Documentation

Inventory overview

 

The default Inventory contains two folders: Materials and Methods.

The basic openBIS entity is called Object. In the openBIS ELN-LIMS for life sciences, the following Object types are preconfigured in the database:

Antibodies, Chemicals, Enzymes, Media, Solutions and Buffers, Plasmids, Oligos, RNAs, Bacteria, Cell lines, Flies, Yeasts, General protocols, PCR protocols, Western blotting protocols. 

These entities are organised in collections in the Materials and Methods sections of the Inventory .

The generic openBIS ELN-LIMS does not have any predefined Object type, but these have to be created by users, based on their needs.

 

Register collections

Collections are organised in two level folders. To create the first folder:

  1. Click on the Materials or Methods folder
  2. Click the + button in the form. 
  3. Provide a description of the collection, if wanted. This is not mandatory.
  4. Enter the code. This will be the name of the folder. Codes only take alphanumeric characters and no spaces. (e.g. Equipment)

To register the second folder, inside the first:

  1. Click on the first folder (e.g. Equipment)
  2. Click the + button in the main form

  3. Replace the automatically generated code with something pertinent to the collection (e.g LAB_INSTRUMENTS)
  4. Fill in the Name field (e.g. Lab instruments). By default, the main menu shows the name. If the name is not provided, the code is shown.
  5. Select the Default Object type from the list of available types. This is the Object for which the Collection is used. In this case, Instrument.

 

Register Objects

 

Single Object registration

To register new Objects, navigate to the relevant Collection:

  1. Click on the Collection folder in the main menu (e.g. Lab instruments)
  2. Click the + button in the main page
  3. Fill in the form
  4. Click Save on top of the form

Alternatively:

  1. Select Create Object from the Operations drop-down menu
  2. Select the relevant Object type (e.g. Instrument)
  3. Fill in the form
  4. Click Save on top of the form

In order to establish connections between Objects of the same type or of different types, parental relationships can be established in openBIS. Objects can have unlimited number of parents and children. How to add parents (or connections) to Objects is explained in the Register Experimental Steps session.

 

To edit the Object, click on the Edit icon in the Object form toolbar.

 

Batch registration

To register several Objects of the same type from a file:

  1. Navigate to the relevant collection (e.g. Lab instruments)
  2. Select Batch Register Objects from the Operations drop-down menu
  3. Select the Object type (e.g. Instrument)
  4. Download the template file and fill in the relevant information
  5. Upload the file

 

Rules to follow to fill in the template .tsv file

  1. Identifiers:
    1. Identifiers are given by /SPACE/OBJECT_CODE, e.g /MATERIALS/INS1. Users can provide their own identifiers, or these can be automatically generated by openBIS.
    2. To have identifiers automatically generated by openBIS, completely remove the identifier column from the file.
  2. In fields that have lists to choose from (called Controlled Vocabularies), the code of the term needs to be entered. Term codes can be seen under Utilities -> Vocabulary Browser.
  3. Use the following syntax to enter parents: identifier1, identifier2, identifier3.
  4. Use the following syntax to annotate parents: identifier:xxx;COMMENTS:xxxx\identifier:yyy;COMMENTS:yyyy. Where COMMENTS is the property used for the annotation in this case (to be replaced with the actual property used).

 

Batch update

To modify the value of one or more fields in several Objects simultaneously:

  1. Navigate to the relevant collection (e.g. Lab instruments).
  2. From the Columns drop down menu select Identifier and the field(s) you want to update. 
  3. Filter the table. You can enter the names or Object codes in the filter field and use the Global OR option to search. Please note that this is a global search, and it will likely return more results than needed. These can be removed afterwards from the exported file.
  4. Export the Object table from the relevant Collection page, choosing the option Export visible columns with visible rows from the Operations drop down menu. DO NOT export the table in plain text for batch update, otherwise all text formatting will be lost on update!
  5. Remove any Object you do not want to update from the exported file.
  6. Fill in or modify the fields to update in the exported file.
  7. Select the Batch Update Objects option from the Operations dropdown menu in the Collection page.
  8. Select the relevant Object type, e.g. Instrument .
  9. Upload the file modified before.

 

Copy Objects

To create a copy of an existing Object, use the copy button in the Object form toolbar:

When an Object is copied, the user has the option to link parents, copy children and copy the comments log.

 

STORAGE

 

Register storage position for a single Object

  1. Navigate to the storage section, at the bottom of the Object form. Click the + button below the table:
  2. In the widget that opens, select the appropriate storage from the dropdown menu:
  3. Select the position in the storage (shelf and rack).
  4. If the Object is in a box, provide a box name.
  5. Select the box size form the list of configured sizes.
  6. Select the position in the box.
  7. Click Accept.

By default, the storage only keeps track of locations. It is, however, possible to configure single storage positions to have additional metadata (e.g. freezing date) that needs to be tracked at the position level, when there are several aliquots of the same sample stored in different locations. The STORAGE_POSITION Object type can be configured by an openBIS Instance admin in the openBIS admin interface (see Entity type registration to check how to edit types).

If additional information is available at the storage position level, this can be added by clicking on the link in the storage table (the link is available after saving the Object, when adding a storage position). The additional information can be entered in the storage position Object form.

 

Batch register storage positions

Storage positions are modelled in openBIS as children of other Objects. To register the positions for several Objects, first the parent Objects need to be registered in openBIS. In a second step, the positions are assigned.

As explained in the Batch registration section, to assign storage positions in batch mode:

  1. Select Storage positions from the Batch Registration drop down menu.
  2. Download the template file.
  3. Remove the identifier column (identifiers need to be automatically generated by openBIS)
  4. Fill in the parents, with their identifiers (/MATERIALS/OBJECT_CODE)
  5. Fill the remaining information about positions

 

An example file can be found here: SAMPLE-STORAGE_POSITION-template.txt

 

Storage manager

The Storage Manager, under Utilities, provides an overview of each single storage.

  1. Select the storage containing the Object to visualise from the Storage drop down menu.
  2. Click on a box to view its content.
  3. When hovering with the mouse over an Object inside a box, the info about the Object will be shown.

The Storage Manager can also be used to move Objects from one storage position to another, if the location of the Object is changed:

  1. Click on Toggle Storage B.
  2. Select the destination storage, from the Storage drop down menu.
  3. Drag and drop the box or Object to move from Storage A to the desired position in Storage B. Please note that the move operation for Objects with multiple positions in the same box or in different boxes is not supported.
  4. Changes are visualised at the bottom of the page. To save them, click the Save Changes button on top of the Storage Manager form.

 


 

Lab notebook overview

 

The Lab Notebook part of the openBIS ELN-LIMS should contain a Space (i.e. folder) for each scientist. Within this Space, scientists can organise their work using the openBIS Projects, Experiments and Objects.

An Experiment is defined as a specific scientific question. The individual attempts to answer this question, are Objects of type Experimental Step. At this level, the user can specify all materials and methods registered in the Inventory that were used to perform the Experimental Step. These are entered as Parents of the Experimental Step. All data produced in the Experimental Step and further processed and analysed can be added at this level.

 

Register Projects

  1. Navigate to the relevant Space in the Lab Notebook menu and click the + button.
  2. Projects do not have a Name field, but only Code. Codes can only take alphanumeric characters and no spaces. Codes are prettified in the Main Menu.
  3. Enter a description.
  4. Click Save on top of the form.

 

Register Experiments

  1. Navigate to the relevant Project in the Lab Notebook menu and click the button.
  2. Fill in the relevant fields in the form.
  3. Select Show in project overview if the Experiment is important and should be shown in the Project form.
  4. Click Save on top of the form.

To embed images in rich text fields:

  1. Click on the icon highlighted in red in the image below.
  2. In the pop-up window, go to the Upload tab.
  3. Browse for your image and click on Send to Server.
  4. To adjust the image size, go to the Image Info tab.
  5. Click OK at the bottom of the widget.

Register Experimental Steps

As mentioned above, the various steps executed when performing an experiment in the lab can be registered in openBIS as Objects of type Experimental Step.

To register a default Experimental Step, with pre-defined fields:

  1. Navigate to the relevant Experiment in the Lab Notebook menu and click the + button, as shown below.
  2. Fill in the relevant information on the form.
  3. It is advisable to leave the auto-generated code unchanged and to provide a Name. The Name is shown by default in the main menu. If a name is not provided, the code is shown.
  4. If Show in project overview is selected, this Experimental Step will be displayed on the Project page.
  5. Click Save on top of the form.

Alternatively, to register a custom Experimental Step:

  1. Select Create Object from the Operations drop down in the Objects section of the Experiment form, as shown below.
  2. Select the desired Object type.
  3. Fill in the form as mentioned above.
  4. Click Save on top of the form.

 

Parents

In the Parents section it is possible to specify links to materials and methods from the Inventory or to any other Object, e.g. another Experimental Step. The name of this section is customisable in the Settings by an Admin.

The default Experimental Step in openBIS ELN-LIMS for life sciences has predefined parents in the form. These can be modified by an Admin in the Settings.

In the generic openBIS ELN-LIMS, the parents section can be fully customised by an Admin in the Settings.

To add a parent (or connection):

  1. The + button next to the section name (Parents, in this case) allows to choose among the list of all available Object types.
  2. The + button next to each pre-defined Object type allows to add parents of that type only.
  3. To add a single parent, click on an Object row in the table.
  4. To add multiple parents:
    1. Select the desired Objects from the table.
    2. Choose Add selected from the Options dropdown menu in the table.
  5. If parents have annotations fields, these can be directly edited in the parent table.

To remove a parent (or connection):

  • Choose Remove from the Operations drop down in the parent table.

 

Children

Children of Experimental Steps are usually derivative Experimental Steps. As for the Parents section, this section can also be customised by an Admin in the Settings. To add a child:

  1. Click on the + button next to the Children section.
  2. Select the relevant Object type from the list of available types.
  3. Proceed as explained above for adding parents.

Children Generator

The Children Generator creates a matrix of all the parents entered in the Experimental Step, as shown below. Combinations of parents needed to generate children can then be selected by the user. The Object type to assign to the children and the number of replicas need to be specified. The children will then be automatically generated by openBIS upon creation of the Experimental Step.

 

Protocols

To create a local copy of a template protocol stored in the Inventory:

  1. Select a protocol as parent.
  2. From the Operations dropdown in the parents table select Use as template.
  3. Provide the Object code for the new protocol.
  4. A copy of the protocol is created under the current Experiment, where the user can modify it. This copy has the original protocol set as parent, so that connection between the two is clear.

Comments Log

Several comments can be added by different users who have write-access to a given user Space:

  1. Click the + button in the Comments Log.
  2. Enter the comment.
  3. Click Save.
  4. The user who added the comment and the time when the comment was entered are shown on the form.

 

Copy an Experimental Step

To copy an Experimental Step, select the copy button in the Experimental Step form.

When an Experimental Step is copied, the user has the option to link parents, copy children and copy the comments log.

 

Data upload

Data can be uploaded to Datasets in openBIS Experiments and Objects (e.g., Experimental Steps). openBIS is agnostic of file formats and types.

First the Experiment/Object must be registered in the database, and then Datasets can be added to it. Data can be uploaded in 3 ways, as explained below.

1) Upload without metadata

Files or zip files can be dropped on the right hand-side of an Experiment/Object form

  1. Choose the Dataset type from the drop-down menu. Please note that fasta files are automatically recognised as Datasets of type SEQ_FILES.
  2. Drag and drop a file in the Files Uploader area. Alternatively, browse for files by clicking Select files to upload.
  3. Select Auto upload on drop to start the upload immediately after dropping the file. This setting is stored in memory.
  4. If Auto upload on drop is not selected, click Create.
  5. Please note that folders cannot be uploaded via the web-browser. Only zip files can be uploaded.

2) Upload with metadata

  1. Click the Upload Dataset button from the Object form toolbar.
  2. Fill in the relevant fields in the form. It is advisable to always enter a Name, because this is shown in the menu. If the name is not provided, the dataset code is shown.
  3. When uploading a zip file, users have the option to uncompress before import.

Note for MacOS users: the default MacOS archiver generates hidden folders that become visible in openBIS upon unarchive. To avoid this there are two options:

  1. Zip using  the following command on the command-line: zip -r  folder-name.zip folder-name  -x “*.DS_Store”
  2. Use an external archiver (e.g. Stuffit Deluxe).

 

3) Upload via dropbox

Web upload is only suitable for files of limited size (few GB). To upload larger data, openBIS uses dropbox scripts that run in the background (see Dropboxes). A default dropbox script is provided with the openBIS ELN-LIMS plugin, and the dropbox folder needs to be configured by a system admin. If this is configured, users need to put their data in a main folder inside the dropbox folder. The main folder with the data to upload can contain several sub-folders. The main folder needs to be named according to a specified convention and the Helper tool for dataset upload using the eln-lims dropbox can be used to generate the correct name.

 

 

Data Navigation

Datasets are displayed  on the left hand-side of the Experiment/Object form.

To navigate and open data registered in openBIS via Finder or Explorer, open the Dataset folder and click on the drive icon next to the Dataset type nameIf SFTP has been configured by a system admin, you will be provided with a link to copy/paste in an application such as Cyberduck or other.

Please check our documentation for SFTP server configuration: Installation and Administrators Guide of the openBIS Data Store Server#CIFSServer

To access the Dataset form and edit the Dataset metadata, click on the Dataset code or Name (if provided).

 

Project overview

All Experiments and Experimental Steps have a Show in project overview checkbox. When selected, these Experiments and/or Experimental Steps will be shown in the Project form.

This allows users to have a better overview of a Project and highlight the most important findings.

 

Edit and delete Projects, Experiments, Experimental Steps

Projects, Experiments and Experimental Steps can be edited at any time, by selecting the Edit icon  on the toolbar of the relevant page.

Projects, Experiments and Experimental Steps can be deleted using the Bin icon  in the toolbar. Selected entities are moved to the trashcan, from where they need to be removed in order to be permanently deleted from the database. Please be aware that, by default, only users with Space Admin and Instance Admin  role have permission to delete. Default permissions can be modified by a system admin (see Changing the openBIS capability role map)

 

 


 

openBIS features

 

Relationships

Parent-child relationships between Objects can be visualised as trees or tables in the ELN.

To see the genealogical tree, select the tree  icon  from the Object toolbar. Large trees can be pruned, by selecting how many levels of parents and/or children and which types to show.

To view the genealogy of an Object in a tabular format, select the table  icon  from the Object toolbar.

 

Search

 

 

Global search

This functionality, available from the main menu, performs a search across all database fields. Results are presented in a table that can be further filtered. The search can be also be further refined (see Advanced search below).

 

Advanced search

The advanced search can be accessed from the main menu, under Utilities. Alternatively, the advanced search can be used after performing a generic search, to refine the obtained results.

In the advanced search users can combine several AND or OR searches. Users can limit the search to Experiments, Objects, or Datasets or can search across all of them. It is also possible to restrict the search to a specific Object type.

The search can be further restricted to specific fields.

 

Multiple conditions can be added to a search, by clicking the + button in the search Criteria table.

 

Search Collection

From a Collection page it is possible to launch an advanced search limited to Objects of the Collection, by selecting Search in Collection from the Operations drop down.

 

BLAST search

This performs a BLAST search over nucleotide sequences contained either in the Sequence Object field or in Datasets of type SEQ_FILES. Results are shown in a table, sorted by E-value.

 

Data Set File search

This allows users to search across names of files stored in openBIS Datasets.

 

Tables

All tables in the ELN have the same format and similar functionalities:

  1. Filter. When multiple values are entered in the Filter field, the filtering can be performed in two ways:
    1. Table AND. This performs an AND search across all entities listed in the table.
    2. Global OR. This performs an OR search on all entities to which the user has access in the database.
  2. Table download. Tables can be exported in different ways, from the Options drop down menu,.  Please remember NOT TO USE plain text tables for batch update!
  3. Column displayUsers can select which properties to display from the Columns drop down menu. This information is stored in the database for each user.
  4. Delete multiple entities. Users can select multiple entities in a table and then choose the Delete selected option from the Options drop down menu.

In all tables there is an Operations column, which allow users to perform certain tasks on an Object:

  1. Open the hierarchy graph.
  2. Open the hierarchy table.
  3. Upload a file to the Object.
  4. Move the Object to another Experiment/Collection.

 

Browse Objects by type

All Objects of the same type and all Experimental Steps, which may be contained in different Experiments/Collections and Projects, can be browsed using the Object Browser under the Utilities main menu.

This is useful when there are Objects of a certain type stored in different collections (e.g. protocols of the same type stored in two different protocol collections), or to have an overview of all Experimental Steps, independently of the Experiment they belong to.

 

 

Trashcan

When Experiments, Objects and Datasets are deleted, they are moved to the openBIS trashcan, under the Utilities main menu. Items can be removed from the trashcan only by someone with Space admin or Instance admin role. Deletion from the trashcan is IRREVERSIBLE.

It is possible to either delete single entities, by selecting Delete Permanently from the Operations dropdown in the table, or to empty the whole trashcan, by clicking the blue Empty Trash button above the table.

If one entity was unintentionally deleted, the operation can be reverted at this stage by choosing the Revert Deletions option from the Operations drop down in the table.

 

 

Vocabulary browser

The Vocabulary browser is accessible from the Utilities main menu. This shows all vocabularies registered in openBIS and the terms they contain. This information is needed for filling the forms for Batch Upload or Batch Update of Objects. If an Object has a property of type Controlled Vocabulary, the codes of the vocabulary have to be entered in the form.

 

Export

All levels of the Lab Notebook and Inventory can be exported, using the export icon  in the Space, Project, Experiment, Object and Dataset forms toolbar.

In this way, users can export their complete lab notebook with all data contained in it. Everything is exported to a zip file, which maintains the same structure used in openBIS. Each folder contains several file formats (.txt, .html, .json, .docx) with the metadata of the corresponding Project, Experiment, Object or Dataset.

It is also possible to export the content of the ELN-LIMS using the Export Builder in the Utilities main menu.  Here users can select items from different spaces and export them.

 

 


 

 

Managing lab stocks and orders

 

It is possible to use openBIS to manage stocks of products and lab orders.

 

Register suppliers

  1. Go to the Supplier Collection folder under Stock -> Stock Catalog in the main menu.
  2. Click the + button in the Collection page.
  3. Follow the steps explained in the Register Objects section

 

Register products

  1. Go to the Product Collection folder under Stock -> Stock Catalog in the main menu.
  2. Click the + button in the Collection page.
  3. Follow the steps explained in section .
  4. In addition, a supplier needs to be added as parent. Select a supplier from the list of suppliers registered in the Supplier Collection.

 

Create product requests

  1. Go to the Request Collection folder under Stock -> Stock Catalog in the main menu.
  2. Click the + button in the Collection page.
  3. Fill in the form:
    1. the Order status is mandatory
    2. Add a product to the Request from the list of registered ones, by clicking the + button next to Products. Alternatively you can also create a new product, by clicking the + button in the Create and add new product table.
  4. Click Save on top of the form.

 

Create product orders

  1. Go to the Order Collection folder under Stock -> Stock Orders in the main menu.
  2. Click the + button in the Collection page.
  3. If the order template form is defined by and Admin in the Settings, most fields will be automatically filled. If not, fill in the fields with the relevant information.
  4. Add one or more requests to the oder, by clicking the + button next to Requests. Only requests with Order status set to not yet ordered will be displayed.
  5. Click Save on top of the form.
  6. Once the order is processed, change the Order status to ordered. This will automatically change the Order status in all connected requests.


 

Admin features

User registration

Users can only be added by someone with Instance admin role:

  1. Go to User Manager, under Utilities.
  2. Select Create User from the Operations drop down. 
  3. Provide a username and, if using file-based authentication, a password. The password can later be changed by the user.

 

User roles

When a user is registered in this way, a Space (folder) with the name of the user is automatically created under the Lab Notebook main menu. The user registered in this way has Space admin rights in his/her Space and Space users rights for the Inventory Spaces (MATERIALS, METHODS by default). Modification to default rights can be granted by an Instance admin using the standard openBIS UI.

Please note that users cannot be removed from openBIS. Users can only be deactivated, using the standard openBIS UI.

 

Settings

A person with Instance admin role can modify some ELN settings from the user interface.

In multi-groups openBIS instances, it is possible to assign a lab admin role to one or more persons of the individual groups. The lab admins can modify the Settings for their own group, without having Instance admin role.

 

Main menu configuration

Individual sections of the Main Menu can be disabled, based on the needs of the lab. By default, everything is enabled.

 

Storage configuration

Fridges and freezers can be configured by clicking the + button above the storage table.

Storage settings:

  1. Code. It is advisable to provide a meaningful code for the storage, rather than using the default, becuase this information is nedded when registering storage positions in Batch mode. For example MINUS80_ROOM_A1
  2. Name. The name is what is shown in most parts of the ELN. E.g. Minus 80°C in Room A1
  3. Number of rows. This is the number of shelves.
  4. Number of columns. This is the number of racks per shelf.
  5. Allowed number of boxes in a rack. This is the maximum number per rack. Enter a very high number if this is not important.
  6. Rack space warning. Enter space as percentage. E.g. 80, means that the system will give a warning when 80% of a rack is occupied.
  7. Box space warning. Enter space as percentage. E.g. 80, means that the system will give a warning when 80% of a box is occupied.
  8. Validation level. This is the minimum level of information required about the storage:
    1. Rack validation. The position in the shelf and rack needs to be specified.
    2. Box validation. In addition to 1, a box name needs to be specified.
    3. Box position validation. In addition to 1 and 2, the position in the box needs to be specified.

 

Orders

Edit the Order Template form in the table to create a template for your lab orders.

 

Force Disable RTF

By default, all multiline text fields have a rich text editor. This is not always desirable and it is possible to convert some multiline text field to plain text. Click the + button in this section to disable RTF for a multiline text field.

 

Forced Monospace Font

Multiline text fields, for which the RTF is disabled, can be forced to use monospace font. Click the + button in this section to enforce monospace font on a multiline text field.

 

Inventory Spaces

By default, only the MATERIALS and METHODS are shown in the Inventory main menu. All other spaces are shown under the Lab Notebook main menu. Click the + button in this section to add Spaces to the Inventory.

 

Assign file types to dataset types

It is possible to configure if a certain file type should always be uploaded to a specific dataset type. In the openBIS ELN-LIMS for life sciences, by default all fasta files are uploaded to the SEQ_FILE dataset type and this should be left unchanged. Additional file extension/dataset type combination can be added, by clicking the + button in this section.

 

Customise Object forms

In this section it is possible to customise Object forms per Object type.

 

 

  1. Use as protocol. If this is enabled, the Object is treated as a protocol. This enables the option to use protocols as templates in Experimental Steps (see Register Experimental Steps).
  2. Enable Storage. If this is enabled, the visual representation of fridges and freezer becomes available in the Object form.
  3. Show. If enabled, the Object type is shown in all Object Type drop downs of the openBIS ELN-LIMS.
  4. Parents/children section:
    1. Section Name. Enter an alternative name for the Parents or  Children section. If empty the default is used (Parents/Children).
    2. Disable the section for the Object type. No parents/children can be added to this Object type.
    3. Disable addition of any object type. This removes the + button next to the section name, which enable to add as parent any Object type (see Register Experimental Steps). In this way only Objects of types pre-defined in the form can be added.
  5. Hints for Parents/Children sections.
    1. To define which Object types should always be shown in the form of a this Object type, click the + button.
    2. Select if this is a Parent or Child from the drop down.
    3.  Enter a label (this is what is shown in the Object form)
    4. Select the Object type from the drop down.
    5. Specify the minimum and maximum number of parents needed. This can be left empty if parents of this type are not mandatory.
    6. Specify annotations for this parent Object type.
    7. Click the + button on the section to add an annotation field.
    8. Select the annotation field from the list of available fields.
    9. Specify if the annotation is mandatory.

 

 

Entity type registration

Entity types, i.e. Experiment/Collection, Object and Dataset types can be created by someone with Instance admin role in the standard openBIS UI.

Register a new Experiment/Collection type

  1. Select Types -> Collection Types from the Admin drop down menu.
  2. Click Add at the bottom of the newly opened page.
  3. Enter a code. Codes only take alphanumeric characters and no spaces. This should be something meaningful for the type of experiment we are creating, e.g. MICROSCOPY_EXPERIMENT.
  4. Provide a description (not mandatory)
  5. Click Entity:Add at the bottom of the page to add properties (fields):
    1. Choose from existing properties.
      1. It is highly recommended to always add the property Name.
      2. Select if the property is mandatory.
      3. Choose or create a section. Sections are ways of grouping together similar properties. Examples of sections used in the ELN are General info, Storage info, Parents, etc.
      4. Choose where the property is to be shown on the Experiment/Collection form.
    2. Register a new property
      1. Provide the Property Code (only alphanumeric characters and no spaces).
      2. Provide the Property Label. This is shown in the forms instead of the code.
      3. Provide a description for the Property.
      4. Select the type from the list of available types.
      5. Select if the property is mandatory.
  6. Click Save at the bottom of the page.

 

Object and Dataset types are registered in a very similar way.

 

Register a new Object type

    1. Select Types -> Object Types from the Admin drop down menu.
    2. Click Add at the bottom of the newly opened page.
    3. Enter a Code. E.g. INSTRUMENT.
    4. Provide a description (not mandatory).
    5. Leave all selectable options as provided by default.
    6. Enter the Generated Code Prefix. It is recommended to use the first 3 letters of the Object code (e.g. INS). This field is used by openBIS to automatically generate Object codes: the codes will be for example INS1, INS2, INS3, etc.
    7. Click Entity:Add at the bottom of the page to add properties (fields). See Register a new Experiment/Collection type.
      • A new Object type should always have the predefined properties Name and Annotations state. The last property is not visible in any of the forms, but it is necessary to establish parent/child relationships between Objects.
    8. Click Save at the bottom of the page.

 

Register a new Dataset type

  1. Select Types -> Data Set Types from the Admin drop down menu.
  2. Click Add at the bottom of the newly opened page.
  3. Enter a code. E.g. RAW_DATA.
  4. Enable Disallow Deletion, if datasets of this type should never be deleted.
  5. Add properties as described in Register a new Experiment/Collection type.
  6. Click Save at the bottom of the page