Figure 1.1

![](media/image1.jpeg){width="10.124305555555555in"
height="0.6201388888888889in"}

Document Change History

  ----------- ------------ ------------------------ --------------------------
  **Version   **Date**     **Contributor**          **Description**
  Number**                                          

  V1.1        11/09/2006   Janet Stone --           Initial Presentation
                           Washington University    

              01/02/2007   Janet Stone --           Included additional
                           Washington University    function details,
                                                    conducted edits and
                                                    updated images to reflect
                                                    recent UI enhancements

              01/07/2007   Janet Stone --           Added additional details
                           Washington University    for simple and advanced
                                                    query. Updated query
                                                    images and changed all
                                                    references to Shopping
                                                    Cart to My List.

              01/30/2007   Janet Stone --           Incorporated Collection
                           Washington University    Protocol based view
                                                    details. Inserted
                                                    additional details
                                                    regarding how biospecimens
                                                    are displayed in the
                                                    system when stored in a
                                                    virtual location.

  V.12        05/17/2007   Washington University    Incorporated enhancement
                                                    made for V1.2.
  ----------- ------------ ------------------------ --------------------------

![](media/image2.jpeg){width="3.9298611111111112in"
height="1.1631944444444444in"}

Copyright and License page

+-------------------+-------------------------------+------------------+
|                   |                               |                  |
+-------------------+-------------------------------+------------------+
| Development       | User's Guide                  | Program          |
|                   |                               | Management       |
+-------------------+-------------------------------+------------------+
| **Names of        | **Names of Technical          | **Names of       |
| developers**      | Writers**                     | program          |
|                   |                               | managers**       |
+-------------------+-------------------------------+------------------+
|                   | **Casey Overby** --           |                  |
|                   | *University of Pennsylvania - |                  |
|                   | Abramson Cancer Center*       |                  |
+-------------------+-------------------------------+------------------+
|                   | **Dennis Mitchell** -- *Duke  |                  |
|                   | Comprehensive Cancer Center*  |                  |
+-------------------+-------------------------------+------------------+
|                   | **Jack London** -- *Kimmel    |                  |
|                   | Cancer Center - Thomas        |                  |
|                   | Jefferson University*         |                  |
+-------------------+-------------------------------+------------------+
|                   | **Min Xu** -- *UNC Lineberger |                  |
|                   | Comprehensive Cancer Center - |                  |
|                   | University of North Carolina  |                  |
|                   | Chapel Hill*                  |                  |
+-------------------+-------------------------------+------------------+
|                   | **Paul Courtney** - *Norris   |                  |
|                   | Cotton Cancer Center -        |                  |
|                   | Dartmouth-Hitchcock Medical   |                  |
|                   | Center*                       |                  |
+-------------------+-------------------------------+------------------+
|                   | **Tara McSherry** --          |                  |
|                   | *University of Pennsylvania - |                  |
|                   | Abramson Cancer Center*       |                  |
+-------------------+-------------------------------+------------------+
|                   | **Zhiqiang Cheng** -- *Wake   |                  |
|                   | Forest Comprehensive Cancer   |                  |
|                   | Center*                       |                  |
+-------------------+-------------------------------+------------------+
|                   | **Janet Stone** --            | Dr. Rakesh       |
|                   | *Washington University --     | Nagarajan        |
|                   | Siteman Cancer Center*        |                  |
|                   |                               | Dr. Mark Watson  |
+-------------------+-------------------------------+------------------+

+----------------------------------+-----------------------------------+
| ***Contacts and Support***       |                                   |
+----------------------------------+-----------------------------------+
| NCICB                            | Telephone: 301-451-4384           |
|                                  |                                   |
|                                  | Toll free: 888-478-4423           |
|                                  |                                   |
|                                  | Monday - Friday, 8 am -- 8 pm EST |
+----------------------------------+-----------------------------------+
| Enter customer support contact   | Email: <ncicb@pop.nci.nih.gov>    |
+----------------------------------+-----------------------------------+

  ---------------- ------------------------------------------------------------------------------------------------------------------ ---------------------
  LISTSERV and                                                                                                                        
  GForge FORUM                                                                                                                        
  Facilities                                                                                                                          
  Pertinent to                                                                                                                        
  software teams                                                                                                                      

  LISTSERV/FORUM   URL                                                                                                                Name

  caDSR_Users      <https://list.nih.gov/archives/cadsr_users.html>                                                                   Cancer Data Standards
                                                                                                                                      Repository

  NCIEVS-L         <https://list.nih.gov/archives/ncievs-l.html>                                                                      NCI Vocabulary
  Listserv                                                                                                                            Services Information

  Cacorecvs        <http://gforge.nci.nih.gov/forum/?group_id=18>                                                                     Forums for caTissue
                                                                                                                                      Core

  caTissue v1.2    http://cabigcvs.nci.nih.gov/viewcvs/viewcvs.cgi/catissuecore/Version1.2/SRSAndUseCases/caTissueCore_v1_2_SRS.doc   Software Requirements
                                                                                                                                      Specifications and
                                                                                                                                      Use Case Document

  caTissue v1.2    <http://gforge.nci.nih.gov/forum/forum.php?forum_id=766>                                                           caTissue v1.2
                                                                                                                                      Discussion Forum
  ---------------- ------------------------------------------------------------------------------------------------------------------ ---------------------

Table of Contents

[Chapter 1 Introduction to the Manual 2](#introduction-to-the-manual)

[Getting Started with caTissue Core
2](#getting-started-with-catissue-core)

[Organization of the User\'s Manual
2](#organization-of-the-users-manual)

[Chapter 2 Overview of the Software 2](#overview-of-the-software)

[Software Overview 2](#software-overview)

[Components of the Software 2](#components-of-the-software)

[Chapter 3 User Interface 2](#user-interface)

[The caTissue Core HOME Page 2](#the-catissue-core-home-page)

Map
feature\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_**7**

Tissue Site
List\_**\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_
9**

[Chapter 4 Overview of User Types and Workflows
2](#overview-of-user-roles-and-workflows)

[Organization of Privileges and Workflow
2](#organization-of-role-based-privileges-and-workflow)

[User Roles 2](#user-roles)

[Workflow Modules 2](#workflow-modules)

[Login Module 2](#login-module)

[**Overview of Login Module Workflow**
2](#overview-of-login-module-workflow)

[Submit User Request 2](#submit-new-user-request)

[Report a Problem 2](#report-a-problem)

[Login 2](#login)

[Edit Profile 2](#edit-profile)

[Change Password 2](#change-password)

[Retrieve Forgotten Password 2](#retrieve-forgotten-password)

[Assign Privileges 2](#assign-privileges)

[Logout 2](#logout)

[View Aggregate Data 2](#view-aggregate-data)

[Administrative Module 2](#administrative-module)

[**Overview of Administrative Module Workflow**
2](#overview-of-administrative-module-workflow)

[Add \| Edit \| Approve User 2](#add-edit-approve-user)

[Add \| Edit Institution 2](#add-edit-institution)

[Add \| Edit Department 2](#add-edit-department)

[Add \| Edit Cancer Research Group 2](#add-edit-cancer-research-group)

[Add \| Edit Site 2](#add-edit-site)

[Add \| Edit Storage Type 2](#add-edit-storage-type)

[Add \| Edit \| View Map - Storage Container
2](#add-edit-view-map---storage-container)

[Add/Edit Specimen Array Type 2](#addedit-specimen-array-type)

[Add \| Edit Biohazard 2](#add-edit-biohazard)

[Add \| Edit Collection Protocol 2](#add-edit-collection-protocol)

[Add \| Edit Distribution Protocol 2](#add-edit-distribution-protocol)

[View Reported Problems 2](#view-reported-problems)

[Bio-Specimen Module 2](#bio-specimen-module)

[**Overview of Bio-Specimen Module Workflow**
2](#overview-of-bio-specimen-module-workflow)

Collection Protocol Based
View\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_
77

[Add \| Edit Participant 2](#collection-protocol-based-view)

[Add \| Edit Participant Registration
2](#add-edit-participant-registration)

[Add \| Edit Specimen Collection Group
2](#add-edit-specimen-collection-group)

[Add \| Edit Specimen 2](#add-edit-specimen)

[Add \| Edit \| Aliquot - Specimen Array
2](#add-edit-aliquot---specimen-array)

[Add Multiple Specimens 2](#add-multiple-specimens)

[Derive Specimen 2](#derive-specimen)

[Create Aliquot 2](#create-aliquot)

[Add Events 2](#add-events)

[Distribution 2](#distribution)

[Query Module 2](#query-module)

[**Overview of Query Module Workflow**
2](#overview-of-query-module-workflow)

[Simple Querying 2](#simple-query)

[Advanced Querying 2](#advanced-query)

[Define Query View 2](#define-query-view)

View My List
\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_152

[Chapter 5: Error Messages/Indicators and Problem Resolutions
2](#chapter-5-error-messagesindicators-and-problem-resolutions)

[Problem List: 2](#problem-list)

[Contents: 2](#contents)

[Problem 1: 2](#problem-1)

[You can see the website, but no tools are available to you.
2](#you-can-see-the-website-but-no-tools-are-available-to-you.)

[Problem 2: 2](#problem-2)

[I do not see where to login to the system.
2](#i-do-not-see-where-to-login-to-the-system.)

[Problem 3: 2](#problem-3)

[I forget my password. 2](#i-forgot-my-password.)

[Problem 4: 2](#problem-4)

[Failed to log in the system. (Error message: 'Incorrect Login ID or
Password')
2](#failed-to-log-into-the-system.-error-message-incorrect-login-id-or-password)

[Problem 5: 2](#problem-5)

[Failed to change password. 2](#failed-to-change-password.)

[Problem 6: 2](#problem-6)

[Other problems with passwords. 2](#other-problems-with-passwords.)

[Problem 7: 2](#problem-7)

[You need to report a problem with using the system.
2](#you-need-to-report-a-problem-with-using-the-system.)

[Problem 8: 2](#problem-8)

[I need to contact system administrator.
2](#i-need-to-contact-a-system-administrator.)

[Problem 9: 2](#problem-9)

[Can't perform some operations in the system. (Error message: "Access
denied: You are not authorized to perform this operation.")
2](#cant-perform-some-operations-in-the-system.-error-message-access-denied-you-are-not-authorized-to-perform-this-operation.)

[Problem 10: 2](#problem-10)

[How to update my email address? 2](#how-to-update-my-email-address)

[Problem 11: 2](#problem-11)

[I can not see the map of storage containers when I click the link 'View
Map' under 'STORAGE CONTAINER' in the left panel of the page in
Administrative Data.
2](#i-can-not-see-the-map-of-storage-containers-when-i-click-the-link-view-map-under-storage-container-in-the-left-panel-of-the-page-in-administrative-data.)

[Problem 12: 2](#problem-12)

[I can not see the map of storage containers when I click the 'Map'
button in Adding New Specimen page in Bio-Specimen Data
2](#i-can-not-see-the-map-of-storage-containers-when-i-click-the-map-button-in-adding-new-specimen-page-in-bio-specimen-data)

[Problem 13: 2](#problem-13)

[I can not register a participant to a collection protocol. (Error
message: 'Submission failed since a Collection Protocol Registration
with the same COLLECTION_PROTOCOL_ID, PARTICIPANT_ID already exists.')
2](#i-can-not-register-a-participant-to-a-collection-protocol.-error-message-submission-failed-since-a-collection-protocol-registration-with-the-same-collection_protocol_id-participant_id-already-exists.)

[Problem 14: 2](#problem-14)

[I can not create a new distribution. (Error message: 'Quantity entered
is greater that the available quantity.')
2](#i-can-not-create-a-new-distribution.-error-message-quantity-entered-is-greater-that-the-available-quantity.)

[Problem 15: 2](#problem-15)

[I can not edit the location of a frozen specimen.
2](#i-can-not-edit-the-location-of-a-frozen-specimen.)

[Problem 16: 2](#problem-16)

[I can not find a specimen. (Error message: 'No Records Found!')
2](#i-can-not-find-a-specimen.-error-message-no-records-found)

[Problem 17: 2](#problem-17)

[How do I start a new search when I have finished one?
2](#how-do-i-start-a-new-search-when-i-have-finished-one)

[Problem 18: 2](#problem-18)

[The sum of all aliquot quantities exceed the quantity of the parent
specimen
2](#the-sum-of-all-aliquot-quantities-exceed-the-quantity-of-the-parent-specimen)

[Chapter 6: Glossary/Acronyms/ Abbreviations
2](#chapter-6-glossaryacronymsabbreviations)

[References 2](#references)

[Technical Manuals/Articles 2](#technical-manualsarticles)

[Scientific Publications 2](#scientific-publications)

[caBIG Material 2](#cabig-material)

[caCORE Material 2](#cacore-material)

[Glossary 2](#glossary)

[Index 2](#index)

# **Introduction to the Manual**

This User's Guide is intended for users who work at or operate a tissue
bank that uses the caTissue system to manage the inventory.

Potential users include:

-   Tissue bank technicians and their associated supervisors, who manage
    the tissue bank

-   Scientists or researchers who use the system to conduct queries for
    specific tissue samples

-   Administrators who manage the overall caTissue Core system (example,
    through user provisioning, creating collection and distribution
    protocols, creating storage containers,and so on).

Topics in this chapter include:

*Overview of the Guide* and *Getting Started with the Software* on this
page.

*Organization of the User\'s Manual*

*The caTissue Core User* (background and experience expected, to use
software)

## Getting Started with caTissue Core {#getting-started-with-catissue-core .unnumbered}

Review the **Organization of the User\'s Manual**, to know what is
available in this manual. If you do not have an account already, browse
to the URL set up by Administrator for the application, and click the
\"Sign Up\" link. This opens a page which has a form that you need to
fill up. For help in identifying your Department or Cancer Research
Group, ask your Administrator for assistance. When you submit this form,
the Administrator approves your request for an account. The
administrator then assigns you a role based on your involvement in the
system.

For more detailed information about caTissue Core, review documents
[online](http://cabigcvs.nci.nih.gov/viewcvs/viewcvs.cgi/catissuecore/).

## Organization of the User\'s Manual {#organization-of-the-users-manual .Style-Heading-2-+-No-underline .unnumbered}

  ------------------- ---------------------------------------------------
  Chapter in caTissue Chapter Contents
  Core User Manual    

  Chapter 1           **Introduction to the User Manual:** This chapter
                      orients the first time user to the data contained
                      within the manual.

  Chapter 2           **Overview of the Software:** This chapter gives a
                      fairly high level overview of the caTissue Core
                      application. It provides the context for the
                      problems that the application must solve. It also
                      explains how it must relate to or interact with the
                      other informatics systems at a medical center and
                      with other TBPT tools.

  Chapter 3           **User Interface:** This chapter gives a general
                      orientation to the application\'s look and feel.
                      Included are instructions on how to login, how to
                      edit your personal information after logging in,
                      and the common screen features in this application.

  Chapter 4           **Overview of User Types and Workflows:** This
                      chapter explores in detail each interactive screen
                      for each type of workflow. This chapter includes
                      screenshots and instructions on how to interact
                      with each screen to add or edit data or conduct a
                      query of the system data.

  Chapter 5           **Error Messages/Indicators and Problem
                      Resolutions:** This chapter addresses the common
                      error messages that a typical user might encounter
                      and how to resolve the problem underlying the
                      message.

  Chapter 6           **Glossary/Acronyms/Abbreviations:** This chapter
                      lists terms, acronyms, and abbreviations along with
                      their definitions.

  Index               **Full Index**
  ------------------- ---------------------------------------------------

# **Overview of the Software**

## Software Overview {#software-overview .unnumbered}

caTissue Core is a web-based application for biospecimen inventory,
tracking, and basic annotation. caTissue Core may be used by biospecimen
resource facilities, regardless of the nature of biospecimen
transactions or the type of biospecimens involved in the transaction.

Advances in molecular technologies and sophistication in clinical trial
design have increased the importance of biospecimen banks in collecting,
processing, storing, and distributing human specimens for correlative
science cancer research. Biospecimen banks are now responsible for the
collection and distribution of multiple human specimen types for
molecular studies.

Biospecimen banks and their associated informatics systems need the
functionality to:

-   Track multiple specimens from the same participant,

-   Track refined materials (RNA, DNA, and Protein) that are used for
    molecular analysis

-   Annotate biospecimens with accumulating experimental and clinical
    data,

Some of the existing tissue banking systems do tracking, some do
financial management, some have automated pathology and clinical
annotations, and some may have ![](media/image3.wmf)experimental data
associated with the specimens, but no one system has all the
functionalities.

The more expansive caTissue Suite system is designed as a central
repository for all the above data. caTissue Core is a component of this
larger system. The other two components are the Cancer Text Information
Extraction System (caTIES) and the Clinical Annotation Engine (CAE).

## Components of the Software {#components-of-the-software .unnumbered}

Principle features of the caTissue Core system include open source
architecture that adheres to caBIG^TM^ compatibility guidelines
regarding architecture, controlled vocabulary and common data elements.
caTissue Core is "Silver Level" compliant and will eventually be "Gold
Level" compliant, once the grid architecture is integrated into the
design.

**Features and Functions of the Software:**

caTissue Core functionality may be categorized into three distinct
groups (See Figure 2.1):

> **Administration**: Contains administrator-specific functionality to
> manage the overall system.
>
> For example, in this tab, the administrator may:

-   approve users who have registered

-   create collection and distribution protocols

-   create the storage container hierarchy at their biospecimen
    repositories

-   curate organization-specific permissible values such as departments,
    institutions, and cancer research groups

> **Biospecimen Data**: Contains the following functionalities:

-   Supervisor and technician-specific (That is, repository-specific)
    functions to add participants

-   Register the participants in the collection protocols

-   Add specimen collection groups

-   Add specimens and related information (See description below and
    Figure 2.2 for more details).

> **Search**: Contains scientist-related functionality to search the
> repository for relevant biospecimens

![](media/image4.png){width="5.766666666666667in"
height="4.766666666666667in"}

**Figure 2.1**: caTissue Core System Block Diagram

> **caTissue Core Object Model:**

All the data contained in the caTissue Core application may be
visualized in a hierarchical structure as shown in Figure 2.2. One
participant may be registered to one or more collection protocols. Each
participant may have one or more biospecimens collected at one or more
points of time. Each of these biospecimens may be infinitely derived
,such as:

-   Frozen tissue that is divided into parts

-   Serum that is aliquoted

-   A paraffin block that is cut into slides

-   Tissue that is molecularly refined into DNA, RNA, or protein

Some of these may be distributed to investigators under a specific
distribution protocol.

> ![](media/image5.png){width="4.427777777777778in"
> height="3.123611111111111in"}

**Figure 2.2**: caTissue Core Data Hierarchy

# **User Interface** 

This chapter describes the caTissue Core User Interface (UI), common
features found through out the system, and simple navigation.

Topics in this chapter include:

-   Display and description of the features included in the caTissue
    Core **HOME** Page

-   Common page elements

-   Common processes

-   Navigation

## The caTissue Core HOME Page {#the-catissue-core-home-page .unnumbered}

Upon invoking the caTissue Core application on your web browser, the
system displays the **HOME** page containing fields for the **Login**
data.

![](media/image6.jpeg){width="5.986111111111111in"
height="3.6645833333333333in"}

**Figure 3. 1**: HOME page

Type your **Email address** and **Password**, and then click the
**Login** button.

![](media/image7.jpeg){width="2.060416666666667in"
height="1.6743055555555555in"}

**Figure 3 .2**: HOME page, left-hand menu

The left hand menu or the user dashboard on the Home page contains the
following links:

**USER PROFILE**:

Edit

Change Password

**PRIVILEGES**:

Assign

**QUICK LINKS:**

caBIG Home Page -- Links to the Cancer Bioinformatics Grid Home Page

NCICB Home -- Links to the National Cancer Institute Center for
Bioinformatics Home Page

Site Home -- Returns you to the caTissue Home Page

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}Quicklinks are located on all pages.

## Common Page Elements and Navigation {#common-page-elements-and-navigation .unnumbered}

All the pages have horizontal tabs containing links to the various
menus. Each tab is linked to a specific set of menus based on the
functional area. The horizontal tabs are as follows:

-   **HOME**: Links to the Home page or Login page

-   **ADMINISTRATIVE DATA:** Contains the tasks that can be done in an
    Administrative module

```{=html}
<!-- -->
```
-   **BIO-SPECIMEN DATA:** Contains the tasks that can be done in a
    bio-specimen module

```{=html}
<!-- -->
```
-   **SEARCH:** Contains menu options for simple or advanced searches of
    system data

-   **SUMMARY** : Displays the aggregate data in the system

-   **HELP:** Links to the on-line help

-   **Sign Out**: Enables you to sign out

![](media/image7.jpeg){width="5.986111111111111in"
height="1.3479166666666667in"}

**Figure 3 .3**: Horizontal tabs and common page features

Click on any of the horizontal tabs to display the following:

-   Entry page for the selected module

-   A left-hand side menu of available options

For example, click the **BIO-SPECIMEN DATA** tab, to display a
function-specific vertical menu on the left-hand side of the biospecimen
page.

![](media/image9.jpeg){width="5.995833333333334in" height="3.2625in"}

**Figure 3. 4**: User Dashboard options based on tab selected

Subsequently click a function-specific task in the user dashboard, such
as **Add** under **SPECIMEN.** This displays the appropriate page with
fields for data entry.

![](media/image10.jpeg){width="5.986805555555556in"
height="4.191666666666666in"}

**Figure 3. 5**: Example User workspace filled with task-related data
entry fields

### **\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_** {#section .unnumbered}

### **Map Feature** {#map-feature .unnumbered}

> []{#MapFeature .anchor}Click the **Map** button located to the right
> in the **Storage Position** row. This displays a hierarchical
> representation of storage containers and all the storage positions in
> the system that is, used or unused.

![](media/image11.png){width="6.493055555555555in" height="4.775in"}

**Figure 3.6**: Map of Storage Containers

> The left pane in the map displays information in the following
> hierarchical format:
>
> ![](media/image12.png){width="1.8229166666666667in"
> height="1.1666666666666667in"}

-   A **red** lid on a storage container node indicates that the
    container is full or restricted.

-   A **blue** lid on a storage container node indicates that the
    container has vacancies and is available for storage.

> The storage container hierarchy is as follows:
>
> Site
>
> Container ID (Name)

Container Collection Protocol

Container Specimen Type

The detail view (See Figure 3.7) presented to the right of the hierarchy
view shows two types of hyperlinks, those which may contain other
containers or those which may hold specimens themselves. Clicking on the
former results in displaying that container's contents on the right
side, while clicking on the latter indicates that the specimen or a
child container should be placed in this position.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}
Once a storage position is vacated by a specimen (via transfer or
disposal), or a container is disabled (i.e. 'deleted' from the system),
the storage position vacated by that specimen or container becomes
immediately available for placement of a new specimen or container.

![](media/image14.png){width="5.997916666666667in"
height="5.540972222222222in"}

**Figure 3.7:** Storage Location Details

Clicking on any of the links in the map table, will display details for
the selected position as displayed in the image below:

![](media/image15.png){width="3.7708333333333335in"
height="4.479166666666667in"}

**Figure 3.8**: Edit Storage Location

### **\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_** {#section-1 .unnumbered}

### **Hierarchy Selection List** {#hierarchy-selection-list .unnumbered}

> For attributes with permissible values that may be arranged
> hierarchically (e.g. tissue site and diagnosis), the caTissue Core
> system has been built to support viewing and selecting values from
> this hierarchy. To make a selection, click on the
> ![](media/image16.png){width="0.3125in"
> height="0.23958333333333334in"} icon located to the right of the data
> field. An example of the hierarchy for tissue site is shown in Figure
> 3.9.
>
> ![](media/image17.png){width="4.03125in" height="3.96875in"}

**Figure 3.9**: Example of hierarchical data presentation

> If a permissible value contains additional items, you can drill down
> in the hierarchy by clicking on the
> ![](media/image18.png){width="0.14583333333333334in"
> height="0.14583333333333334in"} image located to the left of each
> node. Once you have located the desired tissue site/diagnosis,
> clicking on the item will close the window and take you back to the
> original data page with the selected item populated in the field.

### **\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_** {#section-2 .unnumbered}

### **Calendar Feature** {#calendar-feature .unnumbered}

[]{#CalendarFeature .anchor}For easy visualization of dates as well as
ease of use, the caTissue Core system has an embedded calendar feature
beside each date field. The user has the option to manually enter a date
using the following supported formats mm/dd/yyyy or mm-dd-yyyy or select
a date from the calendar provided. To use this feature, click on the
calendar ![](media/image19.png){width="0.21875in" height="0.21875in"}
icon located to the right of the date field. This will prompt the system
to display an interactive calendar from which a date can be selected
(see Figure 3.10). ![](media/image20.png){width="2.7805555555555554in"
height="1.7916666666666667in"} ***Figure 3.10**: Calendar feature*

To use the calendar feature, you can navigate to a month and/or year by
using the drop down selection boxes located at the top. You can also
select to move one month at a time using the single arrows or one year
at a time by using the double arrows. Once you are on the desired
month/year, you can click on any of the boxes marked with the date. Once
the date is selected, you will be returned to the original data page,
with the selected date populated into the date field.

## Add/Edit Objects {#addedit-objects .unnumbered}

The two main function-specific processes for all objects include **Add**
and **Edit**.

**Add Objects:**

Clicking on an **Add** task menu item, will display a data entry page
displaying data entry fields for the selected item. Once all required
items have been entered, you can select to submit that data to the
database or cancel the request.

**\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_**

[]{#EditObjects .anchor}**Edit Objects:**

An **Edit** menu option is used for modification of an existing data
record (e.g. Biospecimen ID 1234); therefore a SEARCH page will be
displayed for location of the desired record to be edited.

[]{#SearchEDIT .anchor}All edit **SEARCH** pages have a common
structure:

-   [Class:]{.underline} The first selection box allows a user to select
    the class object to be searched on (Figure 3.11 displays the object
    class as Specimen)

-   [Attribute:]{.underline} The second selection box allows a user to
    select an attribute to search for in the selected class (figure 3.12
    displays Identifier selected for the Specimen class)

-   [Constraint]{.underline}: The third selection box allows a user to
    specify a search constraint for the attribute (figure 3.13 displays
    a "starts with" constraint for specimen identifier)

-   [Value]{.underline}: The fourth field is a manual entry box for an
    attribute value (figure 3.14).

![](media/image21.png){width="6.559722222222222in"
height="2.1006944444444446in"}

**Figure 3. 11**: Search field for class

![](media/image22.png){width="6.652777777777778in"
height="2.261111111111111in"}

**Figure 3. 12**: Search field for attribute

![](media/image23.png){width="6.679861111111111in" height="1.9625in"}

**Figure 3. 13**: Search field for constraint

> ![](media/image24.png){width="6.679861111111111in"
> height="1.8131944444444446in"}

**Figure 3. 14**: Search field for value

Once query parameters are entered, the page will refresh and display all
records that match the criteria entered. If no data exists in the system
that matches your search parameters, the following message will be
displayed "No Records Found!"

If more than one record is returned, you must select the desired record
you want to edit from the list presented. To select a record,
double-click on the row item in the search results table.

> ![](media/image25.png){width="6.679861111111111in"
> height="3.658333333333333in"}

**Figure 3. 15**: Example of a Search results view

![](media/image13.png){width="0.9479166666666666in" height="0.25in"} You
can change the sort order of the results view by clicking on a column
title at the top of the page.

Example: You can select to sort items by identifier by clicking on the
Identifier title at the top of the column. You can also select to sort
participants by clicking on gender, last name, first name ,etc.

Once an item is selected, an edit page for the selected object will be
displayed (example: Specimen, Storage Container etc), with all contents
from the selected record populated on the page.

**Common User Interface Components:**

The caTissue Core system contains many specific functional buttons that
are found throughout the application. The table below provides a
detailed description for each functional button.

# **Overview of User Roles and Workflows**

## Organization of Role Based Privileges and Workflow {#organization-of-role-based-privileges-and-workflow .unnumbered}

### User Roles {#user-roles .unnumbered}

Functionality within the caTissue Core v1.1 application is limited by
roles assigned to each user within the system. The following five roles
are defined in the application: Administrator, Supervisor, Technician,
Scientist and Public. In order to accommodate adopting institutions that
may have a different privilege for each role, the system allows for the
creation of customized roles with privileges assigned or disallowed
based on the needs of the institution. The table below describes each of
the predefined caTissue Core roles.

  -----------------------------------------------------------------------
  []{#Role .anchor}Role Description
  --------------------- -------------------------------------------------

  -----------------------------------------------------------------------

### Workflow Modules {#workflow-modules .unnumbered}

The workflow of caTissue Core v1.1 is divided among multiple modules.
The purpose of the remainder of this chapter is to provide an
understanding of the tasks that make up the five caTissue Core modules:
Login Module, Administration Module, Biospecimen Module, Distribution
Module and Query Module.

The following topics will be described for each module in the system:

-   Purpose of task

-   Prerequisite information

-   Step by step instructions

-   Related topics

## Login Module {#login-module .unnumbered}

### **Overview of Login Module Workflow** {#overview-of-login-module-workflow .unnumbered}

The login module consists of all features available without having to
log into the system, as well as features that are implemented in order
to gain login credentials, retrieve login data, gain access to the
system and then exit the system.

The login module allows users to:

-   Submit a request to become an authorized user

-   Report a problem to the administrator

-   Login to gain access to the caTissue Core user dashboard

-   Edit personal profile in case of mistakes or changes

-   Change password for enhanced security

-   Retrieve a forgotten password

-   Logout to protect user security

-   View aggregate data

Each of the above tasks will be discussed in detail in this section.

### Submit New User Request {#submit-new-user-request .unnumbered}

#### Purpose of Task {#purpose-of-task .unnumbered}

Due to the sensitive nature of some of the data stored within the
caTissue Core system, all potential users must register and be approved
by an administrator prior to logging into the system. The designated
Institution, Department and Cancer Research Group will assist the
Administrator in assigning a role for the new user. The approved role
will specify what data types the new user can edit/view/use.

#### Prerequisite Information {#prerequisite-information .unnumbered}

A potential caTissue Core user must successfully navigate to the
caTissue Core **HOME** page by entering the URL into the internet
browser.

#### Step by Step Instructions {#step-by-step-instructions .unnumbered}

Step 1: On the caTissue Core **HOME** page, click the **Sign Up** link.

![](media/image34.png){width="6.493055555555555in"
height="3.935416666666667in"}

**Figure 4. 1**: caTissue Core HOME page

This action will direct the user to the **ADD USER** page for entry of
their personal data (An administrator can manually enter a user into the
system, by using the same page along with additional data fields for
administrative data. This process is also covered in the [Add New
User](#submit-new-user-request) section)

![](media/image35.png){width="4.65625in" height="4.6875in"}

**Figure 4. 2**: NEW USER page

Step 2: Enter the following information into the data fields provided:

> **Item 1:** Indicates entry field for an **Email Address** (required)
> for the new user.
>
> **Item 2:** Entry field for User's **Last Name** (Required).
>
> **Item 3:** Entry field for **First Name** (Required).
>
> **Item 4:** Entry field for **Street** address.
>
> **Item 5:** Entry field for **City** (Required).
>
> **Item 6:** Drop down selection box for **State** (Required).
>
> **Item 7:** Entry field for **Zip Code** (Required)
>
> **Item 8:** Drop down selection box for **Country** (Required).
>
> **Item 9:** Entry field for User's **Phone Number** (required)

**Item 10: Fax Number**

> **Item 11:** Drop down selection box for **Institution** associated
> with the new user (Required).
>
> **Item 12:** Drop down selection box for **Department** (Required).
>
> **Item 13:** Drop down selection box for **Cancer Research Group**
> (Required).
>
> Step 3: Click the **Submit** button.

Upon successful submission of New User data, a message stating "Your
membership request has been received. Please wait for an approval email
from caTissue Core Administrator. Thank you." is displayed.
Additionally, an email confirmation is sent to the email address entered
on the submitted registration.

#### Related Topics {#related-topics .unnumbered}

[Login](#login)

[Approve User](#add-edit-approve-user)

[Edit User Profile](#edit-profile)

[Logout](#logout)

### Report a Problem {#report-a-problem .unnumbered}

#### Purpose of Task {#purpose-of-task-1 .unnumbered}

If a problem is encountered at any time while in the caTissue Core
system, all users (registered or potential) must be able to report the
issue. The reported problem will be stored and can only be viewed by
administrators. The individual submitting the problem will be sent an
email indicating a successful submission. Since an email address is part
of the Report Problem submission, an administrator may choose to follow
up with the submitter for additional information or to inform them of
the problem status or to collect additional information.

#### Prerequisite Information {#prerequisite-information-1 .unnumbered}

A user (registered or potential) successfully navigates to the caTissue
Core URL.

#### Step by Step Instructions {#step-by-step-instructions-1 .unnumbered}

Step 1: Click on the **REPORT PROBLEMS** tab located at the bottom of
the page.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}The
Report Problems tab is displayed on ALL pages in the system, therefore
potential users can report problems without logging into the system, and
registered users can report problems at any time from anywhere inside
the application.

![](media/image34.png){width="6.493055555555555in"
height="3.935416666666667in"}

**Figure 4. 3**: caTissue Core HOME page

This action directs the user to the **REPORT PROBLEM** page.

![](media/image36.png){width="5.4375in" height="2.8854166666666665in"}

**Figure 4. 4:** REPORT PROBLEM page

Step 2: Enter the following data into the fields provided:

> **Item 1:** Entry field for **Your** **Email Address** (required).
>
> **Item 2:** Entry field for your **Name** (required)
>
> **Item 3:** Entry field for your **Affiliation** (required). Example:
> John Doe from Washington University School of Medicine. John Doe would
> go in the name field, and Washington University School of Medicine
> would go in the affiliation field.
>
> **Item 4:** Entry field for **Subject** or problem summary (required)
>
> **Item 5:** Entry field for **Message** or problem details (required)

Step 3: Click the **Submit** button

After successful submission of the problem data, a message stating
"*Problem successfully reported*" will be displayed. Additionally, an
email confirmation is sent to the email address entered on the form.

#### Related Topics {#related-topics-1 .unnumbered}

None

### Login {#login .unnumbered}

#### Purpose of Task {#purpose-of-task-2 .unnumbered}

All users must log into the system in order to gain access to the main
functionality of the caTissue Core system. In this task, an approved
user completes the login process, and is granted access to the user
dashboard.

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}The user may be able to view all options in their
dashboard, however the ability to add, edit, or view specific data may
be restricted due to their assigned role and its associated privileges
(e.g. a technician may not add or edit participant data but may enter
biospecimen-related information).

#### Prerequisite Information {#prerequisite-information-2 .unnumbered}

A previously registered and approved user successfully navigates to the
caTissue Core **HOME** page.

#### Step by Step Instructions {#step-by-step-instructions-2 .unnumbered}

Step 1: On the caTissue Core **HOME** page, enter the following details:

-   **Email address**

-   **Password**

    Step 2: Click the **Login** button.

![](media/image37.png){width="6.492361111111111in"
height="4.047916666666667in"}

**Figure 4. 5**: caTissue Core HOME page

![](media/image13.png){width="0.9479166666666666in" height="0.25in"} If
this is the 1^st^ time a new user has logged into the system, or logging
in after using the [Forgot Password?](#retrieve-forgotten-password)
Feature, they will be prompted to change their password (this will be
discussed in the [Change Password](#change-password) section)

#### [If the logged-in user has an Administrator role then default view will be Administrator tab]{.underline} {#if-the-logged-in-user-has-an-administrator-role-then-default-view-will-be-administrator-tab .unnumbered}

![](media/image38.png){width="6.49375in" height="3.5930555555555554in"}

**Figure 4. 6**: caTissue Core User Dashboard

#### [If the logged-in user has a Technician role then default view will be Specimen Search in Bio-Specimen tab]{.underline} {#if-the-logged-in-user-has-a-technician-role-then-default-view-will-be-specimen-search-in-bio-specimen-tab .unnumbered}

![](media/image39.png){width="6.490277777777778in"
height="3.6152777777777776in"}

**Figure 4. 7**: caTissue Core User Dashboard

#### [If the logged-in user has a Supervisor role then default view will be Collection Protocol Based View in Bio-Specimen tab]{.underline} {#if-the-logged-in-user-has-a-supervisor-role-then-default-view-will-be-collection-protocol-based-view-in-bio-specimen-tab .unnumbered}

![](media/image40.png){width="6.497222222222222in"
height="3.908333333333333in"}

**Figure 4. 8**: caTissue Core User Dashboard

#### [the logged-in user has a Scientist role then default view will be Advance Search in Search tab]{.underline} {#the-logged-in-user-has-a-scientist-role-then-default-view-will-be-advance-search-in-search-tab .unnumbered}

#### ![](media/image41.png){width="6.491666666666666in" height="3.5791666666666666in"} {#section-3 .unnumbered}

**Figure 4. 9**: caTissue Core User Dashboard

#### Related Topics  {#related-topics-2 .unnumbered}

[Change Password](#change-password)

[Logout](#logout)

### Edit Profile {#edit-profile .unnumbered}

#### Purpose of Task {#purpose-of-task-3 .unnumbered}

In case a user's information was entered incorrectly or has changed
(i.e. last name changed due to marriage, email changes or the user has
moved to a different Institution or department), he/she can use this
feature to edit their personal information in the system.

#### Prerequisite Information {#prerequisite-information-3 .unnumbered}

A previously registered and approved user successfully logs into
caTissue Core.

#### Step by Step Instructions {#step-by-step-instructions-3 .unnumbered}

Step 1: In the **HOME** tab, go to, **USER PROFILE Edit** located in the
user dashboard.

If you are logged in as an Administrator, this action will take you to
the User Search page where you can enter search parameters and submit
the query, as detailed in the [edit object](#EditObjects) section of the
manual. Otherwise, for any other user, the Edit User page is shown
directly.

Step 2: Edit /update desired data fields.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
Role can only be assigned/edited by an administrator.

Step 3: Click the **Submit** button.

After submission of the data, a message will be displayed notifying the
user that their profile was successfully updated.

#### Related Topics {#related-topics-3 .unnumbered}

[Submit User Request](#submit-new-user-request)

[Approve User](#add-edit-approve-user)

[Add Institution](#add-edit-institution)

[Add Department](#add-edit-department)

[Add Cancer Research Group](#add-edit-cancer-research-group)

[Roles](#Role)

[Login](#login)

[Logout](#logout)

### Change Password {#change-password .unnumbered}

#### Purpose of Task {#purpose-of-task-4 .unnumbered}

Considering that caTissue Core houses sensitive identified data, it is
important to have proper security measures in place. In accordance with
the described rules governing passwords detailed in this section, the
caTissue Core system allows a registered user to change their password
at any time in order to maintain secure control of their access data.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"} If
the user invokes the [forgot password](#retrieve-forgotten-password)
feature, s/he must change her/his password in order to regain access to
the system. This feature protects from unauthorized entry by individuals
who may have gained knowledge of the password via email or other means.
Once the user logs into the system, the old password and the temporary
password become invalid.

#### Prerequisite Information {#prerequisite-information-4 .unnumbered}

A previously registered and approved user successfully logs into
caTissue Core.

#### Step by Step Instructions {#step-by-step-instructions-4 .unnumbered}

Step 1: On the caTissue Core **HOME** page, go to **USER PROFILE**
**Change Password** option in the user dashboard.

This action directs the user to the **Change Password** page.

![](media/image42.png){width="4.604166666666667in" height="1.4375in"}

**Figure 4.7**: Change Password page

Step 2: The following data items must be entered into the page:

**Item 1: Old Password**

**Item 2: New Password**

**Item 3: Confirm New Password**

This feature assures that the password is typed the same in both fields,
thus cutting down on inaccuracy due to misspellings, capitalization etc.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}For
security reasons, the **New Password** must conform to the following
[]{#PasswordRules .anchor}rules:

-   The new password must be different than the last '*n*' passwords

-   The new password can not be the same as the User/Login name

-   Password can not contain spaces

-   Must be at least '*n*' characters long

-   Must include at least one upper case letter, one lower case letter
    and a number

-   Password should expire after '*n*' days

-   A password cannot be changed more than once per session

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
**'***n***'** denotes a configurable number that is set by the installer
of the caTissue Core system at your site. Contact your administrator for
more details.

Step 3: Click the **Submit** button.

After successful submission, a message will be displayed notifying the
user that their password has been successfully changed in the system.

#### Related Topics {#related-topics-4 .unnumbered}

[Login](#login)

[Logout](#logout)

### Retrieve Forgotten Password {#retrieve-forgotten-password .unnumbered}

#### Purpose of Task {#purpose-of-task-5 .unnumbered}

In case a user forgets his/her password; the system allows all
registered user the option to request that the caTissue Core application
send their password to the email account registered in the system. In
this task, a user requests that the system supply their password
information via email.

#### Prerequisite Information {#prerequisite-information-5 .unnumbered}

A previously registered and approved user successfully navigates to the
caTissue Core **HOME** page.

#### Step by Step Instructions {#step-by-step-instructions-5 .unnumbered}

Step 1: On the caTissue Core **HOME** page, click on the **Forgot your
password?** link.

![](media/image34.png){width="6.493055555555555in"
height="3.935416666666667in"}

**Figure 4.8**: caTissue Core HOME page

This action directs the user to the **FORGOT PASSWORD** page.

![](media/image43.png){width="6.426388888888889in"
height="1.3118055555555554in"}

**Figure 4.9**: FORGOT PASSWORD page

Step 2: Enter **Email Address**

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}The
email address entered *must* be the same email address in your profile.
If you enter a secondary email address, the system will not be able to
tie it your account and will state that the user does not exist.

Step 3: Click the **Send** button to submit or **Reset** to clear the
page.

A message will be displayed at the top of the page stating that the
password will be emailed.

#### Related Topics {#related-topics-5 .unnumbered}

[Change Password](#change-password)

### Assign Privileges {#assign-privileges .unnumbered}

#### Purpose of Task {#purpose-of-task-6 .unnumbered}

The caTissue Core application allows a principal investigator or
administrator to assign (Allow) or revoke (Disallow) privileges to other
users or a user group (role) on all data collected under a specific
Collection Protocol. Therefore, a user granting privileges on a
particular object should also decide whether to extend the privilege to
all data in the object hierarchy. E.g. If a PI grants READ privilege on
a particular protocol that he/she owns, they must also decide whether
that privilege applies to all the specimens associated with that
protocol.

Privileges can be granted at two separate levels:

1\. [Object level]{.underline}: A user can grant privilege to another
user in order to access all data of a particular object.

E.g. User X gives READ privilege to user Y on all the specimen objects
he/she owns, but disallows USE privileges, therefore user Y can view
specimen details but can not submit a distribution request for the
specimens.

2\. [Record level]{.underline}: A user can grant privilege to another
user in order to access a subset of data for a particular object.

E.g. User X gives READ privilege to user Y on the specimen objects of a
particular type.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}By
default all users have read privilege to all objects (in compliance with
regulatory specifications- i.e. all users who are not PIs or
coordinators of data collected under a specific protocol may view
de-identified data of all objects in the system) in the system, and the
PI or protocol coordinator must specifically disallow READ access to
other users.

#### Prerequisite Information {#prerequisite-information-6 .unnumbered}

The currently logged in user must have ownership privileges of the items
on which they are assigning privileges.

#### Step by Step Instructions {#step-by-step-instructions-6 .unnumbered}

Step 1: To alter privileges go to, **PRIVILEGES** **Assign** in the user
dashboard.

This action, forwards the user to the Assign Privileges page.

![](media/image44.png){width="5.65625in" height="3.5104166666666665in"}

**Figure 4 .10**: Assign Privileges Page

> Step 2: Enter the following items into the page:
>
> **Item 1**: Indicates drop down selection box to **Assign** (Allow /
> Disallow) a status.
>
> **Item 2**: Indicates drop down selection box for desired
> **Privilege** (Read / Use).
>
> **Item 3**: Selection box for **Object Type** (Collection Protocol).
>
> **Item 4**: Selection box for **Record Id** (list populated based on
> item selected in Object Type field).
>
> **Item 5**: Selection box for **Group** or **User**(s) that you want
> to assign/revoke privileges to.
>
> Step 3: Click the **Assign** button.

Upon successful submission, a confirmation message will be displayed at
the top of the page.

[Possible Scenario]{.underline}: You are the PI for a Collection
Protocol and you want to allow some investigators (e.g. your
collaborators) to use your data/specimens but you want to disallow
others from doing so.

[Solution]{.underline}: Click on Collection Protocol as the Object Type,
then select the desired record(s) on which and the user/group(s) in the
list for whom you want to disallow privileges.

![](media/image45.png){width="5.625in" height="2.8125in"}

**Figure 4.11**: Disallow Read Privileges

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
To select multiple items, hold down the **Ctrl** key during selection.

#### Related Topics  {#related-topics-6 .unnumbered}

[Login](#login)

[Approve User](#add-edit-approve-user)

[Roles](#Role)

[Logout](#logout)

### Logout {#logout .unnumbered}

#### Purpose of Task {#purpose-of-task-7 .unnumbered}

This task involves logging a user out of the system and terminating the
current session.

#### Prerequisite Information {#prerequisite-information-7 .unnumbered}

User must be currently logged into the caTissue Core application.

#### Step by Step Instructions {#step-by-step-instructions-7 .unnumbered}

From any view or any page of the caTissue Core website, click the **Sign
Out** link located in the top right hand corner of the screen.

![](media/image7.jpeg){width="6.061111111111111in"
height="3.6104166666666666in"}

**Figure 4.12**: caTissue Core Sign Out link

This action returns the user to the caTissue Core **HOME** page, where
they can log in again if desired.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}If a
user selects to logout of the system, all data not submitted will be
lost.

#### Related Topics {#related-topics-7 .unnumbered}

[Login](#login)

### View Aggregate Data {#view-aggregate-data .unnumbered}

#### Purpose of Task {#purpose-of-task-8 .unnumbered}

All users (potential or registered) must be able to view aggregate data
without logging into the system.

#### Prerequisite Information {#prerequisite-information-8 .unnumbered}

User (registered or potential) successfully navigates to the caTissue
Core **HOME** page.

#### Step by Step Instructions {#step-by-step-instructions-8 .unnumbered}

On the caTissue Core **HOME** page, click on the **SUMMARY** tab located
at the top of the page.

![](media/image34.png){width="6.493055555555555in"
height="3.935416666666667in"}

**Figure 4. 13**: caTissue Core HOME page

This action prompts the system to display the **caTissue Core Summary**
page.

![](media/image46.png){width="6.426388888888889in"
height="2.4319444444444445in"}

**Figure 4. 14:** caTissue Core Summary page

Aggregate data displayed encompasses summary data for all available
specimens in the system.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}
Summary data does not display identifiable data and cannot be traced to
a specific protocol or participant.

#### Related Topics {#related-topics-8 .unnumbered}

None

## Administrative Module {#administrative-module .unnumbered}

### **Overview of Administrative Module Workflow** {#overview-of-administrative-module-workflow .unnumbered}

This module deals with administrative tasks in the system, i.e. setting
up new user accounts, resolving problems, and entry of required data
elements used during biospecimen submission and distribution.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}
Only users with the role of administrator are allowed to submit or edit
data in the administrative module.

The menu options contained in the **ADMINISTRATIVE DATA** tab include:

-   Add / Edit User / Approve new User

-   Add / Edit Institution

-   Add / Edit Department

-   Add / Edit Cancer Research Group

-   Add / Edit Site

-   Add / Edit Storage Type

-   Add / Edit Storage Container / View Map

-   Add / Edit Specimen Array Type

-   Add / Edit Biohazard

-   Add / Edit Collection Protocol

-   Add / Edit Distribution Protocol

-   View Reported Problems

Each of the above tasks will be discussed in detail in this section.

### Add \| Edit \| Approve User {#add-edit-approve-user .unnumbered}

#### Purpose of Task {#purpose-of-task-9 .unnumbered}

The purpose of Add \| Edit \| Approve New User is to allow an
administrator to add/edit user profiles, assign user roles, and approve
or reject user registration requests.

#### Prerequisite Information {#prerequisite-information-9 .unnumbered}

The currently logged in user must be assigned the role of administrator
in the system.

#### Step by Step Instructions {#step-by-step-instructions-9 .unnumbered}

##### *Add User* {#add-user .unnumbered}

When adding a user into the system, an administrator can enter all data
for a user into the system without the requestor submitting a New User
Request.

> ![](media/image8.png){width="0.6145833333333334in"
> height="0.21875in"}This process leads to direct approval of the user.

Step 1: Click on the **ADMINISTRATIVE DATA** tab located at the top of
the page.

Step 2: Go to, **USER Add** on the user dashboard.

![](media/image47.png){width="5.5625in" height="5.78125in"}

**Figure 4.15**: NEW USER page

Step 3: Enter the following user details into the fields provided:

> **Item 1: Email Address** (Required) for the new user.
>
> **Item 2: Confirm Email Address** (Required). For security reasons,
> the email address must be entered a second time and must match the
> original entry.
>
> **Item 3: Last Name** (Required) of the new user.
>
> **Item 4: First Name** (Required) of the new user.

**Item 5: Street** address

**Item 6: City** (Required)

**Item 7: State** (Required)

**Item 8: Zip Code** (Required)

**Item 9: Country** (Required)

**Item 10: Phone Number** (Required)

**Item 11: Fax Number**

> **Item 12:** Indicates Add New links for
> [Institution](#add-edit-institution),
> [Department](#add-edit-department) or [Cancer
> Research](#add-edit-cancer-research-group) Group. The links can be
> used to direct you to the appropriate pages if the desired items are
> not available in the drop down selections and need to be entered into
> the system.
>
> ![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
> If using any of the Add New links, upon submit, you will be returned
> to the Add New User page.
>
> **Item 13:** Users associated **Institution** (Select from drop down -
> required)
>
> **Item 14:** Users associated **Department** (Select from drop down -
> required)
>
> **Item 15:** Users associated **Cancer Research Group** (Select from
> drop down - required)
>
> **Item 16: Role** (Required) of the new user. This field is active
> only during entry of a new user by an administrator. When a user edits
> his/her profile, the Role field will be inactive.
>
> **Item 17:** Optional **Comments** entry field. This field is not
> displayed if a user is editing their own profile.

Step 4: Click the **Submit** button or **Reset** to clear the page.

Submission status will be displayed at the top page. Additionally, an
email confirmation will be sent to the user's email address entered on
the page.

##### ***Edit User*** {#edit-user .unnumbered}

Step 1: Got to **ADMINISTRATIVE DATA** tab **USER Edit.**

Step 2: In the User Search page enter search parameters for a specified
user (please refer to [Edit - Search section](#SearchEDIT) for
additional details)

Step 3: Once the Edit User page is displayed, update the desired data
items for the selected user. This is the same page and data fields used
for initial creation of the selected user account.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
The Edit User feature differs from the Edit Profile feature in that the
Edit User feature allows for not only modification of the user data, but
also modification of the user's role which defines access privileges in
the system. The administrator can log into the system using his/her
assigned login data, and then select to edit one or more user profiles
without having to leave the system.

Step 4: Click on the **Submit** button

##### ***Activate User*** {#activate-user .unnumbered}

This feature allows an administrator to review all New User Request
details and then select to accept or reject the request.

Step 1: Log into the caTissue Core **HOME** page.

Step 2: Click on the **ADMINISTRATIVE DATA** tab located at the top of
the page.

Step 3: Go to, **USER Approve New Users** on the user dashboard.

![](media/image48.png){width="4.552083333333333in"
height="2.2423611111111112in"}

**Figure 4.16**: APPROVE USERS page

Step 4: Select any of the users by clicking on an **Email Address** (in
the **Login Name** column).

This action results in the **EDIT USER** page being displayed. The page
will be populated with the data from the selected user request.

![](media/image49.png){width="5.166666666666667in"
height="6.072916666666667in"}

**Figure 4.17**: Approve New User page

Step 5: The administrator can change the **Status** of the request in
**Item 1** from **Pending** to **Active** (to approve the user
registration request) OR from **Pending** to **Reject** (to reject the
user registration request).

Step 6: Select **[Role](#Role)** in **Item 2** for the newly approved
user.

**Item 3**: Indicates optional entry fields for **Comments** related to
the user.

Step 7: Click **Submit**.

The submission status will be displayed at the top of the page and the
requestor will be sent an email indicating whether his/her registration
request has been approved or rejected.

#### Related Topics {#related-topics-9 .unnumbered}

[Login](#login)

[Submit New User Request](#submit-new-user-request)

[Approve User](#add-edit-approve-user)

[Assign Privileges](#assign-privileges)

[Logout](#logout)

### Add \| Edit Institution {#add-edit-institution .unnumbered}

#### Purpose of Task {#purpose-of-task-10 .unnumbered}

The purpose of this task is to add the name of a new institution into
the system or edit the name of an existing institution. An institution
is defined as an established society, corporation, foundation or other
organization founded and united for a specific purpose, e.g. for
health-related research; also used to refer to a building or buildings
occupied or used by such organization (e.g. Washington University or
University of Pittsburgh). An institution designation is important when
adding a new user into the system. This feature along with Add/Edit
Department and Add/Edit Cancer Research Group allows the administrator
of a caTissue Core instance to customize the permissible values for
these fields.

#### Prerequisite Information {#prerequisite-information-10 .unnumbered}

Only an administrator has the privilege to perform this task after
successfully logging into the caTissue Core system.

#### Step by Step Instructions {#step-by-step-instructions-10 .unnumbered}

##### *Add Institution* {#add-institution .unnumbered}

Step 1: On the caTissue Core **HOME** page, click on the
**ADMINISTRATIVE DATA** tab.

Step 2: Go to, **INSTITUTION Add** on the user dashboard.

This action results in the **NEW INSTITUTION** page being displayed.

Step 3: Enter a **Name** for the new institution.

Step 4: Click the **Submit** button or **Reset** to clear the page.

![](media/image50.png){width="3.6819444444444445in" height="1.21875in"}

**Figure 4.18:** NEW INSTITUTION page

The submission status will be displayed at the top of the page.

##### *Edit Institution* {#edit-institution .unnumbered}

Step 1: Go to, **INSTITUTION Edit** on the user dashboard.

Step 2: In the **INSTITUTION SEARCH** form enter search parameters
(please refer to [Edit - Search section](#SearchEDIT) for additional
details)

Step 3: Click the **Submit** button.

This action returns and displays any Institutions matching the criteria
entered. If only one record matches the search criteria, the system will
go directly to the requested record. If more than one record matches the
search criteria, the system will display a list of matches for the user
to select from (this will be discussed in more detail in the [query
section](#query-module)).

Step 4: Once you have located the institution you would like to edit,
double clink on the selected record, enter the updated Name into the
field provided in the Edit Institution page and click on the **Submit**
button.

The submission status will be displayed at the top of the page.

#### Related Topics {#related-topics-10 .unnumbered}

[Login](#login)

[Add Institution](#add-edit-institution)

[Add New User](#submit-new-user-request)

[Logout](#logout)

### Add \| Edit Department {#add-edit-department .unnumbered}

#### Purpose of Task {#purpose-of-task-11 .unnumbered}

The purpose of this task is to add a new department into the system or
edit an existing department's profile. A department is defined as a
specialized division of a large organization or Institution (e.g.
Department of Pathology & Immunology or Department of Surgery).
Designating a department affiliation along with a selected Institution
is important when entering user details into the system.

#### Prerequisite Information {#prerequisite-information-11 .unnumbered}

Only an administrator has the privilege to perform this task after
successfully logging into the caTissue Core system.

#### Step by Step Instructions {#step-by-step-instructions-11 .unnumbered}

##### ***Add Department*** {#add-department .unnumbered}

Step 1: Click on the **ADMINISTRATIVE DATA** tab

Step 2: Click on **Department Add** on the user dashboard.

Step 3: Enter the **Name** of the new department.

Step 4: Click the **Submit** button.

![](media/image51.png){width="3.9298611111111112in"
height="1.4784722222222222in"}

**Figure 4.19**: NEW DEPARTMENT page

The submission status will be displayed at the top of the page.

##### ***Edit Department*** {#edit-department .unnumbered}

Step 1: Click on **DEPARTMENT Edit** on the user dashboard.

Step 2: In the Department Search page enter search parameters (please
refer to [Edit - Search section](#SearchEDIT) for additional details)

Step 3: Click the **Search** button.

Step 4: Select desired department if more than one result is returned by
double clicking on this row.

Step 5: Update **Name** of Department.

Step 6: Click the **Submit** button.

The submission status will be displayed at the top of the page.

#### Related Topics {#related-topics-11 .unnumbered}

[Login](#login)

[Add Department](#add-edit-department)

[Logout](#logout)

### Add \| Edit Cancer Research Group {#add-edit-cancer-research-group .unnumbered}

#### Purpose of Task {#purpose-of-task-12 .unnumbered}

The purpose of this task is to add a new Cancer Research Group into the
system or change an existing Cancer Research Group's profile. A Cancer
Research Group is defined as a collection of scientists and/or clinician
users with a common research objective related to diagnosis and
treatment of cancer (e.g. Breast Cancer Research Group or Cancer
Immunology Group).

#### Prerequisite Information {#prerequisite-information-12 .unnumbered}

Only an administrator has the privilege to perform this task after
successfully logging into the caTissue Core system.

#### Step by Step Instructions {#step-by-step-instructions-12 .unnumbered}

##### ***Add Cancer Research Group*** {#add-cancer-research-group .unnumbered}

Step 1. On the caTissue Core **HOME** page, click the **ADMINISTRATIVE
DATA** tab**.**

Step 2: Go to, **Cancer Research Group Add** on the user dashboard.

This action causes the **NEW CANCER RESEARCH GROUP** page to be
displayed.

![](media/image52.png){width="3.5416666666666665in"
height="0.8645833333333334in"}

> **Figure 4. 20**: NEW CANCER RESEARCH GROUP page

Step 3: Enter the **Name** of a new Cancer Research Group.

Step 4: Click the **Submit** button.

The submission status will be displayed at the top of the page.

##### ***Edit Cancer Research Group*** {#edit-cancer-research-group .unnumbered}

Step 1: Go to, **CANCER RESEARCH GROUP Edit** on the user dashboard.

Step 2: In the Cancer Research Group Search page enter search parameters
(please refer to [Edit - Search section](#SearchEDIT) for additional
details)

Step 3: Click the **Submit** button.

Step 4: After selecting the desired record from the search results by
double clicking on the row, update the **Name** of the Cancer Research
Group.

Step 5: Click the **Submit** button to proceed, or **Reset** to
terminate the process.

The submission status will be displayed at the top of the page.

#### Related Topics {#related-topics-12 .unnumbered}

[Login](#login)

[Add Cancer Research Group](#add-edit-cancer-research-group)

[Logout](#logout)

### Add \| Edit Site {#add-edit-site .unnumbered}

#### Purpose of Task {#purpose-of-task-13 .unnumbered}

The purpose of this task is to add a new Site into the system or change
an existing Site's profile. A Site represents a physical location
associated with a biospecimen collection, storage, processing, or
utilization (e.g. Barnes-Jewish Hospital South Operating Room Suite or
Siteman Cancer Center Tissue Procurement Facility). The specification of
a Site is required during entry of a storage container, biospecimen,
specimen collection group, or distribution into the system. The
customization of Site by an administrator allows each instance of
caTissue Core to display only relevant physical locations for that
installation.

#### Prerequisite Information {#prerequisite-information-13 .unnumbered}

Only an administrator has the privilege to perform this task after
successfully logging into the caTissue Core system.

#### Step by Step Instructions {#step-by-step-instructions-13 .unnumbered}

##### *Add New Site* {#add-new-site .unnumbered}

Step 1: On the caTissue Core **HOME** page, click the **ADMINISTRATIVE
DATA** tab**.**

Step 2: Go to, **SITE Add** on the user dashboard.

This action causes the **NEW** **SITE** page to be displayed.

![](media/image53.png){width="4.552083333333333in"
height="3.8020833333333335in"}

**Figure 4. 21**: NEW SITE page

Step 3: Enter the following items into the page:

> **Item 1:** Indicates the entry field for the **Name** of the new site
> being entered (Required).
>
> **Item 2**: Indicates a drop down selection box for designation of the
> site **Type** (Required). In other words, what purpose does the Site
> serve with respect to biospecimens:

-   Collection Site -- location where biospecimens may be procured.

-   Laboratory -- location where biospecimens may be processed.

-   Not Specified -- Site purpose not specified (e.g. a multi-purpose
    site or none of the other permissible values apply).

-   Repository -- location where biospecimens may be stored.

> **Item 3:** Indicates a drop down selection box for selection of a
> **Coordinator** for the Site (Select from drop-down menu - required).
> If the desired coordinator is not in the list presented and therefore
> does not exist in the caTissue system, you can click on the Add New
> link located to the right of the field. This will take you to a page
> for entry of a new coordinator. Once you submit the data you will be
> returned to the New Site page with the newly entered coordinator
> selected.
>
> **Item 4:** Indicates an entry field for **Email Address** for the
> Site.
>
> **Item 5:** Indicates entry field for **Street** address for the Site
> being entered. (Required)

**Item 6:** Indicates an entry field for **City** (Required)

> **Item 7:** Indicates a drop down field for selection of **State**
> (Required)
>
> **Item 8:** Indicates a drop down field for selection of **Country**
> (Required)
>
> **Item 9:** Indicates an entry field for **Zip Code** (Required)
>
> **Item 10:** Indicates an entry field for **Phone Number**
>
> **Item 11:** Indicates an entry field for **Fax Number**

Step 4: Click the **Submit** button.

The submission status will be displayed at the top of the page.

##### *Edit Site* {#edit-site .unnumbered}

Step 1: Go to, **SITE Edit** on the user dashboard.

Step 2: In the Site Search page enter search parameters (please refer to
[Edit - Search section](#SearchEDIT) for additional details)

Step 3: Click on **Search**.

Step 4: Once the desired record is located, select it by double clicking
on the row, and update part or all of the fields on the **EDIT SITE**
page. This is the same page containing the same data fields used for
initial creation of the selected Site.

Step 5: Click the **Submit** button.

The submission status will be displayed at the top of the page.

#### Related Topics {#related-topics-13 .unnumbered}

[Login](#login)

[Add Site](#add-edit-site)

[Logout](#logout)

### Add \| Edit Storage Type {#add-edit-storage-type .unnumbered}

#### Purpose of Task {#purpose-of-task-14 .unnumbered}

The purpose of this task is to add a new storage type into the system or
change an existing storage type's profile. A storage type can be thought
of as a "template" used during creation of new storage containers. This
feature allows an administrator to cut down on the amount of data
entered during storage container creation by using pre-defined
parameters. Examples of storage types include a -80º C freezer
(different makes and models may be created as individual storage types
if they can hold different numbers of racks or boxes or may be
represented as a single storage type), liquid nitrogen freezer, -20º C
freezer, 4º C freezer, etc.

#### Prerequisite Information {#prerequisite-information-14 .unnumbered}

Only an administrator has the privilege to perform this task after
successfully logging into the caTissue Core system.

#### Step by Step Instructions {#step-by-step-instructions-14 .unnumbered}

##### *Add New Storage Type* {#add-new-storage-type .unnumbered}

Step 1: On the caTissue Core **HOME** page, click the **ADMINISTRATIVE
DATA** tab**.**

Step 2: Go to, **STORAGE TYPE Add** on the user dashboard.

This action causes the **NEW** **STORAGE TYPE** page to be displayed.

![](media/image54.png){width="6.497222222222222in"
height="3.248611111111111in"}

**Figure 4. 22**: NEW STORAGE TYPE page

Step 3: Enter the following items onto the page:

> **Item 1**: Indicates the **Name** (required) of the new storage
> container type (e.g. Forma Freezer).
>
> **Item 2**: Indicates the data field for entry of a **Default
> Temperature** (in degrees Celsius- for example -80º C).
>
> **Item 3**: Indicates the **Can hold** (restrictions on what other
> containers or specimen class/array the current storage type can
> contain. For example, a Forma Freezer may only hold Forma Racks)
> section.
>
> ![](media/image13.png){width="0.9479166666666666in" height="0.25in"}To
> make multiple selections, for Storage Type, Specimen Class or Specimen
> Array Type, hold down the **Ctrl** key when selecting items.
>
> caTissue Core v1.1 contains functionality that allows for a detailed
> definition of storage container components along with a strict
> hierarchy of positional elements. This functionality allows the system
> to automatically identify the next available open storage container
> based on "what" the storage container "type" can hold.

*[Storage type]{.underline}*

> ![](media/image55.png){width="1.8333333333333333in"
> height="0.9166666666666666in"}

**Figure 4. 23**: STORAGE TYPE restrictions field

> This new feature allows a user to specify one or more container types
> that can be held in a newly created storage container.
>
> Example: A "freezer" can contain "racks" and "boxes" but a box can not
> contain a freezer.
>
> ![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
> The default value for Storage Type is "All". In other words, no
> restrictions are applied and the storage container can hold ALL
> storage types.

*[Specimen Class]{.underline}*

> This section allows a user to restrict the class of specimens that can
> be stored in the storage container type being created. So, certain
> containers may only hold fluid specimens, while other may be
> restricted to containing frozen tissues. To allow one or more Specimen
> Class(s), click on the radio button located to the left of the column
> title. This will activate the Specimen Class selection list and
> de-activate the Specimen Array Type list.
>
> ![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
> Specimen class(es) that are selected will be allowed to be held by
> that storage type.
>
> ![](media/image56.png){width="1.84375in"
> height="0.9270833333333334in"}
>
> **Figure 4. 24**: Specimen Class restrictions
>
> Example: If the new type of storage container being created is
> intended for only tissue specimens, you would select Tissue in the
> specimen class listbox.
>
> ![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
> The default value for Specimen Class is "All".

*[Specimen Array]{.underline}*

> This section allows you the ability to designate specimen arrays (e.g.
> 96 well plates or 384 well plates) that may be held by the Storage
> Container Type being created. Note that a storage type may be
> restricted to hold one or more specimen classes OR one or more
> specimen arrays. Thus, a storage type cannot be restricted to hold
> either tissue specimens or 8 x 12, 96 well PCR plates since one is a
> specimen class and the other is a specimen array.
>
> ![](media/image57.png){width="1.84375in"
> height="0.9270833333333334in"}

**Figure 4. 25:** Specimen Array Type restrictions

> **Item 4**: Indicates the entry field for the **Capacity in Dimension
> One** (required), i.e. the number of columns in the newly created
> storage type (e.g. a Forma Freezer may have 6 x 4 racks and so the
> total capacity in dimension one is 6).
>
> **Item 5**: Indicates the entry field for **Text Label For Dimension
> One** (required- e.g. racks for a Forma Freezer that holds 6 x 4
> racks).
>
> **Item 6**: Indicates the entry field for the **Capacity in Dimension
> Two** (required), i.e. the number of rows in the newly created storage
> type (e.g. a Forma Freezer may have 6 x 4 racks and so the total
> capacity in dimension two is 4).
>
> **Item 7**: Indicates the entry field for **Text Label for Dimension
> Two**. (e.g. racks for a Forma Freezer that holds 6 x 4 racks).
>
> Step 4: Click the S**ubmit** button.
>
> The submission status will be displayed at the top of the page.

##### *Edit Storage Type* {#edit-storage-type .unnumbered}

> Step 1: Go to, S**TORAGE TYPE** **Edit** on the user dashboard.
>
> Step 2: In the Storage Type Search page enter search parameters
> (please refer to [Edit - Search section](#SearchEDIT) for additional
> details)
>
> Step 3: Once the desired record is located, update part or all of the
> fields on the **EDIT STORAGE TYPE** page. This is the same page and
> data fields used for initial creation of the selected Storage Type.
>
> Step 4: Click the **Submit** button to continue, or [Add
> Container](#add-edit-view-map---storage-container) to go to the [Add
> Storage Container](#add-edit-view-map---storage-container) page.
>
> The submission status will be displayed at the top of the page.

#### Related Topics {#related-topics-14 .unnumbered}

[Login](#login)

[Add Storage Type](#add-edit-storage-type)

[Add/Edit Storage Container](#add-edit-view-map---storage-container)

[Logout](#logout)

### Add \| Edit \| View Map - Storage Container {#add-edit-view-map---storage-container .unnumbered}

#### Purpose of Task {#purpose-of-task-15 .unnumbered}

The purpose of this task is to add a new Storage Container into the
system or change an existing Storage Container's profile. This option
also allows you to view a map of all Storage Containers in the system. A
storage container represents a physically discrete repository that is
used to store a specimen (e.g. Box or Freezer). Any container may be a
child of another container and may have multiple children containers as
well. In addition, each site may have different types of containers in
different kinds of physical arrangements. Thus the storage container
hierarchy is a configurable recursive structure that is provides
flexibility for deployment at all sites.

#### Prerequisite Information {#prerequisite-information-15 .unnumbered}

Only an administrative user has the privilege to perform this task after
successfully logging into the caTissue Core system.

#### ***Step by Step Instructions*** {#step-by-step-instructions-15 .unnumbered}

##### *Add New Storage Container and View Map* {#add-new-storage-container-and-view-map .unnumbered}

Step 1: On the caTissue Core **HOME** page, click the **ADMINISTRATIVE
DATA** tab.

Step 2: Go to, **STORAGE CONTAINER Add** in the user dashboard.

![](media/image58.png){width="6.496527777777778in"
height="5.226388888888889in"}

> **Figure 4. 26**: NEW STORAGE CONTAINER page

Step 3: Select/Enter the following items into the page:

**Item 1:** Indicates the Storage Container **Type** that should be
applied to the newly created Storage Container. For example, you may be
installing a new Forma Freezer. In this case, first the Forma Freezer's
storage type description must be entered using the Add Storage Type link
or by clicking Add New on this page, and then this newly created type
may be selected in this field.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}
Storage type denotes the basic elements of a container and can be used
as a template during entry of new storage containers. If none of the
available storage types represent the type of container being entered,
you can select to add a new storage type by clicking on the Add New link
located to the right of the field.

**Item 2:** Indicates a choice of either selecting **Site** (select from
drop-down menu) or **Parent Container** using the radio buttons
displayed to the left of the fields. This denotes the location where the
new storage container is to reside. You can manually edit the
auto-selected location or user the [map feature](#MapFeature). For
containers that will physically reside in a Site and have no parent
container (e.g. a Forma Freezer would reside in a Tissue Procurement
Facility), select the appropriate Site, and for containers that
themselves are contained by other larger containers (e.g. Forma Racks
are held by a Forma Freezer), select the appropriate Parent Container.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
If the drop-down menu does not have the value you want, click on the
**Add New** link to add a new storage **Site**.

A user can select to assign a new storage container to a Site or to a
Parent Container by clicking on the radio buttons located to the left of
the field. The Parent Container position will be populated with the 1st
suitable vacant position according to the storage container
restrictions.

**Item 3**: Indicates a data field for entry of a **Name** for the new
created container (Required- e.g. Forma Freezer #1). If **Site** is
selected, a Container Name will be auto generated and displayed in the
**Name** field. The name displayed can be reset to the default setting,
by clicking on the [Reset Name]{.underline} link located to the right of
the Container Name field. The Reset Name link resets the name of the
Storage Container to the default name, i.e.
\<Site_name\>\_\<Type_name\>\_\<Id\>. If you want to edit the name, you
can type directly into the field provided.

**Item 4**: Is an entry field where you can specify the **number of
containers** that will be included (Required). Go to [Create Similar
Containers](#create-similar-storage-containers) section for more
details. This feature allows the Administrator to create multiple
similar storage containers in bulk (e.g. add 24 Forma Racks to a Forma
Freezer in batch).

**Item 5:** Is an optional entry field for a **Barcode** for the storage
container.

**Item 6**: Indicates an optional entry field for **Temperature** of the
new Storage Container.

**Item 7:** Indicates listbox for selection of container Restrictions
for **Collection Protocol Title.** A container may be restricted to hold
specimens procured under one or more collection protocols. These
restrictions may be specified by selecting one or more collection
protocols under which specimens are procured.

**Item 8:** Indicates the first section of the Can Hold Restrictions for
the storage container. This specifies which container types may be held
by that storage container (e.g. Forma Freezer #1 may hold Forma Freezer
Racks). Values specified for that container type are automatically
selected by default and may be overridden for the current storage
container instance.

**Item 9:** Restrictions for **Specimen Class** may be entered by
clicking on the radio button located next to specimen class and making
selections in the list provided.

**Item 10:** Restrictions for **Specimen Array Type** may be entered by
clicking on the radio button located next to specimen array type and
making selections in the list provided.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
The default value for Container Type, Specimen Class and Specimen Array
Type restrictions is "All". Please the Storage Type section for more
details on Items 8-10 above.

All restrictions applied to a parent container will transcend to any
existing or future children containers. At the same time it will be
possible to override the privilege at the child level.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}To
select multiple restrictions, hold down the **Ctrl** key when selecting
items in each box. Can hold allowances are selected during creation of a
storage Type, however they may be modified for an individual storage
container without having to create an additional storage type.

**Item 11:** Indicates entry fields for **Dimension One** (Required) and
**Dimension two.**

Step 4. Click on the **Submit** button.

The submission status will be displayed at the top of the page.

##### *Create Similar Storage Containers* {#create-similar-storage-containers .unnumbered}

If more than one container is specified and the form is submitted
(**Item 4** in the [Add New Storage
Container](#add-edit-view-map---storage-container) page), the page will
refresh with entry fields for the specified number of similar
containers, as shown in the image below:

![](media/image59.png){width="6.0in" height="4.7in"}

***Figure 4.27:** Create Similar Containers*

**Item 1**: Indicates a drop down for selection of Storage Container
Type for ALL containers (required).

**Item 2**: Entry box for **Temperature** of the containers.

**Item 3**: Selection box to assign one or more **Collection Protocol
Title**(s) to the containers.

**Item 4**: Indicates selection boxes for the types of sub containers
that may be stored in the newly created containers as well as specimen
types.

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}Multiple Items can be selected for **Collection
Protocol Title** and the **Can Hold** fields by holding down the
**Ctrl** key while making selections.

**Item 5:** Indicates entry fields for container dimensions that will be
applied to ALL containers being created (required).

**Item 6**: Indicates the **Container Name** entry fields for each
container (required). An associated Barcode is optional.

**Item 7**: Indicates a drop down for selection of a **Site** or
**Parent Container**. This field is pre-populated depending on which
item was selected during the initial submit (required).

##### *Edit Storage Container:* {#edit-storage-container .unnumbered}

Step 1: Go to, **STORAGE CONTAINER Edit** on the user dashboard.

Step 2: In the Storage Container Search page enter search parameters
(please refer to [Edit - Search section](#SearchEDIT) for additional
details)

Step 3: Click the **Search** button.

Step 4: Once the desired record is selected, update data fields on the
**EDIT STORAGE CONTAINER** page, and click on the **Submit** button to
proceed or **Reset** to clear the page.

The submission status will be displayed at the top of the page.

##### *View Map:* {#view-map .unnumbered}

In order to easily visualize storage containers in the system, a map
feature has been implemented that allows a user to select appropriate
storage locations from a container hierarchy.

Go to the **BIOSPECIMEN DATA** tab and click on **Storage Container**
**View Map**.

This action will display a map of containers where you can browse
through storage locations (go to [Map feature](#MapFeature) section for
additional details).

#### Related Topics {#related-topics-15 .unnumbered}

[Login](#login)

[Add/Edit Storage Type](#add-edit-storage-type)

[Logout](#logout)

### Add/Edit Specimen Array Type {#addedit-specimen-array-type .unnumbered}

#### Purpose of Task {#purpose-of-task-16 .unnumbered}

The purpose of this task is to add a new Biospecimen Array Type (e.g. 96
well or 384 well PCR plate) into the system or modify an existing array.
An array type can be thought of as a "template" used during creation of
specimen arrays. This feature allows a user to cut down on the amount of
data entered during array creation by using pre-defined parameters. The
array type allows you to predefine the class and types of specimens that
may be contained by that array type (e.g. a 96 well PCR plate may hold
molecular specimens) along with dimensions for the array.

Example: If you work a lot with arrays that hold DNA and/or RNA and have
the dimension of 8 X 12. You can create an array type with a specimen
class of Molecular and Specimen Type of DNA and RNA with dimension 1 set
to 8 and dimension 2 set to 12. This allows you to select a pre-defined
array type during entry of a new array. The system will recognize the
array type selected and will format the page with the proper dimensions
and will restrict entry of biospecimens into the array that do not
conform to the specified specimen class and type.

#### Prerequisite Information {#prerequisite-information-16 .unnumbered}

User must have administrative privileges in the caTissue system.

#### Step by Step instructions {#step-by-step-instructions-16 .unnumbered}

*Add Biospecimen Array Type*

Step 1: Go to, **ADMINISTRATIVE DATA** tab, and click on **SPECIMEN
ARRAY TYPE** **Add** in the user dashboard.

This will prompt the system to display the **ADD SPECIMEN ARRAY TYPE**
page.

![](media/image60.png){width="7.120833333333334in"
height="2.095833333333333in"}

***Figure 4. 28**: ADD SPECIMEN ARRAY TYPE page*

Step 2: Enter/select the following data items into the fields provided:

**Item 1**: Indicates the entry box for the **Name** of the new array
type (Required)

**Item 2**: Drop down for section of a **Specimen Class** (Required)

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}Only one specimen class is allowed. Therefore the
class selected will be the same for all specimens on the array.

**Item 3**: Listbox for selection of one or more **Specimen Type**(s)
(Required)

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
To select multiple items, hold down the **Ctrl** key during selection.

**Item 4**: Indicates an entry box for optional **comments** related to
the new array type.

**Item 5**: Indicates the **Capacity** for the new array type.
**Dimension One** is required and **Dimension Two** is optional.

Step 3: Once you have entered/selected all required data types, click
**Submit** to enter the data into the system.

The submission status will be displayed at the top of the page.

##### *Edit Specimen Array Type* {#edit-specimen-array-type .unnumbered}

Step 1: Go to, **Specimen Array Type Edit** on the user dashboard.

Step 2: In the Specimen Array Search page, enter search parameters
(please refer to [Edit - Search section](#SearchEDIT) for additional
details) and then click the **Search** button.

Step 3: Once the desired record is selected, update part or all of the
fields on the EDIT SPECIMEN ARRAY TYPE page.

This is the same page and data fields used for initial creation of the
selected Storage Type.

Step 4: Click the **Submit** button.

The submission status will be displayed at the top of the page.

#### Related Topics {#related-topics-16 .unnumbered}

[Login](#login)

[Specimen Array](#add-edit-aliquot---specimen-array)

[Logout](#logout)

### Add \| Edit Biohazard {#add-edit-biohazard .unnumbered}

#### Purpose of Task {#purpose-of-task-17 .unnumbered}

The purpose of this task is to add a new Biohazard into the system or
edit an existing Biohazard. An administrator can add biohazard
designations into the system. These designations can then be used by
other users during entry of biospecimens (e.g. to designate that a
particular biospecimen is ^32^P radiolabeled or that it is infected by
HIV). A biohazard is defined as a biological or chemical substance that
exerts toxic or pathologic effects on living entities (e.g. radioactive
or infectious).

#### Prerequisite Information {#prerequisite-information-17 .unnumbered}

Only an administrative user has the privilege to perform this task after
successfully logging into the caTissue Core system.

#### Step by Step Instructions {#step-by-step-instructions-17 .unnumbered}

##### *Add Biohazard* {#add-biohazard .unnumbered}

Step 1: On the caTissue Core **HOME** page, click the **ADMINISTRATIVE
DATA** tab**.**

Step 2: Go to, **BIOHAZARD Add** in the user dashboard.

This action causes the **NEW BIOHAZARD** page to be displayed.

![](media/image61.png){width="4.304861111111111in"
height="2.3944444444444444in"}

**Figure 4. 29:** NEW BIOHAZARD page

Step 3. Select/ enter the following items in the fields provided:

> **Item 1:** Entry field for new biohazard **Name** (required- e.g. HIV
> or 32P)**.**
>
> **Item 2:** Drop down selection box for **Type** of biohazard being
> entered (Required- e.g. Radioactive or Infectious).

**Item 3**: Optional entry field for **Comments** related to the new
biohazard.

Step 4: Click the **Submit** button to proceed, or **Reset** to clear
all data.

The submission status will be displayed at the top of the page.

##### *Edit Biohazard* {#edit-biohazard .unnumbered}

Step 1: Click on **BIOHAZARD Edit**.

> Step 2: In the Biohazard search page enter search parameters (please
> refer to [Edit - Search section](#SearchEDIT) for additional details)

Step 3: Click on the **Search** button**.**

Step 4: Once the desired record is selected, update desired data fields.

Step 5: Click the **Submit** button to proceed or **Reset** to clear the
page.

> The submission status will be displayed at the top of the page.

#### Related Topics {#related-topics-17 .unnumbered}

[Login](#login)

[Add\\Edit Specimen](#add-edit-specimen)

[Logout](#logout)

### Add \| Edit Collection Protocol {#add-edit-collection-protocol .unnumbered}

#### Purpose of Task {#purpose-of-task-18 .unnumbered}

The purpose of this task is to add a new Collection Protocol into the
system or change an existing Collection Protocol's profile. A collection
protocol contains a biospecimen collection schedule for all registered
participants. A collection protocol is managed by a principal
investigator and zero or more protocol coordinators and must have an IRB
approval ID. Once approved, a PI can send a request to an administrator
to enter a new collection protocol into the system. The request must
include specimen requirements (i.e. what is to be collected, when, and
how much, participant requirements, a start date and time points of
collection (e.g. frozen prostate tumor biospecimens having a minimum
mass of 10 grams will be collected for participants registered under the
current collection protocol at 30 days post registration which
corresponds to a post-operative time point). When a participant is
entered into the system, s/he may be assigned to one or more collection
protocols. When a specimen is being entered into the system, the
protocol under which the specimen was collected must be designated.

#### Prerequisite Information {#prerequisite-information-18 .unnumbered}

Only an administrative user has the privilege to perform this task after
successfully logging into the caTissue Core system.

#### Step by Step Instructions {#step-by-step-instructions-18 .unnumbered}

##### *Add Collection Protocol* {#add-collection-protocol .unnumbered}

Step 1: Click on the **ADMINISTRATIVE DATA** tab.

Step 2: Go to, **COLLECTION PROTOCOL Add** in the user dashboard.

This action causes the **ADD COLLECTION PROTOCOL** page to be displayed.

![](media/image62.png){width="6.490277777777778in" height="3.75in"}

**Figure 4. 30**: NEW COLLECTION PROTOCOL page

Step 3: Select/enter the following data into the fields provided:

**Item 1:** Indicates the drop down selection field for selection of **a
Principal Investigator** for the protocol being entered. (Required)

**Item 2:** Indicates selection field for selection of **Protocol
Coordinators** that will be involved with the Collection Protocol being
entered.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}To
make multiple selections, hold down the **Ctrl** key.

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}Click on **Add New** link to add a new Principal
Investigator or Protocol Coordinator into the system. This action will
take the user back to the Collection Protocol page with the new data
displayed.

**Item 3:** Indicates the entry field for the **Title** (required) of
the newly created Collection Protocol.

**Item 4:** Indicates the entry field for the **Short Title** (required)
of the newly created Collection Protocol.

**Item 5:** Indicates the entry field for the associated **IRB ID**
(required).

**Item 6:** Indicates the entry field for **Start Date** (required) of
the collection protocol. For details on how to use the embedded
calendar, please refer to the [calendar feature](#CalendarFeature) help.

**Item 7:** Indicates the entry field for **Number of Participants
Anticipated** in this Collection Protocol.

**Item 8: Description URL.** This field allows you to enter a web
address where additional information regarding the Collection Protocol
may be obtained.

Items 9-11 are repeated for each collection protocol event. Each event
specifies a time point (in days) in the study calendar (item 10) and the
participant's clinical status (item 11) at that time point (e.g. New
Diagnosis, Pre-Operative, or Relapse). Note that each event may have
multiple specimen requirements (Item 11). Each of these items is
described in more detail below:

**Item 9:** Indicates the drop down selection menu for **Clinical
Status** (Required) of biospecimens to be collected at the study
calendar event point specified in Item 10.

**Item 10:** Indicates the entry field for number of days for the
**Study Calendar Event Point** (required).

**Item 11:** Indicates entry fields for Specimen Requirements for the
Study Calendar Event Point specified in Item 10. These include:

-   Biospecimen **Class** (Required) to be collected at that study
    calendar event point.

-   Biospecimen **Type** (Required) to be collected at that study
    calendar event point.

-   Indicates location from which the indicated biospecimen should be
    accessioned. The **Tissue Site** (Required) can be selected from the
    drop down list, or you can use the tissue site hierarchical map by
    clicking on the ![](media/image63.png){width="0.23125in"
    height="0.19305555555555556in"} icon located to the right of the
    field. Please see [Hierarchical List
    section](#hierarchy-selection-list) for additional details on how to
    use this feature.

-   Indicates the **Pathological Status** (Required) of the biospecimen
    collected at that study calendar event point.

-   Indicates the **Quantity (Unit)** (Required) of biospecimen that
    should be collected for the indicated event point for the collection
    protocol.

Example: You want to enter a collection protocol event for 60 days post
operative with the collection of 5 gm of fresh tissue from the
upper-inner quadrant of breast with a pathological status of
malignant/invasive. Select Post-Operative for Clinical Status; enter 60
days for Study Calendar Event Point, select the Specimen Class as
Tissue, Specimen Type could be Fresh Tissue. You can choose either the
tissue map feature (displayed in the image below) or use the drop down
for selection of the tissue site.

Pathological Status should be selected as Malignant, Invasive with 5gm
entered for quantity

![](media/image64.png){width="6.490277777777778in"
height="3.1166666666666667in"}

***Figure 4.31**: Entry example for a Collection Protocol Event*

Step 4: **Delete Collection Protocol Events or Specimen Requirements.**
To delete Collection Protocol Events, select the events to be deleted by
checking the box on the far right and click on the Delete button found
on the upper right of the Collection Protocol Events section. To delete
Specimen Requirements, select the requirement(s) to be deleted by
checking the box in the column labeled "Delete?" and click on the Delete
button found on the upper right of the Specimen Requirements section.

Step 5: Click the **Add More** button to add more **COLLECTION PROTOCOL
EVENT** data entry fields.

The page will refresh and display additional fields for study calendar
events points and the associated specimen requirements.

Step 6: Click the **Add More** button to add more **SPECIMEN
REQUIREMENTS**.

This feature can be used if more than one specimen is to be collected
for a specific study calendar event point.

**Item 12:** If you want all aliquots from this collection protocol to
be stored together, click on the checkbox labeled **Store all Aliquots
in the Same Container,** located at the bottom of the page.

Step 7: Click the **Submit** button.

The submission status will be displayed at the top of the page.

##### *Edit Collection Protocol* {#edit-collection-protocol .unnumbered}

Step 1: Click on **COLLECTION PROTOCOL Edit**.

> Step 2: In the Search page enter search parameters (please refer to
> [Edit - Search section](#SearchEDIT) for additional details)

Step 3: Click the **Search** button.

Step 4: Once the desired record is selected, update part or all the
fields on the **EDIT COLLECTION PROTOCOL** page.

This is the same page and data fields used for initial creation of the
selected Collection Protocol.

Step 5: Click the **Submit** button to proceed.

> The submission status will be displayed at the top of the page.

#### Related Topics {#related-topics-18 .unnumbered}

[Login](#login)

[Add Collection Protocol](#add-edit-collection-protocol)

[Logout](#logout)

### Add \| Edit Distribution Protocol {#add-edit-distribution-protocol .unnumbered}

#### Purpose of Task {#purpose-of-task-19 .unnumbered}

The purpose of this task is to add a new Distribution Protocol into the
system or change an existing Distribution Protocol's profile. An
administrator can enter a distribution protocol which defines a set of
guidelines governing the use of specimens in research (e.g. use of DNA
biospecimens to perform a SNP genotyping experiment). When a user
submits a distribution request for biospecimens, they must indicate the
distribution protocol they are using. All requested biospecimens must
match the specimen requirements in the distribution protocol.

#### Prerequisite Information {#prerequisite-information-19 .unnumbered}

Only an administrative user has the privilege to perform this task after
successfully logging into the caTissue Core system.

#### Step by Step Instructions {#step-by-step-instructions-19 .unnumbered}

##### *Add New Distribution Protocol* {#add-new-distribution-protocol .unnumbered}

Step 1: On the caTissue Core **HOME** page, click the **ADMINISTRATIVE
DATA** tab.

Step 2: Go to, **DISTRIBUTION PROTOCOL Add** in the user dashboard.

This action causes the **ADD DISTRIBUTION PROTOCOL** page to be
displayed.

![](media/image65.png){width="6.49375in" height="3.2430555555555554in"}

> **Figure 4.32**: NEW DISTRIBUTION PROTOCOL page

Step 3: Select or enter the following data items into the fields
provided:

> **Item 1**: Drop down selection field for designation of a **Principal
> Investigator** for the Distribution Protocol being entered (Required).

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}Click on **Add New** link to add a new Principal
Investigator to the system

**Item 2:** Entry field for **Title** of the new Distribution Protocol
(Required)

> **Item 3:** Entry field for **Short** **Title** (Required)
>
> **Item 4:** Entry field for **IRB ID** (Required)
>
> **Item 5:** Entry field for **Start Date** (Required). For details on
> how to use the embedded calendar, please refer to the [calendar
> feature](#CalendarFeature) help.
>
> **Item 6:** Entry field for **Number of Participants Anticipated** in
> this Distribution Protocol.

**Item 7:** Entry field for **Description URL**

> **Item 8:** Indicates Specimen Requirements for the Distribution
> Protocol being created.

-   Dropdown selection box for designation of a Biospecimen **Class**
    (Required)

-   Dropdown selection box for designation of a Biospecimen **Type**
    (Required)

-   Dropdown selection box for designation of a **Tissue Site**
    (Required) for specimens in the distribution protocol. For details
    on how to use the tissue site list, please refer to the
    [Hierarchical List](#hierarchy-selection-list) help section.

-   Dropdown selection box for designation of a **Pathological Status**
    (Required) of biospecimens to be included in the distribution
    protocol.

-   Entry box for biospecimen **Quantity (Unit)** (Required)

Step 4: Click on the **Add More** button if additional **SPECIMEN
REQUIREMENTS** are needed. If you want to delete a specimen requirement,
click on the associated checkbox located in the far right column of the
specimen requirement table, and then click on the **Delete** button.

Step 5: Click the **Submit** button.

The submission status will be displayed at the top of the page.

##### *Edit Distribution Protocol* {#edit-distribution-protocol .unnumbered}

Step 1: Click on **DISTRIBUTION PROTOCOL Edit**.

> Step 2: In the Distribution Protocol Search page enter search
> parameters (please refer to [Edit - Search section](#SearchEDIT) for
> additional details)

Step 3: Click the **Search** button**.**

Step 4: Once the desired record is selected, update part or all the
fields on the of **EDIT DISTRIBUTION PROTOCOL** page.

Step 5: Click the **Submit** button.

The submission status will be displayed at the top of the page.

#### Related Topics {#related-topics-19 .unnumbered}

[Login](#login)

[Add Distribution Protocol](#add-edit-distribution-protocol)

[Distribution](#distribution)

[Logout](#logout)

### View Reported Problems {#view-reported-problems .unnumbered}

#### Purpose of Task {#purpose-of-task-20 .unnumbered}

In case a problem is encountered, all users should be able to report the
issue regardless of their status in the system (logged in versus logged
out). Once a problem is submitted a caTissue Core administrator will be
notified. During review of the reported problem, an administrator can
select to change the status to "close" and remove the problem from the
list, or they can select to leave the status as "pending" and follow up
with the reported person for additional details.

#### Prerequisite Information {#prerequisite-information-20 .unnumbered}

Only an administrative user has the privilege to view reported problems,
after successfully logging into the caTissue Core system.

#### Step by Step Instructions {#step-by-step-instructions-20 .unnumbered}

Step 1: On the caTissue Core **HOME** page, click the **ADMINISTRATIVE
DATA** tab.

This action causes the **Administrative Data Workspace** to be
displayed.

Step 2: Go to, **REPORTED PROBLEMS View** on the user dashboard.

This action causes the **View Reported Problems** page to be displayed.

![](media/image66.png){width="5.55625in" height="2.627083333333333in"}

**Figure 4. 33**: View Reported Problems page

Step 3: In the **Title** column, click on the problem to be viewed.

This action causes the detailed information of the problem to be
displayed.

![](media/image67.png){width="4.8180555555555555in"
height="5.440277777777778in"}

**Figure 4. 34:** View details of a selected problem on the REPORT
PROBLEM page

Step 4: The administrator has the option of changing the Status of the
Problem Report, and adding additional comments if desired.

Step 5: Click the **Submit** button to proceed, or **Reset** to clear
the page.

#### Related Topics {#related-topics-20 .unnumbered}

## None  {#none .unnumbered}

## Bio-Specimen Module {#bio-specimen-module .unnumbered}

### **Overview of Bio-Specimen Module Workflow** {#overview-of-bio-specimen-module-workflow .unnumbered}

The Bio-Specimen Module allows users to create and edit information
pertaining to the collection of a specimen. The Bio-Specimen Workspace
includes menu options for creation and entry of data for:

-   Participant(s)

-   Participant Registration (to a Collection Protocol)

-   Specimen Collection Group(s)

-   Specimen(s)

-   Specimen Array(s)

-   Distributions(s)

In addition, the Collection Protocol Based View allows tissue bank users
to perform all of the steps associated with biospecimen management and
accessioning. Each of the above tasks will be discussed in detail in
this section.

### Collection Protocol Based View {#collection-protocol-based-view .unnumbered}

#### Purpose of Task {#purpose-of-task-21 .unnumbered}

In order to increase the effectiveness of the system it is vital to
provide an interface that allows for ease of use as well as a visual
display that is comprehensive in regards to the relationship between
objects and data stored in the caTissue Core system. The Collection
Protocol view shows participant and biospecimen information in the form
of a hierarchy, allows for more intuitive navigation, and provides
visual cues while performing complex workflows within a tissue bank. For
example, this feature may be used to navigate a common workflow such
as: 1) register a new participant to a collection protocol, 2) create a
specimen collection group for this participant, and 3) accession one or
more specimens under this collection group.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}The
original biospecimen pages are still available for use at anytime as
user dashboard options.

#### Prerequisite Information {#prerequisite-information-21 .unnumbered}

This feature requires the user to be logged in successfully as
Administrator, Supervisor, or Technician.

#### Step by Step Instructions {#step-by-step-instructions-21 .unnumbered}

Go to the **BIO-SPECIMEN DATA** tab and click on **Collection Protocol
Based View** in the user dashboard.

![](media/image68.png){width="5.997916666666667in"
height="4.907638888888889in"}

**Figure 4.35**: Collection Protocol Based View

The Collection Protocol View is organized in hierarchical fashion,
therefore you must make a series of selections in order to view specific
details for an object that falls lower in the hierarchy (as shown
below).

**Figure 4.36**: Object hierarchy in Collection Protocol View

**Item 1**: Indicates a drop down box for selection of a Collection
Protocol in the system.

![](media/image69.png){width="4.593055555555556in"
height="3.2805555555555554in"}

**Figure 4.37**: Register participant to selected protocol

You can also click on the **Register** link located above the Collection
Protocol drop down box in order to register a new participant to the
selected collection protocol.

![](media/image70.png){width="5.995833333333334in"
height="2.013888888888889in"}

**Figure 4.38**: Add Participant Registration to a selected Collection
Protocol in the Collection Protocol View

If registering a new participant in a selected protocol, you would
follow the same procedure outlined in the [Register
Participant](#add-edit-participant-registration) help section.

**Item 2**: Indicates a list of all registered participants for the
Collection Protocol selected in **Item 1**.

![](media/image71.png){width="3.2493055555555554in"
height="2.2083333333333335in"}

**Figure 4.39**: Participant list for selected Collection Protocol

This feature provides an easy way to view all the Participants who are
currently registered in the selected Collection Protocol. Clicking on
any of the participants in the list will display a tree for all specimen
collection group(s) collected till now which is called as active
specimen collection group(s) and their associated specimen(s) in the
section labeled **Item** 3. It also shows the specimen collection groups
which are not yet added for a particular collection protocol event,
these are called as proactive specimen collection group(s) for selected
collection protocol and participant. Different colors are used to
differentiate between these two.

The label for a active specimen collection group node in tree is formed
as "T"\<study calendar event point\>:\<collection point
label\>:\<received date of specimen collection group\>. But for a
proactive specimen collection group it will not include received date in
its label.

Upon selecting an object in **Item 2** or **Item 3** (e.g. a
participant, a specimen collection group or specimen), the main body of
the page (**item 4**) will show that object's data where edits may be
made. But when you select a proactive SCG, **item 4** will display a
page to add a new specimen collection group.

![](media/image72.png){width="6.497916666666667in"
height="4.202083333333333in"}

**Figure 4.40**: Participant data form and all associated specimens
collected for selected participant

The box indicated in **Item 3** contains all of the biospecimens
collection groups for the selected participant who is registered in the
selected collection protocol. In the image below a active specimen
collection group has been selected in the Specimen Details list with all
data displayed in the main body of the page (**Item 4**).

![](media/image73.png){width="6.492361111111111in"
height="3.4652777777777777in"}

**Figure 4.41**: Specimen collection group data

The figure above displays details for the *Case Control Study* specimen
collection group that was selected in the Specimen Details list. The
main body of the page (**Item 4**) allows you to make edits for the
selected record and then save them in the system using the **Submit**
button.

In the image below a proactive specimen collection group has been
selected in the Specimen Details list with all data displayed in the
main body of the page (Item 4). It allows you to add a new specimen
collection group for selected participant under selected collection
protocol.

You can also select to add a specimen to the selected specimen
collection group by using the **Add Specimen** or **Add Multiple
Specimen** buttons.

![](media/image74.png){width="6.496527777777778in" height="4.46875in"}

**Figure 4.41.1**: Proactive Specimen collection group data

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}All
data displayed on the page is filtered based on your role and assigned
access privileges.

If specimens exist in the system for a specimen collection group, you
can click on the plus (+) sign located to the left of the specimen
collection group name. This will "open" the collection group and display
all associated specimens (as displayed in the image below).

![](media/image75.png){width="1.7708333333333333in" height="1.1875in"}

**Figure 4.42**: Specimens in a selected specimen collection group

Once a specimen has been selected from the Specimen Details list, all
associated data for the selected specimen will be displayed in the main
body of the page (as displayed in figure 4.43).

![](media/image76.png){width="6.497916666666667in"
height="4.350694444444445in"}

**Figure 4.43**: Collection Protocol View -- Specimen details

From this page you have the following options:

-   Edit the selected specimen and then save it in the system using the
    **submit** button.

-   Derive a specimen from the currently selected specimen by clicking
    on the **Derive** button. This will display the [Derive Specimen
    Page](#derive-specimen) in the main view.

-   Distribute selected specimen by clicking on the **Distribute**
    button at the bottom of the page. This will display the
    [Distribution page](#distribution) which will be populated with the
    selected specimen data.

-   View/Add/Edit events for the selected specimen by clicking on the
    [Events tab](#add-events) at the top of the page.

![](media/image77.png){width="6.495833333333334in"
height="5.555555555555555in"}

**Figure 4.44**: Specimen events for selected specimen in the Collection
Protocol View

To add a new event, select the desired event from the list provided and
then fill in all required data in the form displayed.

Example: You want to add a fixed event for the selected specimen. Click
on the **Events** tab, then select the desired event from the Add New
Specimen Event section located at the bottom of the page. This will
prompt the system to display the associated data entry page for the
event selected. Once you have entered all data, click on the **Submit**
button. Upon successful submission, the newly entered event will be
displayed in the events table at the top of the page.

![](media/image78.png){width="5.780555555555556in"
height="3.8340277777777776in"}

**Figure 4.45:** Example of Add event for specimen in the Collection
Protocol View

From the specimen page in the Collection Protocol View you can also
select to view the associated **Surgical Pathology Report** or
**Clinical Annotation** for the selected specimen by clicking on the
tabs located at the top of the page.

![](media/image76.png){width="6.05625in" height="0.5854166666666667in"}

**Figure 4.46**: View Surgical Pathology Report/View Clinical Annotation
tabs in the Collection Protocol View

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}View
**Surgical Pathology Report** and **View Clinical Annotation** are not
supported in v1.1 and will be available in a future release

In summary, the Collection Protocol View is a useful tool when trying to
navigate through the caTissue Core system. It provides all of the same
functionality as displayed using the user dashboard menu options.
However it indicates where you are regardless of the object currently
being viewed and provide visual cues that facilitate complex biospecimen
banking workflows.

**Related Sections:**

[Register Participant](#add-edit-participant-registration)

[Add/Edit Specimen Collection Group](#add-edit-collection-protocol)

[Add/Edit Specimen](#add-edit-specimen)

[Add Multiple Specimens](#add-multiple-specimens)

[Aliquot Known Specimen](#create-aliquots-from-known-specimen)

[Add Specimen Event](#add-events)

[Distribute Specimen](#distribution)

### Add \| Edit Participant {#add-edit-participant .unnumbered}

#### Purpose of Task {#purpose-of-task-22 .unnumbered}

This task is designed to enter or edit participant information into the
system. A participant is defined as an individual who has consented to a
collection protocol where one or more biospecimens are procured at one
or more points in time.

#### Prerequisite Information {#prerequisite-information-22 .unnumbered}

This requires the user to be logged in as Administrator or Supervisor.

#### Step by Step Instructions {#step-by-step-instructions-22 .unnumbered}

Please take notice of the lack of required fields, however, enter as
much information as possible to identify the participant. Include
medical identifiers, if known. This information will help ensure that a
participant is not entered more than once.

##### *Add Participant* {#add-participant .unnumbered}

Step 1: In the **BIOSPECIMEN DATA** tab, go to, **PARTICIPANT** **Add**
in the user dashboard.

This prompts the system to display the **ADD NEW PARTICIPANT** page.

![](media/image79.jpeg){width="5.5in" height="5.416666666666667in"}

**Figure 4.47**: NEW PARTICIPANT REGISTRATION page

Step 2: Select/Enter the following data items into the fields presented:

**Item 1**: Entry field for participant's **Last Name.**

**Item 2**: Entry field for **First Name.**

**Item 3**: Entry field for **Middle Name.**

**Item 4:** Entry field for **Birth Date**.

**Item 5:** Radio boxes for selection of **Vital Status** of the
participant.

**Item 6:** Entry field for **Death Date**.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"} The
Death Date field will only be active when Vital Status equals
"Deceased".

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}Both birth date and death date can be selected using
the [calendar feature.](#CalendarFeature)

**Item 7:** Radio boxes for selection of participant **Gender.**

**Item 8:** Drop down selection box for participant **Sex Genotype**.

**Item 9:** Drop down selection box for participant **Race.**

**Item 10:** Drop down selection box for participant **Ethnicity.**

**Item 11:** Entry field for participant's **Social Security Number**.

**Item 12**: Indicates entry/selection fields for participant's
**Medical Identifier(s).**

You can select a **Source** of the Identifier, along with entry of a
**Medical Record Number**. Some participants may have multiple medical
record numbers given by different entities (thus, the Source field).
Example: John Doe has been admitted to Barnes Jewish Hospital and to
Missouri Baptist Hospital and therefore he may have 2 different medical
record numbers that can be tied to biospecimens that were collected at
each hospital (or Site). To enter more than one medical record number,
click the **Add More** button to produce additional lines for the
information. If you need to delete any of the lines in the Medical
Identifier section, click on the checkbox located in the far right
column for the line to be deleted, and then click on the **Delete**
button.

Step 4: The user has the option to enter participant data into the
system using the **Submit Only** button or they can submit the data as
well as register the entered participant to an existing protocol by
using the **Submit and Register to Protocol** button.

In order to prevent entry of duplicate participants into the caTissue
Core system, the system must verify that the participant data being
entered does not match any existing participant data. If any of the
participant details entered match existing participant data in the
system, caTissue will display a list of matches for the user to select
from or continue with the submit process.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
Matching probability is based on the number of attributes entered.

[Participant data does not match:]{.underline}

If the participant data entered does not match any current data existing
in the system, a success message will be displayed at the top of the
page, notifying the user that the participant was successfully created.

[Participant data match:]{.underline}

If the participant data submitted matches any data in the system, a list
will be displayed at the bottom of the **ADD NEW PARTICIPANT** Page.

Example: If a user enters "Doe" for participant last name, then all
participants with the last name of Doe will be displayed as a probable
match, not necessarily an exact match since the probability is only
based on one data item.

![](media/image80.png){width="5.96875in" height="2.15625in"}

**Figure 4.48**: POSSIBLE PARTICIPANT MATCH section

The user now has the following options:

**Item 1**: This option allows the user to select a participant from the
list by either clicking on the desired participant or clicking on the
radio button located to the left of each participant identifier.

**Item 2**: Select the radio button to Ignore matches and create new
participant.

This option allows a user to bypass the list presented and create a new
participant from the initial data entered. The user can also select to
initiate a new search by clicking on the radio button located next to
the Lookup again option. This option allows the user to make edits to
the participant data and conduct another search of the system without
having to go through the entire submit process again.

**Item 3**: You can submit the participant using the **Submit Only**
button or you can submit the participant and register him/her to a
collection protocol by using the **Submit and Register to Protocol**
button. When selecting to submit and register a participant, you will be
directed to the [Add Participant
Registration](#add-edit-participant-registration) page with selected
participant data populated on the page.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
The **Submit Only** option is not available once a participant match is
selected.

The status of the submission will be displayed at the top of the page.

##### *Edit Participant* {#edit-participant .unnumbered}

Step 1: In the **BIO-SPECIMEN DATA** tab, go to, **Participant Edit** in
the user dashboard.

> Step 2: In the Participant Search page enter search parameters (please
> refer to [Edit - Search section](#SearchEDIT) for additional details)

Step 3: Click the **Search** button**.**

Step 4: Once the desired record is selected, update part or all the
fields on the of **EDIT PARTICIPANT** page.

Step 5: Click the **Submit** button.

> The submission status will be displayed at the top of the page.

#### Related Topics {#related-topics-21 .unnumbered}

[Login](#login)

[Add Participant](#add-edit-participant)

[Register Participant](#add-edit-participant-registration)

[Logout](#logout)

### Add \| Edit Participant Registration {#add-edit-participant-registration .unnumbered}

#### Purpose of Task {#purpose-of-task-23 .unnumbered}

This task will allow the user to register a participant to a specific
Collection Protocol or edit a previous registration**.** Registering a
participant to a collection protocol indicates that the participant has
agreed to the terms of the collection protocol by signing a consent
form. For additional information, please refer to the [Add Collection
Protocol section](#add-edit-collection-protocol).

#### Prerequisite Information {#prerequisite-information-23 .unnumbered}

This requires the user to be logged in as Administrator or Supervisor. A
Collection Protocol must be created, as described in the Administrative
Module, before a participant can be registered to that Collection
Protocol.

#### Step by Step Instructions {#step-by-step-instructions-23 .unnumbered}

##### *Add Participant Registration* {#add-participant-registration .unnumbered}

Step 1: In the **BIOSPECIMEN DATA** tab, go to, **PARTICIPANT
REGISTRATION** **Add** on the user dashboard.

The **ADD PARTICIPANT REGISTRATION** page will be displayed.

![](media/image81.png){width="5.072916666666667in"
height="1.8541666666666667in"}

**Figure 4. 49:** **Participant -** **Collection Protocol Registration**
page

Step 2: Select/enter the following items into the fields presented:

**Item 1**: Indicates a drop down selection box for **Collection
Protocol** (Required).

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
If the Collection Protocol to which you would like to register the
participant does not exist, click the **Add New** link located to the
right of the drop-down menu. The **New Collection** **Protocol** screen
will be displayed if the user is an Administrator. Supervisors may only
register participants to existing Collection Protocols but may not add
new collection protocols. Please see the Administrative Module section
for instructions on how to create a new Collection Protocol.

Step 3: To register the participant by name, click on the checkbox
labeled **Participant Name,** indicated at **Item 2**. This will
activate the drop-down menu for selection of the registered
participant's name.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
If a desired participant does not exist in the system, their name will
not appear in the drop-down menu. To add a new participant, click the
[Add New]{.underline} link located next to the drop-down menu. Once you
are finished adding a new participant, you will be directed back to the
Collection Protocol Registration page, with the newly entered
participant name selected in the participant drop down field.

If entering the page from the Add Participant form, the name of the
newly added participant will be populated into the field.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}When
registering a Participant by name, the **Participant Protocol ID** data
field changes from a required field to an optional field.

**Item 3**: Entry field for **Participant Protocol ID** (Required).

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
This field is required if name is *not* used and is optional when
participant name *is* used. This Participant Protocol ID is assigned by
the user, and it uniquely identifies a participant within the selected
collection protocol.

**Item 4**: Entry field for **Registration Date** (Required) or you can
use the [calendar feature](#CalendarFeature) to make your selection.

Step 3: You can select to submit the information by clicking on the
**Submit** button or submit the information and proceed to the Specimen
Collection Group page by clicking on the **Specimen Collection Group
button**. Selecting this option will create the participant registration
and take you to the Add Specimen Collection Group page. The submission
status will be displayed at the top of the page.

##### *Edit Participant Registration* {#edit-participant-registration .unnumbered}

#### Purpose of Task {#purpose-of-task-24 .unnumbered}

This task will allow the user to edit a participant's registration for a
specific Collection Protocol.

#### Prerequisite Information {#prerequisite-information-24 .unnumbered}

This requires the user to be logged in as Administrator or Supervisor.
The participant must be a registered participant in a Collection
Protocol.

#### Step by Step Instructions {#step-by-step-instructions-24 .unnumbered}

Step 1: In the **BIO-SPECIMEN DATA** tab, go to **PARTICIPANT
REGISTRATION** **Edit** on the user dashboard.

Step 2: In the Participant Registration Search page enter search
parameters (please refer to [Edit - Search section](#SearchEDIT) for
additional details)

Step 3: Click the **Search** button**.**

Step 4: Update part or all the fields on the of **EDIT PARTICIPANT
REGISTRATION** page.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
The **Activity Status** of a participant in the Collection Protocol is
set to active by default. If a participant chooses to no longer
participate in the Collection Protocol, their activity status should be
changed to Closed or Disabled. Closed refers to the fact that no future
biospecimen collections are possible but that already accessioned
biospecimens will be visible for query and distribution, while Disabled
refers to the fact that already present biospecimens will not be visible
for query or distribution and that no future collections may take place.

Step 5: Click the **Submit** button.

The submission status will be displayed at the top of the page.

#### Related topics  {#related-topics-22 .unnumbered}

[Login](#login)

[Add Participant Registration](#add-edit-participant-registration)

[Add Collection Protocol](#add-edit-collection-protocol)

[Add Participant](#add-edit-participant)

[Logout](#logout)

### Add \| Edit Specimen Collection Group {#add-edit-specimen-collection-group .unnumbered}

#### Purpose of Task {#purpose-of-task-25 .unnumbered}

This task will allow the user to register a participant into a specific
**Specimen Collection Group**. Collection Groups are defined as a batch
of specimens collected from a single participant as part of a collection
protocol at a particular point in time. Example: If a collection
protocol has a collection event at 30 days in the study calendar where
malignant prostate tissue and non-malignant blood should be collected,
each participant should have these specimens collected at this time
point. This collection represents a single Specimen Collection Group.

#### Prerequisite Information {#prerequisite-information-25 .unnumbered}

This requires the user to be logged in as an Administrator or Supervisor
and working in the **Bio-Specimen Data** Workspace. A **Collection
Protocol** and a **Site** for tissue acquisition must have previously
been created. The **Participant** must exist in the system and must be
registered to collection protocol under which the specimen collection
group is being collected.

#### Step by Step Instructions {#step-by-step-instructions-25 .unnumbered}

##### *Add Specimen Collection Group* {#add-specimen-collection-group .unnumbered}

Step 1: In the **BIO-SPECIMEN DATA** tab, go to **SPECIMEN COLLECTION
GROUP** **Add**.

The **ADD SPECIMEN COLLECTION GROUP** page will appear in the user's
workspace.

![](media/image82.png){width="6.49375in" height="7.1194444444444445in"}

**Figure 4.50: Add Specimen Collection Group page**

Step 2: Enter/select the following data items:

**Item 1**: Drop down selection box for **Collection Protocol Title**
(Required).

**Item 2**: Drop down selection box to indicate **Site** where
collection took place (Required).

**Item 3**: To activate the drop down selection box for **Participant**,
you must click on the radio button located to the left of the field.

**Item 4**: To activate the drop down selection box for Participant
Protocol Identifier, you must click on the radio button located to the
left of the field.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}
Selection of either Participant or Participant Protocol Identifier is
required.

**Item 5**: Entry field for **Specimen Group Name** (Required). You can
clear this field by clicking on the [Reset Name]{.underline} link
located to the right of the field. There are no rules governing the name
of the collection group, however the name must contain enough detail
where it can be differentiated from other collection groups.

**Item 6**: Entry field for **Study Calendar Event Point** for the
Specimen Collection Group. This is a time point in the study calendar
that applies to the current collection group (Required).

**Item 7**: Drop down selection box for **Clinical Diagnosis**
(Required). You can also select a clinical diagnosis by clicking on the
hierarchy located to the right of the field. Once you make a selection,
the selected item will be populated in the field on the page. Please
refer to the [Hierarchical List](#hierarchy-selection-list) help section
for details.

**Item 8**: Drop down selection box for **Clinical Status** of the
participant. Example: New diagnosis or post-operative (Required).

**Item 9**: Entry field for **Medical Record Number**.

**Item 10**: Entry field for **Surgical Pathology Number**.

**Item 11**: Entry field for Comments

**Item 12**: Collected Events. Events related to the collection of the
specimen, they include:

-   Drop down selection box for selection of a **Collector** (Required)
    or name of the individual who accessioned the specimen.

-   Entry box for **Date** of collection or you can use the calendar
    feature located to the right of the field by clicking on the
    calendar icon.

-   Drop down box for selection of **Procedure** or how the specimen was
    collected (Required) Example: Surgical resection or venipuncture.

-   Drop down box for selection of **Container** used for the specimen
    (Required). Example: Heparin Vacutainer or ACD Vacutainer.

-   Optional text entry field for **Comments** related to the collection
    event details.

-   Received Events. Events related to the receipt of the specimen, they
    include:

```{=html}
<!-- -->
```
-   Drop down box for selection of the **Receiver** (Required) or name
    of the individual who received the specimen.

-   Data field for **Date** (Required) or day that the specimen was
    received.

-   Drop down box for selection of specimen **Quality** at the time it
    was received (Required). Example: Acceptable or Lipemic.

-   Optional text entry field for **Comments** related to the received
    event details.

> ![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
> Date fields for both Collection and Received event can be selected
> using the embedded calendar feature. For additional details, go to the
> [Calendar Feature help](#CalendarFeature) section.

**Item 13**: Entry filed to add number of multiple specimens.

**Item 14**: Check box to propagate specimen data from collection
protocol requirements.

The first two drop-down lists, **Site** and **Collection Protocol
Title**, along with the **Study Calendar Event Point** list contain data
created in the Administrative Module. In order to use the [Add
New]{.underline} links for these two fields, you must have
administrative privileges.

Step 3: Select either normal submit by clicking on the **Submit** button
or add a new specimen by clicking on the **Add Specimen** button, which
will take you to the Add Specimen Page.

A message stating the status of the submission will be displayed at the
top of the page.

##### *Edit Specimen Collection Group* {#edit-specimen-collection-group .unnumbered}

#### Purpose of Task {#purpose-of-task-26 .unnumbered}

This task will allow the user to change or update information previously
entered during registration of a participant into a new Specimen
Collection Group.

#### Prerequisite Information {#prerequisite-information-26 .unnumbered}

This requires the user to be logged in as an Administrator or Supervisor
and working in the Bio-Specimen Data Workspace. The participant must be
a registered participant in a Collection Protocol.

#### Step by Step Instructions {#step-by-step-instructions-26 .unnumbered}

Step 1: In the **BIO-SPECIMEN DATA** tab, go to, **SPECIMEN COLLECTION
GROUP** **Edit** on the user dashboard.

Step 2: In the Specimen Collection Group Search page enter search
parameters (please refer to [Edit - Search section](#SearchEDIT) for
additional details)

Step 3: Click the **Search** button**.**

Step 4: Edit desired data fields in the page. This is the same page and
data fields used for initial creation of the selected Specimen
Collection Group.

Step 5: Click on **Submit** to add updates to the system, or save all
updates and add a new specimen to the collection group by clicking on
the **Add Specimen** button.

Step 6: The alert message appears if Collection or Received Events are
modified. Click on OK button to overwrite the events to all specimens
under specimen collection group.

![](media/image83.png){width="5.6715277777777775in"
height="1.1659722222222222in"}

**Alert message to overwrite events to all specimens under that group**

The submission status will be displayed at the top of the page.

##### *Populate Specimen data as per Collection Protocol requirement* {#populate-specimen-data-as-per-collection-protocol-requirement .unnumbered}

#### Purpose of Task {#purpose-of-task-27 .unnumbered}

This task will allow the user to restrict the specimen data information
on Specimen page during adding new Specimen for selected Specimen
Collection Group.

#### Prerequisite Information {#prerequisite-information-27 .unnumbered}

> The SCG and one of the Collection Event Pont must be selected first.

#### Step by Step Instructions {#step-by-step-instructions-27 .unnumbered}

Step 1: In the **BIO-SPECIMEN DATA** tab, go to, **SPECIMEN COLLECTION
GROUP** **Add** on the user dashboard.

Step 2: Follow the steps as mentioned in Add Specimen Collection Group.

> Step 3: When one of the collection events is selected, then the number
> of specimen text box gets populated with the number of specimen
> required for selected study calendar event point. Also the restriction
> checkbox gets checked, except in case of days value is 0.
>
> ![](media/image84.png){width="6.499305555555556in"
> height="1.3381944444444445in"}

**Figure 4.51: Add Multiple Specimens**

Step 4: Click on checkbox "Pre populate specimen data with Collection
Protocol requirements" if it is not checked.

Step 5: Click on Add Specimen button. The specimen collection group will
be updated and specimen page will be shown where,

> ![](media/image85.png){width="6.49375in"
> height="1.7013888888888888in"}

**Figure 4.52: Pre-populate Specimen data on single specimen form**

> If there is only one specimen requirement, the values are
> pre-populated as per specimen requirement with no other options in the
> dropdown boxes in single specimen form.
>
> Step 6: Click on Add Multiple specimen button. The specimen collection
> group will be updated and Multi Specimen form will be displayed where
> the default values will get selected from the list as per specimen
> requirements.
>
> ![](media/image86.png){width="5.478472222222222in"
> height="1.9791666666666667in"}

**Figure 4.53: Pre-populate Specimen data on multiple single specimen
form**

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}When the number of multiple specimen value is entered
is greater than 1, only "Add Multiple Specimen" button is enabled. If
the Pre populate specimen data check box is checked, only "Add Specimen"
and "Add Multiple Specimen" buttons are enabled.

#### Related topics  {#related-topics-23 .unnumbered}

[Login](#login)

[Add Specimen Collection Group](#add-edit-specimen-collection-group)

[Add Collection Protocol](#add-edit-collection-protocol)

[Add Site](#add-edit-site)

[Add Participant](#add-edit-participant)

[Logout](#logout)

### Add \| Edit Specimen {#add-edit-specimen .unnumbered}

#### Purpose of Task {#purpose-of-task-28 .unnumbered}

This task will allow the user to add one or more specimen(s) with
associated biohazard information, selection of a storage position, and
input of events (e.g. collection time, time of specimen receipt at the
biospecimen procurement facility, or time when the specimen was frozen).
Once specimen data is entered, the user has the option to derive
specimens or create aliquots from the specimen being entered. A specimen
is defined as a part of a thing, or of several things, taken to
demonstrate or to determine the character of the whole, e.g. a
substance, or portion of material obtained for use in testing,
examination, or study; particularly, a preparation of tissue or bodily
fluid taken for examination or diagnosis.

#### Prerequisite Information {#prerequisite-information-28 .unnumbered}

This requires the user to be logged in as an Administrator, Supervisor,
or Technician and working in the Bio-Specimen Data Workspace. A Specimen
Collection Group for the specimen(s) being entered must have previously
been created.

#### Step by Step Instructions {#step-by-step-instructions-28 .unnumbered}

##### *Add Single Specimen* {#add-single-specimen .unnumbered}

Step 1: In the **BIO-SPECIMEN DATA** tab, go to, **SPECIMEN** **Add:
Single** on the user dashboard.

![](media/image87.jpeg){width="6.497222222222222in"
height="6.063194444444444in"}![](media/image87.jpeg){width="6.497222222222222in"
height="6.063194444444444in"}

**Figure 4.51: NEW SPECIMEN page**

Step 2: Select/enter the following data items for the specimen being
entered.

**Item 1**: Drop down field for selection of a **Specimen Group Name**
(Required)

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}If
the Specimen Collection Name is not in the drop-down menu, click the Add
New link to the right of the field. The New Specimen Collection Group
will be displayed; however you must be an administrator or supervisor in
order to use the Add New link for Specimen Collection Group.

**Item 2**: Entry box for specimen **Label** (Required).

**Item 3**: Drop down selection box for designation of the specimen
**Class** (Required- e.g. tissue, fluid, or molecular). Note that
options for the Specimen Type (Item 8) will change based on the value
selected in this field.

**Item 4**: Drop down selection box for **Tissue Site** or location
where the specimen came from (Required), or you can make a selection
using the tissue site hierarchy feature. For additional details, go to
[Hierarchical List](#hierarchy-selection-list) help section.

**Item 5**: Drop down box for selection of **Pathological Status** of
the specimen (Required- e.g. malignant or metastatic).

**Item 6**: Entry field for text describing **Initial Quality** of the
specimen (Required).

**Item 7**: Optional entry field for the specimen **Barcode**.

**Item 8**: Drop down box for selection of specimen **Type** (Required-
e.g. frozen tissue if class is tissue or DNA or RNA if the class is
molecular).

**Item 9**: Drop down box for **Tissue Side** (Required). Example: Left
can be selected if the specimen was accessioned from the left breast.

**Item 10**: Optional entry field for **Concentration** of the new
specimen.

**Item 11**: **Storage Position** (Required)

Due to restrictions available for storage container contents, the system
now has the ability to select vacant positions in storage containers
that conform to the specimen characteristics and collection protocol.
This feature is designed to help technicians identify storage positions
quicker and with increased accuracy.

Once **Specimen Group Name** and **Class** are entered, the system will
filter the available containers accordingly and will display the first
available **Storage Position** in a qualifying storage container.

> ![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
> The auto container should return the first container available in
> terms of the order that the containers were added in the system. In
> the example below, container 1 would be selected by default.
>
> Example:
>
> 1\. Container 1 was added on day 1
>
> 2\. Container 2 was added on day 2
>
> 3\. Both containers have free space

The automated position can be edited by manually entering a new position
into the fields provided or selecting a new position using the **Map**
feature.

![](media/image88.png){width="4.28125in" height="0.5625in"}

**Figure 4.52: Storage position section**

To store the specimen in a virtual location, click on the checkbox
located next to the question "**Is** **virtually located?"** If the
checkbox is activated, storage position attributes will be disabled and
thus not required for submission of specimen details. This function is
important when a parent specimen has been entered into the system but is
immediately aliquoted to depletion or when a new specimen is accessioned
into the system and may not be physically available to assign a storage
position (planned accession with imminent possession).

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}A
specimen cannot be moved from a storage container into a virtual
location. In order to use the virtual location, the specimen must be
new.

**Item 12**: Optional text entry box for **Comments** related to the
specimen being entered.

For audit purposes as well as the establishment of a chain of
possession, it is important to note the date, method of collection and
individual who conducted the collection of the specimen (Item 13). In
addition, it is important to know the date and quality of the specimen
along with any support text related to the specimen at the time of
receipt (Item 14).

**Item 13**: Collected Events. Events related to the collection of the
specimen, they include:

-   Drop down selection box for selection of a **Collector** (Required)
    or name of the individual who accessioned the specimen.

-   Entry box for **Date** of collection or you can use the calendar
    feature located to the right of the field by clicking on the
    calendar icon.

-   Drop down box for selection of **Procedure** or how the specimen was
    collected (Required) Example: Surgical resection or venipuncture.

-   Drop down box for selection of **Container** used for the specimen
    (Required). Example: Heparin Vacutainer or ACD Vacutainer.

-   Optional text entry field for **Comments** related to the collection
    event details.

**Item 14**: Received Events. Events related to the receipt of the
specimen, they include:

-   Drop down box for selection of the **Receiver** (Required) or name
    of the individual who received the specimen.

-   Data field for **Date** (Required) or day that the specimen was
    received.

-   Drop down box for selection of specimen **Quality** at the time it
    was received (Required). Example: Acceptable or Lipemic.

-   Optional text entry field for **Comments** related to the received
    event details.

> ![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
> Date fields for both Collection and Received event can be selected
> using the embedded calendar feature. For additional details, go to the
> [Calendar Feature help](#CalendarFeature) section.

**Item 15**: External Identifiers

-   Entry field for additional **Name** that may be used to identify the
    specimen.

-   Entry field for additional **Value** that may be used to describe
    the specimen.

To add data fields for additional external identifiers, click on the
**Add More** button. To delete an external identifier, click on the
associated checkbox located to the right of the field and then click on
the **Delete** button.

**Item 16**: Biohazards

-   Drop down box for selection of the **Type** of biohazard associated
    with the specimen being entered.

-   Drop down box for selection of the **Name** for the biohazard being
    applied.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}When
handling biospecimens it is imperative to inform others of any
biohazard(s) associated with a specimen.

To add data fields for additional biohazards, click on the **Add More**
button. To delete a biohazard, click on the associated checkbox located
to the right of the field and then click on the **Delete** button.

##### *Submit single specimen* {#submit-single-specimen .unnumbered}

To submit the single specimen, click on the **Submit** button.

The submission status will be displayed at the top of the page.

##### *Submit multiple specimens* {#submit-multiple-specimens .unnumbered}

To save the single specimen and add more specimens under the same
specimen collection group, click on the **More** button**.** This will
take you to the Add Single Specimen Page with values filled in from the
previous specimen entry.

##### *Derive specimen from new specimen* {#derive-specimen-from-new-specimen .unnumbered}

To save the single specimen and add derivatives for the newly entered
specimen, click on the **Derive** button. This will take you to the
**Create Derived Specimen** page, with the Parent Specimen label
populated for the new specimen entered.

##### *Distribute new specimen*  {#distribute-new-specimen .unnumbered}

To distribute the newly entered specimen, click on the **Distribute**
button. This will save the new specimen data in the system and take you
to the [Add Distribution Page](#distribution) where the Distribute
Item(s) field is populated with data for the new specimen entered.

##### *Create aliquot from new specimen* {#create-aliquot-from-new-specimen .unnumbered}

If you would like to create an aliquot(s) from the specimen being
entered, you can click on the checkbox located to the left of the
question "**Do you want to create an Aliquot**?" This action will save
the specimen entered and you will be taken to the [Create Aliquot
Page](#create-aliquot) with the Parent Specimen Label field populated
with the label for the new specimen.

Clicking on any of the buttons will save the new specimen data in the
system and display the submission status at the top of the page.

#### Related Topics {#related-topics-24 .unnumbered}

[Login](#login)

[Add Specimen Collection Group](#add-edit-specimen-collection-group)

[Add Specimen](#add-edit-specimen)

[Logout](#logout)

### Editing Specimen Data {#editing-specimen-data .unnumbered}

#### Purpose of Task {#purpose-of-task-29 .unnumbered}

This task will allow the user to edit data or add data for previously
entered specimens. For example, for existing specimens, this task
enables the user to add new specimen events and/or create derived
samples from a parent specimen.

#### Prerequisite Information {#prerequisite-information-29 .unnumbered}

This requires the user to be logged in as an Administrator, Supervisor,
or Technician and working in the Bio-Specimen Data Workspace. The
Specimen to be edited must exist in the system.

#### Step by Step Instructions {#step-by-step-instructions-29 .unnumbered}

Step 1: In the **BIO-SPECIMEN DATA** tab, go to, **SPECIMEN**  **Edit**
on the user dashboard.

Step 2: In the Specimen Search page enter search parameters (please
refer to [Edit - Search section](#SearchEDIT) for additional details)

Step 3: Click on the **Search** button.

Step 4: Once the desired specimen is selected, edit existing data or add
new data to the specimen profile.

Step 5: Select the type of submission (Submit, Derive, More, Distribute)
and click the desired button.

Clicking on any of the buttons will save the updated specimen data in
the system and the submission status will be displayed at the top of the
page.

#### Related Topics {#related-topics-25 .unnumbered}

[Login](#login)

[Add Specimen](#add-edit-specimen)

[Add Specimen Collection Group](#add-edit-specimen-collection-group)

[Logout](#logout)

### Add \| Edit \| Aliquot - Specimen Array {#add-edit-aliquot---specimen-array .unnumbered}

#### Purpose of Task {#purpose-of-task-30 .unnumbered}

This task allows the user to add a new specimen array, or edit/aliquot
an existing specimen array. An Array is defined as a collection of
similar biospecimens arranged in an ordered pattern (i.e. array type).
In some respects, an Array has many of the same attributes as a
specimen, but an Array can not be simply represented as a special
specimen class itself because of the many-to-one specimen to array
relationship. In other respects, an array is like a specialized storage
container, in that it holds a defined arrangement of specimens. However,
unlike a storage container, an array can be distributed and has many
specimen-like properties associated with it.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}When
creating a specimen array, it is considered a single entity; therefore
it must be distributed in its entirety as a single item.

#### Prerequisite Information {#prerequisite-information-30 .unnumbered}

This requires the user to be logged in as an Administrator, Supervisor,
or Technician and working in the **Bio-Specimen Data** Workspace. User
must have access privileges to enter biospecimen data into the system.

#### Step by Step Instructions {#step-by-step-instructions-30 .unnumbered}

##### *Add Specimen Array* {#add-specimen-array .unnumbered}

Step 1: In the **BIO-SPECIMEN DATA** tab, go to **SPECIMEN ARRAY**
**Add** in the user dashboard.

![](media/image89.png){width="7.375694444444444in"
height="2.727777777777778in"}

**Figure 4.53: ADD SPECIMEN ARRAY page**

[]{.mark}

Step 2: Enter/select the following data items for the fields provided.

**Item 1**: Drop down box for selection of an **Array Type** (Required).
Upon selection of the array type, the specimen class and type fields are
populated with the data entered by the Administrator during creation of
this Array Type.

**Item 2**: Entry field for **Array Label** (Required), i.e. an
identifiable name that will distinguish this array from others.

**Item 3**: Drop down box for selection of **Specimen Class**
(Required). This value is non-editable and is filled in upon selection
of an Array Type.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
Specimen Class should be identical for all specimens comprising the
array.

**Item 4**: Drop down box for selection of **Storage Position**
(Required) or you can use the [Map feature](#MapFeature).

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
Storage Location fields will be pre-populated with the next available
position (based on "can hold" restrictions identified during creating of
a storage container). The position displayed can be manually changed by
selecting another position from the drop down or by selecting a new
position using the storage container map feature.

**Item 5**: Optional text box for entry of **Comments** related to the
array being created. To enter comments, click inside the box.

**Item 6**: Radio buttons for selection of entry method. Options include
**Barcode** or **Label**.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}The
method of entry selected, will be applied to ALL specimens in the array.

Example: If Label is selected as the mode of entry, you will not be able
to enter some specimens via their labels and some via their barcodes.

**Item 7**: Drop down box to indicate "who" created the array (Required)

**Item 8**: Indicated entry field for the array Barcode.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
Barcode applies to the entire array as a single object in the system.

**Item 9**: Selection box for **Specimen Type** (Required). This value
is non-editable and is filled in upon selection of an Array Type.

**Item 10**: This section displays the **capacity** of the array, for
**Dimension One** and **Dimension Two**. These values are non-editable
and are filled in upon selection of an Array Type. The page will refresh
and display the Specimen Array dimensions as specified by Dimension One
and Dimension Two.

![](media/image90.png){width="7.001388888888889in"
height="1.5930555555555554in"}

**Figure 4.54: Add/Edit Specimen Array**

##### *Edit specimens in the array* {#edit-specimens-in-the-array .unnumbered}

[New array:]{.underline}

To edit specimens in the array, click on a selected "cell" in the array
table.

**Item 1**: Indicates the **Apply** button, used for entry of specimen
**Concentration** and **Quantity** into selected fields. These fields
may be used to enter the same concentration and quantity for multiple
wells in the array. For example, to make the quantity 10 micrograms and
the concentration 1 microgram/microliter for all wells, set
Concentration to 1, Quantity to 10, select all wells, and click the
Apply button.

**Item 2**: Indicates the table of specimens included in the array.

**Item 3**: Indicates the **Upload Specimen Array** button.

This table can be built manually by entering all array details, or it
can be populated from selected items in "My List".

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}To
select more than one cell, hold down the **Ctrl** or **Shift** key
during selection.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"} The
system checks to make sure each specimen included in the array is of
identical class and type as defined by the array type. If not, an error
will be displayed. If the array is of molecular type, each parent
specimen will be decremented in quantity based on the amount of specimen
placed in the array.

Once you are done, click the **Upload Specimen Array** button.

The submission status will be displayed at the top of the page.

[Existing array:]{.underline}

Step 1: In the **BIO-SPECIMEN DATA** tab, go to **SPECIMEN ARRAY**
**Edit**.

Step 2: In the Specimen Array Search page enter search parameters
(please refer to [Edit - Search section](#SearchEDIT) for additional
details)

Step 3: Click on the **Search** button.

Step 4: Update array, and then click on the **Upload Specimen Array**
button.

The submission status will be displayed at the top of the page.

##### *Create aliquots from existing Specimen Array* {#create-aliquots-from-existing-specimen-array .unnumbered}

Step 1: In the **BIO-SPECIMEN DATA** tab, go to **SPECIMEN ARRAY**
**Aliquot**.

This will prompt the system to display the Create Specimen Array Aliquot
page.

![](media/image91.png){width="6.495833333333334in" height="1.1in"}

**Figure 4.55**: **Create Aliquot for a Specimen Array**

Step 2: Select to enter either a **Parent Specimen Array Label** or
**Barcode**, by clicking on the associated radio button (Required).

Step 3: Enter a numeric **Aliquot Count**.

Step 4: Click on the **Submit** button.

The page will refresh and display entry fields at the bottom of the
page, corresponding with the number of aliquots indicated for Aliquot
Count.

![](media/image92.png){width="6.499305555555556in"
height="3.286111111111111in"}

**Figure 4.56: Create Specimen Array Aliquot page**

The Parent Array Data and number of aliquots can be edited at any time
by entering new data and clicking on the **Resubmit** button. This will
refresh the page to reflect the submitted changes.

**Item 1**: Displays the **Specimen Array Type.**

**Item 2**: Displays the **Specimen Array Class.**

**Item 3**: Displays the **Specimen Type**(s) included in the array.

**Item 4**: Indicates data entry fields for the specified number of
aliquots. In the image above, the Aliquot Count is two; therefore two
rows are displayed at the bottom of the page for entry of aliquot data.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
Storage Location fields will be pre-populated with the next available
position. The position displayed can be manually changed by selecting
another position from the drop down or by selecting a new position using
the **Map** feature.

Once all data has been entered, click on the **Create** button to
proceed.

The submission status will be displayed at the top of the page.

#### Related Topics {#related-topics-26 .unnumbered}

[Login](#login)

[Add Array](#add-edit-aliquot---specimen-array)

[Add/Edit Specimen Array Type](#addedit-specimen-array-type)

[Logout](#logout)

### Add Multiple Specimens {#add-multiple-specimens .unnumbered}

#### Purpose of Task {#purpose-of-task-31 .unnumbered}

This task will allow the user to enter multiple specimens into the
system without having to go through the entire process repeatedly. This
is a time saving feature and does not require that the specimens being
entered share the same characteristics, therefore separate data entry
fields are provided for all specimens.

#### Prerequisite Information {#prerequisite-information-31 .unnumbered}

This requires the user to be logged in as an Administrator, Supervisor,
or Technician and working in the **Bio-Specimen Data** Workspace.

#### Step by Step Instructions {#step-by-step-instructions-31 .unnumbered}

Step 1: To enter multiple specimens concurrently, go to the
**BIO-SPECIMEN DATA** tab, and click on **SPECIMEN** **Multiple** in the
user dashboard.

**Figure 4.57**: **Add Multiple Specimen** page

![](media/image93.jpeg){width="6.492361111111111in"
height="4.066666666666666in"}

**Figure 4.58**: **Add Multiple Specimen** details page

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}The
specimen label will be auto-populated based on the Specimen Group Name.
Example: If group name = IB345, the specimen labels should default to
IB345-1,IB345-2, IB345-3, IB345-4 etc.

**Item 1:** Indicates the **Copy** and **Paste** buttons. To use this
feature you can highlight either a text entry or a drop down selection
on the page and click on the **Copy** button. Then click on the field
where you want to paste the item, and click the **Paste** button.
Multiple fields of a specimen (or an entire specimen) may be copied and
pasted at once by multi-selecting rows using the **Shift** button. This
feature is useful when more than one specimen share a common piece of
data.

**Item 2:** Indicates the specimen count displayed on the page. Since
the page can only display a maximum of 4 specimen entry columns, it must
paginate the specimens to be entered. Example: You select to enter 7
specimens, therefore block 1-4 will be fully populated and block 5-7
will only contain 3 entries for a total of 7 specimens.

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}The current specimen block being displayed will be
indicated with a box drawn around the selection (block 1-5 is displayed
in the image above).

**Item 3**: Indicates the **More** button, which can be used to add
additional columns for entry of specimen data. This feature is useful if
you originally indicated 'n' specimens and then decide to add additional
specimens without having to repeat the process.

**Item 4**: Indicates **Add** buttons for optional Comments, [Specimen
Events](#add-events), External Identifiers, biohazard(s) for the
selected specimen or to [Derive specimens](#derive-specimen) from the
selected specimen.

**Item 5**: In the **Events** field, mouse-over the **Edit** button to
view a tooltip. The tooltip displays **Collected Events** and **Received
Events**.

Collected Events are as follows:

-   Collector

-   Date

-   Procedure

-   Container

Received Events are as follows:

-   Receiver

-   Date

-   Quality

To view another form, click **Edit**.

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}Tissue Site can be selected using the [Hierarchical
List](#hierarchy-selection-list) feature, and the Storage Position can
be selected using the [Map feature](#MapFeature).

All data elements on the page follow the same process outlined in the
[Add Specimen](#add-edit-specimen) section. This page simply allows you
to add more than one specimen without having to go through the process
repeatedly.

Step 3: Once all required data is entered, click on the **Submit**
button located at the top of the page.

The submission status will be displayed at the top of the page.

#### Related Topics {#related-topics-27 .unnumbered}

[Login](#login)

[Add Events](#add-events)

[Derive specimens](#derive-specimen)

[Logout](#logout)

### Derive Specimen  {#derive-specimen .unnumbered}

#### Purpose of Task {#purpose-of-task-32 .unnumbered}

This task will allow the user to create a derived specimen(s) from a
previously collected specimen. A derivative differs from an aliquot
since it does not have to be in equal quantities and can be of a
different specimen class and type. Example: The parent specimen can have
a class = tissue, and type = fresh tissue, but the derivative can have a
class = molecular, and type = DNA.

#### Prerequisite Information {#prerequisite-information-32 .unnumbered}

This requires the user to be logged in as an Administrator, Supervisor,
or Technician and working in the **Bio-Specimen Data** Workspace. The
Specimen to be derived must have been previously generated and have an
existing system identifier.

#### Step by Step Instructions {#step-by-step-instructions-32 .unnumbered}

Step 1: In the **BIO-SPECIMEN DATA** tab, go to, **SPECIMEN** **Derive**
in the user dashboard.

![](media/image94.jpeg){width="6.135416666666667in"
height="5.791666666666667in"}

**Figure 4.59**: **CREATE DERIVED SPECIMEN** page

Step 2: Enter/select the following data items for the fields provided.

**Item 1**: Drop down for selection of either the **Parent Specimen
Label** or the **Parent Specimen Barcode** (Required). If the page is
accessed from the path specified in step 1, the Parent specimen ID field
will be empty. If the page is accessed from the [Add Specimen
Page](#add-edit-specimen), the Parent Specimen Label will be populated
with data from the new specimen being entered.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
You must designate which field you want for **Parent Specimen Label**
and **Parent Specimen Barcode**, by using the radio buttons located to
the left of each field.

**Item 2**: Entry field for **Label** of the specimen being derived
(Required).

**Item 3:** Drop down box for selection of the specimen **Class**
(Required)

**Item 4**: Drop down box for selection of the specimen **Type**
(Required)

**Item 5**: Type the date on which the specimen was created. This field
is populated with the current date, by default.

**Item 6** Entry box for **Concentration** of the specimen being
derived.

**Item 7**: Drop down box for selection of initial **Quantity** of the
specimen being derived (Required).

**Item 8**: Indicates Storage Position entry fields (Required).

Once Specimen **Class** and **Type** are selected, the system will
filter the available containers accordingly and will display the first
available **Storage Position** in a qualifying storage container. The
automated position can be edited by manually entering a new position
into the fields provided or selecting a new position using the [map
feature](#MapFeature).

**Item 9**: Entry field for a Barcode for the derived specimen.

**Item 10**: Optional text entry field for **Comments** related to the
specimen being derived.

**Item 11**: Indicates data fields for **External Identifiers** related
to the specimen.

The **Add More** button, allows you to add additional entry fields for
external identifiers. \<\<Add more creates another derived specimen.
Click on more\_ add specimen page\>\>To delete excess entry fields,
click on the checkbox located to the right of the excess fields and then
click on the **Delete** button.

\<\< Create aliquot checkbox\>\>

Step 3: Click **Submit** to save new derived specimen data. Click
**Distribute** to save new derived specimen data and proceed to the
Distribute Page.

The submission status will be displayed at the top of the page.

#### Related Topics {#related-topics-28 .unnumbered}

[Login](#login)

[Add/Edit Specimen](#add-edit-specimen)

[Distribution](#distribution)

[Logout](#logout)

### Create Aliquot {#create-aliquot .unnumbered}

#### Purpose of Task {#purpose-of-task-33 .unnumbered}

This task will allow the user to create aliquots from an existing
specimen or a newly entered specimen. This feature allows you the
ability to create a large number of indistinguishable specimens from a
single parent specimen without having to repeatedly enter related
biospecimen data (ex: tissue type/site/side, pathological status, and
biohazards) for each aliquot into the system. An aliquot inherits all
the properties and events from its parent specimen. Once an aliquot is
created it is treated as an independent specimen and thereafter all
events/modifications performed on the aliquot will be independent of the
rest of the aliquots. However, the following attributes of the aliquot
cannot be changed from the parent: type, concentration (for molecular),
tissue site, tissue side, pathological status and biohazards. The
following attributes can be different from the parent: Is available,
storage location, barcode, activity status and available quantity.

#### Prerequisite Information {#prerequisite-information-33 .unnumbered}

This requires the user to be logged in as an Administrator, Supervisor,
or Technician and working in the **Bio-Specimen Data** Workspace. The
Specimen used to create the aliquot must exist in the system.

#### Step by Step Instructions {#step-by-step-instructions-33 .unnumbered}

##### *Create aliquots from known Specimen* {#create-aliquots-from-known-specimen .unnumbered}

Step 1: You must locate the desired parent specimen. There are several
ways to do this:

[Path 1]{.underline}: If you know the desired Specimen Label for the
parent specimen to be used for creation of the aliquots. Go to the
**BIO-SPECIMEN DATA** tab, and click on **SPECIMEN** **Aliquot** in the
user dashboard.

> [Path 2]{.underline}: Go to **Specimen** **Edit**, select the desired
> specimen from the search results and click on the **Create Aliquot**
> checkbox and click **Submit.** This page allows for entry of an
> Aliquot Count and quantity per Aliquot, however these fields are
> optional. If data is entered, it will be displayed in the Aliquot page
> upon submission. ![](media/image95.jpeg){width="6.492361111111111in"
> height="4.3493055555555555in"}

**Figure 4.60**: Create aliquot from existing specimen section

![](media/image96.png){width="6.4944444444444445in"
height="1.0069444444444444in"}

**Figure 4.61**: **Create Aliquot page**

**Item 1**: Data entry fields for either the **Parent Specimen Label**
or the Parent Specimen **Barcode** (Required).

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
You must designate which field you want for **Parent Specimen Label**
and Parent Specimen **Barcode**, by using the radio buttons located to
the left of each field.

Step 2: Enter the number of desired aliquots, by entering a numeric
number into the Aliquot Count data field (Indicated by **Item 2**).

**Item 3**: Optional entry field for quantity to be used for each
aliquot.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}If
the parent specimen is completely consumed during creation of the
aliquots, its status will be changed to "Not Available" in the system.

Step 3: Click **Submit**.

The **Create Aliquot** page will be displayed, along with associated
data for the selected Parent Specimen.

![](media/image97.png){width="6.491666666666666in"
height="4.522222222222222in"}

**Figure 4.62**: Create Aliquot(s) detail page

Step 4: If edits are needed in regards to the **Parent Specimen Label**,
**Barcode**, **Aliquot Count** or **Quantity per Aliquot**, you can make
the desired changes and resubmit the form, by clicking on the
**Resubmit** button. This will refresh the page to include updated
information.

Step 5: The aliquot rows will be displayed at the bottom of the page,
along with pre-populated data for **Label**, **Initial Quantity**
(indicated at the top of the page) and **Location**. The storage
location is based on the next qualified / available storage position.
The position can be manually edited by using the [Map
feature](#MapFeature) located to the right of the data field.

Step 6: Click on **Create** to proceed.

Upon successful submission, a message stating **"**Aliquots have been
successfully created**"** is displayed.

##### *Create Aliquots from a New Specimen.* {#create-aliquots-from-a-new-specimen. .unnumbered}

Step 1: In the **BIO-SPECIMEN DATA** tab, go to, **Specimen** **Add**

Step 2: In the Add/Edit Specimen pages click on the **Create Aliquot**
checkbox and click Submit. Parent biospecimen data will be displayed in
the Aliquot page upon submission.

Step 3: Follow the same procedure as specified in the [Create aliquots
from known Specimen](#create-aliquots-from-known-specimen) section.

##### *Aliquot storage properties* {#aliquot-storage-properties .unnumbered}

By default, the system will store the aliquots in the next available
storage locations. Thus there is a chance that aliquots of the same
batch are stored in two different storage containers. For example, if
ten aliquots are created from a specimen, the next storage location has
only five empty locations, the system will store five in one container
and the remaining five in another container. Aliquot positions can be
overwritten by using the [Map](#ViewMap) feature or entering a storage
position directly into the fields provided.

Step 4: Click on **Create** to proceed.

Upon successful submission, a message stating **"**Aliquots have been
successfully created**"** is displayed.

#### Related Topics {#related-topics-29 .unnumbered}

[Login](#login)

[Add/Edit Specimen](#add-edit-specimen)

[Create Aliquots](#create-aliquot)

[Logout](#logout)

### Add Events {#add-events .unnumbered}

#### Purpose of Task {#purpose-of-task-34 .unnumbered}

This task allows a user to easily enter events into the system for a
selected biospecimen without having to go through the specimen edit
pages. An event is characterized as an action taken against a specimen.
In the caTissue core system, events may include: check-in/check-out,
transfer of the specimen from one storage container to another, review
of the specimen, freezing the specimen, allowing the specimen to thaw,
applying fixative, or disposal of the specimen. This page is designed to
help reduce the effort required to search for a specimen, navigate to
the events page, select the event and then enter the event.

#### Prerequisite Information {#prerequisite-information-34 .unnumbered}

This requires the user to be logged in as an Administrator, Supervisor,
or Technician and working in the **Bio-Specimen Data** Workspace. The
Specimen for which events are to be added must exist in the system.

#### Step by Step Instructions  {#step-by-step-instructions-34 .unnumbered}

Step 1: In the **BIO-SPECIMEN DATA** tab, click on **SPECIMEN**
**Events** in the user dashboard.

![](media/image98.png){width="5.995833333333334in"
height="1.1541666666666666in"}

**Figure 4.62**: **ADD SPECIMEN EVENT** page

Step 2: Enter/select the following data items into the fields provided.

**Item 1**: Indicates selection of either **Specimen Label** or
**Barcode** for the specimen that the events are being applied to. You
must select which field you are using by clicking on the associated
radio button.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
The selection of either Specimen Label or Barcode is a required field.

**Item 2**: Indicates the drop down box for selection of the **event**
being applied to the specimen indicated (Required)

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
Check-in event is automatically applied to a specimen when it is
initially entered into the system. If a user checks out a specimen, then
a new check-in event must be entered if the specimen is returned.

**Step 3**: Once all required data items are provided, click on the
**Add Event** button to proceed.

The page will be refreshed to show entry fields for the Event selected.

Example: You want to add a Disposal event for Specimen Label "test111".
You would need to enter the Specimen Label into the field provided, then
select Disposal in the Event dropdown and click **Add Event** to
proceed.

![](media/image99.png){width="6.291666666666667in"
height="2.1979166666666665in"}

***Figure 4.63**: Specimen Event selection*

The page will refresh and take you to the specified event data page.

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}When adding a transfer event, the system will assist
the user in finding a qualifying storage location using the "Holds" and
the "Collection Protocol" values stored for a storage container during
its creation.

![](media/image100.png){width="5.78125in" height="6.020833333333333in"}

***Figure 4.64**: Example of event data page*

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}
Each event has its own data entry page.

Upon successful submission, the page will refresh and will display the
new event entered into the specimen event list.

![](media/image101.png){width="6.229166666666667in" height="3.59375in"}

***Figure 4.65**: Event successfully added for specified specimen*

#### Related Topics {#related-topics-30 .unnumbered}

[Login](#login)

[Add/Edit Specimen](#add-edit-specimen)

[Add Multiple Specimens](#add-multiple-specimens)

[Logout](#logout)

### Distribution {#distribution .unnumbered}

##### *Add Distribution* {#add-distribution .unnumbered}

#### Purpose of Task {#purpose-of-task-35 .unnumbered}

The Distribution Module allows biospecimen bank personnel to distribute
specimens from one site to another. A distribution is a way to log the
chain of custody for a biospecimen between sites (e.g. from the
biospecimen bank to a PI's laboratory or from one bank to another). The
specimens included in the distribution must match the specimen
requirements for the indicated distribution protocol.

#### Prerequisite Information {#prerequisite-information-35 .unnumbered}

This requires the user to be logged in as an Administrator, Supervisor,
or Technician and working in the **Bio-Specimen Data** Workspace.

#### Step by Step Instructions  {#step-by-step-instructions-35 .unnumbered}

Step 1: In the **BIO-SPECIMEN DATA** tab, go to, **DISTRIBUTION Add** on
the user dashboard.

![](media/image102.png){width="6.496527777777778in"
height="3.8361111111111112in"}

**Figure 4. 66:** NEW DISTRIBUTION **page**

Step 2: Select the type of distributed item(s), indicating if it is a
Specimen or Specimen Array.

Step 3: Select the **Distribution Protocol** from the drop-down menu
(Required).

Step 4: Select **Distributed By** from the drop-down menu (Required).

If desired Distribution Protocol or Distributed By person is not in the
list presented, you can click on the Add New links located to the right
of the data fields. This will take you to the appropriate page for data
entry. Once you have submitted the new data, you will be returned to the
distribution page, and the newly entered data will be displayed on the
page. Note that only an Administrator can add new distribution protocols
and users into the system.

Step 5: Enter the **Date** of distribution (Required) or use the [Map
feature](#MapFeature).

Step 6: Select the **Time** from the drop-down menu.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}By
default, the system automatically enters the current date and time.

Step 7: Select **To Site** from the drop-down menu (Required).This is
the name of the site that will be receiving the distributed specimen. If
desired site is not in the list presented, you can click on the Add New
link located to the right of the data field. This will take you to the
[Add Site](#add-edit-site) page. Once you have submitted the new site,
you will be returned to the distribution page, and the newly entered
site will be displayed in the data field. Note that only an
Administrator can add new sites into the system.

Step 8: Optional text entry field for any **Comments** related to the
distribution.

Step 9: Select how the item(s) being distributed will be entered, based
on **Barcode** or **label**.

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}You must select either Barcode or label
[prior]{.underline} to clicking on the Add More button.

Step 10: Click on the **Add More** button.

Step 11: Enter the Barcode or Label.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}If
you select Barcode then ALL specimens must be entered using the barcode
and vise versa. You can not select to add some specimens with their
barcode and some with their label.

Step 12: Enter the **Quantity** of the specimen to be distributed
(Required). The **Quantity** to be distributed must be less than or
equal to the **Available Quantity**.

Step 13: If there is more than one specimen to be distributed, click the
**Add More** button to provide an additional line to include more
specimens.

Step 14: If you need to delete lines, click on the corresponding
checkbox located to the far right of the line, then click on the
**Delete** button.

Step 15: Click the **Submit** button after all items to be distributed
have been entered.

The system will refresh and show a report for the distribution.

![](media/image103.png){width="6.491666666666666in"
height="1.9819444444444445in"}

**Figure 4.67**: **DISTRIBUTION REPORT** page

Step 16: You can select to export the report data to outside the system
by clicking on the Export button.

Step 17: You can also select to define the view of the distribution
report by clicking on the **Define View** button.

![](media/image104.png){width="6.496527777777778in"
height="1.7465277777777777in"}

**Figure 4.57**: Define View page

**Item 1**: Indicates a drop down selection field for **Object Names**.

**Item 2**: This field is populated with associated attribute names
after an object name is selected in Item 1.

**Item 3**: Indicates the functional buttons for the view. To add items
to the view, you must select items from the left box (available) and
move them to the right box (view) by clicking on the **Add to View
button**. If you want to delete an item from view, click on the item in
the right box, then click on the **Delete From View** box. This will
take the item from the right box (view) and put it back in the left box
(available).

**Item 4**: Indicates the attributes that will be shown in the
distribution report.

**Item 5**: Allows you to order attribute columns in the distribution
report. You can also organize items by clicking on them in the view box
and then selecting to move them up in the list or down in the list by
using the **Up** and **Down** buttons. The items in the view will be
displayed from left to right in the distribution report with the items
at the top of the list displayed first.

##### *Distribute Specimen* {#distribute-specimen .unnumbered}

#### Purpose of Task {#purpose-of-task-36 .unnumbered}

This feature allows you to quickly find the desired specimen that you
want to distribute and perform the distribution.

#### Prerequisite Information {#prerequisite-information-36 .unnumbered}

This requires the user to be logged in as an Administrator, Supervisor,
or Technician and working in the **Bio-Specimen Data** workspace. The
desired specimen must exist in the system.

#### Step by Step Instructions  {#step-by-step-instructions-36 .unnumbered}

Step 1: In the **BIO-SPECIMEN DATA** tab, go to, **DISTRIBUTE**
**Specimen**.

This will prompt the system to show the **SPECIMEN DISTRIBUTION SEARCH**
page.

![](media/image105.png){width="6.333333333333333in"
height="1.1979166666666667in"}

**Figure 4.68**: **SPECIMEN DISTRIBUTION SEARCH** page

Step 2: Enter Search criteria and click on the **Search** button.

If only one record matches the search criteria, the system will go
directly to the requested record. If more than one record matches the
search criteria, the system will display a list of matches for the user
to select from. Once the desired Specimen Distribution is selected

Step 3: Follow the same procedure listed in the
[Distribution](#distribution) section.

##### *Distribute Array* {#distribute-array .unnumbered}

#### Purpose of Task {#purpose-of-task-37 .unnumbered}

This feature allows you to quickly find a desired array in the system
that you want to distribute and perform the distribution.

#### Prerequisite Information {#prerequisite-information-37 .unnumbered}

This requires the user to be logged in as an Administrator, Supervisor,
or Technician and working in the **Bio-Specimen Data** workspace. The
desired array must exist in the system.

#### Step by Step Instructions  {#step-by-step-instructions-37 .unnumbered}

Step 1: In the **BIO-SPECIMEN DATA** tab, go to, **DISTRIBUTE**
**Array**.

This will prompt the system to show the **SPECIMEN DISTRIBUTION SEARCH**
page.

![](media/image106.png){width="6.34375in" height="1.1770833333333333in"}

**Figure 4.69**: **ARRAY DISTRIBUTION SEARCH** page

Step 2: Enter Search criteria and click on the **Search** button.

Step 3: Follow the same procedure listed in the
[Distribution](#distribution) section.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}An
array is distributed as a single object.

#### Related Topics {#related-topics-31 .unnumbered}

[Login](#login)

[Query](#query-module)

[Add Biospecimen](#add-edit-specimen)

[Add Array](#add-edit-aliquot---specimen-array)

[Logout](#logout)

## Query Module {#query-module .unnumbered}

### **Overview of Query Module Workflow** {#overview-of-query-module-workflow .unnumbered}

The query module allows users to find biospecimens of interest. This is
done by entering query parameters (rules) for possible items of interest
and then searching the caTissue Core system. Selecting the **SEARCH**
tab located on the top, horizontal navigation bar accesses the query
module. Following this selection, query module options are displayed on
the left, vertical navigation bar.

![](media/image107.png){width="5.809027777777778in" height="2.85in"}

**Figure 4.70**: Query Module options [(Replace Image)]{.mark}

This module contains details for the following query functions:

-   Simple Query

-   Advanced Query

A User may enter query parameters and the system will return the
matching result set. Once the result set is displayed, you can continue
to:

-   Define View -- Change data items displayed

-   Export -- Export data outside of the system (e.g. to request that
    these specimens be distributed to you)

-   Redefine Query -- Change query parameters

### Simple Query {#simple-query .unnumbered}

#### Purpose of Task {#purpose-of-task-38 .unnumbered}

The Simple Query Interface allows a user to perform a simplistic query
on any data element stored in the system. This interface is ideal for
queries based on a few parameters (For example, simple queries like "all
specimens of a particular study ID") and will be commonly used by tissue
bank technicians.

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}When using the simple query the result set may be
very large; therefore the results may taking longer to retrieve.

> ![](media/image13.png){width="0.9479166666666666in"
> height="0.25in"}Before the query result set is displayed it is
> filtered to remove the data for which the logged in user does not have
> READ privilege (e.g. PHI may not be seen by users who do not have
> access this information).

#### Prerequisite Information {#prerequisite-information-38 .unnumbered}

A previously registered and approved user successfully logs into
caTissue Core.

#### General Guidelines {#general-guidelines .unnumbered}

By default, the **SIMPLE SEARCH** page is displayed once the **SEARCH**
tab is selected. Additionally, you can navigate from the simple search
to the advanced search by clicking on the **Advanced** link located
under QUERY in the user dashboard.

AND & OR Operators

When adding multiple operators it is important to know the difference
between each operator prior to entry of query parameters. An ***AND***
constraint is applied when you want to retrieve items that contain more
than one data type, with each data type being present in the result set.

Example: Query for participants over the age of 35 *AND* have gender
equal to female *AND* vital status equals alive.

An ***OR*** operator is applied when you want to retrieve items that
conform to at least one data type, but do not have to match all entered
criteria.

Example: Query for specimens where the type equals cDNA *OR* RNA

![](media/image108.png){width="6.495138888888889in"
height="1.4305555555555556in"}

**Figure 4.71**: Multiple Simple Search parameters using Simple Search

This simple query, displayed above, illustrates a search for all storage
containers located at a site with zip code 19104 OR 63110 that are not
full and in which specimens are stored at -40. The final query in
Boolean format would be:

**Storage Type: Default Temperature Equals -40 AND Storage Container: Is
Container Full, Not Equals, Yes AND Site: Zip Code Equals 19104 OR Site:
Zip Code Equals 63110**.

#### Step by Step Instructions {#step-by-step-instructions-38 .unnumbered}

##### *Simple Search* {#simple-search .unnumbered}

Step 1: On the Simple Search page, select desired object class from the
drop down menu.

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}The process is similar to the search conducted when
[editing](#EditObjects) an object; however you are able to add more than
one object with multiple constraints and AND/OR operators.

![](media/image109.png){width="6.498611111111111in" height="3.06875in"}

***Figure 4.72**: Select object class*

Step 1: Participant is selected from the 1st dropdown menu.

![](media/image110.png){width="6.495138888888889in"
height="2.1506944444444445in"}

***Figure 4.73:** Select search attribute*

This figure shows that the second dropdown menu is populated based on
the selection made in Step 1.

Step 2.1: Select desired attribute for the object. In the example above,
Medical Record Number is selected from the 2nd dropdown menu.

![](media/image111.png){width="6.4944444444444445in" height="1.0in"}

***Figure 4.74**: Select search constraint and enter a value*

Step 2.2: Select constraint that you would like to apply to the
attribute (e.g. Starts with, Ends with, Contains, Equals etc.)

In the image above, "Equals" is selected from the 3rd dropdown and
0098766521 is entered as a value.

Step 3: click on the **Search** button.

##### *Simple Search Using* *AND Operator* {#simple-search-using-and-operator .unnumbered}

Step 1: Follow steps described in [simple search](#simple-query) to add
first part of the query.

![](media/image112.png){width="6.495833333333334in"
height="0.9555555555555556in"}

***Figure 4.75**: Select relationship operator to be applied between
parameters*

Step 2: If you want to execute a query with the result set containing
ALL parameters, you can select to add an **AND** operator by clicking on
the link provided.

Click on the **Add More** button to add another row entry of search
parameters.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
The AND operator is selected by default, therefore you do not need to
select an operator unless you are changing the AND to an OR operator.

![](media/image113.png){width="6.497222222222222in"
height="1.2638888888888888in"}

***Figure 4.76:** Example of multiple parameters entered for simple
search*

The figure above shows a 2^nd^ row added to the simple search parameters
list. The figure also shows that the 1^st^ dropdown menu in the 2^nd^
row is populated based on the object type that is selected in the 1^st^
row.

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}As
each row is added, criteria on subsequent rows are limited to the object
selected on the first row or to associated objects of the object
selected in the first row. For example, Participant was selected in the
first row and so in the second row, Participant and Collection Protocol
Registration are shown since Participant was selected in the first row
and Collection Protocol Registration is associated with a participant.

[]{#ObjectHeriarchy .anchor}[Object Hierarchy:]{.underline}

Participant

Collection Protocol

Specimen Collection Group

Specimen

Step 3: Select one of the available data elements of interest, the
example below shows **Collection Protocol Registration** as being
selected.

![](media/image114.png){width="6.495138888888889in" height="1.8625in"}

***Figure 4.77:** Example of attribute list being populated based on
selected class*

The attribute menu is again populated based on the selection made in the
1st dropdown menu (object class).

Step 4: Select desired attribute. In Step 4.1, **Protocol Title** is
selected from the 2nd dropdown menu.

![](media/image115.png){width="6.497222222222222in"
height="1.2131944444444445in"}

**Figure 4.78**: Example of multiple parameters with an AND condition

In Step 4.2, **Starts With** is selected as the constraint and "White
Blood Cell" is entered into the data field for value.

Step 5: Once you have completed entry of desired conditions, click on
the **Search** button. The view (i.e. which fields are shown in the
resulting spreadsheet) may also be defined prior to performing the
search by clicking the **Define View** button. Rows in the query may be
deleted by selecting the row by clicking the checkbox in the first
column and clicking the Delete button.

##### *Simple Search Using AND & OR Operator* {#simple-search-using-and-or-operator .unnumbered}

Step 1: Follow the appropriate steps for adding an [AND
operator](#simple-search-using-and-operator).

![](media/image116.png){width="6.695138888888889in"
height="1.2638888888888888in"}

> **Figure 4.79**: Simple search with 2 AND operators and 1 OR operator
>
> Step 2: Select the conditions and type a value for each condition.
>
> Step 3: Select **OR** **Operator** for the desired parameter.

The example query above is for reported problems with an affiliation
starting with Washington OR an affiliation containing Pittsburgh.

> Step 4: Click the **Search** button to execute the search or click
> **Define View** to set up the page for the display of the result set.
>
> ![](media/image13.png){width="0.9479166666666666in" height="0.25in"}To
> apply an **OR Operator**, you must have two items of the same object,
> thus either one of the conditions will be applied in the query
> results.

###  {#section-4 .unnumbered}

### *View Query Results* {#view-query-results .unnumbered}

> Once all the desired parameters have been entered, click the
> **Search** button.

![](media/image117.jpeg){width="6.498611111111111in"
height="3.6729166666666666in"}

**Figure 4. 80**: Query Result View

> The system will refresh and display all the matching items that you
> have the privilege to view and use.
>
> ![](media/image13.png){width="0.9479166666666666in"
> height="0.25in"}The query result data is scrubbed prior to display to
> include only items that the user has the privilege to view.
>
> The features of this view are as follows:
>
> **Item 1**: Indicates a drop down list for the selection of the
> desired number of results to view per page.

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}Number of results per page default = 100

> **Item 2**: Indicates which block of results the system currently
> displays out of the total number of returned records.
>
> **Item 3**: The system paginates the Result view to accommodate more
> than one page containing the indicated number of results.
>
> Example: If you select to view 100 results per page and 310 results
> are returned, the view will contain three full pages and a fourth page
> containing the remaining 10 results.
>
> **Item 4**: Indicates checkboxes for individual selection of items.

**Item 5**: Indicates details for all the data returned in the result
set.

> ![](media/image13.png){width="0.9479166666666666in"
> height="0.25in"}Due to the large amount of data available per object
> it may be necessary to scroll across items to find the data of
> interest. You can also select to alter the view using the **Define
> View** feature (as explained later).
>
> The result view can also be sorted by clicking a column header.
> Example: To sort the participant records by the last name; click the
> column title -- Last Name. The page displays all the records in the
> alphabetical order based on a participant's last name. Click the
> column header again to sort in descending order.
>
> **Item 6**: Indicates a checkbox for the selection of all the query
> results. This feature is useful to export or add a large number of
> items or all the items to **My List**. You can export all the items by
> clicking the checkbox, or you can click the checkbox and clear the few
> items that you do not want to include.
>
> **Item 7**: Indicates a checkbox for the selection of the **Specimen
> View.**
>
> **Item 8**: Click the **Add to List** button to save all the selected
> items into **My List** to use when you request a specimen
> distribution.
>
> **Item 9**: Indicates the **Export** button. For details on how to use
> this feature, go to the [Export data](#exportdata) help section.
>
> **Item 10**: Indicates the **Define View** button. For details on how
> to use this feature, please go to the [Define Query
> View](#define-query-view) help section.
>
> **Item 11**: Indicates the **Redefine Query** button. This will take
> you back to the query page for additions,edits,and deletions of query
> parameters.
>
> To edit any detail, click the concerned link.
>
> For details on how to modify a query, go to the [Simple
> Query](#_Simple_Query) help section.

###  {#section-5 .unnumbered}

### *Edit in Simple Search*  {#edit-in-simple-search .unnumbered}

> In the table,the **Query Result View** shows a few cells in the
> columns as hyperlinks. Click the hyperlink to open a popup, where you
> can edit the object to which that attribute column belongs. Click the
> **Submit** button to save the changes.
>
> Refer Figure 4. 80: Query Result ViewHere the **Participant First
> Name**, the **Participant Last Name,** and the **Identifier** columns
> are shown as hyperlink. Click Participant First Name and Participant
> Last Name to open Participant object in the edit mode. Clicking the
> **Identifier** column to open the **Collection Protocol Registration**
> object in the Edit mode.
>
> ![](media/image8.png){width="0.6145833333333334in"
> height="0.21875in"}The columns that are shown as hyperlinks are
> configured in the database by the database initialization scripts.
> These columns represent the attribute of an object which you can use
> to refer to that object. For example, for the specimen object Label,
> and Identifier attributes are hyperlinked. For the **Collection
> Protocol** object the title, the short title, and the identifier are
> shown as hyperlink.
>
> From here you can edit only those objects for which you have the
> privilege to edit.
>
> ![](media/image8.png){width="0.6145833333333334in"
> height="0.21875in"}After editing the object, the **Query Result View**
> is not refreshed immediately. For example, you update the **Title**
> attribute of **Collection Protocol** from **Simple Search,** click the
> **Submit** button and close the popup window. The **Query Result
> View** does not reflect it immediately, because the it is not
> refreshed. The next time you search for the same record, the system
> displays the updated value.

### Advanced Query {#advanced-query .unnumbered}

#### Purpose of Task {#purpose-of-task-39 .unnumbered}

The Advanced Query Interface allows a user to create and execute a
complex query on data elements related to biospecimens, specimen
collection groups, collection protocols, and participants stored within
the system. This interface is ideal for queries conducted across
multiple objects along with multiple parameter operators. Typically,
this interface is intended for use by scientists searching for
biospecimens of interest. For example, "Show all female participants who
have RNA (\>5 ug) AND DNA (\>5 ug) from the same lung tumor specimen".

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}
Before query result data is displayed it is filtered to remove the data
for which the logged in user does not have READ privileges.

#### Prerequisite Information {#prerequisite-information-39 .unnumbered}

A previously registered and approved user successfully logs into
caTissue Core.

##### *\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_* {#section-6 .unnumbered}

##### *Operator rules for advanced query:* {#operator-rules-for-advanced-query .unnumbered}

-   An **AND** operator is applied to all data elements within an object
    as shown below:

![](media/image118.png){width="6.499305555555556in"
height="2.2597222222222224in"}

**Figure 4.70:** Example of multiple AND conditions for the specimen
object

> Once conditions are added (as displayed in the figure 4.70), they will
> be displayed with AND operators applied to all entered items, as
> displayed in figure 4.71.
>
> ![](media/image119.png){width="6.292361111111111in" height="0.8125in"}

**Figure 4.71:** AND operator applied to all conditions entered for
specimen object

-   An **AND** operator can be applied between different types of
    objects.

![](media/image120.png){width="6.270138888888889in"
height="0.8541666666666666in"}

**Figure 4.82**: Example of AND operator between objects

The image above, shows an AND operator between all parameters for
participant and the parameter for Collection Protocol.

-   A pAND (pseudo-AND) operator can be applied to existing rules. This
    signifies that the selected items must be available for the same
    parent object in order for it to be included in the query results.
    An example of this would be to apply a pAND operator when you want
    multiple specimens of different types, from the same specimen
    collection group.

![](media/image121.png){width="4.343055555555556in" height="0.59375in"}

**Figure 4.83**: Example of pAND operator

-   Multiple rules (**pAND** and **OR**) can be applied on the same type
    of object.

    -   OR rules pertain to the selection of multiple items that may not
        occur concurrently. Example: A user may want a specimen
        derivative of DNA **OR** RNA with the result set containing DNA
        or RNA but not both.

> ![](media/image122.jpeg){width="6.927777777777778in"
> height="1.7333333333333334in"}

**Figure 4.84**: Operator examples

> ![](media/image123.png){width="0.21875in"
> height="0.17708333333333334in"} = Participant rule
>
> ![](media/image124.png){width="0.21875in"
> height="0.20833333333333334in"} = Collection protocol rule
>
> ![](media/image125.png){width="0.3229166666666667in"
> height="0.1875in"} = Collection group rule
>
> ![](media/image126.png){width="0.3020833333333333in"
> height="0.22916666666666666in"} = Specimen rule
>
> All line items in the rule section are labeled based on their
> associated object (as displayed above). Alternate lines are shaded in
> order to enhance readability.
>
> Operators are indicated as follows:

![](media/image127.png){width="0.25in" height="0.17708333333333334in"} =
A slashed line with no associated icon indicates a simple AND operator.

![](media/image128.png){width="0.2916666666666667in"
height="0.23958333333333334in"} = A gray circle at the end of the line
indicates an OR operator.

The pAND operator is a little more complicated. The operator must
contain at least 2 conditions and must be underneath a higher node.

![](media/image129.png){width="1.3020833333333333in" height="0.5625in"}

The example on the left shows a pAND operator for 2 specimen rules and
they are located underneath a Collection Group rule.

![](media/image130.png){width="0.3229166666666667in" height="0.1875in"}
= A yellow arrow indicates a pAND operator.

> In the query displayed in figure 4.73; the user is searching for
> specimens derived from all male participants whose last name starts
> with **ABC**. The **COLLECTION PROTOCOL** constraint is that the
> registration title EITHER **Starts With A** **OR** **Starts With**
> **B** (but not necessarily both). If the registration **Title Starts
> With** **B**, the specimen constraint is that BOTH **RNA** **AND**
> **DNA** (two different specimens derived from the same specimen
> collection group) must be available for the participant. The final
> query would be: **(PARTICIPANT: Gender Equals Male AND Last Name
> Starts With ABC) AND \[COLLECTION PROTOCOL: (Title Starts With A) OR
> (Title Starts With B AND (SPECIMEN: Type Equals RNA pAND Type Equals
> DNA)\]**.

#### Step by Step Instructions  {#step-by-step-instructions-39 .unnumbered}

Step 1: Go to, **SEARCH** **Advanced**

![](media/image131.png){width="6.260416666666667in" height="1.65625in"}

> **Figure 4.85**: Initial page presented for Advance query

Step 2: Select a node to start and then click on the **Submit** button.

The page will refresh and a selection box will be displayed for each
node in the system. To select the start node or object, click on the
associated radio button, and then click the **Submit** button. The
advanced query is also governed by the [object
hierarchy](#ObjectHeriarchy), with the objects presented in order from
top to bottom in the selection page. If you select a node lower on the
list, the query form will be built, with a rule for ANY applied to the
higher items (see figure 4.86).

Example: If you select Specimen as you start node, then the advanced
query form will be displayed for Specimen parameters. Once you add
desired specimen parameters, the rules section will be updated with
rules for ANY displayed for Participant, Collection Protocol and
Specimen Collection Group along with the specimen rules just entered.

![](media/image132.png){width="4.457638888888889in" height="0.875in"}

**Figure 4.86**: Example of applied object hierarchy rules in the
advanced query

Step 3: Input conditions in the **Participant Query Rule** form. (Search
for all **Specimens** derived from **Participants** whose **Birth Date**
falls between *12-23-1950* and *12-23-1965 (step 3.1)* **AND** whose
**Genotype** is *Unknown* (step 3.2).

![](media/image133.png){width="6.292361111111111in" height="2.375in"}

**Figure 4.87**: Input parameters

![](media/image8.png){width="0.6145833333333334in" height="0.21875in"}
See [Calendar Feature](#CalendarFeature) for additional details.

Step 4: Click **Add** button located on either the top or bottom of the
page to proceed. The parameters entered will be displayed in the rules
section at the bottom of the page. Alternatively, click **Reset** to
refresh the page and remove all data entered. Note that this does not
clear the rules list. To do this, restart the entire query by clicking
on the Advanced Search link in the left panel.

![](media/image134.png){width="6.280555555555556in"
height="0.6902777777777778in"}

**Figure 4.88**: Rule list

If you select to start on the first node (Participant), then each
subsequent page will display parameter entry fields for the next node.
You can enter additional parameters for existing node rules, by
selecting the checkbox of the object in the rule list and selecting the
desired node using the ADD menu at the top of the rule list.

Step 5: Click on the **Search** button once all query parameters have
been entered.

![](media/image135.png){width="6.301388888888889in"
height="1.1979166666666667in"}

**Figure 4.89**: Execute query

##### *Adding a New Base Rule to an Existing Query* {#adding-a-new-base-rule-to-an-existing-query .unnumbered}

Step 1: Select the check box for the **Rule** that precedes the intended
addition and uncheck all other boxes.

Step 2: Go to the **Add** menu located on the **Rules** bar and click on
desire node (as displayed in the figure below.

![](media/image136.png){width="5.997916666666667in"
height="2.310416666666667in"}

**Figure 4.90**: Add additional rule to existing node

Step 3: The page will refresh and an entry form for the selected node
will be displayed.

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}All pages are labeled in order to indicate current
node (as displayed in the image below).

![](media/image137.jpeg){width="5.990972222222222in"
height="0.30416666666666664in"}

**Figure 4.91**: Page labeled based on node

Step 4: Enter parameters for the selected node and click on the Add
button.

Step 5: Repeat steps 1-4 until all desired parameters have been entered
and are displayed in the rules section.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}
When new rules are added, they will be numbered in the rules list. The
figure below shows two separate rules for Participant.

![](media/image138.png){width="5.927083333333333in"
height="2.3854166666666665in"}

**Figure 4.92**: Example of multiple participant rules with OR operator

> In this figure, **Rule #2** is added to the query. The search is now
> for all **Specimens** derived from **Participants** whose **Birth**
> **Date** falls **Between** **12-23-1950** and **12-23-1965** **AND**
> whose genotype is **Unknown OR** **XY.**

##### *Editing a Previously Added Rule*  {#editing-a-previously-added-rule .unnumbered}

[]{#EditRule .anchor}Step 1: Select the check box next to the rule of
interest (step 1.1) and uncheck all others (step 1.2).

Step 2: Click on the **Edit** link located in the Rules menu.

![](media/image139.png){width="5.997222222222222in"
height="2.701388888888889in"}

**Figure 4.93**: Selecting a rule of interest

The pre-populated form of interest will be displayed.

![](media/image140.png){width="5.999305555555556in"
height="2.6909722222222223in"}

**Figure 4.94**: Editing a rule

Step 3: Make appropriate changes to constraint of interest.

Step 4: Click the **Add** button.

> The page will refresh and display the edited rules.
>
> Step 5: Repeat steps 1-4 on each rules until all desired edits are
> made.

##### *Edit multiple rules for a single query* {#edit-multiple-rules-for-a-single-query .unnumbered}

> Follow the same steps mentioned above for each rule that should be
> edited.

![](media/image141.png){width="5.998611111111111in"
height="2.6944444444444446in"}

**Figure 4.95**: Modify rule with new parameter

In Step 3.1, the selection of the dropdown box for **Title** is changed
from **Contains** to **Any**.

![](media/image142.png){width="5.999305555555556in"
height="2.6798611111111112in"}

**Figure 4.96**: Change search parameter from one attribute to another

> In Step 3.2, **Prostate** is deleted from the text box for **Title**.
> Step 3.3, **Contains** is selected from the dropdown menu and
> **Prostate** typed into the text box for **Short Title**. Step 4, the
> **Add** button is clicked.

![](media/image143.jpeg){width="5.992361111111111in"
height="2.6902777777777778in"}

**Figure 4.97**: Modified rule added to rules section

> In this figure query **Rule #1** is updated to a search for all
> **Specimens** derived from **Participants** whose **Birth Date** falls
> **Between** **12-23-1950** and **12-23-1965 AND** whose **Genotype**
> is **Unknown OR XY AND** with a Collection Protocol **Short Title**
> containing **Prostate**. In addition, the **Specimen Collection Group
> Query Rule** form is displayed after the **COLLECTION PROTOCOL** rule
> has been added.

##### *Add an AND Operator for a Different Object Type* {#add-an-and-operator-for-a-different-object-type .unnumbered}

Step 1: Select the check box of the **Rule** that will precede the
intended addition and uncheck all other boxes.

Step 2: Go to the **Add** menu on the page and select the desired
object. Once page is displayed, enter data onto the page.

Step 3: Once all desired data is entered, click on the **Add** button.

![](media/image144.png){width="5.996527777777778in" height="2.6625in"}

**Figure 4.98**: Add AND operator between objects

> This figure above shows the rule for Collection Protocol is selected
> in Step 1. No input conditions are selected for Step 2. The query will
> be updated to include **ANY Specimen Collection Group** for **Rule
> #1** (i.e. A search for all **Specimens** derived from
> **Participants** whose **Birth Date** falls **Between** **12-23-1950**
> and **12-23-1965 AND** whose **Genotype** is **Unknown OR XY AND**
> with a Collection Protocol **Short Title** containing **Prostate AND**
> belonging to **ANY** **Specimen** **Collection Group**).

##### *Adding an OR Operator of the Same Object Type* {#adding-an-or-operator-of-the-same-object-type .unnumbered}

Step 1: Uncheck all boxes in the rules section

Step 2: In the **Add** menu on the rules bar, select desired object.
Enter constraint details into the page displayed, and then click on the
**Add** button. Following the above steps will automatically add an OR
operator to the new rule entered for the specified object. This varies
from the previous example of how to [add a rule](#EditRule) since the
new rule will stand by itself and will not be included as an addition or
edit to an existing rule.

Step 3: Once desired search parameter is entered, click on the **Add**
button.

The page will refresh and display the new rule in the rules list, along
with the icon indicating that an OR operator has been applied.

![](media/image145.png){width="5.930555555555555in"
height="1.5097222222222222in"}

**Figure 4.99**: Updated rules list

> This figure shows the query is updated to include an **OR**ed operator
> under **Rule #1** (i.e. A search for all **Specimens** derived from
> **Participants** whose **Birth Date** falls **Between** **12-23-1950**
> and **12-23-1965 AND** whose **Genotype** is **Unknown AND** with a
> Collection Protocol **Short Title** containing **Prostate AND**
> belonging to **ANY** **Specimen Collection Group** **AND** with
> **EITHER** a **Malignant OR** **Metastatic** **Pathological Status**).

##### *Modify existing rule(s) in list* {#modify-existing-rules-in-list .unnumbered}

Step 1: Click on the checkbox located to a rule to be modified.

![](media/image146.png){width="5.9944444444444445in"
height="2.7263888888888888in"}

**Figure 4. 100**: Select rule that will be modified

Step 2: Click the Edit link located on the rules menu bar.

![](media/image147.png){width="5.99375in" height="2.751388888888889in"}

**Figure 4.101**: Rule parameter changed

In Step 2.1, **Equals** is chosen from the 1^st^ dropdown menu for
**Pathological Status**.

![](media/image148.png){width="5.99375in" height="2.79375in"}

**Figure 4.102:** Select value for new parameter

In Step 2.2, **Malignant** is chosen from the 2^nd^ dropdown menu for
**Pathological Status**.

![](media/image149.png){width="5.99375in" height="2.6868055555555554in"}

**Figure 4.103**: Add new rule

> Step 3: After all desired data items have been modified scroll to the
> top or bottom of the page and click on the **Add** button.
>
> The query is updated to include **Specimens** with a **Pathological
> Status** **Equal** to **Malignant** for **Rule** **#1**.
>
> ![](media/image13.png){width="0.9479166666666666in"
> height="0.25in"}The list of rules is updated EVERY time a new rule is
> added. This is done automatically and does not require any additional
> action.
>
> ![](media/image8.png){width="0.6145833333333334in"
> height="0.21875in"}The data form for the selected object will remain
> displayed until another object is selected or the user selects to
> execute the query.

![](media/image145.png){width="5.930555555555555in"
height="1.5097222222222222in"}

**Figure 4.104**: Updated rules list

> This figure above show an updated rule list, including updated an
> **OR** operator under **Rule #1** (i.e. A search for all **Specimens**
> derived from **Participants** whose **Birth Date** falls **Between**
> **12-23-1950** and **12-23-1965 AND** whose **Genotype** is **Unknown
> AND** with a Collection Protocol **Short Title** containing **Prostate
> AND** belonging to **ANY** **Specimen Collection Group** **AND** with
> **EITHER** a **Malignant OR** **Metastatic** **Pathological Status**).

##### *Adding a Pseudo AND (pAND) Operator of the Same Object Type* {#adding-a-pseudo-and-pand-operator-of-the-same-object-type .unnumbered}

Step 1: Select the check box for the **Rule** that will precede the
intended addition and uncheck all other boxes.

Step 2: Select object in the **Add** menu.

Step 3: Go to the **Add** menu located on the **Rules** bar and select
the object for the rule being entered.

Step 4: Input data into the page displayed and click the **Add** button.

Step 5: Select the check box of the **Rule** preceding the 2 **Rules**
(the **Rules** have been added as **OR**ed operators by default).
Uncheck all other boxes.

![](media/image150.png){width="5.996527777777778in"
height="2.683333333333333in"}

**Figure 4.105:** Select rule that you want to add a pAND to

> In Step 5.1, the box preceding the location of insertion is selected.
> In Step 5.2, all other selected boxes are deselected.

![](media/image151.png){width="5.99375in" height="2.6868055555555554in"}

**Figure 4.106**: Select pAND as the operator

Step 6: Go to the **Operator** menu located on the **Rules** bar and
click on the **pAND** operator.

![](media/image152.jpeg){width="5.997916666666667in"
height="1.5534722222222221in"}

**Figure 4.107:** Updated operator displayed

> This figure shows the query is updated to include a **pAND** operator
> under **Rule #1**. This would result in a search for all **Specimens**
> derived from **Participants** whose **Birth Date** falls **Between**
> **12-23-1950** and **12-23-1965 AND** whose **Genotype** is
> **Unknown** **AND** with a Collection Protocol **Short Title**
> containing **Prostate** **AND** belonging to **ANY** **Specimen
> Collection Group** **AND** with **BOTH** **Malignant** **AND**
> **Metastatic** **Pathological Status** (two different **Specimens**
> derived from the same **Specimen Collection Group**).

\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_

*Add to List*

> You can select specimens in the query result view using the associated
> check boxes (**Item 4**) on the left of the page, or you can select
> all items by clicking on the **Check All (Item 6)** button located at
> the bottom, left of the page. Once items are selected, click on the
> **Add to Cart** button. This action will add all selected biospecimens
> in "**My List**".
>
> Go to [*View My List*](#purpose-of-task-40) section for more details
> on how to use this feature.

*Export*

> []{#exportdata .anchor}Step 1: Select one or more items in the result
> view by clicking on either individual using the checkboxes indicated
> with **Item 4**, or select ALL results by clicking on the Check All
> checkbox indicted by **Item 6**.
>
> Step 2: Once items are selected, click on the **Export** button.

![](media/image153.png){width="3.479861111111111in"
height="2.314583333333333in"}

**Figure 4.109** Option to Open or Export data Items

Pop up window displays message "Do you want to open or save this file?"

> Step 3: If you select **Open**, the data will be displayed in a MS
> Excel spreadsheet, which you can then save to a location of your
> choice.

![](media/image154.png){width="6.0in" height="1.5034722222222223in"}

**Figure 4.110**: Exported item in Spreadsheet View

> If you select **Save**, you will be presented with a pop-up box for a
> desired location.

![](media/image155.png){width="4.226388888888889in"
height="2.879861111111111in"}

**Figure 4.111:** Save query results

> If you select **Cancel**, the process will be terminated and you will
> be returned to the query result page.

*Define View*

> Please go to the [*Define Query View*](#define-query-view) help
> section for additional details.

*Redefine Query*

This feature allows you to go back to the query and make any desired
edits without having to rebuild a new query from scratch.

#### Related Topics {#related-topics-32 .unnumbered}

[Login](#login)

[Simple Query](#simple-query)

[Advance Query](#advanced-query)

[View My List](#purpose-of-task-40)

[Logout](#logout)

### View My List {#view-my-list .unnumbered}

#### Purpose of Task {#purpose-of-task-40 .unnumbered}

This task involves the selection of items from the result set of a query
and saving them into your list of items. This list can then be used to
place a request for distribution (using email or other means outside the
scope of the caTissue Core system) of available biospecimens in the
system. Additional items can be added or deleted until all desired items
have been included. The user then has the option to export list items.

#### Prerequisite Information {#prerequisite-information-40 .unnumbered}

A previously registered and approved user successfully logs into
caTissue Core and performs a query.

#### Step by Step Instructions {#step-by-step-instructions-40 .unnumbered}

##### *Add Item(s) to My List* {#add-items-to-my-list .unnumbered}

Step 1: On Advanced Query **SEARCH RESULTS** form, select checkbox(s)
for all results to be added to My List. (If all results are to be
included, select **Check All** check box).

![](media/image156.png){width="4.772916666666666in"
height="2.928472222222222in"}

**Figure 4.112**: Advanced Query **SEARCH RESULTS** form

Step 2: Click **Add To List** button.

Step 3: Click **View** under **My List** menu option.

Selected items are visible in the list.

![](media/image157.png){width="5.879861111111111in"
height="3.0520833333333335in"}

> **Figure 4.113**: View of **My List** containing selected items

##### *Delete Item(s) From My List* {#delete-items-from-my-list .unnumbered}

Step 1: Click **View** under **My List** menu.

Previously added items are displayed.

Step 2: Select checkbox for items to be deleted from your list. (If all
results are to be deleted, select **Check All** check box.)

Step 3: Click **Delete** button.

![](media/image158.png){width="4.813194444444444in"
height="2.8159722222222223in"}

**Figure 4.114**: View of **My list**

Pop up window displays message "Are you sure you want to delete the
selected item(s)?"

Step 4: Click **OK** button.

Selected items are deleted and are no longer visible on the My List
page.

##### *Export Item(s) From My List* {#export-items-from-my-list .unnumbered}

Exporting items from My List, following the same steps detailed during
export of query results. Please go to the [Export data](#exportdata)
help for additional information.

##### *Delete My List items* {#delete-my-list-items .unnumbered}

If you want to delete an item from your list, click on the checkbox
located to the far left of each line item you want to delete, and then
click on the **Delete** button.

![](media/image159.png){width="5.551388888888889in" height="2.8375in"}

**Figure 4.115**: Delete items from My List

The page will refresh and display the list of items in My List, minus
the selected items deleted.

#### Related Topics {#related-topics-33 .unnumbered}

[Login](#login)

[Simple Query](#simple-query)

[Advanced Query](#advanced-query)

[Logout](#logout)

### Define Query View {#define-query-view .unnumbered}

#### Purpose of Task {#purpose-of-task-41 .unnumbered}

This task involves configuring the view of the results from a query. As
shown in the figure below, a user must conduct a query and then select
to define the displayed view. This will allow the user to customize the
data they want to view.

#### Prerequisite Information {#prerequisite-information-41 .unnumbered}

A previously registered and approved user successfully logs into
caTissue Core.

#### Step by Step Instructions {#step-by-step-instructions-41 .unnumbered}

The query view can be specified by selecting the **Define View** button
located on the **Simple** or **Advanced query** page *before* a search
is performed, or after a search is performed by clicking on the **Define
View** button located on the query page (before query execution) at
under the query results table (after query execution).

This feature allows a user to select what items they want to view prior
to execution of a query, or reduce the number of attributes displayed to
de-clutter the view or delete attributes that are of no interest.

![](media/image160.png){width="5.995833333333334in"
height="0.8826388888888889in"}

**Figure 4.116**: Define view -- Simple Search

Step 1: Click on the Define View located at the bottom of both the
Simple Search and Advanced Search Query pages.

![](media/image161.png){width="5.993055555555555in"
height="1.5680555555555555in"}

**Figure 4.117**: Define Query View

Step 2: Select the Object Name of interest using the dropdown list. This
will populate all the available attributes for that Object in the
listbox on the left side.

Step 2: Select columns of interest by selecting one or more items from
the available box (left box) and adding them to the view box (right box)
by clicking on the **Add** button.

The reverse is also true; you can delete items from the view by
selecting them in the View box and putting them back in the available
box by clicking on the **Delete** button.

To select more than one item, hold down the **Ctrl** key during
selection.

![](media/image162.png){width="5.99375in" height="1.5659722222222223in"}

**Figure 4.118:** Select object attributes in query view

Step 3: You can also select to rearrange items in the view, by clicking
on a desired item and moving it up or down in the list the **Up** and
**Down** buttons provided. The items at the top of the list will be
displayed 1^st^, from left to right in the view.

Step 4: To edit the data displayed for another object, go to the Object
Names dropdown in the top, left of the page and select another object.
Once a selection is made, the page will refresh to display data items
for the selected object.

In figure 4.118, Participant has been selected from the Object Names
list, with the view box containing all data items available for
participant.

Step 5: Click on the **Submit** button to proceed with the view selected
or Reset to clear all selections.

![](media/image163.png){width="5.993055555555555in"
height="1.6090277777777777in"}

**Figure 4.119**: Selected item moved into "View" list

# **Chapter 5:** **Error Messages/Indicators and Problem Resolutions** {#chapter-5-error-messagesindicators-and-problem-resolutions .unnumbered}

## Problem List: {#problem-list .unnumbered}

1.  [You can see the website, but no tools are available to
    you.](#problem-1)

2.  [I do not see where to login to the system.](#problem-2)

3.  [I forget my password.](#problem-3)

4.  [Failed to log in the system. (Error message: 'Incorrect Login ID or
    Password')](#problem-4)

5.  [Failed to change password.](#problem-5)

6.  [Other problems with passwords.](#problem-6)

7.  [You need to report a problem with using the system.](#problem-7)

8.  [I need to contact system administrator.](#problem-8)

9.  [Can't perform some operations in the system. (Error message:
    'Access denied: You are not authorized to perform this
    operation.')](#problem-9)

10. [How to update my email address?](#p10)

11. [I can not see the map of storage containers when I click the link
    'View Map' under 'STORAGE CONTAINER' in the left panel of the page
    in Administrative Data.](#problem-11)

12. [I can not see the map of storage containers when I click the 'Map'
    button in Adding New Specimen page in Bio-Specimen
    Data.](#problem-12)

13. [I can not register a participant to a collection protocol. (Error
    message: 'Collection Protocol is already marked as
    closed.')](#problem-13)

14. [I can not register a participant to a collection protocol. (Error
    message: 'Submission failed since a Collection Protocol Registration
    with the same COLLECTION_PROTOCOL_ID, PARTICIPANT_ID already
    exists.')](#problem-13)

15. [I can not create a new distribution. (Error message: 'Quantity
    entered is greater that the available quantity.')](#problem-14)

16. [I can not edit the location of a frozen specimen.](#p16)

17. [I can not find a specimen. (Error message: 'No Records
    Found!')](#p17)

18. [How do I start a new search when I have finished one?](#problem-17)

19. [I can not see my search results in "My List". (Error message: 'The
    "My List" is empty.')](#problem-18)

20. [Number of aliquots exceeds storage spaces
    available.](#AliquotNumber)

21. [The sum of all aliquot quantities exceeds the quantity of the
    original
    specimen.](#the-sum-of-all-aliquot-quantities-exceed-the-quantity-of-the-parent-specimen)

## Contents: {#contents .unnumbered}

### Problem 1:  {#problem-1 .unnumbered}

#### You can see the website, but no tools are available to you. {#you-can-see-the-website-but-no-tools-are-available-to-you. .unnumbered}

### Solution:  {#solution .unnumbered}

To use the system, you need to register to the system through the link
'Sign Up' on the right side of home page. The most important thing is
that you must provide a VALID email address which will be used as your
login name when you first register to the system. Please refer to the
submit [new user registration](#submit-new-user-request) details section
for additional information. After you finish your input, click 'Submit'
button to send your registration to the system. An email with the
subject 'Request to join caTissue Core received' will be immediately
sent to the email inbox you provided in your registration by the system
administrator. When your account is approved by the administrator, you
will receive the email with the subject 'Request to join caTissue Core
approved' which includes your login name and a temporary password.

### Problem 2:  {#problem-2 .unnumbered}

#### I do not see where to login to the system.  {#i-do-not-see-where-to-login-to-the-system. .unnumbered}

### Solution:  {#solution-1 .unnumbered}

If you have a small size screen or do not have your browser window
maximized, you may not see the 'Sign In' section on the right side of
your screen.

Click on the maximize button ![](media/image164.png){width="0.1875in"
height="0.11458333333333333in"} in the top, right corner of your screen.

### Problem 3:  {#problem-3 .unnumbered}

#### I forgot my password. {#i-forgot-my-password. .unnumbered}

### Solution:  {#solution-2 .unnumbered}

Open the system's web site, scroll your screen to right side, and click
the link 'Forgot your password?' link. Type your email address, click
the 'Send' button, and you will receive an email with the subject of
'Your login details at caTissue Core' from the administrator. All your
account information will be included in the email.

### Exception**:**  {#exception .unnumbered}

You can not get the password for root administrator 'admin@admin.com'
because the email address does not exist.

Go to the [Forgot Password](#retrieve-forgotten-password) help section
for more details.

### Problem 4:  {#problem-4 .unnumbered}

#### Failed to log into the system. (Error message: 'Incorrect Login ID or Password') {#failed-to-log-into-the-system.-error-message-incorrect-login-id-or-password .unnumbered}

### Solution:  {#solution-3 .unnumbered}

This means you type either an incorrect login ID or a wrong password.
Check both entries carefully. Passwords are case sensitive, so be sure
your caps lock key is not on.

If you continue to have problems, you can contact a system administrator
by following the information in the Contact Us option, or [Report a
Problem](#report-a-problem).

### Problem 5:  {#problem-5 .unnumbered}

#### Failed to change password.  {#failed-to-change-password. .unnumbered}

### Solution:  {#solution-4 .unnumbered}

When attempting to change your password (required after first logon or
after using the "Forgot my password" feature) the password must meet the
minimum requirements stated in the [change password](#change-password)
section.

> If your new password does not meet the minimum requirements, you will
> see the error message describing these requirements. Alternatively,
> you may receive a message stating that the passwords you typed do not
> match. Type the new password in both the text boxes (make sure your
> caps lock is not on).

### Problem 6:  {#problem-6 .unnumbered}

#### Other problems with passwords. {#other-problems-with-passwords. .unnumbered}

### Solution:  {#solution-5 .unnumbered}

1)  To maintain system security and abide by HIPAA compliancy rules, all
    passwords must abide by strict rules as defined
    [here](#PasswordRules).

### Problem 7:  {#problem-7 .unnumbered}

#### You need to report a problem with using the system. {#you-need-to-report-a-problem-with-using-the-system. .unnumbered}

### Solution:  {#solution-6 .unnumbered}

Click the link '**REPORT PROBLEMS**' link at the bottom of the page.
Fill in the requested information along with a summary of the problem,
then click on the **Submit** button. This will send an email to the
system administrator about your problem. For additional information,
please refer to the [Report Problem](#report-a-problem) section.

### Problem 8:  {#problem-8 .unnumbered}

#### I need to contact a system administrator. {#i-need-to-contact-a-system-administrator. .unnumbered}

### Solution: {#solution-7 .unnumbered}

Click on the '**CONTACT US'** link located at the bottom of the page.
This will display detailed information on who to contact in regard to
the system.

### Problem 9:  {#problem-9 .unnumbered}

#### ***Can't perform some operations in the system. (Error message: "Access denied: You are not authorized to perform this operation.")*** {#cant-perform-some-operations-in-the-system.-error-message-access-denied-you-are-not-authorized-to-perform-this-operation. .unnumbered}

### Solution: {#solution-8 .unnumbered}

The system access privileges are controlled by your user role.

There are 4 kinds of [general roles](#Role) in the system.

1)  Administrator: Can access all data and operations;

2)  Supervisor: Can NOT add/edit Administrative Data; Can access
    identified data;

3)  Technician: Individual who is in-charge of entering bio-specimen
    data into the system; Can NOT access identified data; Can add/edit
    de-identified data;

4)  Scientist: Can only use search operation.

When you click an operation which you are not allowed to use based on
your current role, you will see an error message stating 'Access denied:
You are not authorized to perform this operation.' If you need to use
this operation, please contact the system administrator.

Please refer to the [Assign Privileges](#assign-privileges) section for
additional details.

### Problem 10:  {#problem-10 .unnumbered}

#### How to update my email address? {#how-to-update-my-email-address .unnumbered}

### Solution:  {#solution-9 .unnumbered}

Log into the system and select to Edit your user profile.

![](media/image13.png){width="0.9479166666666666in" height="0.25in"}The
new email address is used as an identifier in the system. Therefore you
must remember to not enter your old email address when trying to login
otherwise an error will be displayed.

### Problem 11:  {#problem-11 .unnumbered}

#### I can not see the map of storage containers when I click the link 'View Map' under 'STORAGE CONTAINER' in the left panel of the page in Administrative Data. {#i-can-not-see-the-map-of-storage-containers-when-i-click-the-link-view-map-under-storage-container-in-the-left-panel-of-the-page-in-administrative-data. .unnumbered}

### Solution:  {#solution-10 .unnumbered}

The most probable reason is that you have already opened the map of
storage containers and you minimized the window. Check the task bar at
the bottom of your screen. Another reason is that your system may have a
problem, please contact your system administrator using the Contact Us
option or [report the problem](#report-a-problem).

### Problem 12:  {#problem-12 .unnumbered}

#### I can not see the map of storage containers when I click the 'Map' button in Adding New Specimen page in Bio-Specimen Data {#i-can-not-see-the-map-of-storage-containers-when-i-click-the-map-button-in-adding-new-specimen-page-in-bio-specimen-data .unnumbered}

### Solution:  {#solution-11 .unnumbered}

See the solution for Problem 11.

### Problem 13:  {#problem-13 .unnumbered}

#### I can not register a participant to a collection protocol. (Error message: 'Submission failed since a Collection Protocol Registration with the same COLLECTION_PROTOCOL_ID, PARTICIPANT_ID already exists.') {#i-can-not-register-a-participant-to-a-collection-protocol.-error-message-submission-failed-since-a-collection-protocol-registration-with-the-same-collection_protocol_id-participant_id-already-exists. .unnumbered}

### Solution:  {#solution-12 .unnumbered}

The reason is that you can not register a participant twice to the same
collection protocol.

![](media/image8.png){width="0.6145833333333334in"
height="0.21875in"}This does not prevent you from entering tissues from
the same patient more than once; it simply preserves a unique patient ID
record.

### Problem 14:  {#problem-14 .unnumbered}

#### I can not create a new distribution. (Error message: 'Quantity entered is greater that the available quantity.') {#i-can-not-create-a-new-distribution.-error-message-quantity-entered-is-greater-that-the-available-quantity. .unnumbered}

### Solution:  {#solution-13 .unnumbered}

You can not make a new distribution in which the tissue's quantity is
greater that the tissue's available quantity. This also applies when you
edit an existing distribution.

### Problem 15:  {#problem-15 .unnumbered}

#### I can not edit the location of a frozen specimen. {#i-can-not-edit-the-location-of-a-frozen-specimen. .unnumbered}

### Solution:  {#solution-14 .unnumbered}

Specimens can be moved from one position to another by following the
steps below:

1.  Click '**BIO-SPECIMEN DATA'** tab **Specimen** **Events**.

2.  Select **Transfer** event from drop down list.

3.  Enter new location.

4.  Click **Submit**.

See [Add Event](#add-events) section for a detailed description of the
process.

### Problem 16:  {#problem-16 .unnumbered}

#### I can not find a specimen. (Error message: 'No Records Found!') {#i-can-not-find-a-specimen.-error-message-no-records-found .unnumbered}

### Solution:  {#solution-15 .unnumbered}

If you are assigned the role of 'Scientist', you may see the error
message 'No Records Found!' after query execution.

The main two reasons are:

1)  There are no specimens matching your search parameters in the
    system.

2)  You used wrong or conflicting parameters to search for the specimen.
    (Example, prostate tissue from female participants) Examine your
    search parameters carefully, apply changes if necessary and run the
    search again.

3)  Results are available, but you do no possess proper access
    privileges.

### Problem 17:  {#problem-17 .unnumbered}

#### How do I start a new search when I have finished one? {#how-do-i-start-a-new-search-when-i-have-finished-one .unnumbered}

### Solution:  {#solution-16 .unnumbered}

Do the same procedure as you did to run the first search. Click the same
link in the left panel of your page.

See the [Simple Query](#simple-query) and [Advanced
Query](#advanced-query) section for additional details.

### Problem 18: {#problem-18 .unnumbered}

#### The sum of all aliquot quantities exceed the quantity of the parent specimen {#the-sum-of-all-aliquot-quantities-exceed-the-quantity-of-the-parent-specimen .unnumbered}

### Solution: {#solution-17 .unnumbered}

Correct the quantity and resubmit.

# **Chapter 6:** **Glossary/Acronyms/Abbreviations** {#chapter-6-glossaryacronymsabbreviations .unnumbered}

## References {#references .unnumbered}

This appendix could include lists and hypertext links, where
appropriate, to technical manuals, articles, scientific publications,
etc. Examples are shown:

### Technical Manuals/Articles {#technical-manualsarticles .unnumbered}

National Cancer Institute. \"caCORE 2.0 Technical Guide\",
<ftp://ftp1.nci.nih.gov/pub/cacore/caCORE2.0_Tech_Guide.pdf>

Java Bean Specification:
<http://java.sun.com/products/javabeans/docs/spec.html>

Foundations of Object-Relational Mapping:
<http://www.chimu.com/publications/objectRelational/>

Object-Relational Mapping articles and products:
<http://www.service-architecture.com/object-relational-mapping/>

Hibernate Reference Documentation:
<http://www.hibernate.org/hib_docs/reference/en/html/>

Basic O/R Mapping:
<http://www.hibernate.org/hib_docs/reference/en/html/mapping.html>

Java Programming: <http://java.sun.com/learning/new2java/index.html>

Javadoc tool: <http://java.sun.com/j2se/javadoc/>

JUnit: <http://junit.sourceforge.net/>

Extensible Markup Language: <http://www.w3.org/TR/REC-xml/>

XML Metadata Interchange:
<http://www.omg.org/technology/documents/formal/xmi.htm>

### Scientific Publications {#scientific-publications .unnumbered}

#### caBIG Material {#cabig-material .unnumbered}

1.  **caBIG:** <http://cabig.nci.nih.gov/>

```{=html}
<!-- -->
```
1.  **caBIG Compatibility Guidelines**:
    <http://cabig.nci.nih.gov/guidelines_documentation>

#### caCORE Material {#cacore-material .unnumbered}

1.  **caCORE:** <http://ncicb.nci.nih.gov/core>

```{=html}
<!-- -->
```
2.  **caBIO:** <http://ncicb.nci.nih.gov/core/caBIO>

3.  **caDSR:** <http://ncicb.nci.nih.gov/core/caDSR>

4.  **EVS:** <http://ncicb.nci.nih.gov/core/EVS>

5.  **CSM:** <http://ncicb.nci.nih.gov/core/CSM>

##  Glossary {#glossary .unnumbered}

  ----------------------------------------------------------------------------
  ***Term***            ***Definition***
  --------------------- ------------------------------------------------------
  Administrative Data   One of the three different data types in which
                        caTissue Core data can be categorized. Collection
                        protocol, Distribution protocol, Biohazards, Site,
                        Storage container, User, Department, Institution,
                        Cancer Group.

  Administrator         See Chapter 4 (User Roles) for definition.

  Aggregate data        Data collected and reported

  Aliquot               Pertaining to a portion of the whole; any one of two
                        or more samples of something, of the same volume or
                        weight.

  Anonymous             There must not be any way (within or outside caTissue
  Distribution          ) to link the biospecimens distributed and the
                        participant from whom the biospecimens were accessed.
                        This type of distribution can be performed for any
                        user.

  API                   Application Programming Interface

  Array                 An orderly arrangement of biospecimens.

  Biohazards            An attribute of a Specimen that renders it potentially
                        harmful to a User.

  Bio-Specimen data     One of the three different data types in which
                        caTissue Core data can be categorized. Specimen,
                        Specimen external identifiers, Specimen events,
                        Specimen distribution.

  Boolean AND (AND      Boolean is a logic system. Using the \"AND\" operator
  operator)             between terms retrieves documents containing both
                        terms.

  Boolean OR (OR        Boolean is a logic system. Using \"OR\" retrieves
  operator)             documents containing either term.

  Boolean: FALSE        The value of the data element equals FALSE

  Boolean: TRUE         The value of the data element equals TRUE

  caArray               cancer Array Informatics

  caBIG                 Cancer Biomedical Informatics Grid

  caBIO                 Cancer Bioinformatics Infrastructure Objects

  caCORE                cancer Common Ontologic Representation Environment

  caDSR                 Cancer Data Standards Repository

  caMOD                 Cancer Models Database

  Cancer Research Group A collection of scientist and/or clinician users with
                        a common research objective related to biospecimen
                        collection and utilization.

  cardinality           Cardinality describes the minimum and maximum number
                        of associated objects within a set

  caTissue              Cancer Tissue Banking and Pathology Tools workspace
                        initiatives

  CDE                   Common Data Element

  Cell Specimens        A biospecimen composed of purified single cells not in
                        the context of a tissue or other biospecimen fluid.
                        These are discrete in nature and so will always be
                        measured in cell count in the system.

  CGAP                  Cancer Genome Anatomy Project

  Check-in/Check-out    Event that refers to temporary movement of specimens
  Event                 from stored location.

  Clinical Report       A clinical report associated with the participant at
                        the time of specimen collection event (also referred
                        to as Clinical Annotation).

  CMAP                  Cancer Molecular Analysis Project

  CN                    Common Name

  Collection Event      Event that refers to collection of a specimen from
                        participant under a collection protocol.

  Collection Protocol   A set of written procedures that describe how a
                        biospecimen is collected.

  Collection Protocol   A registration of a Participant to a Collection
  Registration          Protocol.

  Constraint            Data rule or restriction that is enforced within the
                        database rather than at application or object level

  CSM                   Common Security Module

  DAO                   Data Access Objects

  De-identified data    De-identified information excludes all
                        patient-identifiable information but can include
                        biospecimen identifiers.

  De-identified         Only de-identified information can be disclosed to the
  Distribution          receiver of the biospecimens. This type of
                        distribution can be performed for any general
                        researcher.

  Department            A department to which a User belongs.

  Disposal Event        Event that refers disposing/rejecting a specimen.

  Distribution          The act of distributing or spreading or apportioning.

  Distribution Protocol An abbreviated set of written procedures that describe
                        what, how many, and how much of a biospecimen or
                        biospecimens will be utilized for research.
                        Biospecimens may be collected under one collection
                        protocol and then later utilized by single or multiple
                        studies.

  Embedded Event        Event that refers to embedding a specimen in paraffin
                        or plastic material.

  EVS                   Enterprise Vocabulary Services

  Fixed Event           Event that refers to fixing a specimen.

  Fluid Specimens       A single unit of bodily fluid that is collected from a
                        participant or created from another specimen. These
                        are fluid in nature and so will always be measured µl
                        (microliter) in the system.

  Frozen Event          Event that refers freezing a specimen at certain
                        temperature.

  HIPPA                 Health Insurance Portability and Accountability Act

  Identified            Identified information can be disclosed to the
  Distribution          receiver of the biospecimens. This type of
                        distribution can be done only if the receiver of the
                        biospecimens is a PI or coordinator of the collection
                        protocol under which the biospecimen is collected.

  Institution           An institution to which a user belongs.

  Integer/Float/Date:   The value of the data element is less than or equal to
  \<= (or BEFORE for    the supplied value.
  DATE data elements)   

  Integer/Float/Date: = The value of the data element equals the supplied
                        value.

  Integer/Float/Date:   The value of the data element is more than or equal to
  \>= (or AFTER for     the supplied value.
  DATE data elements)   

  Integer/Float/Date:   The maximum or minimum n values of the data element
  MAX n / MIN n         are to be returned.

  metadata              Definitional data that provides information about or
                        documentation of other data.

  MGED                  Microarray Gene Expression Data

  MMHCC                 Mouse Models of Human Cancers Consortium

  MO                    MGED Ontology

  Molecular Specimen    A molecular derivative (i.e. RNA / DNA/ PROTEIN)
                        created from a specimen. This is also known as sample.
                        These can be fluid in nature but it will always be
                        measured in micrograms, and concentration of molecular
                        specimen will determine its volume.

  multiplicity          Multiplicity of an association end indicates the
                        number of objects of the class on that end may be
                        associated with a single object of the class on the
                        other end

  NCI                   National Cancer Institute

  NCICB                 National Cancer Institute Center for Bioinformatics

  NLM                   National Library of Medicine

  Object                An entity that has a well-defined role in the
                        application domain and has state, behavior, and
                        identity. Objects discussed in this document include
                        Participant, Collection Protocol, Specimen Collection
                        Group and Specimen objects.

  Participant           An individual from which a biospecimen is collected.

  Participant data      One of the three different data types in which
                        caTissue Core data can be categorized. Participant,
                        Participant's medical identifiers, Collection protocol
                        registration, Specimen collection group, Clinical
                        report.

  Participant Medical   A medical record identification number that refers to
  Identifier            a Participant.

  Procedure Event       Event that refers customized procedure that is applied
                        on a specimen to process it.

  Pseudo AND (pAND      An "AND" operator based on multiple objects (not a
  operator)             single object) as related to the same parent object.

  PT                    Preferred Term

  Public                See Chapter 4 (User Roles) for definition.

  Query Parameter/      A rule is applied to an object and constrains query to
  Query Rule            retrieve results of interest.

  Query View            Display of desired data elements of object(s) of
                        interest. The query view may be defined once a query
                        is specified.

  Received Event        Event that refers to receiving a specimen in the
                        tissue bank.

  Review Event          Event that refers to performing quality assurance
                        actions on a specimen.

  Scientist             See Chapter 4 (User Roles) for definition.

  Site                  A physical location involved in biospecimen
                        collection, storage, processing, or utilization.

  SOC                   System Organ Class

  Specimen              A single unit of tissue or body fluid collected from a
                        participant as part of a specimen collection event. A
                        new specimen can be created as a derivative of an
                        existing specimen or by dividing it into small pieces.

  Specimen Collection   An event that results in the collection of one or more
  Group                 biospecimens from a participant.

  Specimen Distribution An event that results in transfer of a specimen from a
                        Repository to a Laboratory

  Specimen Events       Specimen events are actions that can be performed on
                        specimen in a tissue bank e.g. collected, received,
                        frozen, fixed, reviewed etc.

  Specimen External     A pre-existing, externally defined identifier
  Identifier            associated with a specimen.

  Spun Event            Event that refers to spinning the specimen.

  SRS                   Software Requirements Specification

  SSC                   Special Search Categories

  Storage Container     A physical container which is used for storing the
                        colleted biospecimens.

  Storage Type          Type of the storage container e.g. Freezer, Box etc.

  String: CONTAINS      The value of the data element contains with the
                        supplied string.

  String: ENDSWITH      The value of the data element ends with the supplied
                        string.

  String: EQUALS        The value of the data element equals with the supplied
                        string.

  String: STARTSWITH    The value of the data element starts with the supplied
                        string.

  Supervisor            See Chapter 4 (User Roles) for definition.

  Surgical Pathology    Detailed findings based on surgical accession and
  Report                examination of biospecimens.

  Technician            See Chapter 4 (User Roles) for definition.

  Thaw Event            Event that refers defrosting a specimen.

  Tissue Specimens      A single unit of tissue that is collected from a
                        Participant or created from another specimen. These
                        are solid in nature and so will always be measured in
                        grams in the system.

  Transfer Event        Event that refers to moving specimen from one storage
                        location to another storage location

  UI                    User Interface

  URL                   Uniform Resource Locators

  User                  A person who interacts with the caTissue Core data
                        system and/or participates in the process of
                        biospecimen collection, processing, or utilization.

  VD                    Value Domain
  ----------------------------------------------------------------------------

## Index {#index .unnumbered}

A

*Activate User*, 38

***Add Biohazard***, 65

*Add Cancer Research Group*, 45

***Add Collection Protocol***, 67

*Add Department*, 43

***Add Institution***, 41

**Add** menu, 131, 132, 135, 136, 141, 145

***Add New Distribution Protocol***, 71

**Add New** link, 55, 68, 72, 81, 82, 88

***Add New Site***, 47

**Add New Specimen Submit**, 86

***Add New Storage Container and View Map***, 54

***Add New Storage Type***, 50

***Adding a New Base Rule to an Existing Query***, 131

***Adding a Pseudo AND (**pAND) **Operator of the Same Object Type***,
145

***Adding an** AND **Operator of a Different Object Type***, 140

***Adding Multiple Conditions on a Single Object as an** AND
**Operator***, 140

**Administrative Data tab**, 5, 34, 35, 37, 38, 41, 43, 45, 47, 65, 67,
71, 74

**Administrative Data Workspace**, 54, 74

**Biohazard menu**, 65, 66

**Cancer Research Group menu**, 45

**Collection Protocol menu**, 67, 70, 72

**Department menu**, 43

**Distribution Protocol menu**, 71

Institution menu, 41

Report Problems menu, 74

Site menu, 47

**Storage Container menu**, 54, 62

**Storage Type menu**, 50, 52

User menu, 35, 37, 38

Administrative Module, 34

Add \| Edit \| Approve User, 35

Add \| Edit \| View Map Storage Container, 54

Add \| Edit Biohazard, 65

Add \| Edit Cancer Research Group, 45

Add \| Edit Collection Protocol, 67

Add \| Edit Department, 43

Add \| Edit Distribution Protocol, 71

Add \| Edit Institution, 41

Add \| Edit Site, 47

Add \| Edit Storage Type, 50

**Overview**, 34

View Reported Problem, 74

*Advanced Query results view*, 152

**AND & OR Operators**, 120

**AND** operator, 128

AND link, 122, 123, 124

***AND, OR & pAND Operators***, 128

**Approve Users** form. See

B

**Bio-Specimen Data tab**, 5, 6

**Bio-Specimen Data** Workspace, 77, 81, 82, 84, 86, 87, 92, 93, 98,
101, 104, 108, 112, 115, 116

**Specimen Collection Group** menu, 84

Specimen menu, 92

Bio-Specimen Module, 76

Add \| Edit New Participant, 77

Creating Derived Specimens from Existing Specimens, 101

*Editing Participant Registration*, 82

Editing Specimen Data, 92

Overview, 76

Participant Registration, 81

Specimen, 87

Specimen Collection Group, 84

C

calendar icon, 129

**Change Password** form, 24

Collection Protocol Events, 70

***Collection Protocol** link*, 136

*Collection Protocol Registration form*, 81, 137

***Collection Protocol Registration** **Rule** form*, 131, 134, 138

**Common Buttons**

**Add** button, 129, 131, 133, 134, 135, 136, 137, 138, 139, 140, 141,
143, 145, 150, 152

Reset button, 10

**Search** button, 92, 121, 125

**Send** button, 27

**Submit** button, 10, 16, 18, 23, 25, 37, 38, 41, 43, 44, 45, 46, 48,
52, 56, 62, 64, 66, 70, 72, 73, 80, 83, 86, 114, 148, 150, 151, 152

*Common Screen Features and Navigation*, 5

***Convention for Input of Query Parameters***, 127

D

**Define View** form, 148, 149, 151

***Defining Query View For a Simple Query***, 148

***Defining Query View for an Advanced Query***, 150

E

***Edit Biohazard***, 66

*Edit Cancer Research Group*, 45

***Edit Collection Protocol***, 70

**Edit Collection Protocol** form, 70

*Edit Department*, 43

***Edit Distribution Protocol***, 72, 80

**Edit Distribution Protocol form**, 73, 80, 83

***Edit Institution***, 41

**Edit** link, 7, 137, 138

***Edit Site***, 48

**Edit Site form**, 48

***Edit Storage Container***, 62

**Edit Storage Container** form, 62

***Edit Storage Type***, 52, 64

Edit Storage Type form, 52, 64

*Edit User*, 37

**Edit User** form, 23, 29

F

**Forgot Password form**, 27

**Forgot your password** link, 26

H

Home page, 4, 5, 14, 17, 19, 20, 24, 26, 31, 32, 38, 41, 45, 47, 50, 54,
65, 71, 74

Home Page, 3

I

Institution **Search** form, 41

L

Login Module, 13

Change Password, 24

Edit Profile, 22

Login, 19

Logout, 31

Overview, 13

Report a Problem, 17

Retrieve Forgotten Password, 26

Submit User Request, 14

View Aggregate Data, 32

N

**New Biohazard** form, 65

**New Cancer Research Group** form, 45

**New Collection Protocol** form, 67, 81

New Department form, 43

*New Distribution form*, 113

**New Distribution Protocol** form, 71

**New Institution** form, 41

***New Participant Registration** form*, 78

**New Site** form, 47

**New Specimen Collection Group** form, 84

***New Specimen form***, 88

***New Storage Container** form*, 55

**New Storage Type** form, 50, 51

**New User** form, 15, 36

Normal Submit, 82, 86

O

***Object Names***, 152

***Object Names** menu*, 149, 151

Online help, 5

**Operator** menu, 146

**OR operator**, 128, 134, 145

*OR link*, 124

Overview of the Software, 1

P

**pAnd** operator, 146

**pAND operator**, 128, 147

***pAnd link***, 146

**Participant** form, 131

**Participant Query Rule**, 129, 131

**Participant Query Rule form**, 129, 131, 132, 133

Q

Query Module, 119

Advanced Querying, 126

Define Query View, 148

**Overview**, 119

Simple Querying, 120

R

References

caBIG materials, 173

caCORE material, 173

scientific publications, 173

technical manuals, guides, 173

**Report Problem** form, 18, 75

**Report Problems tab**, 17

Reported Problem, 123, 124, 125

***Rule #1***, 131, 137, 140, 141, 144, 145, 147

***Rule #2***, 134, 135

**Rules** bar, 131, 132, 135, 136, 138, 141, 145, 146

**Rules** form, 129, 131, 134, 140, 141

S

**Search Results form**, 150, 151

**Search tab**, 5, 119, 120

**Sign Out link**, 6, 31

**Sign Up** link, 14

***Simple Search***, 121

**Simple Search** form, 120, 148, 149

***Simple Search Using AND & OR Operator***, 123

***Simple Search Using AND Operator***, 122

Specific Buttons

**Add More** button, 114

**Define Query** button, 150

**Define View** button, 148

***Delete** button*, 151

**Login** button, 4, 19

***Specimen Collection Group Query Rule***, 140

***Specimen Collection Group Query Rule** form*, 135

***Specimen Query Rule** form*, 141, 142, 144

**Specimen Requirements**, 70, 72

***Start a New Query by Adding a Base Rule***, 129

Storage Container, 54, 55, 120

Study Calendar Event Point, 86

**Summary** page, 32, 33

**Summary tab**, 5, 32

U

User Interface, 3

**User Profile**, 4

User Roles, 11

Administrator, 11

Public, 11

Scientist, 11

Supervisor, 11

Technician, 11

V

**View Reported Problems** form, 74

W

**Workflow Modules, 12**

[]{#_Simple_Query .anchor}