DOC: Data model tutorial.

src/doc/tutorials/data_model_tutorial.rst

+Data model tutorial
+===================
+
+Data models are a central concept of research data management. The
+open-source framework LinkAhead makes it easy to create an `agile
+data model <https://docs.indiscale.com/caosdb-server/Data-Model.html>`__
+which suits your needs, so you can profit from your collected data fast.
+
+.. contents::
+   :local:
+
+Frequently asked questions about data models
+--------------------------------------------
+
+What is a data model?
+~~~~~~~~~~~~~~~~~~~~~
+
+In LinkAhead, the `data model <https://docs.indiscale.com/caosdb-server/Data-Model.html>`__
+describes in a generic way how the data is structured. This document will help you understand this
+concept and how you can adjust the data model to your needs.
+
+Let’s give one example what we mean by the data model describing the
+data structure: In experimental research, the data model may say that
+each experiment has one or more experimenters and also some lab notes.
+
+.. figure:: img/very_simple_data_model.png
+   :alt: The simplest data model consists of just one RecordType
+
+   A very simple data model, consisting of only one RecordType
+
+The data model may also say that there are cell culture experiments,
+which *inherit* all properties of generic experiments, but in addition
+have the number of dishes, the time the cell cultures were started and a
+*reference* to the cell line that was used. When we talk about
+references, we mean that there are other data sets (in this case cell
+lines) which are not embedded directly, but only pointed at. For
+example, a number of cell culture experiments may reference the same
+cell line, and when someone adds a note to that cell line, this note
+will be available to all cell culture experiments.
+
+.. figure:: img/simple_data_model.png
+   :alt: The first data model extended by inheritance and references
+
+   A simple data model, with four RecordTypes
+
+In LinkAhead, the data model consists of *RecordTypes* and *Properties*. Each `*RecordType*
+<https://docs.indiscale.com/caosdb-server/Data-Model.html#record-types>`__ corresponds to one type
+of data set, for example an experiment, a cell culture experiment or a cell line. And each data set
+can have `*Properties* <https://docs.indiscale.com/caosdb-server/Data-Model.html#properties>`__
+which define it further: for example
+the number of dishes in a cell culture experiment, a publication
+describing a cell line or the cell line which was used for an
+experiment.
+
+And what about the data?
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+The data model describes the generic structure of the data, but what
+does this mean for your actual data? When you want to store data in
+LinkAhead, you typically look for a matching *RecordType* and
+then create *Record*\ s of that type. This means for example, that a
+*Record* of type “Cell Culture” should have the *Properties* that the
+*RecordType* provides: experimenters, lab notes, number of dishes, time
+of experiment start and the used cell lines.
+
+.. figure:: img/data_model_and_data.png
+   :alt: Records are always based upon (at least) one RecordType, this defines the relationship between data model and data
+
+   A diagram showing the relationship between RecordTypes (the data
+   model) and Records (the data)
+
+Following a data model greatly simplifies your scientific research data
+management, and this is what LinkAhead is for: You know that all
+(or most) of your cell culture experiments will have the same set of
+properties, so you can search for all experiments where the properties
+match your desired criteria, for example those with cell lines which
+were described in publications of a certain author.
+
+What if need to change my data model?
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Science moves fast, and your infrastructure should be able to follow
+just as swiftly. The data model in LinkAhead was designed to be
+very flexible, so it can adapt to your needs.
+
+There are multiple ways to modify and enhance your data model, for
+example you could use the web application or program the changes with
+the Python client. This document describes how to change the data model
+with the LinkAhead web application.
+
+What happens to my data if the data model changes?
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+With most systems, changing the data model is not possible without
+migrating the existing data. With LinkAhead however, your
+“legacy” data can simply stay where it is, it will not be modified. New
+data, that you enter after changing the data model, will of course
+follow your changes and adhere to your “new” data model.
+
+Modifying the data model in LinkAhead
+-------------------------------------
+
+The easiest way to change the data model is to `use the LinkAhead
+web
+application <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html>`__.
+But the first step is to look at the current data model (*RecordTypes*
+and *Properties*) and your current situation, to find out what you need
+changed. It may help to ask yourself these questions:
+
+- Do you want to describe data of existing types in more detail? -> :ref:`Create
+  *Properties*<new_property>` if necessary, then `add
+  <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html#add-properties-to-an-existing-recordtype>`__
+  these *Properties* to the existing *RecordTypes*.
+- Do you need to add a property more than once? -> Make that property `a list property
+  <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html#make-a-property-into-a-list>`__\
+  .
+-  Are there completely new types of data? -> :ref:`Create a new
+   *RecordType* <new_recordtype>` .
+-  Are there new types of data which would nearly fit into an existing
+   RecordType, but not quite? Do you still want to keep the existing
+   RecordType for some purposes, but require changes or additions for
+   other purposes? -> :ref:`Create a new
+   *RecordType* <new_recordtype>` which inherits from the
+   existing RecordType as a parent.
+-  Do you have a new setup, new devices, new protocols, new software? ->
+   :ref:`Create a new
+   *RecordType* <new_recordtype>` .
+- Are there *Properties* or *RecordTypes* which were created in the past, but will never be used? ->
+   `Delete them
+   <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html#delete-an-entity>`__.
+
+Once you know what you want to do, open the LinkAhead web application, log in and click on the “Edit
+Mode” button in the menu.  Then follow one of the instructions in the next sections or the general `Edit
+Mode documentation <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html>`__..
+
+.. figure:: img/edit_mode_button.png
+   :alt: The Edit Mode button appears when a user is logged in.
+
+   A screen shot of the menu, with the Edit Mode button highlighted
+
+.. _new_property:
+
+Create a new Property
+~~~~~~~~~~~~~~~~~~~~~
+
+Creating the required Properties often is the first step for changes to
+the data model.
+
+1. Check that there is no Property yet which does what you want:
+
+   -  Search for existing Properties: ``FIND PROPERTY *qualit*`` to
+      search for Properties with “qualit” in the name, ``FIND PROPERTY``
+      for all Properties.
+   -  Look at related RecordTypes, maybe they already use a Property
+      which does the thing you need.
+   -  Ask around. If possible at least two persons. Your team mates may
+      have had the same thoughts already, or may know about someone who
+      implemented your desired Property.
+
+2. Activate the *Edit Mode* in the top menu. Now the edit mode toolbox
+   on the right hand side of the screen should be visible.
+3. Click on the “Create Property” button in the toolbox. A dialog for
+   the new Property shows up.
+4. Follow the `WebUI documentation
+   <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html#new-property>`__ for Property
+   creation.
+
+.. _new_recordtype:
+
+Create a new RecordType
+~~~~~~~~~~~~~~~~~~~~~~~
+
+1. Check that there is no RecordType yet which does what you want:
+
+   -  Search for existing RecordTypes: ``FIND RECORDTYPE *experi*`` to
+      search for RecordTypes with “experi” in the name,
+      ``FIND RECORDTYPE`` for all RecordTypes.
+   -  Look at related RecordTypes, maybe you can inherit from one?
+   -  Ask around. If possible at least two persons. You team mates may
+      have had the same thoughts already, or may know about someone who
+      implemented your desired RecordType.
+
+2. Activate the *Edit Mode* in the top menu. Now the edit mode toolbox
+   on the right hand side of the screen should be visible.
+
+3. Click on the “Create RecordType” button in the toolbox. A dialog for
+   the new Property shows up.
+
+4. Follow the `WebUI documentation
+   <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html#new-recordtype>`__ for
+   RecordType creation.
+
+What about letting users only choose from a fixed set of values (a.k.a. enums)?
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+You may ask yourself how you can restrict users (or yourself) to choose
+property values from a fixed set. For example, entering the
+experimenters in an “Experiment” record may be cumbersome and
+error-prone. Or entering a chemical formula again and again may become
+tedious. This is where data management tools like LinkAhead can
+help you by referencing between entities.
+
+In this example, instead of having a TEXT Property “experimenter”, where
+users need to enter the name by hand, you could create a new RecordType
+“Person”. Then create a Record for each experimenter in your team. And
+finally, remove the “experimenter” TEXT Property and create a new
+REFERENCE Property which references to the “Person” records. Now all the
+users have to do is to choose the experimenter from a drop-down menu in
+LinkAhead.
+
+.. figure:: img/screenshot_dropdown.png
+   :alt: Users may choose one of multiple Persons when enums are implemented via REFERENCE Properties
+
+   A screenshot of a drop down menu where one of multiple “Person” records may be chosen
+

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