Getting Started with Chemical Registration

Last Updated: Sep 25, 2016 02:43PM PDT

Summary: An introduction to using ScienceCloud Project Data and Project Documents to perform Chemical 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 Chemical Registration Guide").

Introduction

Chemical Registration can be completed both in Project Data via Single Registration as well as Project Documents via batch registration.

ScienceCloud supports registration for the following kinds of chemical data:

  • Single compound (online via Project Data)
  • Multiple compounds (from a file via Project Documents)

Chemical Data Template Registration

The following information explains how to configure and register chemical templates for use within ScienceCloud during batch registration in Project Documents.

File Content

A properly prepared chemical data registration file must contain the fields shown in the table below. Enter these field names exactly as they are shown. If you do not have information for the optional fields for any of the compounds being registered, do not include the field in your file. (Optional, less frequently used fields are listed in the Appendix in the attached PDF user guide.)

Required Fields for Chemical Data Registration Templates

Field Name Description Mandatory/ Optional/ Good Practice Format Example
batch_group_id Registers the compound to a ScienceCloud project batch group. M Char
(50 max)
OXAZOLE
batch_id

Batch ID for the new batch. Must be unique within your Team in ScienceCloud.

Notes:

  • Multiple Batch IDs are allowed per Batch. Use commas to separate multiple IDs.
  • This field is not required in teams that auto-generate Batch IDs.
M Char
(50 max)
PCUCT01-0002
Project_id Registers the compound to a ScienceCloud project. M Char
(50max)
P027
batch_tag Adds other IDs to the batch (e.g., Vendor ID, Partner ID). Use commas to separate multiple IDs. O Char
(50 max)
PG74
scientist Assigns the compound to a scientist based on the scientist's ScienceCloud username. If blank, the username of the person registering the file is automatically assigned. GP Char
(50 max)
BSMITH
quantity Quantity of the sample. O float 3
unit Unit for the above quantity. O Char
(10 max)
Mg
purity Purity of the sample in % as determined by a standard analytical technique (e.g., HPLC/UV, HPLC/MS). Do not include "%" in your numerical entry. O float 90
batch_comment Text field for adding information relevant to the screener. O Char (500 max) Poor solubility
salt_name Name of the salt. Must be present in the Team's Salt Dictionary prior to registration. O Char
(60 max)
Hydrochloride
salt_coeff Number of occurrences of the salt. O float
(30 max)
2
molecular_weight Molecular weight of the sample. If a chemical structure is included in the registration, leave the molecular weight field blank, as it will be automatically calculated from the structure. O float 234.34
molecular_formula Molecular Formula of the molecule. If a chemical structure is included in the registration, leave the molecular formula field blank, as it will be automatically calculated from the structure. O Char
(no limit)
C18H26CIN3
container_id Identifies the container used to store the compound (e.g., vial number, plate number). If not included, a default container "NA" will be registered. O Char
(50 max)
PL012301
well Well position in a 96-well plate or other kind of plate. If not applicable for a compound, leave blank. If not included, a default well of "-1" will be registered. O Char
(5 max)
A01

Prerequisites (File Formats)

Before registering chemical structures, prepare one SD file containing the structures and the additional information. The field names in the SD file must be the ones specified in the Available Fields list.

An alternative method is to prepare one text file in Excel with the chemical structures represented by their SMILES string in a column labeled "SMILES".  However, for a better representation of the stereochemistry, use SD files when possible.

If you do not have any chemical structures to register, prepare a text file in Excel.  Name each column header with the field name specified in the Available Fields list, fill in the Excel spreadsheet, and then save as a text file (Tab Delimited).

Submit a File for Registration

To submit a file for registration:

  1. From the ScienceCloud home page, go to Project Documents. Or from Project Data, click the Project Documents icon.
  2. Click the Chemistry Smart Folder created for registration.
  3. Click Upload from the toolbar.
  4. Use the Upload Document dialog to browse for and select the file to register. Select any of the required options.

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 green or yellow, and you are okay with the warnings, you can register the file.

  • Click + Register to the right of the filename.

Note: You should receive feedback via email when the registration is complete.

Register Subsequent Batches

To register a subsequent batch using an SD file:

  • Reuse the same structure as the one used in the first batch.

To register subsequent batches without using the structure:

  • Include the "compound_id" column in your text file, and enter the compound ID that should be associated with the new batch.

Notes:

  • The registration fields that affect compound data (molecular_weight, compound_name, etc.) will be ignored if used in a file to create subsequent batches.
  • The parent compound must be updated directly.
  • Any changes to compound level information (structure, comments, etc.) for one batch will update compound level information for all subsequent batches.

Register Multiple Samples

Multiple samples for one batch can be registered in the same file.

To register multiple samples:

  1. Repeat the batch information (e.g., batch_id, project, batch group, etc.) on the following lines.
  2. Change the sample information (e.g., purity, quantity, etc.) to reflect the additional samples.

Note: When entering multiple sample information, container_id and wellare mandatory.

Register Multiple Shipments

Multiple shipments for one batch can be registered in the same file.

To register multiple shipments:

  1. Repeat the batch and sample information on the following lines.
  2. Change the shipping information (e.g., ship_container_id, ship_well, etc.) to reflect the additional shipments.

Modify Chemical Data

You can modify existing chemical information for a set of compounds by preparing the same file format as for registration. The Batch ID field is mandatory because it will be used as the key to identify the compound to modify. The Container ID and Well fields are mandatory when modifying any sample fields (e.g., quantity, location, purity, shipping).

To modify chemical data:

  1. When uploading the file, select the Update Chemical Data check box in the upload dialog. This is used to add new data (samples, shippings, etc.) to existing batches, and to modify values.
  2. After validation, click Update at the right of the filename to update the data in ScienceCloud. You will receive feedback via email when the update is complete. 

Modify Values Using ID Fields

A special process is required to modify existing values. Both the original (current value) and new values must be included using special fields in the file so that ScienceCloud can correctly match and update with appropriate data. During this process, it is not necessary to include the mandatory fields from the original file registration process. However, additional fields need to be included so ScienceCloud can update the appropriate items.

Related

Getting Started with Biological Data Template Registration

Single Biology Registration

Single Chemistry Registration 

Analytical Type File Registration


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