter a number without a % sign). If the value type is units, this is the number of units that should be allocated.

Alloc. Category – Required, use the drop down list to select the category you are allocating material into, either Core, Evaluation, Restricted, or Working.

Germplasm Type – Required, use the drop down list to select the type of material the rule applies to (ex: semen, purified DNA).

Comments – Optional, Text field to add notes about the allocation rule, limited to 100 characters.

Apply Retroactively – Check box allowing you to apply a rule in the past; this will retroactively apply to inventory if it already exists; a pop-up message will confirm this when you save the record.

Save – Commits the data to the database.

After saving the record, the form clears out and you can enter another rule, update or delete the rule you just created, or exit the form; a message is also given at the top of the form summarizing what inventory was affected by the application of the rule.

Allocation Rule Search

Purpose: To allow the user to search for existing allocation rules.

Tables populated by this form: none.

Other forms accessed from this form: allocation rule.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Rule Type, Germplasm Type, Allocation Category, and Effective Date fields from the Allocation Rule form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

The Maximum Results per Page can also be permanently set in your profile (accessed from the Main Menu left bar).

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New button at the bottom of the form.

Results can be sorted by clicking on any of the Results column headers.

Allocation Rule Inventories Search

Purpose: To allow searching for inventory affected by current allocation rules.

Tables populated by this form: none.

Other forms accessed from this form: none.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Rule ID and Inventory ID fields will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Results can be sorted by clicking on any of the Results column headers.

Animal

Purpose: Create a new animal record.

Tables populated by this form: animals, identifications.

Other forms accessed from this form: entity search pop-up.

Live animals should be entered in the Animal Form, making sure the Repository Number is unchecked if the animal is not in the repository,and also making sure the Active field is used to indicate the animal’s status. Then, the animal’s pedigree, image, and observations can be entered.

Fields.

Animal ID – Automatically filled in by database.

Repository Animal – Uncheck the box if the animal does not have material in the repository; otherwise, leave the box checked.

Repository Num – Automatically filled in by database (only filled in if Repository Animal is checked).

Country – Automatically filled in by database.

Taxonomy: Search Criteria – Required, enter the taxonomy name or a partial taxonomy name of the animal you want to enter; select the correct taxonomy from the Results box & the selected taxonomy will display in the Selected Taxonomy field.

Sex – Optional, use the drop down list to select M or F; leave blank for embryos.

Date of Birth – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy, mm/yyyy, or yyyy; used to record the animal’s birth date.

Received Date – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy; the date the animal was first received.

Genomic Information Available – Optional, check this box if there are genomic results available for the animal.

Active – Optional, this is for live animal populations; use the drop down list to state whether the animal is active (Y) or not (N).

Inactive Date – Optional, this is for live animal populations; can use calendar pop-up to select date or manually type in mm/dd/yyyy, enter the date the animal became inactive.

Inactive Reason – Optional, this is for live animal populations, enter the reason the animal was inactivated (ex: Culled, Died, Sold).

Sample Identification – This field is automatically populated from the taxonomy form and allows the user to show an example of how the identifications should look for a particular breed, line, etc.

Rank – Click on the Add button in the Identification section to add identifications; Required if Identification Type or Identification are entered; automatically populated by the database, but can be changed to prioritize the importance of the identifications.

Identification Type – Required if Identification is entered, drop down list of the types of identifications available for an animal.

Ancestors of a Sire can only be entered if the Sire is entered. This holds true throughout the pedigree. The pedigree tree must be filled in from the base outward.

Identification – Required if Identification Type is entered, text field to enter the identification(s) for the animal, limited to 100 characters.

Identification Country – Optional, drop down list of countries that can be assigned to the identification.

Breeder Name – Optional, use the search button to open the entity search pop-up to search for an existing breeder or to access the entity form to create a new one; can delete an attached breeder using the DEL button (this unlinks the breeder from the animal record but does not delete the record from the database).

Description – Optional, text field to add additional information about the animal, limited to 1,000 characters.

Save – Commits the data to the database and assigns the Animal ID and Repository Number.

After saving the record, the form changes to Update mode and you can make changes to the record and save again, use the Quick Picks to create a new animal, or exit the form.

Animal Image

Purpose: To upload images of an animal and provide information about the images.

Tables populated by this form: images.

Other forms accessed by this form: animal search pop-up.

Fields.

Image for – Required, to enter an animal image, select the Animal radio button.

Repository Num – Required, use the search button to search for an existing animal to attach the image to.

Ctry (Country) – Automatically populates when Repository Number is selected.

Identifications – Automatically populates when Repository Number is selected.

Upload File – Required, use the Browse button to bring up a search window to locate the picture file on your computer, select the file, and click on Open; the window will close and the file path will fill in automatically.

Sex – Optional, use the drop down list to select male (M) or female (F).

View – Required, use the drop down list to state whether the image is of the back, front, or profile of the animal.

Caption – Optional, text field displayed on the public web pages when the user mouses over the image, limited to 50 characters.

Tip: For the caption, NAGP follows a standardized format of Breed and Repository Number. For example, the caption could be ‘Angus NAGP ID 1531’.

Copyright / Source – Optional, use the drop down list to select the source of the image; if the person you are looking for is not in the list, a Super User will need to create it using the Information Source form.

Any cropping or photo editing should be done before uploading the image.

Description – Optional, text field to provide information about the image, limited to 300 characters.

Save – Commits the data to the database.

Cancel – Exits the form without saving the data.

After saving, the image thumbnail appears at the bottom of the form; click on Update (UPD) or Delete (DEL) to modify or delete the current image, Upload Animal Images in the Quick Picks list, or return to Main Menu to exit the form.

Animal Image Search

Purpose: To allow the user to search for an existing image.

Tables populated by this form: none.

Other forms accessed by this form: images.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Full Taxonomy Name, Repository Number, Identifications, Caption, Description, Copyright Source, and Breeder Name from the Animal Image form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New button at the bottom of the form.

Results can be sorted by clicking on any of the Results column headers.

Animal Observation

Purpose: To enter genotypic and phenotypic information about an animal.

Tables populated by this form: anm_observations.

Other forms accessed from this form: none.

The Animal Observation form can be accessed through the Animal Search form by searching for an animal and clicking on the Obs link in the Action column.

Fields.

Repository Num – Automatically populated with animal selected from the Animal Search form.

Ctry (Country) – Automatically populated by the database.

Identifications – Automatically populated by the database based on the animal selected.

Descriptor – Required, use the drop down list to select the type of observation you want to enter; if the descriptor you are looking for is not in the list, a Super User will need to create it using the Create New Descriptor form.

Observation Value – Required, for a non-coded observation, enter the value for the animal, using the Units field and the Message field as guidelines for how the data should be reported. For a coded observation, use the drop down list to select the appropriate value; if the code you are looking for is not in the list, a Super User will need to create it using the Descriptor Search – Update Descriptor form.

Units – Automatically populated when the descriptor is selected; provides information about how the descriptor data is to be entered.

Date Observed – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy, mm/yyyy, or yyyy; this is the date the observation occurred.

Variable Name, Reliability, Accuracy, etc. – Optional, this field name changes depending on the Descriptor, but is primarily used to record accuracy data for breeding values; if the field is named ‘Variable Name’, then the selected descriptor doesn’t use this field.

Information Source – Optional, use the drop down list to select the provider of the observation; if the person you are looking for is not in the list, a Super User will need to create it using the Information Source form.

Comments – Optional, text field to add notes about the observation, limited to 100 characters.

Save – Commits the data to the database, displays the new record in a list at the bottom of the form, and shows the save was successful with a message at the top of the form (ex.: Animal observation with ID = 35107 was successfully created.).

Cancel – Clears the entered data from the form.

After creating a new observation, you can continue to create new observations on the form, or use the UPD or DEL buttons in the Action column at the bottom of the form to modify or delete existing observations.

Animal Observation Loader

Purpose: To upload genotypic and phenotypic information about an animal or multiple animals.

Tables populated by this form: anm_observations.

Other forms accessed from this form: none.

Fields.

Upload File – Use the Browse button to search your computer for a prepared file to upload. The data must be in the following format:

Line 1: Variable names.

Ex.: repository_number, descriptor_id, obs_value, date_observed, info source, qualifier, comments.

Look up the Descriptor ID using the Descriptor Search. Search for the Descriptor of interest and record the corresponding ID.

Line 2: Data that corresponds to the variables in line 1.

Ex.: 2989 | 943 | 0.039 | 1/28/2014 | American Angus Association (AAA) | | note: this is estimated.

The fields within the file can be separated by a pipe (|), tab, semicolon (;), or comma (,); use the drop down list to select the delimiter that matches your file.

Click on Submit Query to load the file.

A successful upload will return a message stating the file was successful and also the number of records that were processed and inserted.

If the upload fails, a report will be generated showing where the file had unexpected data. You can correct the file and do the upload again.

After a successful upload, search for the animals in the Animal Search form, then click on Obs in the Action column to verify the data is in the Animal Observation form as expected.

Animal Search

Purpose: Allow searching for existing animals.

Tables populated by this form: none.

Other forms accessed from this form: animals, images, animal observations, public web pages – pedigree, pedigree.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Repository Number, Identifications, Taxonomy, and Breeder fields from the Animal form will be searched for what is entered in this field.

The Lines per Page field can be set to display as many or as few results as you want to see on a page.

Hide/Show Advanced Search Options – Optional, allows narrowing of the search criteria.

Selecting the include non-repository animals box allows for live animal and pedigree animal searching.

Search only on drop down list allows you to search specifically within Breeder, Identifications, or Repository Number.

Search only in taxonomy and child taxonomies drop down list allows you to search within a specified taxonomy.

Sort by drop down list allows you to sort the entire results list (not just the first screen of results) by ID, Full Taxonomy Name, or Repository Number.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) the animal record, access the pedigree (PED), images (IMG), animal observations (OBS), or the public web pages pedigree (PPED), or use the Create New button at the bottom of the form to create a new animal record.

Coefficient of Relationship

Purpose: Stores Wright’s coefficient of relationship between animals.

Tables populated by this form: coefficient_relationships.

Other forms accessed from this form: animal search pop-up, taxonomy search pop-up.

Fields.

Upload File – Use the Browse button to search your computer for a prepared file to upload. The data must be in the following format:

Repository Num for Animal 1 | Country Code | Repository Num for Animal 2 | country Code | Relationship (range 0-1).

The fields within the file can be separated by a pipe (|), tab, semicolon (;), or comma (,); use the drop down list to select the delimiter that matches your file.

Click on Submit Query to load the file.

A successful upload will return a message stating the file was successful and also the number of records that were processed, inserted, and updated. Then, a report of the changes to the database is displayed.

If the upload fails, a report will be generated showing where the file had unexpected data. You can correct the file and do the upload again.

Enter data manually.

Animal 1 Rep. Num – Required (if entering data manually), type in the Repository Number or use the search button to open the animal search pop-up and search for the animal of interest.

Animal 1 Ctry – autopopulates when the Repository Number is entered.

Animal 1 Identification – the first ranked identification of the animal is autopopulated.

Animal 2 Rep. Num, Ctry, and Identification – fields are the same as for Animal 1.

Relationship – Enter Wright’s coefficient of relationship between the two animals, range 0-1.

Save – Commits the data to the database and shows the save was successful with a message at the top of the form (ex: Coefficient of Relationship was successfully created).

Search by Taxonomy, use to search for a list of all relationships within a taxonomy.

Full Taxonomy Name – use the search button to select the taxonomy of interest.

Species Comm. Name – autopopulated based on selected Full Taxonomy Name.

Selecting the Full Taxonomy Name will automatically retrieve a list of relationships in the database for that taxonomy in the Search Results section at the bottom of the form.

You can use the Action buttons at the right of each relationship to Update (UPD) or Delete (DEL) records.

You can use the Clear Form button to clear the search results and do another search or enter data.

Search by Animal, use to search for a list of all relationships for a particular animal.

Repository Number – Required, type the Repository Number of the animal or use the search button to open the animal search pop-up and search for the animal of interest.

Ctry – Autopopulated based on the selected animal.

Identifications – Autopopulated based on the selected animal.

Search – Use the search button to retrieve the list of relationships for the selected animal.

You can use the Action buttons at the right of each relationship to Update (UPD) or Delete (DEL) records.

You can use the Clear Form button to clear the search results and do another search or enter data.

Entity

Purpose: Create people and organizations associated with animals in the database.

Tables populated by this form: entities, addresses.

Other forms accessed from this form: entity search pop-up.

Fields (Person tab).

Entity ID – Automatically populated by the database.

Inactive – Check this box if the entity record is no longer in use, keeps the record as part of historic data but is not used to create new records.

Prefix – Optional, use the drop down list to declare the title (Mr., Dr.) of the person/people.

Name (First) – Optional, enter the first name of the person/people.

Name (Last) – Required, enter the last name of the person/people. If there are multiple people associated with the same organization and they have different last names or addresses, create a new entity record for each person.

Profession – Optional, use the drop down list to select the occupation of the person/people. New codes can be added by a Super User.

Organization – Optional, use the search button popup to search for the organization the person is associated with. If the Organization does not exist, you will need to create that and then associate the person entity record with it.

Primary – Optional, enter the main phone number for the person. You can also enter notes about the phone number (i.e., home phone).

Secondary – Optional, enter a second phone number for the person.

Fax – Optional, enter the fax number for the person.

Email Address – Optional, enter the email address for the person.

Web Address – Optional, enter the website for the person.

Comments – Optional, text field to enter notes related to the person.

Address ID – Automatically populated by the database.

Country – Required, use the drop down list to select the country the person is from; the default is the country the user is logged in under. Additional countries can be added by a Super User as needed.

Address – Optional, enter the street address for the person.

City – Optional, enter the city for the person.

State/Province – Optional, use the drop down list to select the state or province for the person; this list is filtered based on the country selected above.

Postal Code – Optional, enter the postal (zip) code for the person.

Address Type – Optional, use the drop down list to designate the address as the ‘Primary’ or ‘Ship to’. Additional address type codes can be entered by a Super User.

Comments – Optional, use the text fields to add notes about the address portion of the record. For example, the address might be used for delivering UPS shipments, but not for USPS mail. This could be noted here.

Add Address – Optional, use this button to add another address section if, for example, the ranch has a physical address but mail contact is via a P.O. Box.

Save – Use this button to commit the data to the database, which returns a message to the user stating the entity record was successfully created.

Fields (Organization tab).

Entity ID – Automatically populated by the database.

Repository – Check this box if the entity record is being created for a repository.

Inactive – Check this box if the entity record is no longer in use, keeps the record as part of historic data but is not used to create new records.

Organization Name – Required, enter the name of company.

Primary – Optional, enter the main phone number for the organization. You can also enter notes about the phone number (i.e., home phone).

Secondary – Optional, enter a second phone number for the organization.

Fax – Optional, enter the fax number for the organization.

Email Address – Optional, enter the email address for the organization.

Web Address – Optional, enter the website for the organization.

Comments – Optional, text field to enter notes related to the organization.

Address ID – Automatically populated by the database.

Country – Required, use the drop down list to select the country the organization is in; the default is the country the user is logged in under. Additional countries can be added by a Super User as needed.

Address – Optional, enter the street address for the organization.

City – Optional, enter the city for the organization.

State/Province – Optional, use the drop down list to select the state or province for the organization; this list is filtered based on the country selected above.

Postal Code – Optional, enter the postal (zip) code for the organization.

Address Type – Optional, use the drop down list to designate the address as the ‘Primary’ or ‘Ship to’. Additional address type codes can be entered by a Super User.

Comments – Optional, use the text fields to add notes about the address portion of the record. For example, the address might be used for delivering UPS shipments, but not for USPS mail. This could be noted here.

Add Address – Optional, use this button to add another address section if, for example, the ranch has a physical address but mail contact is via a P.O. Box.

Save – Use this button to commit the data to the database, which returns a message to the user stating the entity record was successfully created.

Entity Observation

Purpose: To enter genotypic and phenotypic information about a breeder’s animals.

Tables populated by this form: ent_observations.

Other forms accessed from this form: none.

The Entity Observation form can be accessed through the Entity Search form by searching for an entity and clicking on the Obs link in the Action column.

Fields.

Taxonomy – Optional, use the drop down list to select the taxonomy of the animals owned by the breeder that you want to enter observations for.

Descriptor – Required, use the drop down list to select the type of observation you want to enter; if the descriptor you are looking for is not in the list, a Super User will need to create it using the Create New Descriptor form.

Observation Value – Required, for a non-coded observation, enter the value, using the Units field and the Message field as guidelines for how the data should be reported. For a coded observation, use the drop down list to select the appropriate value; if the code you are looking for is not in the list, a Super User will need to create it using the Descriptor Search – Update Descriptor forms.

Date Observed – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy; this is the date the observation occurred.

Information Source – Optional, use the drop down list to select the provider of the observation; if the person you are looking for is not in the list, a Super User will need to create it using the Information Source form.

Comments – Optional, text field to add notes about the observation, limited to 100 characters.

Save – Commits the data to the database, displays the new record in a list at the bottom of the form, and shows the save was successful with a message at the top of the form (ex.: Descriptor average birth weight with Observation value 45 was successfully created.).

Clear – Clears the entered data from the form.

After creating a new observation, you can continue to create new observations on the form, or use the UPD or DEL buttons in the Action column at the bottom of the form to modify or delete existing observatrions.

Entity Search

Purpose: Allow searching for existing entities.

Tables populated by this form: none.

Other forms accessed from this form: entities, agreements, entity observations, and allocation rules.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Name, Address, and Organization fields from the Entity form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) the entity record, access the agreement (AGR), entity observations (Obs), or the Allocation Rules (ALR), or use the Create New button at the bottom of the form to create a new entity record.

Results can be sorted by clicking on any of the Results column headers.

Incoming Order

Purpose: Track all incoming shipments.

Tables populated by this form: incoming_orders, animals, inventories.

Other forms accessed from this form: entity search pop-up, animal, animal observations, animal images, pedigree, protocol search pop-up, inventory observations.

Fields – Incoming Order Header.

Incoming Order ID – Autopopulated by the database.

Incoming Order Type – Required, use the drop down list to select the type of shipment you are entering (ex: Donation).

Germplasm Owner Name – Required, this is to record the owner of the material included in the shipment. Use the search button popup_search to open the entity search pop-up and search for or create the owner.

Shipper Name – Required, this is to record who sent the material to you. Use the search button popup_search to open the entity search pop-up and search for or create the shipper.

Repository Name – Autopopulated based on your login information, but can be changed by clicking on the search button popup_search to search for or create a new repository.

Date Received – Required, can use calendar pop-up to select date or manually type in mm/dd/yyyy; this is the date the shipment was received and can be a date in the future if you are preparing for a future shipment.

Description – Optional, text field (limited to 1000 characters) to include information about the shipment.

All/Not Done/Done radio buttons – All is the default; these buttons are for a shipment that is in a partial state of completion with at least some inventory records entered. Clicking on All shows all animals in the shipment, Not Done shows animals with no associated inventory records, and Done shows animals with inventory records. These buttons are particularly useful when searching a large shipment for animals that need inventory records entered. As inventory records are entered, they do not move to the Done records until the incoming order is refreshed.

Agreement ID – Automatically populated by the database when an agreement exists for the Germplasm Owner. You can select View All to see the Agreement information.

Comments – Optional, text field (limited to 100 characters) to enter any comments about the shipment.

Breeder Name – Optional, if the breeder is the same for all animals in the shipment, you can enter it here and it will be applied to all animal records created for the shipment. It will not change the breeder for existing animals that are attached to the shipment. The breeder can also be changed in the animal form.

Germplasm Type – Optional, use the drop down list to select the type of material received in the shipment (ex: Embryo, Semen).

Original State – Optional, use the drop down list to state whether the material was Fresh or Cryopreserved upon receipt.

Unit Form – Optional, use the drop down list to select the type of packaging used for the material (ex: straw, ampule). If the shipment was received fresh, this is the type of packaging that will be used. If the material was received cryopreserved and there are more than one unit form types included in the shipment, this can be assigned at the individual inventory level.

Unit Size – Optional, use the drop down list to select the size of packaging used (ex.: 0.25 mL).

Protocol Name – Optional, use the search button popup_search to open the protocol search pop-up and search for the protocol used for the shipment, or to create a new protocol.

Save – Commits the data to the database and assigns the Incoming Order ID.

Cancel – Exits the form without saving the data.

Fields – Incoming Order Animals.

Click on the lower left Animal tab to expand this section.

Clicking on the Incoming Order Header, Animal, or Inventory buttons changes that section from full view to condensed view to hidden.

Attach/Create Animals tab – Click on this tab to search for animals that exist in the database or to create new animal records.

Complete data in any field and click on the Search button to search for animals that exist in the database.

Date of birth searching is flexible. You can search by yyyy, mm/yyyy, or dd/mm/yyyy.

If multiple matches are found based on the search criteria, a pop-up box appears and you can select and attach an animal (Attach Selected), create a new animal if none of the animals in the search are the one you are looking for (Create New), or return to the form to change the search criteria (Cancel).

If a single match is found based on the search criteria, the form populated with that animal. You can use the Attach button to include the animal in the shipment or the Clear button to remove the animal from the shipment.

If the search doesn’t find any matches or if you know the animal is new to the database, use the Create New button to open the Animal form.

After the Animal form is completed, saving the record will return you to the Incoming Order and attach the animal to the shipment with a message at the top of the animal area stating the attachment was successful.

Clicking on the Attach/Create Animals tab will clear the form and allow you to search for or create a new animal to attach to the shipment

View/Update Animals tab – Click on this tab to view or make changes to the animals already attached to the Incoming Order; scroll through the animals using the arrow buttons at the bottom of the form or by entering a number in the box to move to a particular record number.

When the View/Update Animals tab is active, the Enter Animal Observations, Upload Animal Images, and Enter/Edit Pedigree tabs are available for entering additional information about the animals in the shipment. Closing the Animal Observations, Animal Images, or Pedigree forms will return you to the Incoming Order form.

Fields – Incoming Order Inventory.

Click on the lower left Inventory tab to expand this section.

Inventory ID – Automatically populated by the database.

Germplasm Type – Required, automatically filled in if this was entered in the Incoming Order Header area; can be changed by selecting the type of material from the drop down list.

Original State – Required, automatically filled in if this was entered in the Incoming Order Header area; can be changed by selecting the state from the drop down list.

Unit Form – Required, automatically filled in if this was entered in the Incoming Order Header area; can be changed by selecting the form from the drop down list.

Unit Size – Optional, automatically filled in if this was entered in the Incoming Order Header area; can be changed by selecting the size from the drop down list.

Collection Date – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy; this is the date the inventory was collected.

Label Text – Optional, text field (30 characters) to enter the text printed on the packaging for the material.

Comments – Optional, text field (100 characters) to record any details about the inventory.

Beg. Total Quantity – Automatically computed by the database when the location information is saved; is a sum of the beginning inventory count.

Cur. Total Quantity – Automatically computed by the database; shows the sum currently available for that inventory. When a record is first created, the beginning and current quantities are the same and they should only differ by the amount sent out in requests.

Unallocated – Automatically computed by the database; shows the inventory not accounted for in Core, Evaluation, Restricted, and Working.

Core – Automatically computed by the database if the inventory is affected by Allocation Rules. This can be updated manually by the user. Inventory placed in Core is for regeneration purposes.

Evaluation – Automatically computed by the database if the inventory is affected by Allocation Rules. This can be updated manually by the user. Inventory placed in Evaluation is for evaluating the quality of the samples.

Restricted – Automatically computed by the database if the inventory is affected by Allocation Rules. This can be updated manually by the user. Inventory placed in Restricted is not available for Requests.

Working – Automatically computed by the database if the inventory is affected by Allocation Rules. This can be updated manually by the user. Inventory placed in Working is the primary area used for filling Requests.

Protocol Name – Optional, automatically filled in if this was entered in the Incoming Order Header area; can be changed by using the search button popup_search to open the protocol search pop-up.

Date Used – Automatically populated with the date of the Incoming Order, but can be changed using the calendar pop-up or by manually typing in the date (mm/dd/yyyy).

Add/Del (Protocol) – these buttons can be used to add additional protocols or to remove existing ones.

Container Type – Required, use the drop down list to select the type of container the inventory is stored in; additional types can be entered by a Super User.

Loc 1... Loc 7 – These field names and required/optional are determined by the location structure set up by a Super User for each location structure. See the screen shots below for an example.

In this example, Tank, Pie, Canister, Goblet, and Visotube are required, while Pie Section is not.

Beg Qty – Required, enter the quantity in that location (ex: 12 straws in Visotube A).

Beg Unit Count – Optional, default is 1. This field should be entered if there is more than 1 unit in the package (ex: multiple embryos in a straw).

Cur Qty – Automatically populated by the database, the value is the beginning quantity minus any requests taken from this location.

Cur Unit Count - Automatically populated by the database, the value is the beginning unit count minus any requests taken from this location.

Stage – Optional, for Germplasm Type = Embryos, the drop down list can be used to select the stage the embryos were cryopreserved at.

Quality – Optional, for Germplasm Type = Embryos, the drop down list can be used to select the quality assigned to the embryos at preservation.

Dup – Optional, these check boxes can be used to retain the information as location records are entered. For example, if the inventory is all in tank 16, checking the Tank box will keep tank 16 for all location records to make data entry easier.

After entering a location record, you must click on the Add button before it can be saved.

UPD/DEL – these buttons can be used to update (UPD) or delete (DEL) inventory records.

If the quantity in a location is found to be incorrect after the shipment has been entered (ex: straws were miscounted), use the UPD button next to the location and make the change in the Beg Qty (in the location record), not the Cur Qty, select UPD, then Save. Make sure the Allocation Values were recalculated by the database.

Save – Commits the data to the database, generates a message at the top of the inventory area, and populates the Inventory Allocation section.

Clear – Empties the form without commiting the records to the database.

Add Inventory – This button is used to assign another Inventory ID to the animal in the shipment. It is used if the material was received in more than one Unit Form or Unit Size. For example, if the same animal was received in straws and ampules, you need different inventory IDs to properly track the inventory. They will have different location structures, protocols, and inventory observations.

The Add Inventory button is NOT for adding additional location records for the same inventory; the Save button should be used for those records.

Remove Inventory – This button is used to remove an animal from an Incoming Order once inventory has already been assigned to it. If inventory has not been assigned and you want to remove the animal, it can be done in the Animal section. Once inventory has been assigned, all inventory must be deleted, then the Remove Inventory button can be used to remove the inventory record so the animal can be removed from the Animal section. Note this is not for removing inventory for a Request; rather, it is for animals assigned to the wrong Incoming Order or some other mistake.

Use the arrow buttons in the Animal section to move between Inventory records (see figure below).

The Inventory Allocation area can be updated manually after the record is saved. Once it is updated, the record needs to be saved again.

Incoming Order Search

Purpose: Allow searching for existing incoming orders.

Tables populated by this form: none.

Other forms accessed from this form: incoming order, inventory observations.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Incoming Order ID, Germplasm Owner, Shipper Name, Repository Name, Animal Repository Number, and Animal Identification fields from the Incoming Order form will be searched for what is entered in this field. If the check box is selected, the search will be limited to the Animal Repository Number and Animal Identification fields.

The Lines per Page field can be set to display as many or as few results as you want to see on a page.

An Incoming Order can only be deleted if there are no inventory records associated with it.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) the Incoming Order or to enter Inventory Observations (Obs), or use the Create New button at the bottom of the form to create a new Incoming Order.

Results can be sorted by clicking on any of the Results column headers.

Inventory Observation

Purpose: Enter observations about inventory records, either manually or via upload.

Tables populated by this form: inv_observations.

Other forms accessed from this form: incoming order search pop-up, animal search pop-up.

The Inventory Observation form can be accessed directly from the Main Menu or by searching for an Incoming Order and clicking on the Obs link in the Action column.

Fields.

Upload File – Use the Browse button to search your computer for a prepared file to upload. The data must be in the following format.

Line 1: SEMEN.

Line 2: Variable names.

Line 3: Data.

The fields within the file can be separated by a pipe (|), tab, semicolon (;), or comma (,); use the drop down list to select the delimiter that matches your file.

Click on Submit Query to load the file.

A successful upload will return a message stating the file was successful and also the number of records that were processed.

An unsuccesful upload will return a list of where the error(s) occurred. You can correct the file and do the upload again.

Enter data manually.

Incoming Order ID – Required, use the Incoming Order search pop-up to select the incoming order to apply the inventory observations to; selecting the Incoming Order ID will also fill in the Animal Section with all animals associated with the Incoming Order.

Repository Name – Automatically populated based on the Incoming Order selected.

Date Received – Automatically populated based on the Incoming Order selected.

Repository Number – Required, automatically populated when the Incoming Order ID is selected, can also use the Animal Search pop-up to search for a specific animal within the Incoming Order.

Ctry – Automatically populated when the Repository Number is selected.

Identifications – Automatically populated when the Repository Number is selected.

Inventory Germplasm Type – Automatically populated when the Repository Number is selected.

Descriptor – Required, select the descriptor you want to enter data for from the drop down list. Selecting the descriptor automatically populates the Units and text box below the Observation Value to provide information about the parameters and formatting for the observation.

Observation Value – Required, use the information provided in the Units and text box to enter the observation data.

Units – Automatically populated when the descriptor is selected; provides information about how the descriptor data is to be entered.

Date Observed – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy, mm/yyyy, or yyyy; this is the date the observation occurred.

Information Source – Optional, use the drop down list to select the provider of the observation; if the person you are looking for is not in the list, a Super User will need to create it using the Information Source form.

Comments – Optional, text field to add notes about the observation, limited to 100 characters.

Save – Commits the data to the database, provides a message at the top of the form (Inventory Observation was successfully created), displays the record at the bottom of the form, and clears the form to enter another observation.

Clear – Removes the data from the Observation Entry section and leaves the data in the Inventory section.

Pedigree

Purpose: To store sire, dam, and other ancestors for an animal.

Tables populated by this form: animals.

Other forms accessed from this form: more info pop-up.

The Pedigree form can be accessed through the Animal Search form by searching for an animal and clicking on the Ped link in the Action column.

Alternatively, and particularly for a file upload, the pedigree form can be accessed by selecting the Loader menu, then Pedigree.

Fields.

Upload File – Use the Browse button to search your computer for a prepared file to upload rather than entering the data manually. The data must be in the following format.

Line 1: Identification Type.

Ex.: Registration Number.

Line 2: Full Taxonomy Name | Animal Identification | Sex | Sire Full Taxonomy Name | Sire | Dam Full Taxonomy Name | Dam.

Ex.: Bovidae Bos taurus – beef Angus | 10392792 | M | Bovidae Bos taurus - beef Angus | 9958208 | Bovidae Bos taurus - beef Angus | 9433106.

Missing data must be represented by a “.”.

The fields within the file can be separated by a pipe (|), tab, space, semicolon (;), or comma (,); use the drop down list to select the delimiter that matches your file.

Click on Upload File to load the file

If multiple matches are detected, you will be prompted to select the correct animal(s) and upload the file again.

After processing the file, the database provides a message at the top of the form indicating the upload was successful.

All of the loaded pedigree records are displayed starting at the root of the tree and you can then scroll through each pedigree record.

Repository Number – Automatically populated with the animal from the previous form (Animal Search or Animal); can be changed using the animal search pop-up.

Ctry – Automatically populated based on the animal selected.

Identifications – Automatically populated based on the animal selected.

Taxonomy – Automatically populated based on the animal selected.

Search Taxonomy – Automatically populated with the taxonomy of the animal selected. If additional taxonomies should be searched for matches for the pedigree animals, use the Add button and then the drop down list to select additional taxonomies. For example, in the U.S., when the taxonomy is Hereford, the child taxonomies Hereford Line 1 and Hereford Prospector should also be included in the pedigree searching since they all belong to the same breed.

Animal ID / Repository Number / Country / Identification / Identification Type / F – Automatically populated with information about the animal selected.

Sire ID – Identification – Optional, enter the identification for the sire of the selected animal.

Sire ID – Ident. Type – Required if Identification is entered, use the drop down list to select the type of identification entered. If multiple matches are found for the combination of Identification and Identification Type, a pop-up will show the user the animals available to select from. Clicking on Attach Selected will associate the selected animal with the pedigree.

Sire ID – You can click on the word Sire to bring up a pedigree pop-up with the Sire as the selected animal.

More info... – use this link to open the more info pop-up if you have more data that you want to add about the sire.

Birth Place – use the drop down list to select the place where the animal was born. If an additional Birth Place is needed, a Super User will need to add the code in the Birth Place References form. Birth Place isn’t needed for animals with unique IDs, such as Registration Numbers. This is more for use with animals that only have ear tags that could be repeated at another location and is a different animal. When the pedigree finds a match for a previously entered animal, this information can be used by the user to decide which animal is the correct match, or if it is a new animal.

Animal ID / Repository Number / Country – Automatically populated by the database.

Full Taxonomy Name – Required, automatically populated with the taxonomy of the selected animal, but the search button can be used to open the taxonomy search form to change the taxonomy. Continuing with the Hereford example, the selected animal might be a Hereford, but the Sire is a Hereford Line 1. The taxonomy search pop-up would be used to change the taxonomy.

Species Common Name – Automatically filled in by the database based on the taxonomy selected.

Rank – The first line is automatically populated by the database from the pedigree form, but can be changed to prioritize the importance of the Identifications if additional Identifications are entered.

Identification Type – The first line is automatically populated by the database from the pedigree form; if additional Identifications are entered, this is required. Use the drop down list to select from the types of identifications available.

Identification – The first line is automatically populated by the database from the pedigree form, if additional Identification Types are entered, this is required. Use the text field to enter the identification(s) for the animal, limited to 100 characters.

Identification Country – Optional, drop down list of countries that can be assigned to the identification.

Save – If the pedigree record has already been saved in the pedigree form and you have made changes in the more info pop-up, the changes are applied to the existing record (same Animal ID). If this animal exists elsewhere in the database, the changes are applied everywhere. If the pedigree record has not been saved in the pedigree form and you have made changes in the more info pop-up, clicking on save will commit the animal to the database and return you to the pedigree form.

If an incorrect ID is entered, you can clear it out of the Identification field and change the Identification Type to “Please Select” and save. Then, enter the correct ID and Identification Type. To permanently remove the incorrect ID from the database, search for it in the Animal Search form and select Del.

Cancel – Returns you to the pedigree form without saving changes made in the more info pop-up

Dam / PGS / PGD / MGS / MGD / ... – Optional, fill in the identifications as explained above for the Sire

Save – Commits the data to the database and produces a message at the top of the form ‘Pedigree was successfully created’.

Pop-ups

Purpose: To search for existing information from another area of the database without leaving the form you are working in.

Tables populated by this form: none.

Other forms accessed from this form: animal form for animal pop-up, taxonomy form for taxonomy pop-up, etc.

Agreement Search Pop-up

Fields.

Search Criteria – If field is left empty, all results from the Agreement form will be displayed after selecting the Search button; otherwise, matches for anything typed in the Search Criteria field will be returned from the Agreement form.

Results – If the Agreement you are looking for is displayed in the Results section, click on it and make sure it is displayed in the Selected Agreement CB field.

Selected Agreement CB / Record Source – Once an agreement is selected from the Results, displays the Created By user ID and Record Source for the Agreement.

OK – Uses the selected data and returns to the form.

Cancel – Returns to the form.

Animal Search Pop-up

Fields.

Search Criteria – If search fields are left empty, all results from the Animal form will be displayed after selecting the Search button; otherwise, matches for anything typed in the Search Criteria fields will be returned from the Animal form.

Results – If the Animal you are looking for is displayed in the Results section, click on it and make sure it is displayed in the Selected Animal field.

Selected Animal – Once an animal is selected from the Results, it is displayed here.

OK – Uses the selected data and returns to the form.

Cancel – Returns to the form.

Entity Search Pop-up

Fields.

Search Criteria – If field is left empty, all results from the Entity form will be displayed after selecting the Search button; otherwise, matches for anything typed in the Search Criteria field will be returned from the Entity form.

Results – If the Entity you are looking for is displayed in the Results section, click on it and make sure it is displayed in the Selected Entity Name field.

Selected Entity Name / Address / Organization – Once an entity is selected from the Results, it is displayed here.

OK – Uses the selected data and returns to the form.

Create New – Opens a new Entity form.

Update – Select the entity you want to view or update, select Update, and view or make necessary changes to the entity.

Cancel – Returns to the form.

Incoming Order Search Pop-up

Fields.

Search Criteria – If search fields are left empty, all results from the Incoming Order form will be displayed after selecting the Search button; otherwise, matches for anything typed in the Search Criteria fields will be returned from the Incoming Order form.

Results – If the Incoming Order you are looking for is displayed in the Results section, click on it and make sure it is displayed in the Selected Incoming Order field.

Selected Incoming Order – Once an incoming order is selected from the Results, it is displayed here.

OK – Uses the selected data and returns to the form.

Cancel – Returns to the form.

Protocol Search Pop-up

Fields.

Search Criteria – If search fields are left empty, all results from the Protocol form will be displayed after selecting the Search button; otherwise, matches for anything typed in the Search Criteria fields will be returned from the Protocol form.

Results – If the Protocol you are looking for is displayed in the Results section, click on it and make sure it is displayed in the Selected Protocol field.

Selected Protocol – Once an incoming order is selected from the Results, it is displayed here.

OK – Uses the selected data and returns to the form.

Create New – Opens a new Protocol form.

Update – Select the protocol you want to view or update, select Update, and view or make necessary changes to the protocol.

Cancel – Returns to the form.

Recipe Search Pop-up

Fields.

Search Criteria – If search fields are left empty, all results from the Recipe form will be displayed after selecting the Search button; otherwise, matches for anything typed in the Search Criteria fields will be returned from the Recipe form.

Results – If the Recipe you are looking for is displayed in the Results section, click on it and make sure it is displayed in the Selected Recipe field.

Selected Recipe – Once a recipe is selected from the Results, it is displayed here.

OK – Uses the selected data and returns to the form.

Create New – Opens a new Recipe form.

Update – Select the recipe you want to view or update, select Update, and view or make necessary changes to the recipe.

Cancel – Returns to the form.

Taxonomy Search Pop-up

Fields.

Search Criteria – If field is left empty, all results from the Taxonomy form will be displayed after selecting the Search button; otherwise, matches for anything typed in the Search Criteria field will be returned from the Taxonomy form.

Results – If the Taxonomy you are looking for is displayed in the Results section, click on it and make sure it is displayed in the Selected Taxonomy field.

Selected Taxonomy / Species Common Name – Once a taxonomy is selected from the Results, displays the Taxonomy and Species Common Name for the Taxonomy.

OK – Uses the selected data and returns to the form.

Cancel – Returns to the form.

Protocol

Purpose: To store information about procedures used in shipping, cryopreserving, evaluating, and storing samples for the repository.

Tables populated by this form: protocols, protocol_recipes.

Other forms accessed from this form: recipe search pop-up, taxonomy search pop-up.

Fields.

Protocol ID – Automatically populated by the database when the protocol record is saved.

Active Date – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy; this is the date the protocol was established for use with repository samples.

Inactive Date – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy; this is the date the protocol is replaced with another, or is no longer used.

Protocol Name – Required, the name of the protocol.

Details – Required, text field (limited to 4,000 characters) to describe the protocol.

Protocol URL – Optional, text field (limited to 100 characters) to enter a web link to the protocol.

References – Optional, text field (2,000 characters) to enter citations for the protocol.

Recipe Use Order – Automatically populated by the database in the order recipes are attached to the protocol; can be changed by the user.

In the Recipe area, the Add button can be used to add more than 1 recipe to a protocol; the Update (UPD) button can be used to modify the recipe, and the Delete (DEL) link can be used to remove the Recipe from the protocol (it does not delete the Recipe from the database). The Add and Delete links work the same way in the Taxonomy section.

Recipe ID/Recipe Name/Recipe Type/Active Date/Inactive Date – Optional, use the search button to open the recipe search pop-up; selecting a recipe will autopopulate the recipe area.

Tax. ID/Full Taxonomy Name – Optional, use the search button to open the taxonomy search pop-up; selecting a taxonomy will automatically populate the taxonomy area.

Save – Commits the data to the database and provides a message at the top of the form (Records have been saved).

Clear – Removes the data from the form without saving the record.

Protocol Search

Purpose: Allow searching for existing protocols.

Tables populated by this form: none.

Other forms accessed from this form: protocol.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Protocol Name, Active Date, Recipes, URL, Details, References, and Taxonomies fields from the Protocol form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) the record or the Create New button at the bottom of the form to start with a blank form.

The delete (DEL) button is only available for protocols that are not in use in the database.

Results can be sorted by clicking on any of the Results column headers.

Recipe

Purpose: To store information about media used in lab protocols.

Tables populated by this form: recipes.

Other forms accessed from this form: none.

Fields.

Recipe ID – Automatically populated by the database when the record is saved.

Active Date – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy; indicates the date the recipe went into effect.

Inactive Date – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy; indicates the date the recipe stopped being used in protocols.

Recipe Name – Required, name of the extender or other recipe.

Type – Optional, used the drop down list to select the type of media the recipe is for; new recipe types can be added by a Super User.

Details – Required, text field (limited to 4,000 characters) to describe the formuation for the recipe.

Recipe URL – Optional, text field (limited to 100 characters) to enter a web link to the recipe.

References – Optional, text field (up to 2,000 characters) to enter citations for the recipe.

Save – Commits the data to the database and provides a message at the top of the form (Recipe has been saved with the ID=2).

Clear – Removes the data from the form without saving the record.

Recipe Search

Purpose: Allow searching for existing recipes.

Tables populated by this form: none.

Other forms accessed from this form: recipe.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Recipe ID, Recipe Name, and Protocols fields from the Recipe form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) the record or the Create New button at the bottom of the form to start with a blank form.

Results can be sorted by clicking on any of the Results column headers.

Request

Purpose: Track material that is requested from the repository.

Tables populated by this form: request_headers, request_lines, request_line_locs, request_results.

Other forms accessed from this form: entity search pop-up, address pop-up, animal search pop-up.

Fields – Request Header.

Request ID – Automatically populated by the database when the Request Header is saved.

Request Type – Optional, use the drop down list to select whether the request is internal to the repository or an external one.

Germplasm Type – Required, use the drop down list to select the type of material being requested. Separate requests should be created if multiple germplasm types are being requested.

Status – Required, default is ‘New’ for a new Request; use the drop down list to change the Status of the Request as material is prepared and shipped.

Request Reason – Optional, use the drop down list to select for what purpose the material will be used.

Repository Name – Required, use the drop down list to select the repository the material is being requested from.

Status Date – Required, default is today’s date; can use calendar pop-up to select date or manually type in mm/dd/yyyy; this date corresponds with the Status field. For example, Status is New on 6/25/2013 and Shipped on 6/27/2013.

Request Date – Required, default is today’s date; can use calendar pop-up to select date or manually type in mm/dd/yyyy; this is the date the material was initially requested.

Requestor Name – Required, use the search button to open the entity search pop-up; search for and select the person/company that made the request. If the person/company doesn’t exist, open another database window and create the record using the entity form. Then, search again for the record.

Ship to Address – Required, the address will automatically populate with the address of the Requestor if only one address exists; otherwise, use the search button to open the address search pop-up. If more than one address exists for the Requestor, the Results section of the pop-up will display the addresses to choose from. Select the address and click on OK. If no address exists for the Requestor, select the Create New button to open the Update Entity form to add an address. Close the Entity form and return to the address search pop-up. Click on the Refresh List and select the address. Click on OK to return to the Request form.

Processed By – Optional, used for quality control purposes to record the person responsible for packaging the material to fill the request.

Verified By – Optional, used for quality control purposes to record the person responsible for ensuring the correct material was packaged and shipped.

Purpose – Optional, text field (limited to 1,000 characters) to describe the reason for the request.

Intended Use – Optional, text field (limited to 1,000 characters) to describe what the requested material will be used for.

Use Protocol – Optional, text field (1,000 characters) to describe the protocols and procedures that will be used for the material.

Info. Return – Optional, text field (1,000 characters) to describe the information expected to be returned about the material (ex.: conception rate, citations for publications).

Comments – Optional, text field to add notes about the request, limited to 100 characters.

Save – Commits the data to the database and generates a Request ID.

Clear – Clears the data in the Request Header without saving it to the database.

Fields – Request Animals.

Ctry – Autopopulated by the database.

Rep. Num – Required, either type in the Repository Number or use the search button to open the animal search pop-up to find the animal being requested.

Identifications – Automatically populated by the database when the Repository Number is entered.

Lowest Level Taxonomy – Automatically populated by the database when the Repository Number is entered.

Qty Req. – Required, the number of units being requested for the animal.

Qty Picked – Automatically calculated and filled in by the database as units are selected from the available inventory.

Qty Avail. – Automatically populated by the database with the units of material that are available for request for the animal and germplasm type selected.

Status – Required, automatically populated with New by default, but the drop down list can be used to select a different status for the selected animal. For example, the Status in the Request Header might be Pending for the overall request, but the Status of one particular Animal is Cancelled.

Status Date – Required, automatically populated with today’s date, but can be changed, format is mm/dd/yyyy. This date corresponds to the Status field.

Comments – Optional, details (100 character limit) about the request of this animal. For example, the reason why the line was cancelled.

Save – Commits the record to the database and allows another animal to be added, or allows locations to be picked for the animal.

Add – Empties the Animal line so another animal can be entered.

Remove – Removes an animal from the Request; a pop-up message is displayed to confirm the delete before the deletion is committed.

Cancel Changes – Undoes changes to the request line.

Fields – Pick Locations.

Select a Location – Required, use the drop down list to select from the locations available for the animal. The drop down list includes the location, quantity, Incoming Order ID, and motility (if available).

When selecting the Locations, make sure the Animal you expect is the one displayed in the Animals section. You can use the ‘<<’ button to move to the first Animal.

Location/Current Inventory/Inventory Allocation – Automatically populated once a location is selected.

Inventory Picked – Use the Quantity Requested field in the Animals section in conjunction with the Current Inventory and Inventory Allocation to enter the quantity to remove from each Allocation Type. For example, in the first screen shot below, 2 units are requested and all allocation is in Unallocated. So, a 2 should be entered in the Unallocated Qty. field. If the quantity requested is a partial unit (for example, 10 µl of DNA from a 100 µl vial), this is entered in the Unit Count field instead of the Qty. field, as shown in the second screen shot below.

Add – Empties out the Inventory Picked section and adds the selected location to the Picked Locations section at the bottom of the form.

If additional locations need to be selected, the next one can be selected from the Select a Location drop down list.

Records in the Picked Locations lists can be changed using the Action buttons to Update (UPD) or Delete (DEL).

Once the locations have all been selected for an animal, the Qty Picked field in the Animals section will reflect that. If a different quantity is Picked than was Requested, a comment as to why would be useful documentation.

To move to the next animal in the Request, click on the Next link at the bottom of the Animals section.

Once the locations have been selected for all animals, you can use the Quick Picks list on the left sidebar to open and print the Picking List Report. This provides a list to assist in pulling the material from the repository.

After a shipment is sent out, you will need to change the Status in the Request Header to shipped and change the Status Date to reflect that.

Once the Status has been changed to shipped, to make any changes to the Request, you must change the Status to pending, make the change, and change the Status back to shipped.

Request Results

Purpose: Store results returned from material shipped out to requestors.

Tables populated by this form: request_results.

Other forms accessed from this form: none.

The Request Results form can be accessed through the Request Search form by searching for a request and clicking on the Results link in the Action column.

Fields.

Request Header ID / Request Type / Germplasm Type / Status / Requestor Name – Automatically populated by the database based on the selected Request.

Animal Specific Result – if checked, shows a list of animals associated with the request to enter results for.

Request Result – 4,000 character text field to enter the results for the Request or for the animal if the Animal Specific Result box is checked.

Save – Commits the data to the database and displays a message at the top of the form ‘Result was successfully created’.

Cancel – Clears unsaved data from the form.

Request Search

Purpose: Allow searching for existing requests.

Tables populated by this form: none.

Other forms accessed from this form: request, request results.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Repository, Requestor, Request Date, Request Reason, Request Type, Animal Repository Number, Animal Identification, Germplasm Type, and Status fields from the Request form will be searched for what is entered in this field. If the check box is selected, the search will be limited to the Animal Repository Number and Animal Identification fields.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or Cancel the record, go to the Request Results form (Results), or the Create New button at the bottom of the form to start with a blank form.

Results can be sorted by clicking on any of the Results column headers.

Taxonomy Image

Purpose: To store pictures that represent males and females of each taxonomy.

Tables populated by this form: images.

Other forms accessed from this form: taxonomy search pop-up.

Fields.

Image for – Required, to enter a taxonomy image, select the Taxonomy radio button.

Full Taxonomy Name – Required, use the search button to search for a taxonomy to attach the image to.

Upload File – Required, use the Browse button to bring up a search window to locate the picture file on your computer, select the file, and click on Open; the window will close and the file path will fill in automatically.

Sex – Optional, use the drop down list to select male (M) or female (F).

View – Required, use the drop down list to state whether the image is of the back, front, or profile of the animal.

Caption – Optional, text field displayed on the public web pages when the user mouses over the image, limited to 50 characters.

Copyright / Source – Optional, use the drop down list to select the source of the image; if the person you are looking for is not in the list, a Super User will need to create it using the Information Source form.

Description – Optional, text field to provide information about the image, limited to 300 characters.

Save – Commits the data to the database and provides a message at the top of the form that the save was successful.

Cancel – Exits the form without saving the data.

After saving, the image thumbnail appears at the bottom of the form; click on Update (UPD) or Delete (DEL) to modify or delete the current image, Upload Taxonomy Images in the Quick Picks list, or return to Main Menu to exit the form.

Taxonomy Image Search

Purpose: To allow the user to search for an existing image.

Tables populated by this form: none.

Other forms accessed by this form: images.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the ID, Full Taxonomy Name, Caption, Description, and Copyright Source fields from the Taxonomy Image form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New button at the bottom of the form.

Results can be sorted by clicking on any of the Results column headers.

Taxonomy Observation

Purpose: To enter average, minimum, and maximum genotypic and phenotypic information about a taxonomy at a point in time.

Tables populated by this form: tax_observations.

Other forms accessed from this form: none.

The Taxonomy Observation form can be accessed through the Taxonomy Search form by searching for a taxonomy and clicking on the Obs link in the Action column.

Fields.

Taxonomy – Automatically populated with taxonomy selected from the Taxonomy Search form; can use the drop down list or the arrows or previous/next links to select another taxonomy.

Descriptor – Required, use the drop down list to select the type of observation you want to enter; if the descriptor you are looking for is not in the list, a Super User will need to create it using the Create New Descriptor form.

Min. Value – Optional, enter the minimum value for the taxonomy, using the Units field and the Message field as guidelines for how the data should be reported.

Max. Value – Optional, enter the maximum value for the taxonomy, using the Units field and the Message field as guidelines for how the data should be reported.

Avg. Value – Optional, enter the average value for the taxonomy, using the Units field and the Message field as guidelines for how the data should be reported.

Avg. M – Optional, enter the average value for males in the taxonomy, using the Units field and the Message field as guidelines for how the data should be reported.

Avg. F – Optional, enter the average value for females in the taxonomy, using the Units field and the Message field as guidelines for how the data should be reported.

Although each of the Value fields (Min., Max., Avg., Avg. M, and Avg. F) is optional, at least one of them is required to save the record.

Units – Automatically populated when the descriptor is selected; provides information about how the descriptor data is to be entered.

Date Observed – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy, mm/yyyy, or yyyy; this is the date the observation occurred.

Information Source – Optional, use the drop down list to select the provider of the observation; if the person you are looking for is not in the list, a Super User will need to create it using the Information Source form.

Comments – Optional, text field to add notes about the observation, limited to 100 characters.

Save – Commits the data to the database, displays the new record in a list at the bottom of the form, and shows the save was successful with a message at the top of the form (ex: Observation was successfully created.).

Clear – Removes the entered data from the form without saving it to the database.

After creating a new observation, you can continue to create new observations on the form, or use the UPD or DEL buttons in the Action column at the bottom of the form to modify or delete existing observations.

Taxonomy Search

Purpose: Allow searching for existing taxonomies.

Tables populated by this form: none.

Other forms accessed from this form: taxonomy, images, taxonomy observations, allocation rule.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Taxonomy ID, Category, Full Taxonomy Name, Common Names, and Purposes fields from the Taxonomy form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) the taxonomy record, access the images (Img), the taxonomy observations (Obs), or the allocation rules (Alr) or use the Create New button at the bottom of the form to create a new taxonomy record. Create new, update, and delete are only available to Administrators and Super Users. Delete is only available for taxonomies that are not in use in the database.

Results can be sorted by clicking on any of the Results column headers.

Form Descriptions (Super Users)

This module provides information about database forms that are accessible only by Administrators and Super Users.

Agreement History

Purpose: Allow searching for current and past agreements.

Tables populated by this form: none.

Other forms accessed by this form: none.

You should apply the descriptor to the highest level taxonomy possible. For example, Horn Status applies to Sheep, Cattle, and Goats, who all belong to the Family Bovidae. The descriptor can be applied to Bovidae instead of separately to each species.This does not apply to a descriptor like Birth Weight since the species have a different range of acceptable values.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Agreement ID, Document Number, and Details fields from the Agreement form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to View the Agreement History.

Agreement Notifications Search

Purpose: Allow searching for notifications sent about expired agreements.

Tables populated by this form: none.

Other forms accessed by this form: agreement notification.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Agreement Entity Name and Notified User Name from the Agreement Notifications table will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to View the Agreement Notifications.

The screens below show the Agreement Notification and the accompanying email sent to the Super User.

Allocation Rules Notifications

Purpose: Allow searching for notifications sent about expired allocation rules.

Tables populated by this form: none.

Other forms accessed by this form: allocation rules notification.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Allocation Rule ID and Notified User Name from the Allocaton Rules Notifications table will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to View the Allocation Rule Notifications.

The screens below show the Allocation Rule Notification and the accompanying email sent to the Super User.

Birth Place

Purpose: To search for and store birth place data to aid in indentification of pedigree animals.

Tables populated by this form: birth_place_refs.

Other forms accessed from this form: birth place.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Birth Place ID and Birth Place from the Birth Place form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New button at the bottom of the form.

To create a new record.

ID – automatically populated when the record is saved.

Birth Place – Required, text field (30 characters) to enter a birth place location.

Save – Commits the data to the database, displays a message at the top of the form that the record was successfully created, and enters Edit mode if you want to make modifications to the record.

Clear – Removes any data from the form and enters into New mode to allow a new record to be created.

Country Reference / Country Subdivision Reference

Purpose: To search for and store country names for use in addresses.

Tables populated by this form: country_refs.

Other forms accessed from this form: country refs.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Country Name and Country Abbreviation from the Country Refs form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New button at the bottom of the form.

To create a new record.

Country Abbr. – Required, assign a 2 letter code to represent the country; ISO standards should be used when possible: http://www.iso.org/iso/home.htm.

Country Name – Required, enter the name of the country.

Old Country ID – If a country’s name changes, use this field to enter the old Country ID to link the old record to the new one.

Inactive Flag – Check this box if the country record is no longer in use. It will maintain the old records without allowing it to be used for new records.

Record Source Flag – Check this box if the country is using the database; this will allow the country to be included as part of a Record Source.

Create – Commits the data to the database, displays a message at the top of the form that the record was successfully created, enters Edit mode if you want to make modifications to the record, and displays a list of Associated Country Subdivision Refs.

To create new Country Subdivisions.

Click on the New Country Subdivsion Ref button from the Update Country Ref form.

Fields.

Subdivision Abbreviation – Optional, enter the abbreviation for the subdivision, limited to 5 characters. For example, the U.S. subdivisions are states and the abbreviation for Colorado is CO.

Subdivision Name – Required, enter the name of the state, province, territory, etc., limited to 50 characters.

Subdivision Type – Optional, this is the way the subdivision is described by the country, for example, state, province, district.

Inactive Flag – Check this box if the subdivision record is no longer in use. It will maintain the old records without allowing it to be used for new records.

Save – Commits the data to the database, displays a message at the top of the form that the record was successfully created, and enters Edit mode if you want to make modifications to the record.

Use the Return to Country Edit link in the left sidebar if you are done entering subdivision records.

DB Codes

Purpose: To search for and store codes assigned to db objects.

Tables populated by this form: db_codes.

Other forms accessed from this form: db codes.

To create a new record.

DB Object – Required, use the drop down list to select the database object to assign a new code to; if the DB object doesn’t exist, you can use the Create New DB Object button to access the Create New DB Object form.

DB_Object ID – Automatically filled in based on the DB Object selected.

Code Name – Required, enter the name of the new code.

Code Definition – Optional, text field (limited to 1,000 characters) to describe the code.

Comments – Optional, text field (100 characters) for any notes about the code.

Save – Commits the data to the database, displays a message at the top of the form that the record was successfully created, enters Edit mode if you want to make modifications to the record, and displays a list of DB Codes associated with the selected DB Object.

To search for a record, select Go to Search from the Quick Picks menu.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the DB Code ID, Code Name, Code Definition, and Comments from the DB Codes form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New button at the bottom of the form.

Descriptor

Purpose: To create the fields the animal, entity, inventory, and taxonomy observations will be assigned to.

Tables populated by this form: descriptors, descriptor_codes, descriptor_taxonomies.

Other forms accessed from this form: taxonomy search pop-up.

Fields.

Descriptor ID – Automatically populated by the database when the record is saved.

Descriptor Type – Required, use the drop down list to select whether the descriptor is for an animal, entity, inventory, or taxonomy.

Descriptor Name – Required, enter the name of the descriptor, Birth Weight, for example.

Descriptor Group – Optional, use the drop down list to select whether the descriptor is genotypic, phenotypic, etc. This is used to group observations in the public web pages.

Descriptor Format – Optional, use the drop down list to select whether the observations should be automatically formatted to initial capitalization, lowercase, or uppercase. This is not necessary for numeric data.

Proportion – Required, default is No. Use the drop down list to select Yes if the data should be summarized as a proportion for reports. In most cases, coded descriptors should be reported as a proportion.

Data Type – Use the drop down list to select whether the observations will be alphanumeric or numeric.

Unit – Optional, use the drop down list to select the units the observation will be reported in. Additional Unit types can be added in the DB Codes form (Super User).

Minimum Value – Optional, provide a minimum value allowed for the observations. This will be displayed in the Message area on the Descriptor form to provide guidelines for the user.

Maximum Value – Optional, provide a maximum value allowed for the observations. This will be displayed in the Message area on the Descriptor form to provide guidelines for the user.

Data Format – Optional, should be filled in for Numeric descriptors. This field is used to show how many decimal places the data should be rounded to (99.999) and an ‘S’ should be placed at the front if the data should be displayed at a + or - (S99.999).

Coded – Required, default is No. Use the drop down list to change the field to Yes if the observations are coded. The form will change so codes can be entered.

Definition – Optional, text field (limited to 1,000 characters) to describe the descriptor.

Comments – Text field (100 characters) to add notes about the descriptor.

If Coded = Yes.

Code Name – Required, add the name of the first code. Ex.: Horned.

Code Definition – Optional, provide a brief description of what the code means.

Comments – Optional, add notes about the code.

Use the Add and DEL links to manage additional codes.

If Descriptor Type = Animal.

Qualifier Name – Optional, this field is used in conjunction with breeding values and this sets the name to be displayed on the Descriptor form. Examples are Accuracy, Predicted Error, and Reliability.

Qualifier Min – The minimum value allowed for the qualifier.

Qualifier Max – The maximum value allowed for the qualifier.

You should apply the descriptor to the highest level taxonomy possible. For example, Horn Status applies to Sheep, Cattle, and Goats, who all belong to the Family Bovidae. The descriptor can be applied to Bovidae instead of separately to each species.This does not apply to a descriptor like Birth Weight since the species have a different range of acceptable values.

If Descriptor Type = Animal, Entity, or Taxonomy.

Full Taxonomy Name – Use the taxonomy search pop-up to search for the taxonomy the descriptor applies to. The Add link can be used to add additional taxonomies and the Del link can be used to remove them.

Descriptor Cross Refs

Purpose: To link matching animal descriptors and taxonomy descriptors to generate collection vs. industry reports.

Tables populated by this form: descriptor_cross_refs.

Other forms accessed from this form: descriptor cross refs.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Descriptor Cross Refs ID, Collection Descriptor Name, Collection Descriptor Code and Industry Descriptor Name from the Descriptor Cross Refs form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to delete (DEL) or the Create New button at the bottom of the form.

To create a new record.

Common Name – Either Common Name or Species are required, use the drop down list to select the common name of the animals you want to match descriptors for.

Species – Either Common Name or Species are required, use the drop down list to select the species of the animals you want to match descriptors for.

Sublevel – Optional, Species must be selected before this field can be selected; use the drop down list to select the species of the animals you want to match descriptors for.

Search – Shows the Descriptor Cross Reference Entry form with a drop down lists of descriptors filtered by the search criteria, displays a list of existing matches that meet the search criteria, and changes the Search button to New Search if you want to change your search.

Descriptor Cross Reference Entry.

Collection Descriptor Name – Required, use the drop down list to select the animal descriptor to match to the taxonomy descriptor.

Collection Descriptor Code – Required if Collection Descriptor Name is a coded descriptor. Use the drop down list to select a code to match to the taxonomy descriptor.

Industry Descriptor Name – Required, use the drop down list to select the taxonomy descriptor to match to the animal descriptor.

Save – Commits the data to the database, provides a message at the top of the form stating the Descriptor Cross Ref was successfully created, clears the entry form, and displays the record at the bottom of the form in the Descriptor Cross Reference list.

Descriptor Cross Reference List.

DEL – Use this link to delete Descriptor Cross References.

Descriptor Search

Purpose: Allow searching for existing descriptors.

Tables populated by this form: none.

Other forms accessed by this form: descriptor.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Descriptor ID, Descriptor Group, Descriptor Name, Descriptor Definition, Descriptor Type, Descriptor Codes, and Taxonomy from the Descriptor form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

The delete (DEL) button is only available for descriptors that are not currently in use in the database.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) the descriptors or the Create New button at the bottom of the form.

Help Pages

Purpose: To provide information about each form.

Tables populated by this form: help_pages.

Other forms accessed by this form: help page.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Controller Name and Page Title from the Birth Place form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New button at the bottom of the form.

To create a new record.

Controller Name – Required, this is the first part of the page URL after http://nrrc.ars.usda.gov/A-GRIN/, for example, allocation_rules.

Page Title – Required, this is the text displayed in the title bar of your browser, see below for example.

Help Text – Optional, text field to provide information about the form. If HTML tags are used, they will be included in the output and interpreted by the browser. There is no checking for correct HTML syntax.

Create – Commits the data to the database and displays a message at the top of the form that the Help Page was successfully created.

Information Source

Purpose: To search for and store sources of information (people or places).

Tables populated by this form: info_source_refs.

Other forms accessed from this form: information source.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Information Source ID and Information Source from the Information Source form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New button at the bottom of the form.

The delete (DEL) button is only available for information sources that are not being used in the database.

To create a new record.

ID – automatically populated when the record is saved.

Info Source – Required, text field (30 characters) to enter a source of information in the database. For example, the provider of Birth Weight data for a Hereford bull.

Save – Commits the data to the database, displays a message at the top of the form that the record was successfully created, and enters Edit mode if you want to make modifications to the record.

Clear – Removes any data from the form and enters into New mode to allow a new record to be created.

Location Structure Reference

Purpose: To provide a framework for storing inventory locations.

Tables populated by this form: location_structure_refs.

Other forms accessed from this form: location structure reference.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Location Structure References ID, Container Type, and Level Title from the Location Structure References form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New button at the bottom of the form.

To create a new record.

Container Type – Required, use the drop down list to select the type of container you will be creating the location structure for. If the code is not in the list, a Super User can add it in the DB codes form under the DB object: locations.container_type.

Level Title – Required, use the drop down list to select the level of the location structure you want to create. If the code is not in the list, a Super User can add it in the DB codes form under the DB object: locations.loc_level.

Capacity – Optional, stores the maximum quantity of units that can be stored at that level.

Parent Loc Structure – Required, use the drop down list to either select ‘No Parent’ if the location level is the highest level, or the parent structure (ex: the parent of Pie is Tank).

Required Flag – Use this check box if this location level is required for this location structure; leave unchecked if it is optional.

Sublevel Flag – Use this check box if this location level has a child location level (ex: Pie will have Canister as a sublevel); leave unchecked if this is the lowest possible location level.

Create – Commits the data to the database, displays a message at the top of the form that the record was successfully created, shows the created record, and provides a link to Edit the record or a Back link to return to the location structure reference search form.

Profession

Purpose: To store professions for use in the entity form.

Tables populated by this form: profession_refs.

Other forms accessed from this form: profession.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Profession ID and Profession from the Profession form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New button at the bottom of the form.

To create a new record.

ID – automatically populated when the record is saved.

Profession – Required, text field (50 characters) to enter a profession for use in the entity form.

Save – Commits the data to the database, displays a message at the top of the form that the record was successfully created, and enters Edit mode if you want to make modifications to the record.

Clear – Removes any data from the form and enters into New mode to allow a new record to be created.

Taxonomy

Purpose: To store taxonomy data for animals in the database.

Tables populated by this form: taxonomies, tax_comm_names, taxonomy_purposes.

Other forms accessed from this form: none.

Fields.

Enter Parent Taxonomy Structure – Category/Taxonomy Name – This section can be used to select the Family, Family & Genus, Family, Genus, & Species, or Family, Genus, Species, & Breed for a new taxonomy record using the drop down lists, if those records exist (see screenshot below).

Taxonomy Level Information – Category – Required, use the drop down list to select the type of taxonomy you want to create. If the Parent Taxonomy Structure is filled out, the Category selected must fit within a standard taxonomy structure. For example, if Family & Genus are filled out above, the next Category must be Species. If the Parent Taxonomy Structure isn’t filled out, any Category can be selected.

Taxonomy Level Information – Taxonomy Name – Required, text field (up to 100 characters) to enter the name of the taxonomy that corresponds with the Category selected.

Web Classification – Use the drop down list to select the how the animal type should be grouped for the public web pages. This is only relevant for certain taxonomy levels and is dependent on the animal type. For example, clarki is the Species level for Cutthroat trout and the Web Classification would be set to Aquatic Freshwater Fish at the Species level. The Family Bovidae is the same for cattle, sheep, and goats, so no Web Classification is appropriate here.

Full Taxonomy Name – Automatically populated with all levels of the taxonomy structure, allowing you to make sure it is what you expect it to be.

Sample Identification – Optional, what is entered in this text field (50 characters) will be displayed in the Animal form above the animal identifications section. This field is to serve as a guide to the user about how identifications should be entered; this is to promote uniformity of data entry. For example, U.S. Holstein registration numbers can be found as 123456789 or HOUSA123456789 or HOUSA000123456789. Entering one of these in this field will serve as a reminder to the user of what has been decided upon for the repository.

Taxonomy Label Abbr – Optional, this field is the abbreviation for printing on straws or other storage unit. For example, the abbreviation for U.S. Hog Island sheep is OVHi (Ovis aries Hog Island).

Target Core Qty – Optional, this is the goal number of units or doses for the Core allocation for this taxonomy. This value is used to calculate percentage of Core met for reports and public web pages.

Description – Optional, this 1,000 character text field is used to describe the taxonomy. Examples of information to include are the origin, when imported into your country, physical description of the animals, conservation efforts, etc.

Common Names – Optional, this is the name the taxonomy is usually referred to as. For example, in the U.S., the taxonomy Salmonidae Oncorhynchus clarki is commonly known as Cutthroat trout. The Add link can be used to add additional Common Names and the DEL link can be used to delete them.

Purposes – Rank – Required if Purpose is selected; automatically populated by the database, but can be changed to prioritize the importance of the purposes (ex: meat, milk, fiber).

Purpose – Optional, use the drop down list to select the function of the animals within the taxonomy. Additional codes can be added by a Super User. The Add link can be used to add additional Purposes and the DEL link can be used to delete them.

Save – Commits the data to the database, displays a message at the top of the form that the record has been saved, adds the record to the appropriate taxonomy list, and clears the form so additional records can be created.

Taxonomy Cross Reference

Purpose: To match equivalent taxonomies across countries; used in generating comparison reports and web pages.

Tables populated by this form: tax_cross_refs.

Other forms accessed from this form: none.

Fields.

Country 1 - Ctry – Required, use the drop down list to select the Country of Taxonomy 1.

Country 1 - Tax ID – Automatically populated with the taxonomy ID when the taxonomy is selected.

Country 1 - Full Taxonomy Name – Required, use the drop down list to select the first taxonomy you want to relate to the the other taxonomy.

Country 2 – Ctry – Required, use the drop down list to select the country of Taxonomy 2.

Country 2 – Tax ID – Automatically populated with the taxonomy ID when the taxonomy is selected.

Country 2 – Full Taxonomy Name – Required, use the drop down list to select the taxonomy to relate to the first taxonomy.

Save – Commits the record to the database, provides a message at the top of the page (TaxCrossRef was successfully created. ID = 1), shows the record at the bottom of the form, and clears the form so another record can be entered.

Newly created records can be modified using the Actions buttons to the right of the record. Use the Edit button to move the record back up to the main part of the form to make changes. Use the DEL button to delete the record.

More than one taxonomy from one country can be assigned to one taxonomy from another country. For example, Angus and Red Angus breeds from the U.S. are assigned to Angus in Brazil. See the figure below.

Taxonomy Cross Reference Search

Purpose: Allow searching for existing taxonomy cross references.

Tables populated by this form: none.

Other forms accessed from this form: taxonomy cross references.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Full Taxonomy Name 1, Full Taxonomy Name 2, and Cross Reference ID from the Taxonomy Cross Reference form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) the record, or the Create New button at the bottom of the form to start with a blank form.

Results can be sorted by clicking on any of the Results column headers.

Taxonomy Purpose

Purpose: To store what the animals within the taxonomy are used for.

Tables populated by this form: tax_purpose_refs.

Other forms accessed from this form: taxonomy purpose.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Taxonomy Purpose ID, Purpose, and Definition from the Taxonomy Purpose form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New button at the bottom of the form.

To create a new record.

Purpose – Required, text field (50 characters) to enter a code representing what a taxonomy is used for (ex: meat, milk).

Definition – Optional, text field to provide details about what the purpose code means, limited to 1,000 characters.

Save – Commits the data to the database, displays a message at the top of the form that the record was successfully created, and enters Edit mode if you want to make modifications to the record.

Clear – Removes any data from the form and enters into New mode to allow a new record to be created.

Unit Form

Purpose: To store codes for the type of storage container the repository material is contained in.

Tables populated by this form: unit_form_refs.

Other forms accessed from this form: unit form.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Unit Form ID and Unit Form from the Unit Form form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New button at the bottom of the form.

To create a new record.

ID – Automatically populated by the database when the record is saved.

Unit Form – Required, enter the name of the type of storage container, limited to 30 characters (ex: straw, vial).

Save – Commits the data to the database, displays a message at the top of the form that the record was successfully created, and enters Edit mode if you want to make modifications to the record.

Clear – Removes any data from the form and enters into New mode to allow a new record to be created.

Unit Size

Purpose: To store the size of the storage container the repository material is contained in.

Tables populated by this form: unit_size_refs.

Other forms accessed from this form: unit size.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Unit Size ID and Unit Size from the Unit Size form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New button at the bottom of the form.

To create a new record.

ID – Automatically populated by the database when the record is saved.

Unit Size – Required, enter the value for the size of the storage container (ex: 0.25 mL, 0.5 mL).

Save – Commits the data to the database, displays a message at the top of the form that the record was successfully created, and enters Edit mode if you want to make modifications to the record.

Clear – Removes any data from the form and enters into New mode to allow a new record to be created.

Users

Purpose: To store information allowing the database users to access the database and enter, modify, and delete data in the database.

Tables populated by this form: db_users.

Other forms accessed from this form: user.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the User Name, Last Name, First Name, and Email from the User form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New Animal Germplasm User link at the bottom of the form.

To create a new record.

User Name – Required, used for logging into the database; current standard format is first name.last name (ex: Joe.Smith).

Last Name – Required, enter the last name of the user.

First Name – Required, enter the first name of the user.

Email – Required, enter the email address for the user; this is used for notifications and to send the user instructions for changing their password if they request it at login.

Organization – Required, use the drop down list to select the organization the user is associated with and will be entering data for.

User Grp – Required, use the drop down list to select whether the user is going to be an Administrator, Super User, or User. An Administrator has the ability to create new countries and has full control over the database. This should be limited to 1 or 2 people (in total, not per country). A Super User can access and edit any data within their country. This should be limited to 1 or 2 people within each country. A User can add, edit, and delete data within their country, but cannot access or create data in the administrative forms (creating users, codes, taxonomies, etc.).

Users in Brazil are limited to records within their location and assigned taxonomy(ies).

Record Source – Required, use the drop down list to select the country the user will be entering data for.

Password – Required, create a password for the user to enter at login. Currently, the only restriction is that is must be at least 4 characters.

Password Confirmation – Required, replicate the password created above for verification purposes.

Inactive Flag – Check this box for a user that is no longer accessing the database. Because a User’s history of record creation, record modification, etc. is important to the database, we do not want to delete a user from the database. Making the user inactive prevents them from accessing the database while keeping the history intact.

Comments – Optional, text field to add notes about the user. If the user is made inactive, this would be a good place to make a note about when and why. This field is limited to 100 characters.

Create – Commits the data to the database, displays a message at the top of the form that the record was successfully created, and shows a summary of the new record.

Users x Taxonomies

Purpose: To limit database users to a specific taxonomy(ies) for data entry.

Tables populated by this form: db_users_taxonomies.

Other forms accessed from this form: db user x taxonomies.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the ID, User Name, and Taxonomy from the DB User x Taxonomy form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New button at the bottom of the form.

To create a new record.

DB Users – Required, use the drop down list to select a DB user to assign a taxonomy to.

Taxonomy Entry – Required, use the drop down list to select a taxonomy.

Add – Commits the data to the database and displays the record at the bottom of the form.

Web Classification

Purpose: To group animal taxonomies for public web page and reporting purposes.

Tables populated by this form: web_classification_refs.

Other forms accessed from this form: web classification.

Fields.

Search Criteria – Optional, if field is left empty, all results will be displayed after selecting the Search button; otherwise, the Web Classification ID and Web Classification from the Web Classification form will be searched for what is entered in this field.

The Maximum Results per Page field can be set to display as many or as few results as you want to see on a page.

Once the results are displayed, you can use the Action links in the right column to update (UPD) or delete (DEL) or the Create New button at the bottom of the form.

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To create a new record.

ID – Automatically populated by the database when the record is saved.

Web Classification – Required, enter the name for the animal grouping to be used on the web pages and reports.

Save – Commits the data to the database, displays a message at the top of the form that the record was successfully created, and enters Edit mode if you want to make modifications to the record.

Clear – Removes any data from the form and enters into New mode to allow a new record to be created.

Entering Shipments

This module provides a step-by-step tutorial about the process of entering an incoming shipment.

E-R Diagram for Incoming Orders

Data Gathering

Get all of the information together that you will need to enter the shipment.

Inventory list from the shipper.

Association websites, AI stud websites, breeder websites, etc.

Legal agreements.

Inventory paperwork completed by staff.

It is helpful to have a standardized set of forms for employees that do the physical inventorying process. NAGP has a form for inventorying straws into goblets and a separate form for ampules. Employees write down everything on the straw or ampule and the quantity they place in each location. See below for examples.

Enter Legal Agreement

If there is a restriction or legal agreement that applies to the shipment, enter it before creating the Incoming Order.

Fields.

Entity Name – Required, use the search button to open the entity search pop-up and select the entity the agreement is with.

Agreement ID – automatically filled in by database.

Established Date – Required, can use calendar pop-up to select date or manually type in mm/dd/yyyy; this is the date an agreement started.

Amended Date – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy; this can be used to track the date an agreement was modified or renewed.

Termination Date – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy; this is the date the agreement ends. This date triggers the Agreement Notifications to let Super Users know the Agreement is about to expire so it can either be renewed or any restrictions on the material will expire.

Details – Required, text field to describe the agreement, limited to 2000 characters.

Document Number – Optional, text field to enter the agreement reference number, limited to 30 characters.

Document URL – Optional, test field to enter the web address of the agreement document, limited to 100 characters.

Repository Name – Required, automatically populated with the repository the user is associated with, but the entity search pop-up can be used to select another repository.

Save – Commits the data to the database.

Cancel – Exits the form without saving the data.

Once an agreement is saved, the new record is listed at the bottom of the form; clicking on update (UPD) in the Action column allows you to enter Allocation Rules associated with the agreement.

Fields.

The form automatically populates the Agreement ID and Germplasm Owner fields with the data from the agreement.

Although the Germplasm Owner is populated on the form, Incoming Order ID, Animal, or Taxonomy could be selected instead, if that is appropriate for the agreement.

Rule ID – Automatically populated by the database.

Effective Date – Required, can use calendar pop-up to select date or manually type in mm/dd/yyyy; indicates the date the rule goes into effect, can be past, present, or future.

Duration – Optional, enter in years as a decimal (ex: 5.5).

Termination Date – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy; indicates the date the rule expires.

Priority – Required, automatically set by the database, but can be changed. Look at the list of current rules to decide if the rule you are creating should be higher or lower than existing rules.

Value Type – Required; use the drop down list to select either percent or units.

Alloc. Value – Required, if the value type is percent, this is the percentage of material that should be allocated (enter a number without a % sign). If the value type is units, this is the number of units that should be allocated.

Alloc. Category – Required, use the drop down list to select the category you are allocating material into, either Core, Evaluation, Restricted, or Working.

Germplasm Type – Required, use the drop down list to select the type of material the rule applies to (ex: semen, purified DNA).

Comments – Optional, text field to add notes about the allocation rule, limited to 100 characters.

Apply Retroactively – Check box allowing you to apply a rule in the past; this will retroactively apply to inventory if it already exists; a pop-up message will confirm this when you save the record.

Save – Commits the data to the database.

After saving the record, the form clears out and you can enter another rule, update or delete the rule you just created, or exit the form.

Create Incoming Order – Header

If there is no agreement to enter, or once the agreement has been entered, the next step is to create the Incoming Order.

An Incoming Order starts with the Header information, which contains who, what, when, and where the shipment came from.

Fields – Incoming Order Header.

Incoming Order ID – Autopopulated by the database.

Incoming Order Type – Required, use the drop down list to select the type of shipment you are entering (ex: Donation).

Germplasm Owner Name – Required, this is to record the owner of the material included in the shipment. Use the search button to open the entity search pop-up and search for or create the owner.

Shipper Name – Required, this is to record who sent the material to you. Use the search button to open the entity search pop-up and search for or create the shipper.

Repository Name – Autopopulated based on your login information, but can be changed by clicking on the search button to search for or create a new repository.

Date Received – Required, can use calendar pop-up to select date or manually type in mm/dd/yyyy; this is the date the shipment was received and can be a date in the future if you are preparing for a future shipment.

Description – Optional, text field (limited to 1000 characters) to include information about the shipment.

All/Not Done/Done radio buttons – All is the default; these buttons are for a shipment that is in a partial state of completion with at least some inventory records entered. Clicking on All shows all animals in the shipment, Not Done shows animals with no associated inventory records, and Done shows animals with inventory records. These buttons are particularly useful when searching a large shipment for animals that need inventory records entered. As inventory records are entered, they do not move to the Done records until the incoming order is refreshed.

Agreement ID – Automatically populated by the database when an agreement exists for the Germplasm Owner. You can select View All to see the Agreement information.

Comments – Optional, text field (limited to 100 characters) to enter any comments about the shipment.

Breeder Name – Optional, if the breeder is the same for all animals in the shipment, you can enter it here and it will be applied to all animal records created for the shipment. It will not change the breeder for existing animals that are attached to the shipment. The breeder can also be changed in the animal form.

Germplasm Type – Optional, use the drop down list to select the type of material received in the shipment (ex.: Embryo, Semen).

Original State – Optional, use the drop down list to state whether the material was Fresh or Cryopreserved upon receipt.

Unit Form – Optional, use the drop down list to select the type of packaging used for the material (ex.: straw, ampule). If the shipment was received fresh, this is the type of packaging that will be used. If the material was received cryopreserved and there are more than one unit form types included in the shipment, this can be assigned at the individual inventory level.

Unit Size – Optional, use the drop down list to select the size of packaging used (ex.: 0.25 mL).

Protocol Name – Optional, use the search button to open the protocol search pop-up and search for the protocol used for the shipment, or to create a new protocol.

Save – Commits the data to the database and assigns the Incoming Order ID.

Cancel – Exits the form without saving the data.

Create Incoming Order – Animals

Once the Incoming Order Header has been created, the animals need to be associated with the shipment.

Clicking on the Incoming Order Header, Animal, or Inventory buttons changes that section from full view to condensed view to hidden.

Fields – Incoming Order Animals.

Click on the lower left Animal tab to expand this section.

Attach/Create Animals tab – Click on this tab to search for animals that exist in the database or to create new animal records.

Complete data in any field and click on the Search button to search for animals that exist in the database.

Date of birth searching is flexible. You can search by yyyy, m/yyyy ou dd/mm/yyyy.

If multiple matches are found based on the search criteria, a pop-up box appears and you can select and attach an animal (Attach Selected), create a new animal if none of the animals in the search are the one you are looking for (Create New), or return to the form to change the search criteria (Cancel).

If a single match is found based on the search criteria, the form populated with that animal. You can use the Attach button to include the animal in the shipment or the Clear button to remove the animal from the shipment.

If the search doesn’t find any matches or if you know the animal is new to the database, use the Create New button to open the Animal form.

Create Animal

Fields.

Animal ID – Automatically filled in by database.

Repository Animal – Uncheck the box if the animal does not have material in the repository; otherwise, leave the box checked.

Repository Num – Automatically filled in by database (only filled in if Repository Animal is checked).

Country – Automatically filled in by database.

Taxonomy: Search Criteria – Required, enter the taxonomy name or a partial taxonomy name of the animal you want to enter; select the correct taxonomy from the Results box & the selected taxonomy will display in the Selected Taxonomy field.

Sex – Optional, use the drop down list to select M or F; leave blank for embryos.

Date of Birth – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy, mm/yyyy, or yyyy; used to record the animal’s birth date.

Received Date – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy; the date the animal was first received. When the Animal form is accessed from the Incoming Order, this field is automatically populated, but can be changed.

Genomic Information Available – Optional, check this box if there are genomic results available for the animal.

Active – Optional, this is for live animal populations; use the drop down list to state whether the animal is active (Y) or not (N).

Inactive Date – Optional, this is for live animal populations; can use calendar pop-up to select date or manually type in mm/dd/yyyy, enter the date the animal became inactive.

Inactive Reason – Optional, this is for live animal populations, enter the reason the animal was inactivated (ex.: Culled, Died, Sold).

Sample Identification – This field is automatically populated from the taxonomy form and allows the user to show an example of how the identifications should look for a particular breed, line, etc.

Rank – Click on the Add button in the Identification section to add identifications; Required if Identification Type or Identification are entered; automatically populated by the database, but can be changed to prioritize the importance of the identifications.

If the animal’s information is available online from an Association website, etc., you can copy and paste the information into the database to improve the speed and accuracy of data entry.

Identification Type – Required if Identification is entered, drop down list of the types of identifications available for an animal.

Identification – Required if Identification Type is entered, text field to enter the identification(s) for the animal, limited to 100 characters.

Identification Country – Optional, drop down list of countries that can be assigned to the identification.

Breeder Name – Optional, use the search button to open the entity search pop-up to search for an existing breeder or to access the entity form to create a new one; can delete an attached breeder using the DEL button (this unlinks the breeder from the animal record but does not delete the record from the database).

Description – Optional, text field to add additional information about the animal, limited to 1,000 characters.

Save – Commits the data to the database, assigns the Animal ID and Repository Number, closes the Animal form, and returns you to the Incoming Order form.

Create Incoming Order – Animals (cont.)

Saving the animal record will return you to the Incoming Order and attach the animal to the shipment with a message at the top of the animal area stating the attachment was successful.

Clicking on the Attach/Create Animals tab will clear the form and allow you to search for or create a new animal to attach to the shipment.

View/Update Animals tab – Click on this tab to view or make changes to the animals already attached to the Incoming Order; scroll through the animals using the arrow buttons at the bottom of the form or by entering a number in the box to move to a particular record number.

When the View/Update Animals tab is active, the Enter Animal Observations, Upload Animal Images, and Enter/Edit Pedigree tabs are available for entering additional information about the animals in the shipment. Closing the Animal Observations, Animal Images, or Pedigree forms will return you to the Incoming Order form.

Pedigree, Animal Observations, Animal Images.

Once an Animal record is attached to the Incoming Order, it is a good idea to enter all information available about the animal at one time.

Accessing the forms from Incoming Order manages the data entry for you since the animal ID is retained in the pop-up forms.

Pedigree

A large amount of pedigree data can be uploaded using the Upload File option; only the manual data entry for one animal is explained here.

Fields.

Repository Number – Automatically populated with the animal from the Incoming Order.

Ctry – Automatically populated based on the animal selected.

Identifications – Automatically populated based on the animal selected.

Taxonomy – Automatically populated based on the animal selected.

Search Taxonomy – Automatically populated with the taxonomy of the animal selected. If additional taxonomies should be searched for matches for the pedigree animals, use the Add button and then the drop down list to select additional taxonomies. For example, in the U.S., when the taxonomy is Hereford, the child taxonomies Hereford Line 1 and Hereford Prospector should also be included in the pedigree searching since they all belong to the same breed.

Animal ID / Repository Number / Country / Identification / Identification Type / F – Automatically populated with information about the animal selected.

Sire ID – Identification – Optional, enter the identification for the sire of the selected animal.

Sire ID – Ident. Type – Required if Identification is entered, use the drop down list to select the type of identification entered. If multiple matches are found for the combination of Identification and Identification Type, a pop-up will show the user the animals available to select from. Clicking on Attach Selected will associate the selected animal with the pedigree.

Ancestors of a Sire can only be entered if the Sire is entered. This holds true throughout the pedigree. The pedigree tree must be filled in from the base outward.

Sire ID – You can click on the word Sire to bring up a pedigree pop-up with the Sire as the selected animal.

More info... – use this link to open the more info pop-up if you have more data that you want to add about the sire.

Birth Place – use the drop down list to select the place where the animal was born. If an additional Birth Place is needed, a Super User will need to add the code in the Birth Place References form. Birth Place isn’t needed for animals with unique IDs, such as Registration Numbers. This is more for use with animals that only have ear tags that could be repeated at another location and is a different animal. When the pedigree finds a match for a previously entered animal, this information can be used by the user to decide which animal is the correct match, or if it is a new animal.

Animal ID / Repository Number / Country – Automatically populated by the database.

Full Taxonomy Name – Required, automatically populated with the taxonomy of the selected animal, but the search button can be used to open the taxonomy search form to change the taxonomy. Continuing with the Hereford example, the selected animal might be a Hereford, but the Sire is a Hereford Line 1. The taxonomy search pop-up would be used to change the taxonomy.

Species Common Name – Automatically filled in by the database based on the taxonomy selected.

Rank – The first line is automatically populated by the database from the pedigree form, but can be changed to prioritize the importance of the Identifications if additional Identifications are entered.

Identification Type – The first line is automatically populated by the database from the pedigree form; if additional Identifications are entered, this is required. Use the drop down list to select from the types of identifications available.

Identification – The first line is automatically populated by the database from the pedigree form, if additional Identification Types are entered, this is required. Use the text field to enter the identification(s) for the animal, limited to 100 characters.

Identification Country – Optional, drop down list of countries that can be assigned to the identification.

Save – If the pedigree record has already been saved in the pedigree form and you have made changes in the more info pop-up, the changes are applied to the existing record (same Animal ID). If this animal exists elsewhere in the database, the changes are applied everywhere. If the pedigree record has not been saved in the pedigree form and you have made changes in the more info pop-up, clicking on save will commit the animal to the database and return you to the pedigree form.

If an incorrect ID is entered, you can clear it out of the Identification field and change the Identification Type to “Please Select” and save. Then, enter the correct ID and Identification Type. To permanently remove the incorrect ID from the database, search for it in the Animal Search form and select Del.

Cancel – Returns you to the pedigree form without saving changes made in the more info pop-up.

Dam / PGS / PGD / MGS / MGD / ... – Optional, fill in the identifications as explained above for the Sire.

Save – Commits the data to the database.

Animal Observations

Fields.

Repository Num – Automatically populated with the animal from the Incoming Order.

Ctry (Country) – Automatically populated by the database.

Identifications – Automatically populated based on the animal selected.

Descriptor – Required, use the drop down list to select the type of observation you want to enter; if the descriptor you are looking for is not in the list, a Super User will need to create it using the Create New Descriptor form.

Observation Value – Required, for a non-coded observation, enter the value for the animal, using the Units field and the Message field as guidelines for how the data should be reported. For a coded observation, use the drop down list to select the appropriate value; if the code you are looking for is not in the list, a Super User will need to create it using the Descriptor Search – Update Descriptor forms.

Units – Automatically populated when the descriptor is selected; provides information about how the descriptor data is to be entered.

Date Observed – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy, mm/yyyy, or yyyy; this is the date the observation occurred.

Variable Name, Reliability, Accuracy, etc. – Optional, this field name changes depending on the Descriptor, but is primarily used to record accuracy data for breeding values; if the field is named ‘Variable Name’, then the selected descriptor doesn’t use this field.

Information Source – Optional, use the drop down list to select the provider of the observation; if the person you are looking for is not in the list, a Super User will need to create it using the Information Source form.

Comments – Optional, text field to add notes about the observation, limited to 100 characters.

Save – Commits the data to the database, displays the new record in a list at the bottom of the form, and shows the save was successful with a message at the top of the form (ex: Animal observation with ID = 35107 was successfully created).

Cancel – Clears the entered data from the form.

After creating a new observation, you can continue to create new observations on the form, or use the UPD or DEL buttons in the Action column at the bottom of the form to modify or delete existing observations.

Once you are done entering observations, click on the ‘X’ in the top right corner of the form to close Animal Observations and return to Incoming Order.

Animal Images

Fields.

Repository Num – Automatically populated with the animal selected from the Incoming Order.

Ctry (Country) – Automatically populated based on animal selected.

Identifications – Automatically populated based on selected animal.

Upload File – Required, use the Browse button to bring up a search window to locate the picture file on your computer, select the file, and click on Open; the window will close and the image name will fill in automatically.

Tip: For the caption, NAGP follows a standardized format of Breed and Repository Number. For example, the caption could be ‘Angus NAGP ID 1531’.

Sex – Optional, use the drop down list to select male (M) or female (F).

View – Required, use the drop down list to state whether the image is of the back, front, or profile of the animal.

Caption – Optional, text field displayed on the public web pages when the user mouses over the image, limited to 50 characters.

Copyright / Source – Optional, use the drop down list to select the source of the image; if the person you are looking for is not in the list, a Super User will need to create it using the Information Source form.

Any cropping or photo editing should be done before uploading the image.

Description – Optional, text field to provide information about the image, limited to 300 characters.

Save – Commits the data to the database, displays the new image as a thumbnail at the bottom of the form, and shows the save was successful with a message at the top of the form (ex: Animal image with ID = 1333 was successfully created).

Cancel – Exits the form without saving the data.

Create Incoming Order – Inventory

Once the animals are associated with the Incoming Order, you can use your inventory sheets to fill in the location of the samples.

Fields – Incoming Order Inventory.

Click on the lower left Inventory tab to expand this section.

Inventory ID – Automatically populated by the database.

Germplasm Type – Required, automatically filled in if this was entered in the Incoming Order Header area; can be changed by selecting the type of material from the drop down list.

Original State – Required, automatically filled in if this was entered in the Incoming Order Header area; can be changed by selecting the state from the drop down list.

Unit Form – Required, automatically filled in if this was entered in the Incoming Order Header area; can be changed by selecting the form from the drop down list.

Unit Size – Optional, automatically filled in if this was entered in the Incoming Order Header area; can be changed by selecting the size from the drop down list.

Collection Date – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy; this is the date the inventory was collected.

Label Text – Optional, text field (30 characters) to enter the text printed on the packaging for the material.

Comments – Optional, text field (100 characters) to record any details about the inventory.

Beg. Total Quantity – Automatically computed by the database when the location information is saved; is a sum of the beginning inventory count.

Cur. Total Quantity – Automatically computed by the database; shows the sum currently available for that inventory. When a record is first created, the beginning and current quantities are the same and they should only differ by the amount sent out in requests.

Unallocated – Automatically computed by the database; shows the inventory not accounted for in Core, Evaluation, Restricted, and Working.

Core – Automatically computed by the database if the inventory is affected by Allocation Rules. This can be updated manually by the user. Inventory placed in Core is for regeneration purposes.

Evaluation – Automatically computed by the database if the inventory is affected by Allocation Rules. This can be updated manually by the user. Inventory placed in Evaluation is for evaluating the quality of the samples.

Restricted – Automatically computed by the database if the inventory is affected by Allocation Rules. This can be updated manually by the user. Inventory placed in Restricted is not available for Requests.

Working – Automatically computed by the database if the inventory is affected by Allocation Rules. This can be updated manually by the user. Inventory placed in Working is the primary area used for filling Requests.

Protocol Name – Optional, automatically filled in if this was entered in the Incoming Order Header area; can be changed by using the search button to open the protocol search pop-up.

Date Used – Automatically populated with the date of the Incoming Order, but can be changed using the calendar pop-up or by manually typing in the date (mm/dd/yyyy).

Add/Del (Protocol) – these buttons can be used to add additional protocols or to remove existing ones.

Container Type – Required, use the drop down list to select the type of container the inventory is stored in; additional types can be entered by a Super User.

Loc 1... Loc 7 – These field names and required/optional are determined by the location structure set up by a Super User for each location structure. See the screen shots below for an example.

In this example, Tank, Pie, Canister, Goblet, and Visotube are required, while Pie Section is not.

Beg Qty – Required, enter the quantity in that location (ex: 12 straws in Visotube A).

Beg Unit Count – Optional, default is 1. This field should be entered if there is more than 1 unit in the package (ex: multiple embryos in a straw).

Cur Qty – Automatically populated by the database, the value is the beginning quantity minus any requests taken from this location.

Cur Unit Count – Automatically populated by the database, the value is the beginning unit count minus any requests taken from this location.

Stage – Optional, for Germplasm Type = Embryos, the drop down list can be used to select the stage the embryos were cryopreserved at.

Quality – Optional, for Germplasm Type = Embryos, the drop down list can be used to select the quality assigned to the embryos at preservation.

Dup – Optional, these check boxes can be used to retain the information as location records are entered. For example, if the inventory is all in tank 16, checking the Tank box will keep tank 16 for all location records to make data entry easier.

UPD/DEL – these buttons can be used to update (UPD) or delete (DEL) inventory records.

After entering a location record, you must click on the Add button before it can be saved.

Save – Commits the data to the database, generates a message at the top of the inventory area, and populates the Inventory Allocation section.

If the quantity in a location is found to be incorrect after the shipment has been entered (ex: straws were miscounted), use the UPD button next to the location and make the change in the Beg Qty (in the location record), not the Cur Qty, select UPD, then Save. Make sure the Allocation Values were recalculated by the database.

Clear – Empties the form without commiting the records to the database.

Add Inventory – This button is used to assign another Inventory ID to the animal in the shipment. It is used if the material was received in more than one Unit Form or Unit Size. For example, if the same animal was received in straws and ampules, you need different inventory IDs to properly track the inventory. They will have different location structures, protocols, and inventory observations.

The Add Inventory button is NOT for adding additional location records for the same inventory; the Save button should be used for those records.

Remove Inventory – This button is used to remove an animal from an Incoming Order once inventory has already been assigned to it. If inventory has not been assigned and you want to remove the animal, it can be done in the Animal section. Once inventory has been assigned, all inventory must be deleted, then the Remove Inventory button can be used to remove the inventory record so the animal can be removed from the Animal section. Note this is not for removing inventory for a Request; rather, it is for animals assigned to the wrong Incoming Order or some other mistake.

Use the arrow buttons in the Animal section to move between Inventory records (see figure below).

The Inventory Allocation area can be updated manually after the record is saved. Once it is updated, the record needs to be saved again.

Inventory Observations

If you have information about the quality of the samples, this can be entered in the Inventory Observations form. This is primarily associated with motility data for semen samples. When the data is a product of Computer Assisted Sperm Analysis (CASA), an upload of the data is the most practical way to get the data into the database.

For non-CASA data, manual data entry will be appropriate.

Fields.

Upload File – Use the Browse button to search your computer for a prepared file to upload. The data must be in the following format.

Line 1: SEMEN.

Line 2: Variable names.

Line 3: Data.

The fields within the file can be separated by a pipe (|), tab, semicolon (;), or comma (,); use the drop down list to select the delimiter that matches your file.

Click on Submit Query to load the file.

A successful upload will return a message stating the file was successful and also the number of records that were processed.

An unsuccesful upload will return a list of where the error(s) occurred. You can correct the file and do the upload again.

Enter data manually.

Incoming Order ID – Required, use the Incoming Order search pop-up to select the incoming order to apply the inventory observations to; selecting the Incoming Order ID will also fill in the Animal Section with all animals associated with the Incoming Order.

Repository Name – Automatically populated based on the Incoming Order selected.

Date Received – Automatically populated based on the Incoming Order selected.

Repository Number – Required, automatically populated when the Incoming Order ID is selected, can also use the Animal Search pop-up to search for a specific animal within the Incoming Order.

Ctry – Automatically populated when the Repository Number is selected.

Identifications – Automatically populated when the Repository Number is selected.

Inventory Germplasm Type – Automatically populated when the Repository Number is selected.

Descriptor – Required, select the descriptor you want to enter data for from the drop down list. Selecting the descriptor automatically populates the Units and text box below the Observation Value to provide information about the parameters and formatting for the observation.

Observation Value – Required, use the information provided in the Units and text box to enter the observation data.

Units – Automatically populated when the descriptor is selected; provides information about how the descriptor data is to be entered.

Date Observed – Optional, can use calendar pop-up to select date or manually type in mm/dd/yyyy, mm/yyyy, or yyyy; this is the date the observation occurred.

Information Source – Optional, use the drop down list to select the provider of the observation; if the person you are looking for is not in the list, a Super User will need to create it using the Information Source form.

Comments – Optional, text field to add notes about the observation, limited to 100 characters.

Save – Commits the data to the database, provides a message at the top of the form (Inventory Observation was successfully created), displays the record at the bottom of the form, and clears the form to enter another observation.

Clear – Removes the data from the Observation Entry section and leaves the data in the Inventory section.

Entering Requests

This module provides a step-by-step tutorial about the process of entering a request.

E-R Diagram for Requests

Receiving the Request

The primary way to receive a request for material from the repository is via the public web pages. Designated Super Users will receive the request via email.

The email contains the information needed to complete the request in the database. Other details, such as shipping arrangements, will need to be worked out separately.

Create a Request

Fields – Request Header.

Request ID – Automatically populated by the database when the Request Header is saved.

Request Type – Optional, use the drop down list to select whether the request is internal to the repository or an external one.

Germplasm Type – Required, use the drop down list to select the type of material being requested. Separate requests should be created if multiple germplasm types are being requested.

Status – Required, default is ‘New’ for a new Request; use the drop down list to change the Status of the Request as material is prepared and shipped.

Request Reason – Optional, use the drop down list to select for what purpose the material will be used.

Repository Name – Required, use the drop down list to select the repository the material is being requested from.

Status Date – Required, default is today’s date; can use calendar pop-up to select date or manually type in mm/dd/yyyy; this date corresponds with the Status field. For example, Status is New on 6/25/2013 and Shipped on 6/27/2013.

Request Date – Required, default is today’s date; can use calendar pop-up to select date or manually type in mm/dd/yyyy; this is the date the material was initially requested.

Requestor Name – Required, use the search button to open the entity search pop-up; search for and select the person/company that made the request. If the person/company doesn’t exist, open another database window and create the record using the entity form. Then, search again for the record.

Ship to Address – Required, the address will automatically populate with the address of the Requestor if only one address exists; otherwise, use the search button to open the address search pop-up. If more than one address exists for the Requestor, the Results section of the pop-up will display the addresses to choose from. Select the address and click on OK. If no address exists for the Requestor, select the Create New button to open the Update Entity form to add an address. Close the Entity form and return to the address search pop-up. Click on the Refresh List and select the address. Click on OK to return to the Request form.

Processed By – Optional, used for quality control purposes to record the person responsible for packaging the material to fill the request.

Verified By – Optional, used for quality control purposes to record the person responsible for ensuring the correct material was packaged and shipped.

Purpose – Optional, text field (limited to 1,000 characters) to describe the reason for the request.

Intended Use – Optional, text field (limited to 1,000 characters) to describe what the requested material will be used for.

Use Protocol – Optional, text field (1,000 characters) to describe the protocols and procedures that will be used for the material.

Info. Return – Optional, text field (1,000 characters) to describe the information expected to be returned about the material (ex.: conception rate, citations for publications).

Comments – Optional, text field to add notes about the request, limited to 100 characters.

Save – Commits the data to the database and generates a Request ID.

Clear – Clears the data in the Request Header without saving it to the database.

Fields – Request Animals.

Ctry – Autopopulated by the database.

Rep. Num – Required, either type in the Repository Number or use the search button to open the animal search pop-up to find the animal being requested.

Identifications – Automatically populated by the database when the Repository Number is entered.

Lowest Level Taxonomy – Automatically populated by the database when the Repository Number is entered.

Qty Req. – Required, the number of units being requested for the animal.

Qty Picked – Automatically calculated and filled in by the database as units are selected from the available inventory.

Qty Avail. – Automatically populated by the database with the units of material that are available for request for the animal and germplasm type selected.

Status – Required, automatically populated with New by default, but the drop down list can be used to select a different status for the selected animal. For example, the Status in the Request Header might be Pending for the overall request, but the Status of one particular Animal is Cancelled.

Status Date – Required, automatically populated with today’s date, but can be changed, format is mm/dd/yyyy. This date corresponds to the Status field.

Comments – Optional, details (100 character limit) about the request of this animal. For example, the reason why the line was cancelled.

Save – Commits the record to the database and allows another animal to be added, or allows locations to be picked for the animal.

Add – Empties the Animal line so another animal can be entered.

Remove – Removes an animal from the Request; a pop-up message is displayed to confirm the delete before the deletion is committed.

Cancel Changes – Undoes changes to the request line.

Fields – Pick Locations.

Select a Location – Required, use the drop down list to select from the locations available for the animal. The drop down list includes the location, quantity, Incoming Order ID, and motility (if available).

When selecting the Locations, make sure the Animal you expect is the one displayed in the Animals section. You can use the ‘<<’ button to move to the first Animal.

Location/Current Inventory/Inventory Allocation – Automatically populated once a location is selected.

Inventory Picked – Use the Quantity Requested field in the Animals section in conjunction with the Current Inventory and Inventory Allocation to enter the quantity to remove from each Allocation Type. For example, in the first screen shot below, 2 units are requested and all allocation is in Unallocated. So, a 2 should be entered in the Unallocated Qty. field. If the quantity requested is a partial unit (for example, 10 µl of DNA from a 100 µl vial), this is entered in the Unit Count field instead of the Qty. field, as shown in the second screen shot below.

Add – Empties out the Inventory Picked section and adds the selected location to the Picked Locations section at the bottom of the form.

If additional locations need to be selected, the next one can be selected from the Select a Location drop down list.

Records in the Picked Locations lists can be changed using the Action buttons to Update (UPD) or Delete (DEL).

Once the locations have all been selected for an animal, the Qty Picked field in the Animals section will reflect that. If a different quantity is Picked than was Requested, a comment as to why would be useful documentation.

To move to the next animal in the Request, click on the Next link at the bottom of the Animals section.

Once the locations have been selected for all animals, you can use the Quick Picks list on the left sidebar to open and print the Picking List Report. This provides a list to assist in pulling the material from the repository.

After a shipment is sent out, you will need to change the Status in the Request Header to shipped and change the Status Date to reflect that.

Once the Status has been changed to shipped, to make any changes to the Request, you must change the Status to pending, make the change, and change the Status back to shipped.

Request Results

It is important to not only show material from the repository is being used, but also that results are being obtained as a result of providing material to requestors. These results could include number of offspring obtained, fertility statistics, genomic sequence data, and citations for publications.

Fields.

Request Header ID / Request Type / Germplasm Type / Status / Requestor Name – Automatically populated by the database based on the selected Request.

Animal Specific Result – if checked, shows a list of animals associated with the request to enter results for.

Request Result – 4,000 character text field to enter the results for the Request or for the animal if the Animal Specific Result box is checked.

Save – Commits the data to the database and displays a message at the top of the form ‘Result was successfully created’.

Cancel – Clears unsaved data from the form.

Reports

This module provides details about generating reports for both managers and database data entry personnel.

Managerial Reports

Managerial reports provide summary data useful for managers to assess the overall collection status over time or at a point in time, generate statistics for use in presentations, and to aid in management decisions.

Allocation at Any Date

This report shows how semen in the repository is allocated into Core, Working, Evaluation, Restricted, and Unallocated fields at any point in time. It also shows what percentage of the Core requirement is being met at that time.

Fields.

Repository – Required, use the drop down list to select the Repository you want to generate a report for. Additional repositories can be selected by using the Add Row link.

Date – Required, can use calendar pop-up to select date or manually type in mm/dd/yyyy. This is the date you want to view the allocation for; today’s date is the default.

Taxonomy – Required, use the drop down list to select a taxonomy you want to view the allocation for. All taxonomies are the default. You can use the Add Row link to add taxonomies.

Submit – Once your report criteria have been selected, use this button to generate the report to the screen.

You can use the Reset Form link from the Quick Picks list to generate a new report.

If you want to download the data, click on the Download CSV link.

Inventory at Any Date

This report shows the inventory for any germplasm type at any date for any taxonomy.

Fields.

Repository – Required, use the drop down list to select the Repository you want to generate a report for. Additional repositories can be selected by using the Add Row link.

Date – Required, can use calendar pop-up to select date or manually type in mm/dd/yyyy. This is the date you want to view the inventory for; today’s date is the default.

Germplasm Type – Required, use the drop down list to select the germplasm type to include in the report. You can use the Add Row link to select additional germplasm types. The default value is all germplasm types.

Taxonomy or Web Classification – Select the top radio button if you want a report based on taxonomy and then use the drop down list to select the taxonomy of interest. The Add Row link can be used to select additional taxonomies. Select the bottom radio button if you want a report based on animal type grouping (Beef Cattle, Dairy Cattle, Aquatic Freshwater Fish, etc.). The Add Row link can be used to select additional animal types.

Submit – Once your report criteria have been selected, use this button to generate the report to the screen.

If you want to download the data, click on the Download CSV link.

Summary of Germplasm Received

This report summarizes donations to the repository for a specified date range.

Fields.

Repository – Required, use the drop down list to select the Repository you want to generate a report for.

Start Date – Required, use the calendar pop-up or manually type in the date (mm/dd/yyyy) that the report should start.

End Date – Required, use the calendar pop-up or manually type in the date (mm/dd/yyyy) that the report should end; today’s date is the default.

Submit – Once your report criteria have been selected, use this button to generate the report to the screen.

If you want to download the data, click on the Download CSV link.

Summary of Germplasm Requests

This report summarizes material leaving the repository for a specified date range.

Fields.

Repository – Required, use the drop down list to select the Repository you want to generate a report for.

Start Date – Required, use the calendar pop-up or manually type in the date (mm/dd/yyyy) that the report should start.

End Date – Required, use the calendar pop-up or manually type in the date (mm/dd/yyyy) that the report should end; today’s date is the default.

Request Reason – Required, use the drop down list to select the request category to include in the report. You can use the Add Row link to select additional request types. The default value is ‘Any’.

Submit – Once your report criteria have been selected, use this button to generate the report to the screen.

If you want to download the data, click on the Download CSV link.

CASA Summary by Taxonomy

This report summarizes CASA data (n, average, and range) by taxonomy.

Fields.

Taxonomy – Required, use the drop down list to select the taxonomy you want to run the report for.

Start Date – Optional, use the calendar pop-up or manually type in the date (mm/dd/yyyy) that the report should start.

End Date – Optional, use the calendar pop-up or manually type in the date (mm/dd/yyyy) that the report should end; today’s date is the default.

Search – Once your report criteria have been selected, use this button to generate the report to the screen.

User Reports

User reports provide information to assist in the data entry process, such as locating the last storage location used and locating animals with missing data.

Get Animal Record ID for Uploads

This produces an export file of animals for a specified taxonomy (or taxonomies) that can be matched with an external file to create data for database uploads (pedigree, CASA, etc.).

Fields.

Taxonomy – Required, use the drop down list to select the taxonomy you want to create a list of animals for. You can use the Add link to select additional taxonomies.

Identification Type – Required, use the drop down list to select the type of identification to include in the list, registration number for example.

Submit – Use this button to generate the export file.

A message to the screen tells you how many records are going to be generated and asks if you want to proceed or cancel.

Selecting OK generates the export file containing the Repository Number, Record Source, Sex, Identification, and Full Taxonomy Name.

Cryo Location Search Tool

This report allows the user to search for inventory locations at any level (tank, pie, goblet, etc.) or by incoming order, repository number, inventory ID, or germplasm type.

Fields.

Location Level Name – Use the drop down list to select the top location type (loc 1), tank for example.

Location Value – Use the drop down list to select the value that corresponds with the top location type, tank 32 for example.

Repeat the above process until you get to the lowest level you want to search for.

Incoming Order ID – This can be used in conjuction with the location fields above or alone; enter the Incoming Order ID you want to see inventory locations for.

Animal Repository Number – This can be used in conjunction with the location fields above or alone; enter the Repository Number you want to see inventory locations for.

Inventory ID – This can be used in conjunction with the location fields above or alone; enter the Inventory ID you want to see inventory locations for.

Germplasm Type – This can be used in conjunction with the location fields above or alone; use the drop down list to select the type of germplasm you want to see inventory locations for.

Submit – Once your report criteria have been selected, use this button to generate the report to the screen.

If you want to download the data, click on the Download CSV link.

Animal Summary

This report shows a snapshot of information about a selected animal, including animal, shipment, inventory, and request data.

Fields.

Repository ID – Required, either type in the desired Repository ID to search, or use the search button to bring up a box to locate the Repository Number via drop down lists for Common Name, Species, Species Sublevel, and Animal Identification.

Search – Once the Repository Number has been selected, use this button to generate the report to the screen.

Missing Data

This report shows a count of empty data fields by taxonomy to assist the user in identifying animals that need additional data.

Fields.

Taxonomy – Required, use the drop down list to select the taxonomy you want to run the report for.

Search – Once the Taxonomy has been selected, use this button to generate the report to the screen.

In the example shown above, there are 64 animals in the repository for the selected taxonomy. There are 3 with a missing birth date, suggesting this information should be available for the taxonomy. There are 64 with a missing value for mature weight, suggesting this information may not be available for the taxonomy. Based on this information, use the check boxes at the right side of the screen to select fields to include in the report.

Once you have selected the fields you want to include in the report, click on the Submit button.

The report shows the animals by Repository Number; if the field displays ‘NO’, then information is missing for that field.

CASA Missing Data

This report shows missing Inventory Observations by Taxonomy, Incoming Order, or Repository Number.

Fields.

Taxonomies – Optional, use the drop down list to select a taxonomy to view missing inventory observations for. You can use the Add Row link to select additional taxonomies.

Incoming Order ID – Optional, enter the Incoming Order to view missing inventory observations for.

Animal Repository Number – Optional, enter the Repository Number to view missing inventory observations for.

Descriptors – Required, use the drop down list to select a descriptor to check for missing observations. Use the Add Row link to select additional descriptors.

Search – Once the Taxonomy, Incoming Order, or Repository Number has been selected, use this button to generate the report to the screen.

As shown on the report above, fields with a ‘NO’ are missing data for that descriptor.

Animal x Inventories

This report lists all inventory for an animal of interest.

Fields.

Repository ID – Required, either type in the desired Repository ID to search, or use the search button to bring up a box to locate the Repository Number via drop down lists for Common Name, Species, Species Sublevel, and Animal Identification.

Search – Once the Repository Number has been selected, use this button to generate the report to the screen.

You can click on an Inventory ID to display the Inventory Observations.

Glossary

Core: Quantity of units in the repository for a taxonomy to be considered secure.

Descriptor: Data entry field allowing the user to enter observations about a taxonomy, entity, animal, or inventory. For example, Birth Weight is an animal descriptor, while Progressive Motility is an inventory descriptor.

Entity-Relationship (ER) Diagram: Graphical representation of the entities (tables) in a database and their relationship to one another. The relationship shows how data is shared via primary and foreign keys. The relationships between tables can be 1-to-1, 1-to-many, or many-to-many.

Foreign Key: Field(s) that creates a link between two database tables.

Form: User interface for data entry; contains fields for users to populate underlying tables.

In situ: Latin word meaning ‘in place’; in situ conservation means maintaining genetic diversity through a live animal population.

Loader: Data entry form that allows a user to process a file of data directly into the database tables rather than manually entering the data.

Parent-Child Relationship: Database structure where the child record can have 0 or 1 parent records, but a parent record can have many child records. This 1-to-many relationship can be visualized as a hierarchical tree structure.

Primary Key: Unique identifier for a database record, usually assigned as a number.

Taxonomy Structure: Hierarchical relationship of an animal type containing at least the Family, Genus, and Species; other options in the hierarchy include Variety, Breed, Line, and Strain.

Appendix

E-R Diagram for Animal Area

E-R Diagram for Taxonomy Area

E-R Diagram for Entity Area

E-R Diagram for Protocol Area