diff --git a/docs/user-documentation/advance-features/img/ELN-data-model.png b/docs/user-documentation/advance-features/img/ELN-data-model.png new file mode 100644 index 0000000000000000000000000000000000000000..7465fcb1c81f1fb24b2e498c9d1937d204c3b2de Binary files /dev/null and b/docs/user-documentation/advance-features/img/ELN-data-model.png differ diff --git a/docs/user-documentation/advance-features/img/dataset-parents-children.png b/docs/user-documentation/advance-features/img/dataset-parents-children.png new file mode 100644 index 0000000000000000000000000000000000000000..5d116d4b44879bdbd494b450c9691f6f3632fd0e Binary files /dev/null and b/docs/user-documentation/advance-features/img/dataset-parents-children.png differ diff --git a/docs/user-documentation/advance-features/img/exp-step-parents-children.png b/docs/user-documentation/advance-features/img/exp-step-parents-children.png new file mode 100644 index 0000000000000000000000000000000000000000..0f12316173391009672f89951a4e8881ddc27e94 Binary files /dev/null and b/docs/user-documentation/advance-features/img/exp-step-parents-children.png differ diff --git a/docs/user-documentation/advance-features/img/exp-step-parents.png b/docs/user-documentation/advance-features/img/exp-step-parents.png new file mode 100644 index 0000000000000000000000000000000000000000..9fd0c2733e5a2feddeaed829024c084962f58581 Binary files /dev/null and b/docs/user-documentation/advance-features/img/exp-step-parents.png differ diff --git a/docs/user-documentation/advance-features/img/inventory-data-model.png b/docs/user-documentation/advance-features/img/inventory-data-model.png new file mode 100644 index 0000000000000000000000000000000000000000..dc96dd2fb85c6b20e6dc57a7806b8c5202436ac0 Binary files /dev/null and b/docs/user-documentation/advance-features/img/inventory-data-model.png differ diff --git a/docs/user-documentation/advance-features/img/labnotebook-data-model.png b/docs/user-documentation/advance-features/img/labnotebook-data-model.png new file mode 100644 index 0000000000000000000000000000000000000000..c44c64c3192e13695f1edf3682dc9972675e7fc8 Binary files /dev/null and b/docs/user-documentation/advance-features/img/labnotebook-data-model.png differ diff --git a/docs/user-documentation/advance-features/img/objects-parents-children.png b/docs/user-documentation/advance-features/img/objects-parents-children.png new file mode 100644 index 0000000000000000000000000000000000000000..defa7f49be856ba77edfc69cf9a57b2d78e03da5 Binary files /dev/null and b/docs/user-documentation/advance-features/img/objects-parents-children.png differ diff --git a/docs/user-documentation/advance-features/img/openbis-data-model.png b/docs/user-documentation/advance-features/img/openbis-data-model.png new file mode 100644 index 0000000000000000000000000000000000000000..d5df0e55da34206d0cef753803c91184b347750d Binary files /dev/null and b/docs/user-documentation/advance-features/img/openbis-data-model.png differ diff --git a/docs/user-documentation/advance-features/img/sample-vials.png b/docs/user-documentation/advance-features/img/sample-vials.png new file mode 100644 index 0000000000000000000000000000000000000000..4644e3012ad77ff1cc60f10482c58f800e14b4e7 Binary files /dev/null and b/docs/user-documentation/advance-features/img/sample-vials.png differ diff --git a/docs/user-documentation/advance-features/openbis-data-modelling.md b/docs/user-documentation/advance-features/openbis-data-modelling.md index c11e73b84e0a34504dc6d5b9c9cdb489139d3875..6afcb1b7b15e1d0a412bad69409f542bc8bfec80 100644 --- a/docs/user-documentation/advance-features/openbis-data-modelling.md +++ b/docs/user-documentation/advance-features/openbis-data-modelling.md @@ -1,147 +1,89 @@ openBIS Data Modelling ====================== -Overview +# Overview -openBIS has a hierarchical data structure: +openBIS has the following data structure: -1. **Space**: folder with *Code and *Description** -2. **Project**: folder with *Code* and *Description* -3. **Experiment/Collection:** folder with *user-defined properties* +1. **Space**: entity with *Code and *Description** +2. **Project**: entity with *Code* and *Description* +3. **Experiment/Collection:** entity with *user-defined properties* 4. **Object**: entity with *user-defined properties* -5. **Data set**: folder where data files are stored. A data set has - *user-defined properties* +5. **Dataset**: folder where data files are stored. A dataset has *user-defined properties* - + - - -Access to openBIS is controlled either at the *Space* level or *Project* -level. - - - -Data model in openBIS ELN-LIMS -------------------------------- - -In the openBIS ELN-LIMS the following structure is used. - -## Inventory - -The inventory is usually conceived to be shared by all lab members. The -inventory is used to store all materials and protocols (i.e. standard -operating procedures) used in the lab. It is possible to create -additional inventories, for example of instruments and equipment. - -The following structure is used in the Inventory: +*Space* is the top level. Below *Spaces* there are *Projects* and below *Projects* there are *Experiments/Collections*. +In the general openBIS data model, *Objects* can: +- be shared across *Spaces* (i.e. they do not belong to any Space) +- belong to a *Space* +- belong to a *Project* +- belong to an *Experiment/Collection* +*Datasets* can be associated only to *Experiments/Collections* or to *Objects*. -**Materials** (=*Space*) - -**Methods** (=*Space*) +Access to openBIS is controlled at the *Space* level, *Project* level or openBIS instance level (see [openBIS roles ](../general-admin-users/admins-documentation/user-registration.md#openbis-roles)). -In the generic ELN-LIMS, the *Materials* folder is empty and everything -has to be defined by an admin user. - -The *Methods* folder has default folders for general protocols defined: - - +## Data model in openBIS ELN-LIMS +------------------------------- -**Methods** (=*Space*) +In the openBIS ELN-LIMS a simplified data model is used, as shown below. -**Protocols** (=*Project*) +. -**General Protocols** (=*Collection*) +In this case, *Objects* can only belong to *Experiments/Collections*. - -In the ELN-LIMS for life sciences, some folders are already predefined -in the *Materials* folder. For example: - -**Materials** (=*Space*) +## Inventory -**Reagents** (=*Project*) +The inventory is usually conceived to be shared by all lab members. The +inventory is used to store all materials and protocols (i.e. standard +operating procedures) used in the lab. It is possible to create +additional inventories, for example of instruments and equipment. -**Chemicals Collection** (=*Collection*) +The picture below shows an example of an Inventory with the different openBIS levels. -**Enzymes Collection** (=*Collection*) + -**Antibodies Collection** (=*Collection*) - -An openBIS Instance admin can customise the Inventory folders for the -lab and create the needed Object types ([Register Master Data via the Admin Interface](../../uncategorized/register-master-data-via-the-admin-interface.md)). ## Lab Notebook By default, the lab notebook is organised per user. Each user has a personal folder (=*Space*), where to create *Projects*, *Experiments* -and *Experimental Steps (*=Objects). Data files can be uploaded to *Data -Sets*. Example structure: +and Experimental Steps (=*Objects*). Data files can be uploaded to *Datasets*. Example structure: + -**Username** (=*Space*) -**Master thesis project** (=*Project*) - -**Experiment 1** (=*Experiment*) - -**Experimental step 1** (=*Object*) - -**Experimental step 2** (=*Object*) - -**Raw Data** (=*Data set*) - - - - - -Some labs prefer to organise their lab notebook using a classification -per project rather than per user. In this case an openBIS space would -correspond to a lab Project and an openBIS project could be a -sub-project. Example structure: -**SNF projects** (=*Space*) - -**Project 1** (=*Project*) - -**Experiment** (=*Experiment*) - -**Experimental Step** (=*Object*) - -**Raw Data** (=*Data set*) - -**Project 2** (=*Project*) - -**Experiment** (=*Experiment*) - -**Experimental step 1** (=*Object*) - -**Experimental step 2** (=*Object*) - -**Raw Data** (=*Data set*) - +Some labs prefer to organise their lab notebook using an organization +per project rather than per user. In this case an openBIS *Space* would +correspond to a lab Project and an openBIS *Project* could be a +sub-project or a user folder (one folder per user working on the same project). -openBIS parents and children +# openBIS parents and children ---------------------------- -Objects can be linked to other objects, datasets to other datasets with +*Objects* can be linked to other *Objects*, *Datasets* to other *Datasets* with N:N relationship. In openBIS these connections are known as *parents* and *children*. - + + + @@ -149,29 +91,22 @@ and *children*. 1. One or more samples are derived from one main sample. This is the parent of the other samples: - + + + -2. One Experimental step is written following a protocol stored in the - Inventory and using a sample stored in the inventory. The protocol - and the sample are the parents of the Experimental - +2. One Experimental step is performed following a protocol stored in the + inventory, on a sample stored in the inventory, using a given equipment. The protocol, the sample and the equipment are the parents of the Experimental step + + + + 3. One Experimental Step is done after another and we want to keep - track of the links between the steps: - + track of the links between the steps: + + + -Protocols ---------- - -Protocols are standard procedures that can be followed to perform given -experiments in a lab. Usually protocols are stored in the common -inventory and are linked to Experimental procedures using the -parent-child relationships described above. - -The protocol contains the standard steps to follow. The parameters -measured during one experiment following a give protocol should be -recorded in the Experimental Step. -Not all labs have standard procedures in place. In this case, the -*Methods* section of the Inventory does not need to be used.