Inventory Of Materials And Methods

The default Inventory contains two folders: Materials and Methods.

These are used to organise respectively samples and materials of any type and lab protocols.

Samples, materials and protocols are modelled in openBIS as Objects.

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, Plants, Oligos, RNAs, Bacteria, Cell lines, Flies, Yeasts, General protocols, PCR protocols, Western blotting protocols.

These Objects are organised in Collections in the Materials and Methods sections of the Inventory.

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The generic openBIS ELN-LIMS only has one predefined Object type for the Inventory, General Protocol, in the General Protocols Collection in the Methods folder. The Material folder is empty. Additional Object types and Collections must be created by an openBIS instance admin, based on the needs of the lab(s).

Customise Collection View

It is possible customise the view of Collections in the ELN.

The default Collection can have a Form View or a List View. Depending on this selection, the collection view will be different.

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Form View: This shows the metadata of the Collection along with the table of objects. This view is useful when a user wants to see specific metadata for a Collection.

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If you do not see the table with the Objects in the form, you need to enable this by selecting Show Objects from the More.. dropdown

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List View: The metadata of the Collection is not shown in this view, but only the table of objects is shown.

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In this case a user would need to click on More.., and Edit Collection in order to see the metadata and be able to edit the Collection.

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Updated on April 25, 2023

Register single entries in a Collection

In this example, we will see how to register one Object of type Sample in the Raw Samples Collection. The same procedure should be followed to register any other Object in other Collections.

  1. Click on the Raw Samples Collection folder in the main menu.

  2. Click the New Sample in the main page

  3. Fill in the form

  4. Save

Please note that the Object type shown in the +New button (in this case Sample), is what is defined as default object type for the Collection. If this is missing in the Collection, the button will not be present.

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To register a different object type in the Collection:

  1. Select New Object from the More drop down menu (as shown below)

  2. Select the relevant Object type from the list (Sample, in this case).

  3. Fill in the form

  4. Save

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Updated on April 25, 2023

Batch register entries in a Collection

It is possible to register several samples at once via file upload. Two methods are currently available:

  1. Batch registration via Excel template file (XLS Batch Register Objects)

  2. Batch registration via TSV template file (TSV Batch Register Objects)

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Warning

In openBIS versions prior to 20.10.6, the XLS batch registration is not recommended to register several hundreds of entries. The use of the TSV batch upload to register several hundreds of entries is recommended in those cases.

Batch registration via Excel template file

To register several entries of the same type with an Excel file:

  1. Navigate to the relevant collection (e.g. Samples).

  2. Select XLS Batch Register Objects from the More drop-down menu (see figure above)

  3. Download the template file and fill in the relevant information. (Example file: SAMPLE-COLLECTION-REGISTRATION-SAMPLE-STORAGE_POSITION-template)

  4. Upload the file.

Codes

In most cases, Object types have the option to auto-generate codes set to true in the admin UI. In this case, openBIS automatically generates codes and identifiers when Objects are registered. If that is not the case, the code needs to be manually entered by the users in the Excel template. The current template does not have a Code column. This can however be manually added if codes should be provided by the user and not automatically generated by openBIS.  If codes should be manually entered and are missing, openBIS will show the error message “UserFailureExceptionmessage: Code cannot be empty for a non auto generated code.

Controlled vocabularies

For Controlled Vocabularies fields, i.e. fields with a drop down menu, you can enter either the code or the label of the terms in the Excel file.

Please note that codes are not case-sensitive, but labels are.

Codes and labels of vocabulary terms can be seen under Utilities -> Vocabulary Browser.

Assign parents

  1. Assign already existing parents

If the parents you want to assign to your Objects are already registered in openBIS, in the Parents column of the Excel file, you can assign the relationship, by providing the identifier of the parent (i.e. /SPACE code/PROJECT code/OBJECT code). If you want to add multiple parents to one Object, every identifier should be in a new line in the corresponding Excel cell. A new line in an Excel cell is entered with the keyboard shortcuts Alt + Enter.

Example file: SAMPLE-COLLECTION-REGISTRATION-ANTIBODY-STORAGE_POSITION-template

Note: no other separators (e.g “,” or  “;”) should be used, otherwise an error will be thrown.

  1. Register Objects and assign parents in the same batch registration process.

If you want to register a few Objects and at the same time establish a parent-child relationship between some of them, you can do so by using the $ and Parents columns. In the example below we want to register 2 Objects, antibody 1 and antibody 2. We want to assign antibody 1 as parent of antibody 2. In the $ column corresponding to antibody 1 we need to enter numbers or letters proceeded by the $ symbol (i.e. $1, or $parent1). In the Parents column of antibody 2, we need to use the same value used in the $ column for antibody 1.

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Date format

For date fields, the expected format is YYYY-MM-DD.

Register storage positions and samples in the same XLS file

A sample and its storage position can be registered together, as shown in the template provided above:

  • The info in the $ column of the sample spreadsheet should match the Parents column in Storage Positions spreadsheet. In the $ column you can enter numbers or letters proceeded by the $ symbol (i.e. $1, $2 or $parent1, $parent2).

Batch registration via TSV template file

  1. Select TSV Batch Register Objects from the More drop-down menu

  2. Select the Object type (E.g. Sample or Storage)

  3. Download the template file and fill in the relevant information

  4. Upload the file

Rules to follow to fill in the template .tsv file

  1. Identifiers:

    1. Identifiers are given by /SPACE code/PROJECT code/OBJECT code, e.g /MATERIALS/EQUIPMENT/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. Lists. 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. Parents. Use the following syntax to enter parents: identifier1, identifier2, identifier3.

  4. Parents annotations. 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).

  5. Date fields. The expected syntax for dates is YYYY-MM-DD.

Advantages of XLS batch registration vs the old batch registration

  1. XLS batch registration uses labels instead of codes in the column headers in the template file.

  2. Fields which are Controlled Vocabularies can use labels instead of codes.

  3. The template can be used as it is, and no modifications are necessary by removing the identifier column, as it was in case of the old batch registration.

  4. Upload of samples and storage positions can now be performed using single template file.

The old batch register mode is being maintained for backward compatibility and will be phased out.

Updated on April 25, 2023

Batch register entries in several Collections

It is possible to batch register Objects that belong to different Collections.

This can be done from the Object Browser page, under Utilities. Two options are available:

  1. XLS Batch Register Objects: batch registration via Excel template file.

  2. TSV Batch Register Objects: batch registration via .tsv template file.

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XLS Batch Register Objects

This option for batch registration is available since openBIS version 20.10.3. It allows to register Objects of different types to multiple Collections.

You can select which types you want to register from the list of available types.

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You can then download the template that will allow you to register Objects of the selected types to single or multiple Collections. The Space, Project, Collection need to be entered in the file. The complete path for Projects and Collections need to be used, as shown in this example file: SAMPLE-GENERAL-REGISTRATION-EXPERIMENTAL_STEP-MASS_MEASUREMENT-SAMPLE-template

TSV Batch Register Objects

The batch registration via .tsv file allows to batch register only one type of Object at a time. Objects however can be registered to several Collections.

This batch upload method is kept for backward compatibility, but it will be phased out.

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In this case, if Objects are to be registered to multiple Collections, an identifier for the Objects needs to be provided, as shown below. This is not the case with the XLS batch registration, where identifiers can be automatically generated by openBIS.

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Updated on April 25, 2023

Batch update entries in a Collection

It is possible to modify the values of one or more fields in several objects simultaneously via batch update. This can be done in two ways:

  1. XLS Batch Update Objects

  2. TSV Batch Update Objects

XLS Batch Update Objects

  1. Navigate to the relevant collection (e.g. Raw Samples).

  2. In the Collection table, from the Columns, select Identifier and the field(s) you want to update (e.g. Source), as shown below

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3. If you have several entries you can filter the table (see Tables)

4. Export the table choosing the options Import Compatible= YES; Selected Columns; All pages/Current page/Selected rows (depending on what you want to export).

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5. Modify the file you just exported and save it.

6. Select XLS Batch Update Objects from the More.. dropdown

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6. Upload the file you saved before and click Accept. Your entries will be updated.

Note:

If a column is removed from the file or a cell in a column is left empty the corresponding values of updated samples will be preserved.

To delete a value or a parent/child connection from openBIS one needs to enter    image info   into the corresponding cell in the XLS file.

TSV Batch Update Objects

  1. Navigate to the relevant collection (e.g. Raw Samples).

  2. Select TSV Batch Update Objects from the More… dropdown.

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  1. Select the relevant Object type, e.g. Sample

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  1. Download the available template

  2. Fill in the identifiers of the objects you want to update (identifiers are unique in openBIS. This is how openBIS knows what to update). You can copy the identifiers from the identifier column in the table and paste them in the file. Identifiers have this format: /MATERIALS/SAMPLES/SAMPLE1.

  3. Fill in the values in the columns you want to update

  4. Save the file and upload it via the XLS Batch Update Objects from the More.. dropdown

Note:

If a column is removed from the file or a cell in a column is left empty the corresponding values of updated samples will be preserved.

To delete a value/connection from openBIS one needs to enter image info _ _DELETE_ _ into the corresponding cell in the file.

Updated on April 25, 2023

Batch update entries in several Collections

It is possible to batch update Objects that belong to different Collections.

This can be done from the Object Browser page, under Utilities. Two options are available:

  1. XLS Batch Update Objects: batch update via Excel template file.

  2. TSV Batch Update Objects: batch update via .tsv template file.

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XLS Batch Update Objects

This option for batch update is available since openBIS version 20.10.3. It allows to update Objects of different types that belong to different Collections.

You can select which types you want to update from the list of available types.

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You can then download the template that will allow you to update Objects of the selected types to single or multiple Collections. The Space, Project, Collection need to be entered in the file. The complete path for Projects and Collections need to be used. In addition, identifiers for the Objects need to be provided: identifiers are unique in openBIS, by providing them openBIS will know which Objects have to be updated. Example file: SAMPLE-GENERAL-REGISTRATION-EXPERIMENTAL_STEP-MASS_MEASUREMENT-SAMPLE-template

TSV Batch Update Objects

The batch update via .tsv file allows to batch update only one type of Object at a time. However, it is possible to update Objects that belong to several Collections.

This batch update method is kept for backward compatibility, but it will be phased out.

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The Space, Project, Collection need to be entered in the file. The complete path for Projects and Collections need to be used. In addition, identifiers for the Objects need to be provided: identifiers are unique in openBIS, by providing them openBIS will know which Objects have to be updated.

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Updated on April 25, 2023

Copy entries

To create a copy of an existing entry, select Copy from the More.. drop down menu in the Collection page.

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When an entry is copied, the user has the option to link parents, copy children into the Parents’ collection and copy the comments log.

All these options are disabled by default.

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Updated on July 27, 2022

Move entries to a different Collection

You can move entries to a different Collection either from the entry form or from a Collection table.

Move from entry form

To move entries to a different Collection, select Move from the More… drop down menu in the entry form.

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You have the option to move to an existing Collection or to create a new Collection.

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Move from Collection Table

It is also possible to move objects from Collection tables. You can select one or multiple entries from a table and click on the Move button.

Also in this case you can move to an existing Collection or create a new one.

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Updated on July 27, 2022

Register Protocols in the Methods Inventory

Protocols are standard operating procedures (SOPs) used in the lab. If such procedures are in place, they should be organised in folders in the Methods Inventory which, by default, is accessible by all lab members.

openBIS provides a General Protocol Object type that can be used. If different specific metadata is needed for protocols, new Object types can be created by an Instance admin in the admin UI and the corresponding Collections can be created in the ELN UI.

To register a new General Protocol in the General Protocols folder, follow these steps:

  1. Go to the General Protocols Collection in the Methods folder.

  2. Click the + New General Protocol button in the main page.

  3. Fill in the relevant fields in the form or choose from available templates.

  4. Save

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