Getting Started with Biological Data Template Registration

Last Updated: Jul 17, 2016 04:29PM PDT

Summary: An introduction to using ScienceCloud Project Data and Project Documents to perform biological registration tasks.

Covered Topics

The following topics are covered in this article. Clicking a link will scroll the page to the relevant section.

Note: The following information provides a high-level summary. For additional details, see the attached PDF ("ScienceCloud Project Data Biological Registration Guide").

Introduction

Biological Registration cand be completed both in Project Data via New Biological Data as well as Project Documents via batch registration

ScienceCloud supports registration for the following kinds of biological data:

  • Single Biological, ADME or PK result (online via Project Data)
  • Multiple biological, ADME or PK results (from a file via Project Documents)

Biological Data Templates

The following Excel biological templates are available in ScienceCloud and can be found in the Details section of New Data Entry | Register Multiple Biological, ADME, or PK Results from a File.

  • Generic – Offers maximum flexibility, but might require some information to be entered more than once. It is possible to repeat the same batch number from one line to another.
  • In Vitro Generic – Selects all parameter information once in the top header, and then only fills up Batch Number values. It offers the entry of multiple assays at the same time. It is possible to repeat the same assay from one column to another.
  • MTS & in vitro Generic – Accepts data entry for multiple doses and types of assays (e.g., percent inhibition at multiple doses).
  • PK – Supports data entry for the PK assay. Select the number of data sets to enter, the relevant PK parameters, and then fill them out. You can also enter PK raw data (concentration vs. doses) that will be used to draw the PK curves
  • DMPK – A preconfigured template intended for all types of ADMET information. The assay name can be used to switch from one assay to another. It is always possible to use any other biological template to register ADMET data.

These templates are equivalent—they all place data into ScienceCloud in the same way. They were designed to offer different data entry solutions based on the characteristics of the assay.  

Define a Biological Data Model

ScienceCloud provides three hierarchal levels to describe and organize the biological values. These levels include:

  • Level 1 – Assay
  • Level 2 – Organism/Descriptor
  • Level 3 – Test Parameter

To report a biological value, each level needs to be defined. Examples are provided in the table below.

Biological Values Examples

Level 1 (Assay) Level 2 (Organism/Descriptor) Level 3 (Test Parameter)
Malaria in vitro

P. Falciparum / K1

P. Falciparum / 3D7

P. Falciparum / NF54

EC50

% inhibition

Solubility

PBS - pH 7.4 /OD_RT

PBS - pH 6.0 /LCMS_RT

0.01M HCl - pH 2 /NEPH_RT

Kinetic

Thermodynamic

PK

Mouse / Plasma po Mouse / Plasma iv

Rat / Blood iv

Cmax

CL

Enter your data into these three levels in whatever way makes sense for organizing your information. It is not necessary to use all three levels. ScienceCloud will dynamically build the SAR table by creating a new column every time information changes at any level.

Level 2 is made out of two fields – organism name and descriptor, in case you want to describe one organism name and multiple variations (for example, multiple strains or multiple conditions). Any change in either of those two fields will create a new column in the SAR table.

If your biological value has more than three hierarchy levels, it will be necessary to combine extra levels to fit into the proposed levels. For example, in the table shown below, the route information is merged in Level 2 with species and matrix for PK. Regardless, the SAR table will be preserved, as the change of any of this information creates a separate column.

Configure the Biological Template Assay Header Sheet

To provide a convenient method for data entry, all biological templates are in Microsoft Excel .xlsm format. These templates can be populated with biological results and uploaded into Project Documents for registration.

Each template includes a first worksheet named "Assay Header" that configures the template for the assay. It describes the three hierarchy levels designed for your assay, as explained previously.

The following information is required when configuring the template.

Required Information for Biology Registration Templates

Field Name Description Example

Assay Name

Assay Type

Name of Assay (500 characters max).

Type of Assay (20 characters max).

Malaria

In vitro

Organism Name and Organism Descriptor

Enter the authorized Organism Names (100 characters max) and Organism Descriptors (500 characters max).

If Descriptor is left empty, "unknown" is used.

P. falciparum/K1

P.falciparum/NF54

P.falciparum/GHA

P.falciparum/3D7

Test Parameter

Enter the authorized test parameters (100 characters max).

% inhibition

IC50

The Assay Header sheet can be used to list the authorized values for the other key parameters. The table below provides details. 

Authorized Values for Key Parameters

Field Name Description Example
Project ID Project in ScienceCloud to check compound existence (Team ID can also be used) P027; BIOVIA

Tester Information:

First name, Last name, Username, Email

Authorized testers (must be valid ScienceCloud user accounts)

Bob Nare; BNARE; bnare@sciencecloud.com

John Smith; JSMITH; jsmith@sciencecloud.com

Test Unit Authorized value units %, uM, nM, mg/kg
Test Operator Authorized value operators >, <, =, <=, >=
SOP/Trial ID SOP or Trial IDs (or experiment #) SOPMALVT1, SOPMALVT2
Time Point Time point values 12, 24, 48, 72, 96
Time Unit Authorized time point units hour, minute, second

All entries on the Assay Header tab must already exist in the Team dictionary. If any values do not exist in the dictionary (for example, operator, organism, test parameter, units, assays), contact the Team Admin to get these entries added). Note that Time Point and SOP/Trial ID are not controlled by the Team dictionary.

Enter Result Values into the Assay Info Sheet

After the template is configured, use the Assay Info sheet to enter the biological values. When a list of authorized values is managed from the Assay Header sheet, a drop-down list of options is available.

The following information can be reported in the template.

Assay Info Sheet Options

Field Name Description

 

Mandatory/Optional Example
Batch ID or Container ID/Well

To identify the compound for attaching results, enter the Batch ID or a combination of Container ID and Well.

Note: When using the External ID option, it works just like the Batch ID column, where the External ID value listed must be unique and will actually be a Batch ID in ScienceCloud. If both a Batch ID and External ID are provided, the Batch ID is used.

M DEACC1234
Three hierarchy levels Assay will be copied from the Assay Header. Organism and Test Parameter must be chosen from the generated drop-down list. M Malaria, P. falciparum/K1, IC50
Operator, Value, Value Unit

To keep the value numeric and allow further sorting and filtering within ScienceCloud, separate the Value from the Operator.

If an operator is not entered, the Equals operator (=) will be automatically assigned.

Value Unit must be chosen from the drop-down list.

M <, 0.5, uM
Dose and Dose Unit Dose is a numeric value. Dose Unit must be chosen from the drop-down list. O 5, mg/kg
Time Point and Time Unit Can be used to capture a Time Point relevant to the assay. Both must be chosen from the drop-down list O 24, hour
Test Date Format is dd-mmm-yyyy. M 03-JUN-2012
Tester Name Must be chose from the drop-down list. M Bob Nare
Trial ID/SOP Can be used to capture a SOP or Trial ID (or experiment #). Must be chosen from the drop-down list. O SOPMALVT1
Test Comment Free text to provide any additional information (1000 characters maximum). O Activity to be confirmed
File to Load Filename of document to load and associate with the value in ScienceCloud. O StudyReport.pdf

Submit a Template for Registration

To submit a template for registration:

  1. From the Apps menu on the ScienceCloud Home page, select Project Documents.
  2. Or from the Project Data page, click the Project Documents icon  (right side of search box in blue header.)
  3. Click on the Biology Smart Folder created for registration and select Upload from menu bar.
  4. Browse for and select the file, and then select the options needed for your template.

Note: The file icon will change appearance based on the status. See the attached PDF user guide for further details.

Resolve Errors

To resolve errors:

  1. Click the filename to download the file.
  2. Open the file.
  3. The content will be modified to guide you to the issue(s).
  4. Resolve any issues.
  5. Save the file again.
  6. Import the newest version of the file.

Register a File

To register the file: If the file icon is displayed in green or yellow, and you are okay with the warnings, you can register the file.

  • Click + Register to the right of the filename.
Related

Analytical Type File Registration

Single Biology Registration

Getting Started with Chemical Registration

Single Chemistry Registration 


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