Project Data Entry Reference

Last Updated: Dec 13, 2017 06:46AM PST

Overview

ScienceCloud has a new way to upload and register data. Users can create their own data readers to support their own files. Additionally, ScienceCloud now supports more ways to represent entity structures. Teams can define their own entity types and specify how entities of each type are represented in the system.

Accessing the Project Data Entry Page

The new Project Data Entry page can be reached by clicking on the “Project Data Entry” application tile on the home page. Please note that only users who have been granted access to the “Project Data Entry” application will see this tile on their homepage. If you believe you should have access to this application but don’t see it, please contact your Team Permission Administrator. Clicking on the “Project Data Entry” application tile will open the Project Data Entry page in a new tab.

Contents of the Project Data Entry Page

At the top of the page there is a button titled “My Registrations.” Clicking this button will navigate to the “My Registrations” page. For more details about this page, please see the section “Managing My Registrations.”
 
Next, the Project Data Entry page contains three sections, which can be expanded or collapsed by clicking on the small triangle to the left of the section title. The sections are:

  • Register entities. This section contains options for adding new entities to ScienceCloud.
  • Add data to entities. This section contains options for adding more information to existing entities in ScienceCloud.
  • Custom entity registration & data additions. Some teams and users have custom registration options, which will appear here.


Registering Entities

The “Register entities” options can be used to add new entities to ScienceCloud, add additional data to existing entities, and modify existing entities in ScienceCloud. Entities can be registered through Single Registration (“Online”) or by uploading a file(s) containing all the data (“From file”). Online registration may be simpler for small amounts of data, but registering data from a file is much more efficient for large amounts of data.


Online

Clicking the “Online” link in the “Register entities” section will navigate to the “Single Registration” page. This page contains a form where you can enter data for a single entity you would like to add to the system. The form contains the following sections:

  • Entity Type: this section allows you to specify the entity type.

  • Type (dropdown menu): specifies the entity type. For more details about Entity Types, please see the “Entity Types” section below. This dropdown menu is populated by values from the Entity Type Dictionary. If you do not see an Entity Type, please contact your Team Data Administrator.
  • Entity: this section contains fields relevant to the entity.

 

  • IDs (text list field): you may enter zero or more IDs for this entity here. The entity may have more than one ID, but no two entities in your team may have the same ID. That is, entity IDs must be unique. To add IDs to this field, click the notepad icon or on the field itself to open the “Entity IDs” dialog. Type the ID to add in the text field. If you have another ID to add, click the plus sign button to make another empty field appear. Use the minus sign buttons to delete entries as necessary. When you are finished, click OK to transfer the IDs to the IDs field. If you don’t enter any IDs, the entity will be automatically assigned an entity ID.
  • Tags (text list field): you may enter zero or more tags for this entity here. The entity may have more than one tag, and, unlike IDs, entities in your team may share tags. To add tags to this field, click the notepad icon or the field itself to open the “Entity Tags” dialog. Type the tag to add in the text field. If you have another tag to add, click the plus sign button to make another empty field appear. Use the minus sign buttons to delete entries as necessary. When you are finished, click OK to transfer the tags to the Tags field.
  • Status (dropdown menu): specifies the entity status. This dropdown menu is populated by values from the Entity Status Dictionary. If you do not see an Entity Status, please contact your Team Data Administrator.
  • Status Comment (link): click to open the “Add Entity Status” dialog box. This dialog box contains a large text field where you can enter a comment about the entity’s status, if necessary. The link will become active after you have selected a Status from the dropdown.
  • Name (text field): specify a name for the entity here.
  • Trivial Name (text field): specify a trivial name for the entity here.
  • Comments (text field): enter any additional comments about the entity here.
  • Representation Comment (text field): enter any comments about the entity’s representation here.
  • Custom Properties (button): click to open the “Entity Custom Properties” dialog box. You can specify custom properties for the entity here. For more details about custom properties, see the “Custom Properties” section below.
  • Batch: this section contains fields relevant to a specific batch of the entity. Entities in ScienceCloud will have at least one batch, so the entity registration process will create a batch according to the data you specify in this section.
 

 
 

  • IDs (text list field): you may enter zero or more IDs for the batch here. The batch may have more than one ID, but no two batches in your team may have the same ID. That is, batch IDs must be unique. To add IDs to this field, click the notepad icon or on the field itself to open the “Batch IDs” dialog. Type the ID to add in the text field. If you have another ID to add, click the plus sign button to make another empty field appear. Use the minus sign buttons to delete entries as necessary. When you are finished, click OK to transfer the IDs to the IDs field.
  • Tags (text list field): you may enter zero or more tags for the batch here. The batch may have more than one tag, and, unlike IDs, batches in your team may share tags. To add tags to this field, click the notepad icon or the field itself to open the “Batch Tags” dialog. Type the tag to add in the text field. If you have another tag to add, click the plus sign button to make another empty field appear. Use the minus sign buttons to delete entries as necessary. When you are finished, click OK to transfer the tags to the Tags field.
  • Salt (dropdown menu): specifies any salt associated with the batch. This dropdown menu is populated by values from the Salt Dictionary. If you do not see a correct salt, please contact your Team Data Administrator.
  • Coef (number field): specify the coefficient of the salt in this batch here.
  • Scientist (dropdown menu): specifies the user to associate the registration with. (You may register data on behalf of another user.) This dropdown menu is populated by users on your team who have permission to create entities and batches in your team. If you do not see a user, please contact your Team Permission Administrator.
  • Comments (text field): enter any additional comments about the batch here.
  • Experiment Number (text field): enter any notebook application experiment number related to the batch here.
  • Custom Properties (button): click to open the “Batch Custom Properties” dialog box. You can specify custom properties for the batch here. For more details about custom properties, see the “Custom Properties” section below.
  • Structure: this section allows you to enter a structure for the entity.

 

  • Representation Type (unlabeled dropdown menu): specifies how the entity’s structure is represented in the system. The options are determined by the Entity Type selected in the upper left corner of the Single Registration form. If you do not see a representation type, please verify you have selected the correct Entity Type, or contact your Team Data Administrator.
  • Structure (appearance varies depending on representation type; appears below Representation Type dropdown menu): click here to enter a structure for the entity. The method for entering a structure depends on the representation type. Please see the “Entity Types” section below for more details.
  • Exact Mass (number field): enter the exact mass of the structure here.
  • Molecular Weight (number field): enter the molecular weight of the structure here. This is auto-calculated for you after an entity representation/structure has been entered.
  • Molecular Formula (text field): enter the molecular formula here. This is auto-calculated for you after an entity representation/structure has been entered.
  • “Check for existing structure and save batch as a subsequent batch” (checkbox): checking this box will cause ScienceCloud to avoid creating a new entity, if possible. If there is already an entity with the specified structure, it will create a new batch associated with that existing entity (rather than creating a new entity and a new batch).
  • “Validated Structure” (checkbox): checking this box will cause ScienceCloud to validate the specified structure against a validation protocol that your team has created. If you check this box and the structure you enter does not pass validation, you will encounter an error.
  • Project(s)/Batch Group(s): this section allows you specify which batch group the batch should be created in.
 

 

  • Filter (text field): enter text in this field to filter the project/batch group tree and quickly locate the batch group in which the batch should be registered.
  • Project/Batch Group (tree): tree items can be expanded and collapsed to locate the batch group in which the batch the batch should be registered. This tree is populated by all the batch groups in projects you have permission to create entities in. If you do not see a project or batch group, please contact your Team Permission Administrator.
  • Samples tab: this tab at the bottom of the page allows you to specify data for samples of the batch. Click the “Add Sample” button to add a new sample to the batch. Fill in the applicable fields, and use the “Custom Properties” button to add custom properties for the sample, as necessary. You may add multiple samples. Each sample can have additional shipping data, which can be added once you add a sample. You can remove an entered sample by clicking the “X” at the end of the sample’s row. If you would like to delete all sample data related to the batch, you can do so by clicking the “Remove all samples” button. The sample tab also allows you to manage your shipping data related to that sample. Click the “Add shipping” button to add new shipping data related to the sample. To remove a shipping entry, click the “X” at the end of the shipping’s row. If you would like to delete all associated shipping data associated with a sample, click “Remove all shippings”.
 

  • Biological tab: this tab at the bottom of the page allows you to specify data for assay results associated with the batch. Click the “Add assay result” button to add a new assay result to the batch. Fill in the applicable fields, and use the “Custom Properties” button to add custom properties for the assay result, as necessary. With the exception of the Tester dropdown menu, the dropdown menus in this section are populated by values from the Assay, Assay Parameter, Result Type, Operator and Unit Dictionaries. If you do not see an entry for any of these, please contact your Team Data Administrator. The Tester dropdown menu is populated with users who have permission to create assay result data in your team. If you do not see a user in this dropdown menu, please contact your Team Permission Administrator. If you would like to add additional data related to your assay result(s) click the “+” sign next to the assay result and the following additional information can be added:
            - Trial ID
            - Group ID
            - Assay Run ID: the associated run ID in the Assay application.
            - File: a file associated with your assay result.
            - Test Comment: a comment associated with your assay result.


When you are finished entering data, click the “Save” button near the top of the page to submit the form. If your data is registered successfully, you will see a dialog box saying that registration is successful. This dialog box will contain any automatically-generated Entity IDs or Batch IDs. Please record these IDs if you wish to access the new entity and/or batch using these IDs later.

If there is an error registering your data, you will see a list of problems preventing your data from being registered. Please correct this issues and click “Save” again.

 

From File

Clicking “From file” under the “Register entities” section will navigate to the “Register entities from file” page. This page contains a form with four sections:


 

  • File(s): use the “Browse…” button to select a file or files on your computer to upload. You may choose multiple files in the file picker dialog box, or you may use the Browse button multiple times to upload more than one file. When you choose files, they will be uploaded to ScienceCloud (although the system will not attempt to register their contents at this point). If you upload a file but change your mind about registering it, use the checkbox to select it, and click the “Remove Selected” button to remove all the checked files from the upload set. You can click on the table headers to sort the list according to each field.
  • Reader: choose the file reader you want to use here. For more information on readers, see the “Readers” section below. If you do not see a useful reader, you may need to create it. Click the “Interactive Reader Creation” link to walk through the steps of creating a new reader. (For more details on this process see the “Creating a New Reader” section below). If you are unsure what format your registration file should be, click the “Download Template” button to download a template for the selected reader. You can use the downloaded template as an example, or modify it to fill in your own values.
  • Settings:
    • Registration behavior: specifies how errors are handled during registration.
      • Register records only if no errors: if there are any errors in your data, none of it will be registered and you will be notified of the errors
      • Register any record without error: as much of your data will be registered as possible. Data with errors will be skipped. When you view the results of the registration, you will be able to see which records were registered successfully and which had errors.
      • Validate only: select this if you want to do a dry run. No data will be registered, but you will be able to see the results of the hypothetical registration, including any errors in your data.
      • Send Email: check this box if you want to receive an email notification when the registration is complete and results are available.
      • Check existing entities: check this box if you want ScienceCloud to add batches to existing entities where possible, rather than creating new entities.
      • Use validation task: check this box if you want ScienceCloud to run your team’s validation task to validate new entities. If there is an entity in your file(s) that does not pass validation, you will encounter an error.
      • Update data: check this box if you want to allow this registration to add new data to existing batches or modify existing ScienceCloud data. If you do not check this box, but specify new values for existing entities, batches, samples or shippings, you will encounter an error.
      • Available Values: links in this section open new windows containing valid options for registration fields, as well as your team’s salts, analytical types, entity types, entity statuses, and monomers. The lists of salts, analytical types, entity types, entity statuses, and monomers are populated from your team’s Dictionaries. If one of these lists appears incomplete, please contact your Team Data Administrator.
 

Click the “Submit” button when you are ready to start running the registration. This will navigate you to the “My Registrations” page. For more details about the “My Registrations” page, please see the section “Managing My Registrations” below.
 

Adding Data To Entities
The “Add data to entities” options can be used to add new data to existing entities. Data can be added either using a web form (“Online”) or by uploading file(s) containing all the new data (“From file”). Online registration may be simpler for small amounts of data, but registering data from a file is much more efficient for large amounts of data.


Online

Clicking the “Online” link will navigate you to the “New Biological Data” page. Near the top of this page is a “Project” dropdown menu. This specifies the project into which new data will be registered. This dropdown menu is populated by the projects to which you have permission to add biological data. If you do not see a project, please contact your Team Permission Administrator.
 



Once you select the project to register in, click the “Add” button to add a row to the assay results table. Enter the batch ID to associate the new assay result to, and fill in values for the rest of the columns in the row. Use the “Custom Properties” button to add custom properties for the assay result, as necessary. With the exception of the Tester dropdown
menu, the dropdown menus in this section are populated by values from the Assay, Parameter, Result Type, Operator and Unit Dictionaries. If you do not see an option for any of these, please contact your Team Data Administrator. The Tester dropdown menu is populated with users who have permission to create assay result data in your team. If you do not see a user in this dropdown menu, please contact your Team Permission Administrator. If you would like to add additional data related to your assay result(s) click the “+” sign next to the assay result and the following additional information can be added:
  • Trial ID
  • Group ID
  • Assay Run ID: the associated run ID in the Assay application.
  • File: a file associated with your assay result.
  • Test Comment: a comment associated with your assay result.
If you would like to add multiple assay results to the project, click the “Add” button again to add another row to the table to fill in. When you are finished entering assay results, click “Save” to add your data to the project.


From File

Clicking the “From file” link will navigate to the “Add more data entities from a file” page. The page has two sections, which can be expanded and collapsed with the small arrow icons next to the section titles.


Assay Results

The “Assay Results” section on the “Add more data to entities from a file” page can be used to add more assay results to an entity. This section contains the following items:

  • Registration File: this file picker allows you to choose one file containing the new assay results to add to an entity. The file should be in CSV format.
  • Attachments: this multiple file picker allows you to choose anywhere from zero to multiple attachments to upload along with the assay results. This is necessary when the assay result refers to a file attachment. Please ensure that all attachments referenced by the assay results file are selected in this file picker.
  • Reader: choose the file reader you want to use here. For more information on readers, see the “Readers” section below. If you do not see a useful reader, you may need to create it. Click the “Interactive Reader Creation” link to walk through the steps of creating a new reader. (For more details on this process see the “Creating a New Reader” section below). If you are unsure what format your registration file should be, click the “Download Template” button to download a template for the selected reader. The template is a file containing just column headers that the reader will understand, so you can fill in your own values for the data in order to register it.
  • Settings:
    • Registration behavior: specifies how errors are handled during registration.
      • Register records only if no errors: if there are any errors in your data, none of it will be registered and you will be notified of the errors.
      • Register any record without error: as much of your data will be registered as possible. Data with errors will be skipped. When you view the results of the registration, you will be able to see which records were registered successfully and which had errors.
      • Validate only: select this if you want to do a dry run. No data will be registered, but you will be able to see the results of the hypothetical registration, including any errors in your data.
      • Send Email: check this box if you want to receive an email notification when the registration is complete and results are available.
      • Check Duplicate: check this box if you want to prevent adding duplicated data points to the entity. A data point is considered a duplicate if it is taken under the same conditions on the same date and have the same result. If you have multiple assay results taken on the same conditions on the same date that happen to have the same result and you want all of your data to be added to the entity, ensure this box is unchecked.
      • Available Values: clicking the “Available Assay Dictionary” link in this section opens a new window containing valid options for assay fields. Custom properties can be registered in addition to these fields. For more details on how to register custom properties from files, please see the “Custom Properties” section below. 

Click the “Submit” button when you are ready to start running the registration. This will navigate you to the “My Registrations” page. For more details about the “My Registrations” page, please see the section “Managing My Registrations” below.


Analytical Type File

The “Analytical Type File” section on the “Add more data entities from a file” page can be used to add analytical type files to entities. This section contains the following items:

  • File(s): use the “Browse…” button to select a file or files from your computer to upload. You may choose multiple files in the file picker dialog box, or you may use the Browse button multiple times to upload more than one file. The files should follow a specific file naming convention (see “Analytical Type File Name Convention”) to identify the batch and/or sample the file should be attached to. When you choose files, they will be uploaded to ScienceCloud (although the system will not attempt to register their contents at this point). If you upload a file but change your mind about registering it, use the checkbox to select it, and click the “Remove Selected” button to remove all the checked files from the upload set. You can click on the table headers to sort the list according to each field.
  • Settings:
    • Registration behavior: specifies how errors are handled during registration.
      • Register any record without error: as much of your data will be registered as possible. Data with errors will be skipped. When you view the results of the registration, you will be able to see which records were registered successfully and which had errors.
      • Validate only: select this if you want to do a dry run. No data will be registered, but you will be able to see the results of the hypothetical registration, including any errors in your data.
      • Send Email: check this box if you want to receive an email notification when the registration is complete and results are available.
      • Available Values: the “Available Analytical Types” link in this section opens a new window containing valid options for types of analytical files. The list is populated from your team’s analytical type Dictionary. If the list appears incomplete, please contact your Team Data Administrator.
 

Click the “Submit” button when you are ready to start running the registration. This will navigate you to the “My Registrations” page. For more details about the “My Registrations” page, please see the section “Managing My Registrations” below.


Analytical Type File Name Convention

In order for ScienceCloud to match an analytical type file up to the correct batch and/or sample, you will need to ensure the analytical type file is named correctly. The naming convention for analytical type files is as follows:
 
<team name or project ID>$<batch id>$<analytical type>$<container ID>$<well>$<rest of file name>.<file extension>
 
Container and well are optional for batches that contain only one sample.
Otherwise container and well are required and if you do not supply them you will encounter an error.
 
Click “Available Analytical Types” to see a list of options to fill in the <analytical type> part of the file name.
 
Some examples of well-formed analytical type files names:

  • BIOVIA$EX0000031$HPLC$MyFile2HPLC.pdf: team name is “BIOVIA”, batch ID is “EX0000031”, analytical type is “HPLC”, the rest of the file name is “MyFile2HPLC” and the file extension is “pdf” — this example assumes a batch with ID EX0000031 exists in team BIOVIA and the BIOVIA analytical type Dictionary contains an “HPLC” analytical type. Additionally, since the container and well are missing, this example assumes there is only one sample of batch EX0000031.
  • P027$EX0000031$HPLC$MyFile2HPLC.pdf: project ID is “P027”, batch ID is “EX0000031”, analytical type is “HPLC” the rest of the file name is “MyFile2HPLC” and the file extension is “pdf” — this example assumes a batch with ID EX0000031 exists in project P027 and the BIOVIA analytical type Dictionary contains an “HPLC” analytical type. Additionally, since the container and well are missing, this example assumes there is only one sample of batch EX0000031.
  • P027$EX0000031$NMR$Plate0001$A01$MyFile1NMR.pdf: project Id is “P027”, batch ID is “EX0000031”, analytical type is “NMR”, container is “Plate0001”, well is “A01”, rest of filename is “MyFile1NMR” and file extension is “pdf” — this example assumes a batch with ID EX0000031 exists in project P027, that the batch has a sample with container Plate02 and well A01, and that the BIOVIA analytical type Dictionary contains an “NMR” analytical type.


Managing My Registrations

The “My Registrations” page contains a summary of your currently running registrations, as well as any recent registrations that have been completed. The table will only show a limited number of entries at once, so use the First/Previous/Next/Last buttons to page through the table entries. Also, by clicking the gear icon you can choose what types of registrations will appear in the table.



 

The table contains the following columns:

  • Submission: this is the file name. Clicking the file name will download the file.
  • Origin: this indicates the means by which the registration was initiated. This column will contain “File” for file-based registration, or “UI” for online registration, to be supported at a later date.
  • Objects: this indicates the type of registration. The types can be Entity, Assay Result or Analytical Type.
  • Author: this indicates the user who started the registration. Team Data Administrators will see registrations by all users in the team.
  • Submitted: this indicates the date and time the registration began.
  • Status: this indicates the current state of the registration. The possible states are:
    • Pending: the system has received the request to register or validate the file, but has not yet begun.
    • Validating: the registration dry run is in progress. You can click “Stop” to cancel it.
    • Registering: the registration is in progress. You can click “Stop” to cancel it.
    • Validated: the registration was executed as a dry run, and results are available. Click the link to view any warnings or errors. If it is possible to proceed to register this file, a “Register” link will display. You can click this link to go ahead and register this file’s data.
    • Registered: the registration has completed. Click the link to view the results, as well as any warnings or errors.
    • Stopping: the system has received a request to cancel the registration, and is attempting to cancel it.
    • Stopped: the registration was cancelled. Click the link to view a report.
    • Failed: the registration has failed. Click the link to view a report.
    • Timed Out: the registration has taken too long and/or has become unresponsive. Please contact ScienceCloud support for assistance.
  • Trash can icon: clicking this icon on a row will remove the registration from your history. Use this feature to clean up your registration history as necessary. Note, however, after you remove a registration from your history, any results or reports associated with it will become unavailable.


Entity Types

ScienceCloud has introduced more options for the types of entities you can register. Previously, entities were compounds (that is, small molecules). Now, in addition to small molecules, entities can be biologics—DNA sequences, peptides, proteins, or any other type that your team might define. Each Entity Type is associated with one or more representation types. The representation type determines how ScienceCloud stores structures for entities of that type in the system. For example, the “Small Molecule” Entity Type would have a representation type of “Chemical structure,” and when registering or searching for entities with this type, you would use a chemistry sketcher application to draw the entity’s structure. On the other hand, the “DNA Plasmid” Entity Type would have a representation type of “Sequence,” and when registering or searching for entities with this type, you would enter a sequence of letters to indicate the entity’s structure.
 
ScienceCloud supports the following representation types:

  • Chemical structure, either in Molfile format, or SMILES string
  • HELM: ScienceCloud supports a default set of monomers, which HELM representations may contain. To review the default monomers, please see the attached Helm_Standard_Monomers PDF. Additionally, Team Data Administrators may add more monomers to your team’s monomer Dictionary to support more monomers. 
  • Sequence: ScienceCloud supports representing protein sequences as strings of single letters, each representing a single amino acid. Please see attached The_20_Amino_Acids PDF. Additionally, it is possible to define a custom amino acid in monomer administration by setting its polymer type to "PEPTIDE".
  • None: some Entity Types do not have representation types. In this case, the representation type is “None.”
  • When HELM or Sequence representations are saved, if the representation contains non-standard monomers, ScienceCloud looks them up in your team’s monomer Dictionary. If the monomer cannot be resolved, you will encounter an error: “Could not find HELM reference monomer, please create this monomer in your team’s monomer Dictionary.” If you encounter this error, please contact your Team’s Data Administrator, who will be able to create the monomer in your team’s monomer Dictionary.

 
Each team has a default Entity Type, which affects how entities are registered when their Entity Type is not specified. Your Team Data Administrator will configure the default Entity Type for your team.

 

Entity Types and Representations in Online Registration

In online registration the “Structure” section of the “Single Registration” page will behave differently based on which Entity Type is selected in the “Entity Type” dropdown in the upper left corner of the form.

  • Entities with a chemical structure representation will allow you to enter a structure using a chemical sketcher or by entering SMILES.
  • Entities with a HELM representation will allow you to enter a structure by pasting the HELM string into the structure pop-up window. Your team’s monomer Dictionary will be used to interpret the structure before it is saved. Your team’s monomer Dictionary is managed by your Team Data Administrator, so if you encounter errors with HELM notation, please contact your Team Data Administrator and verify that your team’s monomer Dictionary is configured correctly.
  • Entities with a Sequence representation will allow you to enter a structure by pasting a sequence string into the structure pop-up window. Your team’s monomer Dictionary will be used to interpret the structure before it is saved. Your team’s monomer Dictionary is managed by your Team Data Administrator, so if you encounter errors with sequence notation, please contact your Team Data Administrator and verify that your team’s monomer Dictionary is configured correctly.
  • Entities with no representation will not allow you to enter a structure.


Entity Types in File-Based Registration

The field compound_type has been replaced by entity_type. If the entity_type field is not specified for a record during file-based registration, ScienceCloud will use your team’s default Entity Type for that record. In that case, that default Entity Type will define the valid representations for that record.
 
Since different representations for an entity may be provided during 
representation, what ScienceCloud does with the provided representation varies from situation to situation.
 

Case 1: Provided representation is of correct type for the entity’s type

Suppose your team has an Entity Type of “PEP” with a representation type of “Sequence.” (This is defined in your team’s Entity Type Dictionary, managed by your team’s Team Data Administrator.) When registering the following example data, ScienceCloud determines that “sequence” is the appropriate representation for the entity, and stores the given sequence as the entity’s structure. 

project_id batch_group_id entity_type sequence
ENTITIES MY_BATCH_GROUP PEP CGTA
 

Case 2: Different type of representation is provided

Again, suppose your team has an Entity Type of “PEP” with a representation type of “Sequence.” (This is defined in your team’s Entity Type Dictionary, managed by your team’s Team Data Administrator.) When registering the following example data, ScienceCloud determines that “sequence” is the appropriate representation for the entity, however, no sequence is given. No structure will be saved for the entity. (Although the SMILES value will be retained in the database for reference; however it will not be searchable in structure searching.)

project_id batch_group_id entity_type smiles
ENTITIES MY_BATCH_GROUP PEP COc(cc1)ccc1C#N
 

Case 3: No representation for Entity Type

Suppose your team has an Entity Type of “VAC” with a representation type of “None.” (This is defined in your team’s Entity Type Dictionary, managed by your team’s Team Data Administrator.) When registering the following example data, ScienceCloud determines that the entity requires no structural representation, so no structure is saved for the entity even though a SMILES string is given. (Although the SMILES value will be retained in the database for reference; however it will not be searchable in structure searching.)
 

project_id batch_group_id entity_type smiles
ENTITIES MY_BATCH_GROUP VAC COc(cc1)ccc1C#N


Custom Properties

ScienceCloud supports Custom Properties on various objects. Custom Properties are additional fields you may specify in order to contain information that the ScienceCloud built-in fields are not designed to contain. Custom Properties may be specified on the following objects in both online and file-based registration:

  • Entity
  • Batch
  • Sample
  • Shipping
  • Assay Results


Specifying Custom Properties in Online Registration

When you click a Custom Properties button for an object in one of the online registration pages, a Custom Properties editor window will open. This window contains a table with the Custom Properties currently defined for the object, along with their current values. You can sort the table by clicking on the column headers, and filter the table by typing in the filter text field.

Click the “Add Custom” button at the top of the table to add a new Custom Property to the table. You will be prompted to enter the property name and the value. If you want to remove a Custom Property from the table, click its row in the table to select it, and click the “Delete” button.
 
If you make a mistake while editing Custom Properties, you can click the “Cancel” button to dismiss the editor and your changes will not be saved.
 
Once you are finished editing the Custom Properties, click the Save button to save your changes.

 

Specifying Custom Properties in File-Based Registration

Custom Properties can also be added to objects in file-based registration. You can configure a reader to map fields in your file to Custom Properties (for more details on this, please see “Configuring Custom Property Fields in Readers” below). Even without a reader mapping, you can still register Custom Property values by using a column header with the following format in an entity registration file:
 
cp:<object type>:<property name>
 
where <object type> is replaced by either “entity,” “batch,” “sample,” or “shipping,” and <property name> is replaced by the name of the Custom Property to read field values into. So, for example, the following header in an entity registration file adds a Custom Property called “Priority” to a shipping record:
 

cp:shipping:Priority
 
Here is another example—the following data defines two Custom Properties, one on the batch and one on the shipping:

project_id batch_group_id batch_id quantity unit ship_quantity ship_unit cp:entity:is_chiral cp:shipping:method
ENTITIES SMALL MOLECULES ENT_B_1 10 g 3 g yes UPS

 
In assay result registration files, the <object type> is not necessary (since the object type is always “result”); therefore it is omitted.
 
So, for example, the following header in an assay result registration file adds a Custom Property called “secondary_tester” to the assay result:
 
cp:secondary_tester

 

Readers

File-based registration uses a “reader”. The reader determines how ScienceCloud extracts data from your registration files. Different data conventions within different files will require different readers in order toregister, since ScienceCloud will need to use a different approach to extract data from files using different conventions. For example, some of your files might label an entity’s molecular weight as “molweight” and other files might label it as “molecular_weight.” Different readers would allow you to upload files using these different conventions, without having to edit every file to follow the convention ScienceCloud supports by default.
 
Readers support the following file formats:

  • CSV text file (Comma-Separated Values)
  • TSV text file (Tab-Separated Values)
  • SD file
  • Excel file

 If you have files in a format other than the above, you can create your own Pipeline Pilot components and/or protocol to support your format. Please see “Custom Registration Protocols” below for more details.


The Generic Reader

By default, the only reader available is the Generic Reader. This reader reads the uploaded file and matches up column headers to ScienceCloud fields based on the field names in the “Available Fields” list. (You can view this list by clicking the “Available Fields” link under the “Available Values” section of the “Register entities from file” page.) In order to use this reader, you must ensure that your column headers are contained in the “Available Fields” list.

Creating A Reader

If your registration file contains column headers that aren’t contained in the “Available Fields” list, but those column headers match up to fields that do appear on the list, you can create your own reader, which will map your data to ScienceCloud fields, so that you don’t have to change your column headers.
To create your own reader, click the “Interactive Reader Creation” link in the file-based registration page. This will open a new tab containing the Interactive Reader Creation page.
 

 

Complete the following steps to create your reader:
  1. Upload an example file. Click the “Choose File” button to pick a file to upload. This will be used as an example in order to set up the columns your reader will be able to process. If you choose the wrong file, click the red X button to remove it and choose a different file.
  2. Click “Upload” to upload the file. ScienceCloud will read it and detect the column headers you’re using.
  3. The “Map Fields” page will appear. At the top of the page is a table of column headers that ScienceCloud has detected in your example file. The “File Field” column contains these column headers. In the “Available ScienceCloud Fields” column, each row has a dropdown menu where you can select the field in ScienceCloud that the column in your example file should map to. Select a ScienceCloud field for each of the fields in your file. For example, you may have a column header “FedEx_Tracking_Number” that should be stored as the shipping tracking number in ScienceCloud. Since the shipping tracking number’s field name is “ship_track_no,” select “ship_track_no” from the available fields drop down menu. Then, whenever you use this reader, values in the “FedEx_Tracking_Number” column will be stored as the shipping tracking number.
  4. Enter a name for your reader in the text field under the “Reader Name” section. Alternatively, you can overwrite an existing reader with this new configuration by selecting it from the dropdown menu in this section.
  5. Optionally, you may enter a purpose and a description for the reader.
  6. When you are finished, click “Save Mapping.”
When you return to the file-based registration page, your new reader will appear in the dropdown menu of readers.
 

Custom Registration Protocols

If your file format is too complex for the above process, you may need to develop your own custom registration protocol. The tools for doing so are found under the “Custom entity registration & data additions” section of the “Project Data Entry” page. You will need to make use of the Authoring application to create the protocol and go through the publishing process.
 
For more details or for assistance, please contact 
BIOVIA support at biovia.support@3ds.com
 
Once you have published the custom registration protocol, it will appear under “Custom entity registration & data additions” section of the “Project Data Entry” page for users in your team. You will be able to run it directly from that page.

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