Summary: An introduction to using ScienceCloud Project Data and Project Documents to perform biological registration tasks.
The following topics are covered in this article. Clicking a link will scroll the page to the relevant section.
- Biological Data Templates
- Define a Biological Data Model
- Configure the Biological Template Assay Header Sheet
- Resolve Errors
- Register a File
Note: The following information provides a high-level summary. For additional details, see the attached PDF ("ScienceCloud Project Data Biological Registration Guide").
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
PBS - pH 7.4 /OD_RT
PBS - pH 6.0 /LCMS_RT
0.01M HCl - pH 2 /NEPH_RT
Mouse / Plasma po Mouse / Plasma iv
Rat / Blood iv
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
Name of Assay (500 characters max).
Type of Assay (20 characters max).
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.
Enter the authorized test parameters (100 characters max).
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
|Project ID||Project in ScienceCloud to check compound existence (Team ID can also be used)||P027; BIOVIA|
First name, Last name, Username, Email
|Authorized testers (must be valid ScienceCloud user accounts)||
Bob Nare; BNARE; firstname.lastname@example.org
John Smith; JSMITH; email@example.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
|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.
|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:
- From the Apps menu on the ScienceCloud Home page, select Project Documents.
- Or from the Project Data page, click the Project Documents icon (right side of search box in blue header.)
- Click on the Biology Smart Folder created for registration and select Upload from menu bar.
- 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.
To resolve errors:
- Click the filename to download the file.
- Open the file.
- The content will be modified to guide you to the issue(s).
- Resolve any issues.
- Save the file again.
- 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.