From d7d36d243a1b0f97ffe807236835865fa44054aa Mon Sep 17 00:00:00 2001
From: Marco Del Tufo <marco.deltufo@exact-lab.it>
Date: Thu, 6 Jul 2023 14:02:02 +0000
Subject: [PATCH] Update inventory-of-materials-and-methods.md
---
.../inventory-of-materials-and-methods.md | 216 +++---------------
1 file changed, 26 insertions(+), 190 deletions(-)
diff --git a/docs/user-documentation/general-users/inventory-of-materials-and-methods.md b/docs/user-documentation/general-users/inventory-of-materials-and-methods.md
index c8de3535b03..803df57a6f3 100644
--- a/docs/user-documentation/general-users/inventory-of-materials-and-methods.md
+++ b/docs/user-documentation/general-users/inventory-of-materials-and-methods.md
@@ -3,10 +3,6 @@ Inventory Of Materials And Methods
## Customise Collection View
-[](# "Print this article")
-
-Â
-
It is possible customise the view of *Collections* in the ELN.
The default *Collection* can have a **Form View** or a **List View**.
@@ -16,10 +12,6 @@ Depending on this selection, the collection view will be different.
-Â
-
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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*.
@@ -58,41 +50,27 @@ Updated on April 25, 2023
## Register single entries in a Collection
-[](# "Print this article")
-
-Â
-
-Â
+[](# "Print this article")Â
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*.
-Â
-
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**
-Â
-
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.
-Â
-
-Â
-
To register a different object type in the Collection:
-Â
-
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
@@ -100,8 +78,6 @@ To register a different object type in the Collection:
3. Fill in the form
4. **Save**
-Â
-
Updated on April 25, 2023
@@ -110,8 +86,6 @@ Updated on April 25, 2023
[](# "Print this article")
-Â
-
It is possible to register several samples at once via file upload. Two
methods are currently available:
@@ -120,22 +94,15 @@ methods are currently available:
2. Batch registration via TSV template file (TSV Batch Register
Objects)
-Â
-
-
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.
-Â
-
-## Batch registration via Excel template fileÂ
-
-Â
+### Batch registration via Excel template file
To register several entries of the same type with an Excel file:
@@ -147,12 +114,8 @@ To register several entries of the same type with an Excel file:
[SAMPLE-COLLECTION-REGISTRATION-SAMPLE-STORAGE\_POSITION-template](https://openbis.ch/wp-content/uploads/2022/02/SAMPLE-COLLECTION-REGISTRATION-SAMPLE-STORAGE_POSITION-template-2.xlsx))
4. Upload the file.
-Â
-
#### **Codes**
-Â
-
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
@@ -162,14 +125,10 @@ 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.*â€Â
-
-Â
+generated code.*â€
#### **Controlled vocabularies**
-Â
-
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.
@@ -179,16 +138,10 @@ Please note that codes are not case-sensitive, but labels are.
Codes and labels of vocabulary terms can be seen under
**Utilities -> Vocabulary Browser**.
-Â
-
#### Assign parents
-Â
-
1. **Assign already existing parents**
-Â
-
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
@@ -200,18 +153,12 @@ the keyboard shortcuts **Alt** + **Enter.**
Example file:
[SAMPLE-COLLECTION-REGISTRATION-ANTIBODY-STORAGE\_POSITION-template](https://openbis.ch/wp-content/uploads/2022/02/SAMPLE-COLLECTION-REGISTRATION-ANTIBODY-STORAGE_POSITION-template-1.xlsx)
-Â
-
** Note:** no other separators (e.g “,†or “;â€) should be used,
otherwise an error will be thrown.
-Â
-
**2. Register Objects and assign parents in the same batch registration
process. **
-Â
-
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
@@ -221,37 +168,23 @@ 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.
-Â
-
-Â
-
#### Date format
For date fields, the expected format is YYYY-MM-DD.
-Â
-
### Register storage positions and samples in the same XLS file
-Â
-
A **sample** and its **storage** **position** can be registered
together, as shown in the template provided above:
-Â
-
- 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)**.**
-Â
-
-## Batch registration via TSV template file
-
-Â
+### Batch registration via TSV template file
1. Select **TSV** **Batch Register Object*****s***Â from the
**More***Â *drop-down menu
@@ -261,9 +194,7 @@ together, as shown in the template provided above:
**Â **
-### **Rules to follow to fill in the template .tsv file**
-
-Â
+#### **Rules to follow to fill in the template .tsv file**
1. **Identifiers**:
1. Identifiers are given by **/SPACE code/PROJECT code/OBJECT
@@ -286,9 +217,7 @@ together, as shown in the template provided above:
5. **Date fields**. The expected syntax for dates is YYYY-MM-DD.
-## Advantages of XLS batch registration vs the old batch registration
-
-Â
+### 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.
@@ -300,46 +229,30 @@ together, as shown in the template provided above:
4. Upload of samples and storage positions can now be performed using
single template file.Â
-Â
-
The *old* batch register mode is being maintained for backward
compatibility and will be phased out.Â
-Â
-
-Â
-
Updated on April 25, 2023
## Batch register entries in several Collections
[](# "Print this article")
-Â
-
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:
-Â
-
1. **XLS Batch Register Objects**: batch registration via Excel
template file.
2. **TSV Batch Register Objects**: batch registration via .tsv template
file.
-Â
-
-Â
-
### XLS Batch Register Objects
-Â
-
This option for batch registration is available since openBIS version
20.10.3. It allows to register *Objects* of different types to multiple
*Collections*.
@@ -349,8 +262,6 @@ available types.
-Â
-
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
@@ -358,12 +269,8 @@ 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](https://openbis.ch/wp-content/uploads/2022/03/SAMPLE-GENERAL-REGISTRATION-EXPERIMENTAL_STEP-MASS_MEASUREMENT-SAMPLE-template.xlsx)
-Â
-
### TSV Batch Register Objects
-Â
-
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*.
@@ -371,54 +278,34 @@ several *Collections*.
This batch upload method is kept for backward compatibility, but it will
be phased out.
-Â
-
-Â
-
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.
-Â
-
-Â
-
Updated on April 25, 2023
## Batch update entries in a Collection
[](# "Print this article")
-Â
-
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:
-Â
-
1. **XLS Batch Update Objects**
2. **TSV Batch Update Objects**
-Â
-
-Â
-
### XLS Batch Update Objects
-Â
-
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
-Â
-
3\. If you have several entries you can filter the table
@@ -428,23 +315,18 @@ objects simultaneously via batch update. This can be done in two ways:
Selected Columns; All pages/Current page/Selected rows** (depending on
what you want to export)**.**
-Â
-
5\. Modify the file you just exported and save it.
6\. Select **XLS Batch Update Objects** from the **More..** dropdown
-Â
6\. Upload the file you saved before and click **Accept**. Your entries
will be updated.
-Â
-
**Note**:Â
If a column is removed from the file or a cell in a column is left empty
@@ -455,25 +337,16 @@ enter Â
 into the corresponding cell in the XLS file.
-
### TSV Batch Update Objects
-Â
-
1. Navigate to the relevant collection (e.g. **Raw Samples**).
2\. Select **TSV** **Batch Update Objects** from the **More…** dropdown.
-Â
-
-Â
-
3\. Select the relevant *Object* *type*, e.g. **Sample **
-Â
-
4\. Download the available **template**
@@ -489,8 +362,6 @@ table and paste them in the file. Identifiers have this format:
7\. Save the file and upload it via the **XLS Batch Update
Objects** from the **More..** dropdown
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-
**Note**:
If a column is removed from the file or a cell in a column is left empty
@@ -506,25 +377,17 @@ Updated on April 25, 2023
[](# "Print this article")
-Â
-
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:
-Â
-
1. **XLS Batch Update Objects**: batch update via Excel template file.
2. **TSV Batch Update Objects**: batch update via .tsv template file.
-Â
-
-
-
### XLS Batch Update Objects
This option for batch update is available since openBIS version 20.10.3.
@@ -536,8 +399,6 @@ types.
-Â
-
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
@@ -547,14 +408,8 @@ 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](https://openbis.ch/wp-content/uploads/2022/03/SAMPLE-GENERAL-REGISTRATION-EXPERIMENTAL_STEP-MASS_MEASUREMENT-SAMPLE-template-1.xlsx)
-Â
-
-Â
-
### TSV Batch Update Objects
-Â
-
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*.
@@ -562,51 +417,33 @@ belong to several *Collections*.
This batch update method is kept for backward compatibility, but it will
be phased out.
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-
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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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-
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-
Updated on April 25, 2023
## Copy entries
[](# "Print this article")
-
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-
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-
To create a copy of an existing entry, select **Copy** from the
**More..** drop down menu in the *Collection* page.
-Â
-
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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
@@ -615,39 +452,23 @@ Updated on July 27, 2022
[](# "Print this article")
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-
You can move entries to a different *Collection* either from the e*ntry*
form or from a *Collection* table.
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-
### Move from entry form
-Â
-
To move entries to a different *Collection*, select **Move** from the
**More…** drop down menu in the entry form.
-Â
-
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-
You have the option to move to an existing *Collection* or to create a
new *Collection*.
-Â
-
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-
### Move from Collection Table
-Â
-
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.
@@ -655,12 +476,27 @@ button.
Also in this case you can move to an existing *Collection* or create a
new one.
-Â
-
-Â
+Updated on July 27, 2022
-Â
+## Register Protocols in the Methods Inventory
-Updated on July 27, 2022
+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
+
+
+
+### LINKS TO SAMPLES, MATERIALS, OTHER PROTOCOLS
+
+When writing a protocol, it is possible to create links to samples, materials or other protocols stored in the Inventory. These are parent-child relationships in openBIS.
+
+Everything that is used in the protocol can be added as Parent of the protocol itself. This can be done as described fo Experimental Steps: [Add parents and children to Experimental Steps](lab-notebook.md)
--
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