From f23669878ea9d87a4929d483217f4a61959fd9ea Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Sun, 15 Dec 2024 19:00:44 +0100
Subject: [PATCH 01/59] Updated dataset, including the following changes:   -
 Allow to add other types of entries to the triplestore that are not    
 datasets. Ex: samples, models, instruments, people, projects...   - Renamed
 list_data_iris() to search_iris(). It can now be use to search     for all
 types of entries.   - Renamed prepare() to as_jsonld() and made it part of
 the public API

---
 tests/dataset/test_dataset.py    |  14 ++--
 tests/input/semdata.yaml         |  12 ++--
 tripper/context/0.2/context.json |   4 +-
 tripper/dataset/__init__.py      |   3 +-
 tripper/dataset/dataset.py       | 120 +++++++++++++++++++------------
 5 files changed, 91 insertions(+), 62 deletions(-)

diff --git a/tests/dataset/test_dataset.py b/tests/dataset/test_dataset.py
index 4aa8fbdb..105db426 100644
--- a/tests/dataset/test_dataset.py
+++ b/tests/dataset/test_dataset.py
@@ -116,12 +116,7 @@ def test_datadoc():
     # pylint: disable=too-many-statements
 
     from tripper import CHAMEO, DCAT, EMMO, OTEIO, Triplestore
-    from tripper.dataset import (
-        list_dataset_iris,
-        load_dict,
-        save_datadoc,
-        save_dict,
-    )
+    from tripper.dataset import load_dict, save_datadoc, save_dict, search_iris
 
     pytest.importorskip("dlite")
     pytest.importorskip("rdflib")
@@ -188,20 +183,19 @@ def test_datadoc():
 
     # Test searching the triplestore
     SAMPLE = ts.namespaces["sample"]
-    datasets = list_dataset_iris(ts)
+    datasets = search_iris(ts)
     named_datasets = {
         SEMDATA["SEM_cement_batch2/77600-23-001/77600-23-001_5kV_400x_m001"],
         SEMDATA["SEM_cement_batch2/77600-23-001"],
         SEMDATA["SEM_cement_batch2"],
-        SAMPLE["SEM_cement_batch2/77600-23-001"],
     }
     assert not named_datasets.difference(datasets)
-    assert set(list_dataset_iris(ts, creator="Sigurd Wenner")) == {
+    assert set(search_iris(ts, creator="Sigurd Wenner")) == {
         SEMDATA["SEM_cement_batch2/77600-23-001/77600-23-001_5kV_400x_m001"],
         SEMDATA["SEM_cement_batch2/77600-23-001"],
         SEMDATA["SEM_cement_batch2"],
     }
-    assert set(list_dataset_iris(ts, _type=CHAMEO.Sample)) == {
+    assert set(search_iris(ts, type=CHAMEO.Sample)) == {
         SAMPLE["SEM_cement_batch2/77600-23-001"],
     }
 
diff --git a/tests/input/semdata.yaml b/tests/input/semdata.yaml
index 0e99919f..2d1da201 100644
--- a/tests/input/semdata.yaml
+++ b/tests/input/semdata.yaml
@@ -1,4 +1,5 @@
 ---
+
 # This extends the list of prefixes that are already defined in the context
 prefixes:
   sem: https://w3id.com/emmo/domain/sem/0.1#
@@ -62,10 +63,6 @@ datasets:
       downloadURL: sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2
       mediaType: inode/directory
 
-  - "@id": sample:SEM_cement_batch2/77600-23-001
-    "@type": chameo:Sample
-    title: Series for SEM images for sample 77600-23-001.
-
 
 parsers:
   - "@id": parser:sem_hitachi
@@ -81,3 +78,10 @@ generators:
     generatorType: application/vnd.dlite-generate
     configuration:
       driver: hitachi
+
+
+# Other entities, like samples, instruments, persons, models etc...
+other_entries:
+  - "@id": sample:SEM_cement_batch2/77600-23-001
+    "@type": chameo:Sample
+    title: Series for SEM images for sample 77600-23-001.
diff --git a/tripper/context/0.2/context.json b/tripper/context/0.2/context.json
index d5903ba9..3f658c0d 100644
--- a/tripper/context/0.2/context.json
+++ b/tripper/context/0.2/context.json
@@ -32,8 +32,8 @@
     "hasCurrentVersion": "dcat:hasCurrentVersion",
     "hasVersion": "dcat:hasVersion",
     "inSeries": {
-      "@id" : "dcat:inSeries",
-      "@type" : "@id"
+      "@id": "dcat:inSeries",
+      "@type": "@id"
     },
     "keyword": "dcat:keyword",
     "landingPage": "dcat:landingPage",
diff --git a/tripper/dataset/__init__.py b/tripper/dataset/__init__.py
index 0a3a5088..d6435b8d 100644
--- a/tripper/dataset/__init__.py
+++ b/tripper/dataset/__init__.py
@@ -2,12 +2,13 @@
 
 from .dataaccess import load, save
 from .dataset import (
+    as_jsonld,
     get_jsonld_context,
     get_partial_pipeline,
     get_prefixes,
-    list_dataset_iris,
     load_dict,
     read_datadoc,
     save_datadoc,
     save_dict,
+    search_iris,
 )
diff --git a/tripper/dataset/dataset.py b/tripper/dataset/dataset.py
index 0387328d..ba4a0fde 100644
--- a/tripper/dataset/dataset.py
+++ b/tripper/dataset/dataset.py
@@ -9,12 +9,13 @@
   - `save_datadoc()`: Save documentation from YAML file to the triplestore.
 
 Functions for searching the triplestore:
-  - `list_dataset_iris()`: Get IRIs of matching datasets.
+  - `search_iris()`: Get IRIs of matching entries in the triplestore.
 
 Functions for working with the dict-representation:
   - `read_datadoc()`: Read documentation from YAML file and return it as dict.
   - `save_dict()`: Save dict documentation to the triplestore.
   - `load_dict()`: Load dict documentation from the triplestore.
+  - `as_jsonld()`: Return the dict as JSON-LD (represented as a Python dict)
 
 Functions for interaction with OTEAPI:
   - `get_partial_pipeline()`: Returns a OTELib partial pipeline.
@@ -28,7 +29,6 @@
 
 """
 
-# pylint: enable=line-too-long
 # pylint: disable=invalid-name,redefined-builtin,import-outside-toplevel
 import functools
 import io
@@ -41,7 +41,7 @@
 import requests
 import yaml  # type: ignore
 
-from tripper import DCAT, EMMO, OTEIO, RDF, Triplestore
+from tripper import DCAT, EMMO, OTEIO, OWL, RDF, Triplestore
 from tripper.utils import AttrDict, as_python
 
 if TYPE_CHECKING:  # pragma: no cover
@@ -90,6 +90,12 @@
         "datadoc_label": "datasets",
         "@type": [DCAT.Dataset, EMMO.DataSet],
     },
+    "entry": {
+        # General datacatalog entry that is not one of the above
+        # Ex: samples, instruments, models, people, projects, ...
+        "datadoc_label": "other_entries",  # XXX better label?
+        "@type": OWL.NamedIndividual,
+    },
 }
 
 
@@ -120,14 +126,15 @@ def save_dict(
 
     Notes:
         The keys in `dct` and `kwargs` may be either properties defined in the
-        [JSON-LD context](https://raw.githubusercontent.com/EMMC-ASBL/oteapi-dlite/refs/heads/rdf-serialisation/oteapi_dlite/context/0.2/context.json)
-        or one of the following special keywords:
+        [JSON-LD context] or one of the following special keywords:
           - "@id": Dataset IRI.  Must always be given.
           - "@type": IRI of the ontology class for this type of data.
             For datasets, it is typically used to refer to a specific subclass
             of `emmo:DataSet` that provides a semantic description of this
             dataset.
 
+    References:
+    [JSON-LD context]: https://raw.githubusercontent.com/EMMC-ASBL/oteapi-dlite/refs/heads/rdf-serialisation/oteapi_dlite/context/0.2/context.json
     """
     if "@id" not in dct:
         raise ValueError("`dct` must have an '@id' key")
@@ -136,7 +143,7 @@ def save_dict(
     if prefixes:
         all_prefixes.update(prefixes)
 
-    d = prepare(type=type, dct=dct, prefixes=all_prefixes, **kwargs)
+    d = as_jsonld(dct=dct, type=type, prefixes=all_prefixes, **kwargs)
 
     # Bind prefixes
     for prefix, ns in all_prefixes.items():
@@ -199,8 +206,7 @@ def save_extra_content(ts: Triplestore, dct: dict) -> None:
                 except (
                     dlite.DLiteMissingInstanceError  # pylint: disable=no-member
                 ):
-                    # __FIXME__: check session whether want to warn or re-reise
-                    # in this case
+                    # __FIXME__: check session whether to warn or re-reise
                     warnings.warn(f"cannot load datamodel: {uri}")
                 else:
                     add_dataset(ts, dm)
@@ -476,7 +482,7 @@ def save_datadoc(
     for spec in dicttypes.values():
         label = spec["datadoc_label"]
         for dct in get(d, label):
-            dct = prepare(types[label], dct, prefixes=prefixes)
+            dct = as_jsonld(dct=dct, type=types[label], prefixes=prefixes)
             f = io.StringIO(json.dumps(dct))
             with Triplestore(backend="rdflib") as ts2:
                 ts2.parse(f, format="json-ld")
@@ -505,52 +511,65 @@ def prepare_datadoc(datadoc: dict) -> dict:
     for type, spec in dicttypes.items():
         label = spec["datadoc_label"]
         for i, dct in enumerate(get(d, label)):
-            d[label][i] = prepare(type, dct, prefixes=d.prefixes)
+            d[label][i] = as_jsonld(dct=dct, type=type, prefixes=d.prefixes)
 
     return d
 
 
-def prepare(
-    type: str, dct: dict, prefixes: dict, _recur: bool = False, **kwargs
+def as_jsonld(
+    dct: dict,
+    type: "Optional[str]" = "dataset",
+    prefixes: "Optional[dict]" = None,
+    _entryid: "Optional[str]" = None,
+    **kwargs,
 ) -> dict:
-    """Return an updated copy of dict `dct` with additional key-value
-    pairs needed for serialisation to RDF.
+    """Return an updated copy of dict `dct` as valid JSON-LD.
 
     Arguments:
-        type: Type of dict to prepare.  Should be one of: "dataset",
-            "distribution", "parser" or "generator".
         dct: Dict to return an updated copy of.
+        type: Type of dict to prepare.  Should either be one of the
+            pre-defined names: "dataset", "distribution", "accessService",
+            "parser" and "generator" or an IRI to a class in an ontology.
+            Defaults to "dataset".
         prefixes: Dict with prefixes in addition to those included in the
             JSON-LD context.  Should map namespace prefixes to IRIs.
-        _recur: Whether this function is called recursively. Intended for
-            internal use.
+        _entryid: Id of base entry that is documented. Intended for
+            internal use only.
         kwargs: Additional keyword arguments to add to the returned dict.
             A leading underscore in a key will be translated to a
-            leading "@"-sign.  For example, "@id=..." may be provided
-            as "_id=...".
+            leading "@"-sign.  For example, "@id" or "@context" may be
+            provided as "_id" or "_context", respectively.
+
 
     Returns:
-        An updated copy of `dct`.
+        An updated copy of `dct` as valid JSON-LD.
     """
     # pylint: disable=too-many-branches
-    if type not in dicttypes:
-        raise ValueError(
-            f"`type` must be one of: {', '.join(dicttypes.keys())}. "
-            f"Got: '{type}'"
-        )
-    spec = dicttypes[type]
-
     d = AttrDict()
-    if not _recur:
+    if not _entryid:
         d["@context"] = CONTEXT_URL
-    add(d, "@type", spec["@type"])  # get type at top
-    d.update(dct)
-    add(d, "@type", spec["@type"])  # readd type if overwritten
+
+    if type:
+        t = dicttypes[type]["@type"] if type in dicttypes else type
+        add(d, "@type", t)  # get type at top
+        d.update(dct)
+        add(d, "@type", t)  # readd type if overwritten
+    else:
+        d.update(dct)
 
     for k, v in kwargs.items():
         key = f"@{k[1:]}" if re.match("^_([^_]|([^_].*[^_]))$", k) else k
         add(d, key, v)
 
+    if "@id" not in d and not _entryid:
+        raise ValueError("Missing '@id' in dict to document")
+
+    if not _entryid:
+        _entryid = d["@id"]
+
+    if "@type" not in d:
+        warnings.warn(f"Missing '@type' in dict to document: {_entryid}")
+
     all_prefixes = get_prefixes()
     if prefixes:
         all_prefixes.update(prefixes)
@@ -584,9 +603,11 @@ def prepare(
                 if isinstance(e, str):
                     v[i] = expand_iri(e, all_prefixes)
                 elif isinstance(e, dict) and k in nested:
-                    v[i] = prepare(k, e, prefixes=prefixes)
+                    v[i] = as_jsonld(
+                        e, k, _entryid=_entryid, prefixes=prefixes
+                    )
         elif isinstance(v, dict) and k in nested:
-            d[k] = prepare(k, v, prefixes=prefixes)
+            d[k] = as_jsonld(v, k, _entryid=_entryid, prefixes=prefixes)
 
     return d
 
@@ -711,31 +732,42 @@ def get_partial_pipeline(
     return pipeline
 
 
-def list_dataset_iris(ts: Triplestore, **kwargs):
-    """Return a list of IRIs for all datasets matching a set of criterias
-    specified by `kwargs`.
+def search_iris(ts: Triplestore, type=DCAT.Dataset, **kwargs):
+    """Return a list of IRIs for all entries of the given type.
+    Additional matching criterias can be specified by `kwargs`.
+
 
     Arguments:
         ts: Triplestore to search.
+        type: Search for entries that are individuals of the class with
+            this IRI.  The default is `dcat:Dataset`.
         kwargs: Match criterias.
 
     Examples:
         List all dataset IRIs:
 
-            list_dataset_iris(ts)
+            search_iris(ts)
 
         List IRIs of all datasets with John Doe as `contactPoint`:
 
-            list_dataset_iris(ts, contactPoint="John Doe")
+            search_iris(ts, contactPoint="John Doe")
+
+        List IRIs of all samples:
 
-        List IRIs of all datasets with John Doe as `contactPoint` AND that are
+            search_iris(ts, type=CHAMEO.Sample)
+
+        List IRIs of all datasets with John Doe as `contactPoint` AND are
         measured on a given sample:
 
-            list_dataset_iris(
+            search_iris(
                 ts, contactPoint="John Doe", fromSample=SAMPLE.batch2/sample3
             )
     """
     crit = []
+
+    if type:
+        crit.append(f"  ?iri rdf:type <{type}> .")
+
     expanded = {v: k for k, v in get_shortnames().items()}
     for k, v in kwargs.items():
         key = f"@{k[1:]}" if k.startswith("_") else k
@@ -748,14 +780,12 @@ def list_dataset_iris(ts: Triplestore, **kwargs):
             )
         else:
             value = v
-        crit.append(f"  ?dataset <{predicate}> {value} .")
+        crit.append(f"  ?iri <{predicate}> {value} .")
     criterias = "\n".join(crit)
     query = f"""
     PREFIX rdf: <{RDF}>
-    PREFIX dcat: <{DCAT}>
-    SELECT ?dataset
+    SELECT ?iri
     WHERE {{
-      ?dataset rdf:type dcat:Dataset .
     {criterias}
     }}
     """

From 94fa59a0788f49a33964aad14d0008b91ea4cf18 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 16 Dec 2024 00:18:00 +0100
Subject: [PATCH 02/59] Added new TableDoc class providing a table interface
 for data documentation.

---
 docs/api_reference/dataset/tabledoc.md |  3 +
 pyproject.toml                         |  7 ++-
 tests/dataset/dataset_paths.py         | 12 ++++
 tests/dataset/test_dataaccess.py       | 16 ++----
 tests/dataset/test_dataset.py          | 47 +++++++++------
 tests/dataset/test_tabledoc.py         | 79 ++++++++++++++++++++++++++
 tripper/dataset/__init__.py            |  1 +
 tripper/dataset/dataaccess.py          |  4 +-
 tripper/dataset/dataset.py             | 79 +++++++++++++++++++++++---
 tripper/dataset/tabledoc.py            | 68 ++++++++++++++++++++++
 10 files changed, 275 insertions(+), 41 deletions(-)
 create mode 100644 docs/api_reference/dataset/tabledoc.md
 create mode 100644 tests/dataset/dataset_paths.py
 create mode 100644 tests/dataset/test_tabledoc.py
 create mode 100644 tripper/dataset/tabledoc.py

diff --git a/docs/api_reference/dataset/tabledoc.md b/docs/api_reference/dataset/tabledoc.md
new file mode 100644
index 00000000..f3a73929
--- /dev/null
+++ b/docs/api_reference/dataset/tabledoc.md
@@ -0,0 +1,3 @@
+# tabledoc
+
+::: tripper.dataset.tabledoc
diff --git a/pyproject.toml b/pyproject.toml
index d5f7f94a..21196860 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -104,7 +104,8 @@ max-public-methods = 25
 max-locals = 20
 disable = [
     "fixme",
-    "too-many-positional-arguments",
+    "invalid-name",
+    #"too-many-positional-arguments",
 ]
 good-names = [
     # Default
@@ -115,8 +116,8 @@ good-names = [
     "s", "p", "o",
     # Namespaces
     "EX",
-    # dict, value, file, ...
-    "d", "v", "f",
+    # dict, value, file, keyword...
+    "d", "v", "f", "kw",
 ]
 
 [tool.pytest.ini_options]
diff --git a/tests/dataset/dataset_paths.py b/tests/dataset/dataset_paths.py
new file mode 100644
index 00000000..e84b2f47
--- /dev/null
+++ b/tests/dataset/dataset_paths.py
@@ -0,0 +1,12 @@
+"""Defines paths for tests.
+
+It defines some directories and some utility functions that can be used
+with or without conftest.
+"""
+
+from pathlib import Path
+
+testdir = Path(__file__).resolve().parent.parent
+ontodir = testdir / "ontologies"
+indir = testdir / "input"
+outdir = testdir / "output"
diff --git a/tests/dataset/test_dataaccess.py b/tests/dataset/test_dataaccess.py
index c3a7b75d..bdc0ef45 100644
--- a/tests/dataset/test_dataaccess.py
+++ b/tests/dataset/test_dataaccess.py
@@ -2,18 +2,12 @@
 
 # pylint: disable=invalid-name,too-many-locals,duplicate-code
 
-from pathlib import Path
-
 import pytest
+from dataset_paths import outdir
 
 pytest.importorskip("yaml")
 pytest.importorskip("requests")
 
-thisdir = Path(__file__).resolve().parent
-testdir = thisdir.parent
-inputdir = testdir / "input"
-outputdir = testdir / "output"
-
 
 # if True:
 def test_save_and_load():
@@ -38,7 +32,6 @@ def test_save_and_load():
     # Test save dict
     save_dict(
         ts,
-        type="dataset",
         dct={
             "@id": SEMDATA.img1,
             "distribution": {
@@ -49,6 +42,7 @@ def test_save_and_load():
                 "format": "tiff",
             },
         },
+        type="dataset",
     )
     newdistr = load_dict(ts, SEMDATA.img1)
     assert newdistr["@type"] == [DCAT.Dataset, EMMO.DataSet]
@@ -57,12 +51,12 @@ def test_save_and_load():
 
     save_dict(
         ts,
-        type="generator",
         dct={
             "@id": GEN.sem_hitachi,
             "generatorType": "application/vnd.dlite-generate",
             "configuration": {"driver": "hitachi"},
         },
+        type="generator",
     )
 
     # Test load dataset (this downloads an actual image from github)
@@ -70,7 +64,7 @@ def test_save_and_load():
     assert len(data) == 53502
 
     # Test save dataset with anonymous distribution
-    newfile = outputdir / "newimage.tiff"
+    newfile = outdir / "newimage.tiff"
     newfile.unlink(missing_ok=True)
     buf = b"some bytes..."
     save(
@@ -94,7 +88,7 @@ def test_save_and_load():
     assert newimage.distribution.downloadURL == f"file:{newfile}"
 
     # Test save dataset with named distribution
-    newfile2 = outputdir / "newimage.png"
+    newfile2 = outdir / "newimage.png"
     newfile2.unlink(missing_ok=True)
     save(
         ts,
diff --git a/tests/dataset/test_dataset.py b/tests/dataset/test_dataset.py
index 105db426..4e43cd10 100644
--- a/tests/dataset/test_dataset.py
+++ b/tests/dataset/test_dataset.py
@@ -2,18 +2,12 @@
 
 # pylint: disable=invalid-name,too-many-locals,duplicate-code
 
-from pathlib import Path
-
 import pytest
+from dataset_paths import indir
 
 pytest.importorskip("yaml")
 pytest.importorskip("requests")
 
-thisdir = Path(__file__).resolve().parent
-testdir = thisdir.parent
-inputdir = testdir / "input"
-outputdir = testdir / "output"
-
 
 def test_get_jsonld_context():
     """Test get_jsonld_context()."""
@@ -73,12 +67,31 @@ def test_add():
     from tripper.dataset.dataset import add
 
     d = {}
-    add(d, "a", 1)
-    add(d, "b", 1)
-    add(d, "b", 1)
-    add(d, "a", 2)
-    add(d, "a", 1)
-    assert d == {"a": [1, 2], "b": 1}
+    add(d, "a", "1")
+    add(d, "b", "1")
+    add(d, "b", "1")
+    add(d, "a", "2")
+    add(d, "a", "1")
+    add(d, "a", {"c": "3"})
+    assert d == {"a": ["1", "2", {"c": "3"}], "b": "1"}
+
+
+def test_addnested():
+    """Test help-function addnested()."""
+    from tripper.dataset.dataset import addnested
+    from tripper.utils import AttrDict
+
+    d = AttrDict()
+    addnested(d, "a.b", "1")
+    assert d == {"a": {"b": "1"}}
+
+    addnested(d, "a", "2")
+    assert d == {"a": ["2", {"b": "1"}]}
+
+    addnested(d, "a.b.c", {"d": "3"})
+    assert d.a[0] == "2"
+    assert d.a[1].b[1].c == {"d": "3"}
+    assert d == {"a": ["2", {"b": ["1", {"c": {"d": "3"}}]}]}
 
 
 def test_get():
@@ -124,7 +137,7 @@ def test_datadoc():
     ts = Triplestore("rdflib")
 
     # Load data documentation into triplestore
-    datadoc = save_datadoc(ts, inputdir / "semdata.yaml")
+    datadoc = save_datadoc(ts, indir / "semdata.yaml")
     assert isinstance(datadoc, dict)
     assert "@context" in datadoc
 
@@ -167,8 +180,8 @@ def test_datadoc():
     # Test save dict
     save_dict(
         ts,
-        "distribution",
-        {"@id": SEMDATA.newdistr, "format": "txt"},
+        dct={"@id": SEMDATA.newdistr, "format": "txt"},
+        type="distribution",
         prefixes={"echem": "https://w3id.org/emmo/domain/electrochemistry"},
     )
     newdistr = load_dict(ts, SEMDATA.newdistr)
@@ -210,7 +223,7 @@ def test_pipeline():
 
     # Prepare triplestore
     ts = Triplestore("rdflib")
-    save_datadoc(ts, inputdir / "semdata.yaml")
+    save_datadoc(ts, indir / "semdata.yaml")
 
     SEMDATA = ts.namespaces["semdata"]
 
diff --git a/tests/dataset/test_tabledoc.py b/tests/dataset/test_tabledoc.py
new file mode 100644
index 00000000..77e81dcc
--- /dev/null
+++ b/tests/dataset/test_tabledoc.py
@@ -0,0 +1,79 @@
+"""Test the dataset module."""
+
+from tripper import Triplestore
+from tripper.dataset import TableDoc
+
+
+# if True:
+def test_as_dicts():
+    """Test the as_dicts() method."""
+
+    from tripper import DCAT, EMMO, Namespace
+
+    ONTO = Namespace("http:/example.com/onto#")
+    DS = Namespace("http:/example.com/datasets#")
+
+    td = TableDoc(
+        header=[
+            "@id",
+            "@type",
+            "@type",
+            "inSeries",
+            "distribution.downloadURL",
+        ],
+        data=[
+            ("ds:s1", "onto:T1", "onto:T2", None, "file:///data/"),
+            ("ds:d1", "onto:T1", None, "ds:s1", "file:///data/d1.txt"),
+            ("ds:d2", "onto:T2", None, "ds:s1", "file:///data/d2.txt"),
+        ],
+        prefixes={
+            "onto": "http:/example.com/onto#",
+            "ds": "http:/example.com/datasets#",
+        },
+        # context={
+        #    "ds": "http:/example.com/datasets#",
+        # },
+    )
+
+    s1, d1, d2 = td.asdicts()  # pylint: disable=unbalanced-tuple-unpacking
+
+    assert s1["@id"] == DS.s1
+    assert set(s1["@type"]) == {
+        DCAT.Dataset,
+        EMMO.DataSet,
+        ONTO.T1,
+        ONTO.T2,
+    }
+    assert "inSeries" not in s1
+    assert s1.distribution == {
+        "@type": DCAT.Distribution,
+        "downloadURL": "file:///data/",
+    }
+
+    assert d1["@id"] == DS.d1
+    assert set(d1["@type"]) == {
+        DCAT.Dataset,
+        EMMO.DataSet,
+        ONTO.T1,
+    }
+    assert d1.inSeries == DS.s1
+    assert d1.distribution == {
+        "@type": DCAT.Distribution,
+        "downloadURL": "file:///data/d1.txt",
+    }
+
+    assert d2["@id"] == DS.d2
+    assert set(d2["@type"]) == {
+        DCAT.Dataset,
+        EMMO.DataSet,
+        ONTO.T2,
+    }
+    assert d2.inSeries == DS.s1
+    assert d2.distribution == {
+        "@type": DCAT.Distribution,
+        "downloadURL": "file:///data/d2.txt",
+    }
+
+    ts = Triplestore(backend="rdflib")
+    td.save(ts)
+    print(ts.serialize())
diff --git a/tripper/dataset/__init__.py b/tripper/dataset/__init__.py
index d6435b8d..e0b53d58 100644
--- a/tripper/dataset/__init__.py
+++ b/tripper/dataset/__init__.py
@@ -12,3 +12,4 @@
     save_dict,
     search_iris,
 )
+from .tabledoc import TableDoc
diff --git a/tripper/dataset/dataaccess.py b/tripper/dataset/dataaccess.py
index 672b2a59..3e248e36 100644
--- a/tripper/dataset/dataaccess.py
+++ b/tripper/dataset/dataaccess.py
@@ -175,9 +175,9 @@ def save(
     # Update triplestore
     ts.add_triples(triples)
     if save_dataset:
-        save_dict(ts, "dataset", dataset, prefixes=prefixes)
+        save_dict(ts, dataset, "dataset", prefixes=prefixes)
     elif save_distribution:
-        save_dict(ts, "distribution", distribution, prefixes=prefixes)
+        save_dict(ts, distribution, "distribution", prefixes=prefixes)
 
     return dataset["@id"]
 
diff --git a/tripper/dataset/dataset.py b/tripper/dataset/dataset.py
index ba4a0fde..2bb5e6a1 100644
--- a/tripper/dataset/dataset.py
+++ b/tripper/dataset/dataset.py
@@ -101,8 +101,8 @@
 
 def save_dict(
     ts: Triplestore,
-    type: str,
     dct: dict,
+    type: str = "dataset",
     prefixes: "Optional[dict]" = None,
     **kwargs,
 ) -> dict:
@@ -111,9 +111,11 @@ def save_dict(
 
     Arguments:
         ts: Triplestore to save to.
-        type: Type of dict to save.  Should be one of: "dataset",
-            "distribution", "parser" or "generator".
         dct: Dict with data to save.
+        type: Type of data to save.  Should either be one of the
+            pre-defined names: "dataset", "distribution", "accessService",
+            "parser" and "generator" or an IRI to a class in an ontology.
+            Defaults to "dataset".
         prefixes: Dict with prefixes in addition to those included in the
             JSON-LD context.  Should map namespace prefixes to IRIs.
         kwargs: Additional keyword arguments to add to the returned dict.
@@ -333,6 +335,9 @@ def get_values(
     return values
 
 
+# TODO: update this function to take an initial argument `context`,
+# which can be an URL (string), dict with raw context or a list of
+# strings or dicts.
 @cache  # type: ignore
 def get_jsonld_context(timeout: float = 5, fromfile: bool = True) -> dict:
     """Returns the JSON-LD context as a dict.
@@ -355,6 +360,8 @@ def get_jsonld_context(timeout: float = 5, fromfile: bool = True) -> dict:
     return context
 
 
+# TODO: update this to take an initial argument `context`.
+# See get_jsonld_context()
 def get_prefixes(timeout: float = 5) -> dict:
     """Loads the JSON-LD context and returns a dict mapping prefixes to
     their namespace URL."""
@@ -367,6 +374,8 @@ def get_prefixes(timeout: float = 5) -> dict:
     return prefixes
 
 
+# TODO: update this to take an initial argument `context`.
+# See get_jsonld_context()
 def get_shortnames(timeout: float = 5) -> dict:
     """Loads the JSON-LD context and returns a dict mapping IRIs to their
     short names defined in the context."""
@@ -407,9 +416,61 @@ def add(d: dict, key: str, value: "Any") -> None:
         d[key] = value
     else:
         klst = d[key] if isinstance(d[key], list) else [d[key]]
-        vlst = value if isinstance(value, list) else [value]
-        v = list(set(klst).union(vlst))
-        d[key] = v[0] if len(v) == 1 else sorted(v)
+        if isinstance(value, dict):
+            v = klst if value in klst else klst + [value]
+        else:
+            vlst = value if isinstance(value, list) else [value]
+            try:
+                v = list(set(klst).union(vlst))
+            except TypeError:  # klst contains unhashable dicts
+                v = klst + [x for x in vlst if x not in klst]
+        d[key] = (
+            v[0]
+            if len(v) == 1
+            else sorted(
+                # Sort dicts at end, by representing them with a huge
+                # unicode character
+                v,
+                key=lambda x: "\uffff" if isinstance(x, dict) else x,
+            )
+        )
+
+
+def addnested(d: "Union[dict, list]", key: str, value: "Any"):
+    """Like add(), but allows `key` to be a dot-separated list of sub-keys.
+
+    Each sub-key will be added to `d` as a corresponding sub-dict.
+
+    Example:
+
+        >>> d = {}
+        >>> addnested(d, "a.b.c", "val")
+        {'a': {'b': {'c': 'val'}}}
+
+    """
+    if "." in key:
+        first, rest = key.split(".", 1)
+        if isinstance(d, list):
+            for ele in d:
+                if isinstance(ele, dict):
+                    addnested(ele, key, value)
+                    break
+            else:
+                d.append(addnested({}, key, value))
+        elif first in d and isinstance(d[first], (dict, list)):
+            addnested(d[first], rest, value)
+        else:
+            addnested(d, first, addnested(AttrDict(), rest, value))
+    elif isinstance(d, list):
+        for ele in d:
+            if isinstance(ele, dict):
+                add(ele, key, value)
+                break
+        else:
+            d.append({key: value})
+    else:
+        add(d, key, value)
+    return d
 
 
 def get(
@@ -516,6 +577,8 @@ def prepare_datadoc(datadoc: dict) -> dict:
     return d
 
 
+# TODO: update this function to correctly handle multiple contexts
+# provided with the `_context` keyword argument.
 def as_jsonld(
     dct: dict,
     type: "Optional[str]" = "dataset",
@@ -526,8 +589,8 @@ def as_jsonld(
     """Return an updated copy of dict `dct` as valid JSON-LD.
 
     Arguments:
-        dct: Dict to return an updated copy of.
-        type: Type of dict to prepare.  Should either be one of the
+        dct: Dict with data documentation represent as JSON-LD.
+        type: Type of data to document.  Should either be one of the
             pre-defined names: "dataset", "distribution", "accessService",
             "parser" and "generator" or an IRI to a class in an ontology.
             Defaults to "dataset".
diff --git a/tripper/dataset/tabledoc.py b/tripper/dataset/tabledoc.py
new file mode 100644
index 00000000..b1a8ef51
--- /dev/null
+++ b/tripper/dataset/tabledoc.py
@@ -0,0 +1,68 @@
+"""Basic interface for tabular documentation of datasets."""
+
+from typing import TYPE_CHECKING
+
+from tripper import Triplestore
+from tripper.dataset.dataset import addnested, as_jsonld, save_dict
+from tripper.utils import AttrDict
+
+if TYPE_CHECKING:  # pragma: no cover
+    from typing import List, Optional, Sequence, Union
+
+
+class TableDoc:
+    """Representation of tabular documentation of datasets.
+
+    Arguments:
+        header: Sequence of column header labels.  Nested data can
+            be represented by dot-separated label strings (e.g.
+            "distribution.downloadURL")
+        data: Sequence of rows of data. Each row documents an entry.
+        type: Type of data to save (applies to all rows).  Should
+            either be one of the pre-defined names: "dataset",
+            "distribution", "accessService", "parser" and "generator"
+            or an IRI to a class in an ontology.  Defaults to
+            "dataset".
+        prefixes: Dict with prefixes in addition to those included in the
+            JSON-LD context.  Should map namespace prefixes to IRIs.
+        context: Dict with user-defined JSON-LD context.
+
+    """
+
+    # pylint: disable=redefined-builtin,too-few-public-methods
+
+    def __init__(
+        self,
+        header: "Sequence[str]",
+        data: "Sequence[Sequence[str]]",
+        type: "Optional[str]" = "dataset",
+        prefixes: "Optional[dict]" = None,
+        context: "Optional[Union[dict, list]]" = None,
+    ):
+        self.header = header
+        self.data = data
+        self.type = type
+        self.prefixes = prefixes
+        self.context = context
+
+    def asdicts(self) -> "List[dict]":
+        """Return the table as a list of dicts."""
+        kw = {"_context": self.context} if self.context else {}
+
+        results = []
+        for row in self.data:
+            d = AttrDict()
+            for i, colname in enumerate(self.header):
+                cell = row[i]
+                if cell:
+                    addnested(d, colname, cell)
+            jsonld = as_jsonld(
+                d, type=self.type, prefixes=self.prefixes, **kw  # type: ignore
+            )
+            results.append(jsonld)
+        return results
+
+    def save(self, ts: Triplestore) -> None:
+        """Save tabular datadocumentation to triplestore."""
+        for d in self.asdicts():
+            save_dict(ts, d)

From 028054fad4ae6a7e0055ad746b90f200c807e965 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 16 Dec 2024 00:39:21 +0100
Subject: [PATCH 03/59] Import indir/outdir inside test functions

---
 tests/dataset/test_dataaccess.py | 3 ++-
 tests/dataset/test_dataset.py    | 5 ++++-
 tripper/dataset/dataset.py       | 3 ++-
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/tests/dataset/test_dataaccess.py b/tests/dataset/test_dataaccess.py
index bdc0ef45..0cbc7727 100644
--- a/tests/dataset/test_dataaccess.py
+++ b/tests/dataset/test_dataaccess.py
@@ -3,7 +3,6 @@
 # pylint: disable=invalid-name,too-many-locals,duplicate-code
 
 import pytest
-from dataset_paths import outdir
 
 pytest.importorskip("yaml")
 pytest.importorskip("requests")
@@ -14,6 +13,8 @@ def test_save_and_load():
     """Test save() and load()."""
     # pylint: disable=too-many-statements
 
+    from dataset_paths import outdir
+
     from tripper import DCAT, DCTERMS, EMMO, Triplestore
     from tripper.dataset import load, load_dict, save, save_dict
 
diff --git a/tests/dataset/test_dataset.py b/tests/dataset/test_dataset.py
index 4e43cd10..1a0cffbd 100644
--- a/tests/dataset/test_dataset.py
+++ b/tests/dataset/test_dataset.py
@@ -3,7 +3,6 @@
 # pylint: disable=invalid-name,too-many-locals,duplicate-code
 
 import pytest
-from dataset_paths import indir
 
 pytest.importorskip("yaml")
 pytest.importorskip("requests")
@@ -128,6 +127,8 @@ def test_datadoc():
     """Test save_datadoc() and load_dict()/save_dict()."""
     # pylint: disable=too-many-statements
 
+    from dataset_paths import indir
+
     from tripper import CHAMEO, DCAT, EMMO, OTEIO, Triplestore
     from tripper.dataset import load_dict, save_datadoc, save_dict, search_iris
 
@@ -219,6 +220,8 @@ def test_pipeline():
     from tripper import Triplestore
 
     otelib = pytest.importorskip("otelib")
+    from dataset_paths import indir
+
     from tripper.dataset import get_partial_pipeline, save_datadoc
 
     # Prepare triplestore
diff --git a/tripper/dataset/dataset.py b/tripper/dataset/dataset.py
index 2bb5e6a1..13fdb935 100644
--- a/tripper/dataset/dataset.py
+++ b/tripper/dataset/dataset.py
@@ -445,7 +445,8 @@ def addnested(d: "Union[dict, list]", key: str, value: "Any"):
 
         >>> d = {}
         >>> addnested(d, "a.b.c", "val")
-        {'a': {'b': {'c': 'val'}}}
+        >>> d == {'a': {'b': {'c': 'val'}}}
+        True
 
     """
     if "." in key:

From ef5239ad7e96f586c5ce970cec834cf7881864ff Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 16 Dec 2024 00:56:02 +0100
Subject: [PATCH 04/59] Fixed doctest issue

---
 tripper/dataset/dataset.py | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/tripper/dataset/dataset.py b/tripper/dataset/dataset.py
index 13fdb935..8db5b497 100644
--- a/tripper/dataset/dataset.py
+++ b/tripper/dataset/dataset.py
@@ -38,9 +38,6 @@
 from pathlib import Path
 from typing import TYPE_CHECKING
 
-import requests
-import yaml  # type: ignore
-
 from tripper import DCAT, EMMO, OTEIO, OWL, RDF, Triplestore
 from tripper.utils import AttrDict, as_python
 
@@ -171,6 +168,8 @@ def save_extra_content(ts: Triplestore, dct: dict) -> None:
     - data models (require that DLite is installed)
 
     """
+    import requests
+
     # Save statements and mappings
     statements = get_values(dct, "statements")
     statements.extend(get_values(dct, "mappings"))
@@ -351,6 +350,8 @@ def get_jsonld_context(timeout: float = 5, fromfile: bool = True) -> dict:
         fromfile: Whether to load the context from local file.
 
     """
+    import requests
+
     if fromfile:
         with open(CONTEXT_PATH[7:], "r", encoding="utf-8") as f:
             context = json.load(f)["@context"]
@@ -436,16 +437,18 @@ def add(d: dict, key: str, value: "Any") -> None:
         )
 
 
-def addnested(d: "Union[dict, list]", key: str, value: "Any"):
+def addnested(
+    d: "Union[dict, list]", key: str, value: "Any"
+) -> "Union[dict, list]":
     """Like add(), but allows `key` to be a dot-separated list of sub-keys.
+    Returns the updated `d`.
 
     Each sub-key will be added to `d` as a corresponding sub-dict.
 
     Example:
 
         >>> d = {}
-        >>> addnested(d, "a.b.c", "val")
-        >>> d == {'a': {'b': {'c': 'val'}}}
+        >>> addnested(d, "a.b.c", "val") == {'a': {'b': {'c': 'val'}}}
         True
 
     """
@@ -508,6 +511,8 @@ def expand_iri(iri: str, prefixes: dict) -> str:
 
 def read_datadoc(filename: "Union[str, Path]") -> dict:
     """Read YAML data documentation and return it as a dict."""
+    import yaml  # type: ignore
+
     with open(filename, "r", encoding="utf-8") as f:
         d = yaml.safe_load(f)
     return prepare_datadoc(d)

From 331878a1756ed225d48fc3a2e0acdd567ccc4774 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 16 Dec 2024 01:01:22 +0100
Subject: [PATCH 05/59] Skip test_tabledoc if rdflib isn't available

---
 tests/dataset/test_tabledoc.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/dataset/test_tabledoc.py b/tests/dataset/test_tabledoc.py
index 77e81dcc..49902b69 100644
--- a/tests/dataset/test_tabledoc.py
+++ b/tests/dataset/test_tabledoc.py
@@ -1,5 +1,7 @@
 """Test the dataset module."""
 
+import pytest
+
 from tripper import Triplestore
 from tripper.dataset import TableDoc
 
@@ -10,6 +12,8 @@ def test_as_dicts():
 
     from tripper import DCAT, EMMO, Namespace
 
+    pytest.importorskip("rdflib")
+
     ONTO = Namespace("http:/example.com/onto#")
     DS = Namespace("http:/example.com/datasets#")
 

From 5fe9cf7c387a9fb3ccd02856c0878ef8dceb8eba Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 16 Dec 2024 01:04:02 +0100
Subject: [PATCH 06/59] More pylint fixes...

---
 tests/dataset/test_dataaccess.py | 2 +-
 tests/dataset/test_dataset.py    | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/dataset/test_dataaccess.py b/tests/dataset/test_dataaccess.py
index 0cbc7727..ecf98dba 100644
--- a/tests/dataset/test_dataaccess.py
+++ b/tests/dataset/test_dataaccess.py
@@ -13,7 +13,7 @@ def test_save_and_load():
     """Test save() and load()."""
     # pylint: disable=too-many-statements
 
-    from dataset_paths import outdir
+    from dataset_paths import outdir  # pytest: disable=import-error
 
     from tripper import DCAT, DCTERMS, EMMO, Triplestore
     from tripper.dataset import load, load_dict, save, save_dict
diff --git a/tests/dataset/test_dataset.py b/tests/dataset/test_dataset.py
index 1a0cffbd..4fb5ec09 100644
--- a/tests/dataset/test_dataset.py
+++ b/tests/dataset/test_dataset.py
@@ -127,7 +127,7 @@ def test_datadoc():
     """Test save_datadoc() and load_dict()/save_dict()."""
     # pylint: disable=too-many-statements
 
-    from dataset_paths import indir
+    from dataset_paths import indir  # pytest: disable=import-error
 
     from tripper import CHAMEO, DCAT, EMMO, OTEIO, Triplestore
     from tripper.dataset import load_dict, save_datadoc, save_dict, search_iris
@@ -220,7 +220,7 @@ def test_pipeline():
     from tripper import Triplestore
 
     otelib = pytest.importorskip("otelib")
-    from dataset_paths import indir
+    from dataset_paths import indir  # pytest: disable=import-error
 
     from tripper.dataset import get_partial_pipeline, save_datadoc
 

From 4aaeed8551b56ece4c7c9af151ce3152a2779077 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 16 Dec 2024 01:08:20 +0100
Subject: [PATCH 07/59] Placed importskip before importing EMMO

---
 tests/dataset/test_tabledoc.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/tests/dataset/test_tabledoc.py b/tests/dataset/test_tabledoc.py
index 49902b69..4a1c0613 100644
--- a/tests/dataset/test_tabledoc.py
+++ b/tests/dataset/test_tabledoc.py
@@ -2,18 +2,16 @@
 
 import pytest
 
-from tripper import Triplestore
-from tripper.dataset import TableDoc
-
 
 # if True:
 def test_as_dicts():
     """Test the as_dicts() method."""
 
-    from tripper import DCAT, EMMO, Namespace
-
     pytest.importorskip("rdflib")
 
+    from tripper import DCAT, EMMO, Namespace, Triplestore
+    from tripper.dataset import TableDoc
+
     ONTO = Namespace("http:/example.com/onto#")
     DS = Namespace("http:/example.com/datasets#")
 

From 0f21fbbde6f6b6eaaf6583145f403fb7f841c0a7 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 16 Dec 2024 01:12:12 +0100
Subject: [PATCH 08/59] typo

---
 tests/dataset/test_dataaccess.py | 2 +-
 tests/dataset/test_dataset.py    | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/dataset/test_dataaccess.py b/tests/dataset/test_dataaccess.py
index ecf98dba..af058440 100644
--- a/tests/dataset/test_dataaccess.py
+++ b/tests/dataset/test_dataaccess.py
@@ -13,7 +13,7 @@ def test_save_and_load():
     """Test save() and load()."""
     # pylint: disable=too-many-statements
 
-    from dataset_paths import outdir  # pytest: disable=import-error
+    from dataset_paths import outdir  # pylint: disable=import-error
 
     from tripper import DCAT, DCTERMS, EMMO, Triplestore
     from tripper.dataset import load, load_dict, save, save_dict
diff --git a/tests/dataset/test_dataset.py b/tests/dataset/test_dataset.py
index 4fb5ec09..9bdec2c6 100644
--- a/tests/dataset/test_dataset.py
+++ b/tests/dataset/test_dataset.py
@@ -127,7 +127,7 @@ def test_datadoc():
     """Test save_datadoc() and load_dict()/save_dict()."""
     # pylint: disable=too-many-statements
 
-    from dataset_paths import indir  # pytest: disable=import-error
+    from dataset_paths import indir  # pylint: disable=import-error
 
     from tripper import CHAMEO, DCAT, EMMO, OTEIO, Triplestore
     from tripper.dataset import load_dict, save_datadoc, save_dict, search_iris
@@ -220,7 +220,7 @@ def test_pipeline():
     from tripper import Triplestore
 
     otelib = pytest.importorskip("otelib")
-    from dataset_paths import indir  # pytest: disable=import-error
+    from dataset_paths import indir  # pylint: disable=import-error
 
     from tripper.dataset import get_partial_pipeline, save_datadoc
 

From 4cc88cb0fb119697f35184177e9dbfb697141ac4 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 16 Dec 2024 15:53:34 +0100
Subject: [PATCH 09/59] Fixed pylint errors

---
 tripper/dataset/dataset.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/tripper/dataset/dataset.py b/tripper/dataset/dataset.py
index b98eaeaa..bbb4a178 100644
--- a/tripper/dataset/dataset.py
+++ b/tripper/dataset/dataset.py
@@ -42,9 +42,6 @@
 from pathlib import Path
 from typing import TYPE_CHECKING
 
-import requests
-import yaml  # type: ignore
-
 from tripper import DCAT, EMMO, OTEIO, OWL, RDF, Triplestore
 from tripper.utils import AttrDict, as_python
 

From 92b213d7b2a292b04ddbaf0921d4e046a27e95db Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Thu, 19 Dec 2024 10:10:35 +0100
Subject: [PATCH 10/59] added csv file

---
 tests/input/semdata.csv | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 tests/input/semdata.csv

diff --git a/tests/input/semdata.csv b/tests/input/semdata.csv
new file mode 100644
index 00000000..631d9e69
--- /dev/null
+++ b/tests/input/semdata.csv
@@ -0,0 +1,5 @@
+@id;@type;title;description;creator;contactPoint;inSeries;datamodel;datamodelStorage;distribution.downloadURL;distribution.mediaType;distribution.parser;fromSample;isDescriptionOf
+semdata:SEM_cement_batch2/77600-23-001/77600-23-001_5kV_400x_m001;sem:SEMImage;SEM image of cement;Back-scattered SEM image of cement sample 77600 from Heidelberg, polished with 1 µm diamond compound.;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>;semdata:SEM_cement_batch2/77600-23-001;http://onto-ns.com/meta/matchmaker/0.2/SEMImage;https://github.com/HEU-MatCHMaker/DataDocumentation/blob/master/SEM/datamodels/SEMImage.yaml;https://github.com/EMMC-ASBL/tripper/raw/refs/heads/dataset/tests/input/77600-23-001_5kV_400x_m001.tif;image/tiff;parser:sem_hitachi;sample:SEM_cement_batch2/77600-23-001;mat:concrete1
+semdata:SEM_cement_batch2/77600-23-001;sem:SEMImageSeries;Series of SEM image of cement sample 77600;Back-scattered SEM image of cement sample 77600, polished with 1 µm diamond compound.;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>;semdata:SEM_cement_batch2; ;;sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2/77600-23-001;inode/directory;;;
+semdata:SEM_cement_batch2;sem:SEMImageSeries;Nested series of SEM images of cement batch2;…;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>; ;;;sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2;inode/directory;;;
+mple:SEM_cement_batch2/77600-23-001;chameo:Sample;Series for SEM images for sample 77600-23-001.; ;;;;;;;;;;

From ae20a0a3dc36926c90511f522b47dbbce5b04259 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Thu, 19 Dec 2024 10:54:48 +0100
Subject: [PATCH 11/59] Added csv parser

---
 tests/dataset/test_tabledoc.py | 28 ++++++++++++++++++++++++++++
 tests/input/semdata.csv        |  8 ++++----
 tripper/dataset/tabledoc.py    | 25 +++++++++++++++++++++++++
 3 files changed, 57 insertions(+), 4 deletions(-)

diff --git a/tests/dataset/test_tabledoc.py b/tests/dataset/test_tabledoc.py
index 4a1c0613..52ea9236 100644
--- a/tests/dataset/test_tabledoc.py
+++ b/tests/dataset/test_tabledoc.py
@@ -79,3 +79,31 @@ def test_as_dicts():
     ts = Triplestore(backend="rdflib")
     td.save(ts)
     print(ts.serialize())
+
+
+if True:
+    # def test_parse_csv():
+    """Test parsing a csv file."""
+    from dataset_paths import indir  # pylint: disable=import-error
+
+    from tripper.dataset import TableDoc
+
+    td = TableDoc.parse_csv(
+        indir / "semdata.csv",
+        delimiter=";",
+        prefixes={
+            "sem": "https://w3id.com/emmo/domain/sem/0.1#",
+            "semdata": "https://he-matchmaker.eu/data/sem/",
+            "sample": "https://he-matchmaker.eu/sample/",
+            "mat": "https://he-matchmaker.eu/material/",
+            "dm": "http://onto-ns.com/meta/characterisation/0.1/SEMImage#",
+            "parser": "http://sintef.no/dlite/parser#",
+            "gen": "http://sintef.no/dlite/generator#",
+        },
+    )
+
+    img, series, batch, sample = td.asdicts()
+    assert img["@id"] == (
+        "https://he-matchmaker.eu/data/sem/SEM_cement_batch2/"
+        "77600-23-001/77600-23-001_5kV_400x_m001"
+    )
diff --git a/tests/input/semdata.csv b/tests/input/semdata.csv
index 631d9e69..4df732ef 100644
--- a/tests/input/semdata.csv
+++ b/tests/input/semdata.csv
@@ -1,5 +1,5 @@
 @id;@type;title;description;creator;contactPoint;inSeries;datamodel;datamodelStorage;distribution.downloadURL;distribution.mediaType;distribution.parser;fromSample;isDescriptionOf
-semdata:SEM_cement_batch2/77600-23-001/77600-23-001_5kV_400x_m001;sem:SEMImage;SEM image of cement;Back-scattered SEM image of cement sample 77600 from Heidelberg, polished with 1 µm diamond compound.;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>;semdata:SEM_cement_batch2/77600-23-001;http://onto-ns.com/meta/matchmaker/0.2/SEMImage;https://github.com/HEU-MatCHMaker/DataDocumentation/blob/master/SEM/datamodels/SEMImage.yaml;https://github.com/EMMC-ASBL/tripper/raw/refs/heads/dataset/tests/input/77600-23-001_5kV_400x_m001.tif;image/tiff;parser:sem_hitachi;sample:SEM_cement_batch2/77600-23-001;mat:concrete1
-semdata:SEM_cement_batch2/77600-23-001;sem:SEMImageSeries;Series of SEM image of cement sample 77600;Back-scattered SEM image of cement sample 77600, polished with 1 µm diamond compound.;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>;semdata:SEM_cement_batch2; ;;sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2/77600-23-001;inode/directory;;;
-semdata:SEM_cement_batch2;sem:SEMImageSeries;Nested series of SEM images of cement batch2;…;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>; ;;;sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2;inode/directory;;;
-mple:SEM_cement_batch2/77600-23-001;chameo:Sample;Series for SEM images for sample 77600-23-001.; ;;;;;;;;;;
+semdata:SEM_cement_batch2/77600-23-001/77600-23-001_5kV_400x_m001;sem:SEMImage;SEM image of cement;Back-scattered SEM image of cement sample 77600 from Heidelberg, polished with 1 um diamond compound.;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>;semdata:SEM_cement_batch2/77600-23-001;http://onto-ns.com/meta/matchmaker/0.2/SEMImage;https://github.com/HEU-MatCHMaker/DataDocumentation/blob/master/SEM/datamodels/SEMImage.yaml;https://github.com/EMMC-ASBL/tripper/raw/refs/heads/dataset/tests/input/77600-23-001_5kV_400x_m001.tif;image/tiff;parser:sem_hitachi;sample:SEM_cement_batch2/77600-23-001;mat:concrete1
+semdata:SEM_cement_batch2/77600-23-001;sem:SEMImageSeries;Series of SEM image of cement sample 77600;Back-scattered SEM image of cement sample 77600, polished with 1 um diamond compound.;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>;semdata:SEM_cement_batch2; ;;sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2/77600-23-001;inode/directory;;;
+semdata:SEM_cement_batch2;sem:SEMImageSeries;Nested series of SEM images of cement batch2;...;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>; ;;;sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2;inode/directory;;;
+sample:SEM_cement_batch2/77600-23-001;chameo:Sample;Series for SEM images for sample 77600-23-001.; ;;;;;;;;;;
diff --git a/tripper/dataset/tabledoc.py b/tripper/dataset/tabledoc.py
index b1a8ef51..50fe86b7 100644
--- a/tripper/dataset/tabledoc.py
+++ b/tripper/dataset/tabledoc.py
@@ -1,5 +1,7 @@
 """Basic interface for tabular documentation of datasets."""
 
+import csv
+from pathlib import Path
 from typing import TYPE_CHECKING
 
 from tripper import Triplestore
@@ -66,3 +68,26 @@ def save(self, ts: Triplestore) -> None:
         """Save tabular datadocumentation to triplestore."""
         for d in self.asdicts():
             save_dict(ts, d)
+
+    @classmethod
+    def parse_csv(
+        self,
+        csvfile: "Union[Path, str]",
+        type: "Optional[str]" = "dataset",
+        prefixes: "Optional[dict]" = None,
+        context: "Optional[Union[dict, list]]" = None,
+        dialect="excel",
+        **kwargs,
+    ) -> None:
+        """Parse a csv file."""
+        with open(csvfile, newline="") as f:
+            reader = csv.reader(f, dialect=dialect, **kwargs)
+            header = next(reader)[0].split(reader.dialect.delimiter)
+            data = [row for row in reader]
+        return TableDoc(
+            header=header,
+            data=data,
+            type=type,
+            prefixes=prefixes,
+            context=context,
+        )

From 543e99e743876f68eaa8913c02d9df33ffc3ca07 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Thu, 19 Dec 2024 10:59:01 +0100
Subject: [PATCH 12/59] Updated the test

---
 tests/dataset/test_tabledoc.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/tests/dataset/test_tabledoc.py b/tests/dataset/test_tabledoc.py
index 52ea9236..ae7ca348 100644
--- a/tests/dataset/test_tabledoc.py
+++ b/tests/dataset/test_tabledoc.py
@@ -81,13 +81,16 @@ def test_as_dicts():
     print(ts.serialize())
 
 
-if True:
-    # def test_parse_csv():
+#if True:
+def test_parse_csv():
     """Test parsing a csv file."""
     from dataset_paths import indir  # pylint: disable=import-error
 
+    from tripper import Triplestore
     from tripper.dataset import TableDoc
 
+    pytest.importorskip("rdflib")
+
     td = TableDoc.parse_csv(
         indir / "semdata.csv",
         delimiter=";",
@@ -107,3 +110,7 @@ def test_as_dicts():
         "https://he-matchmaker.eu/data/sem/SEM_cement_batch2/"
         "77600-23-001/77600-23-001_5kV_400x_m001"
     )
+
+    ts = Triplestore(backend="rdflib")
+    td.save(ts)
+    print(ts.serialize())

From b3e3d0723f879547099aabcc45f9148e4a959700 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 19 Dec 2024 09:59:28 +0000
Subject: [PATCH 13/59] [pre-commit.ci] auto fixes from pre-commit hooks

For more information, see https://pre-commit.ci
---
 tests/dataset/test_tabledoc.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/dataset/test_tabledoc.py b/tests/dataset/test_tabledoc.py
index ae7ca348..00179810 100644
--- a/tests/dataset/test_tabledoc.py
+++ b/tests/dataset/test_tabledoc.py
@@ -81,7 +81,7 @@ def test_as_dicts():
     print(ts.serialize())
 
 
-#if True:
+# if True:
 def test_parse_csv():
     """Test parsing a csv file."""
     from dataset_paths import indir  # pylint: disable=import-error

From 700c514282a8374f32dd5d858be87e466be1eb4a Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Thu, 19 Dec 2024 13:17:46 +0100
Subject: [PATCH 14/59] Fixed failing tests

---
 tests/dataset/test_tabledoc.py |  8 +++++---
 tripper/dataset/tabledoc.py    | 35 +++++++++++++++++++++++++++-------
 2 files changed, 33 insertions(+), 10 deletions(-)

diff --git a/tests/dataset/test_tabledoc.py b/tests/dataset/test_tabledoc.py
index ae7ca348..f1640dbc 100644
--- a/tests/dataset/test_tabledoc.py
+++ b/tests/dataset/test_tabledoc.py
@@ -81,16 +81,16 @@ def test_as_dicts():
     print(ts.serialize())
 
 
-#if True:
+# if True:
 def test_parse_csv():
     """Test parsing a csv file."""
     from dataset_paths import indir  # pylint: disable=import-error
 
+    pytest.importorskip("rdflib")
+
     from tripper import Triplestore
     from tripper.dataset import TableDoc
 
-    pytest.importorskip("rdflib")
-
     td = TableDoc.parse_csv(
         indir / "semdata.csv",
         delimiter=";",
@@ -105,7 +105,9 @@ def test_parse_csv():
         },
     )
 
+    # pylint: disable=unused-variable,unbalanced-tuple-unpacking
     img, series, batch, sample = td.asdicts()
+
     assert img["@id"] == (
         "https://he-matchmaker.eu/data/sem/SEM_cement_batch2/"
         "77600-23-001/77600-23-001_5kV_400x_m001"
diff --git a/tripper/dataset/tabledoc.py b/tripper/dataset/tabledoc.py
index 50fe86b7..1dc37098 100644
--- a/tripper/dataset/tabledoc.py
+++ b/tripper/dataset/tabledoc.py
@@ -69,21 +69,42 @@ def save(self, ts: Triplestore) -> None:
         for d in self.asdicts():
             save_dict(ts, d)
 
-    @classmethod
+    @staticmethod
     def parse_csv(
-        self,
         csvfile: "Union[Path, str]",
         type: "Optional[str]" = "dataset",
         prefixes: "Optional[dict]" = None,
         context: "Optional[Union[dict, list]]" = None,
-        dialect="excel",
+        dialect: "Union[csv.Dialect, str]" = "excel",
         **kwargs,
-    ) -> None:
-        """Parse a csv file."""
-        with open(csvfile, newline="") as f:
+    ) -> "TableDoc":
+        # pylint: disable=line-too-long
+        """Parse a csv file using the standard library csv module.
+
+        Arguments:
+            csvfile: CSV file to parse.
+            type: Type of data to save (applies to all rows).  Should
+                either be one of the pre-defined names: "dataset",
+                "distribution", "accessService", "parser" and "generator"
+                or an IRI to a class in an ontology.  Defaults to
+                "dataset".
+            prefixes: Dict with prefixes in addition to those included in the
+                JSON-LD context.  Should map namespace prefixes to IRIs.
+            context: Dict with user-defined JSON-LD context.
+            dialect: A subclass of csv.Dialect, or the name of the dialect,
+                specifying how the `csvfile` is formatted.  For more details,
+                see [Dialects and Formatting Parameters].
+            kwargs: Additional keyword arguments overriding individual
+                formatting parameters.  For more details, see
+                [Dialects and Formatting Parameters].
+
+        References:
+        [Dialects and Formatting Parameters]: https://docs.python.org/3/library/csv.html#dialects-and-formatting-parameters
+        """
+        with open(csvfile, encoding="utf-8") as f:
             reader = csv.reader(f, dialect=dialect, **kwargs)
             header = next(reader)[0].split(reader.dialect.delimiter)
-            data = [row for row in reader]
+            data = list(reader)
         return TableDoc(
             header=header,
             data=data,

From 4d7d77adc9233b39ad05dfd6fb4222feef814b94 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Thu, 19 Dec 2024 13:33:10 +0100
Subject: [PATCH 15/59] Added encoding to keyword arguments

---
 tests/input/semdata.csv     | 4 ++--
 tripper/dataset/tabledoc.py | 5 ++++-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/tests/input/semdata.csv b/tests/input/semdata.csv
index 4df732ef..c3cf536c 100644
--- a/tests/input/semdata.csv
+++ b/tests/input/semdata.csv
@@ -1,5 +1,5 @@
 @id;@type;title;description;creator;contactPoint;inSeries;datamodel;datamodelStorage;distribution.downloadURL;distribution.mediaType;distribution.parser;fromSample;isDescriptionOf
-semdata:SEM_cement_batch2/77600-23-001/77600-23-001_5kV_400x_m001;sem:SEMImage;SEM image of cement;Back-scattered SEM image of cement sample 77600 from Heidelberg, polished with 1 um diamond compound.;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>;semdata:SEM_cement_batch2/77600-23-001;http://onto-ns.com/meta/matchmaker/0.2/SEMImage;https://github.com/HEU-MatCHMaker/DataDocumentation/blob/master/SEM/datamodels/SEMImage.yaml;https://github.com/EMMC-ASBL/tripper/raw/refs/heads/dataset/tests/input/77600-23-001_5kV_400x_m001.tif;image/tiff;parser:sem_hitachi;sample:SEM_cement_batch2/77600-23-001;mat:concrete1
-semdata:SEM_cement_batch2/77600-23-001;sem:SEMImageSeries;Series of SEM image of cement sample 77600;Back-scattered SEM image of cement sample 77600, polished with 1 um diamond compound.;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>;semdata:SEM_cement_batch2; ;;sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2/77600-23-001;inode/directory;;;
+semdata:SEM_cement_batch2/77600-23-001/77600-23-001_5kV_400x_m001;sem:SEMImage;SEM image of cement;Back-scattered SEM image of cement sample 77600 from Heidelberg, polished with 1 μm diamond compound.;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>;semdata:SEM_cement_batch2/77600-23-001;http://onto-ns.com/meta/matchmaker/0.2/SEMImage;https://github.com/HEU-MatCHMaker/DataDocumentation/blob/master/SEM/datamodels/SEMImage.yaml;https://github.com/EMMC-ASBL/tripper/raw/refs/heads/dataset/tests/input/77600-23-001_5kV_400x_m001.tif;image/tiff;parser:sem_hitachi;sample:SEM_cement_batch2/77600-23-001;mat:concrete1
+semdata:SEM_cement_batch2/77600-23-001;sem:SEMImageSeries;Series of SEM image of cement sample 77600;Back-scattered SEM image of cement sample 77600, polished with 1 μm diamond compound.;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>;semdata:SEM_cement_batch2; ;;sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2/77600-23-001;inode/directory;;;
 semdata:SEM_cement_batch2;sem:SEMImageSeries;Nested series of SEM images of cement batch2;...;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>; ;;;sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2;inode/directory;;;
 sample:SEM_cement_batch2/77600-23-001;chameo:Sample;Series for SEM images for sample 77600-23-001.; ;;;;;;;;;;
diff --git a/tripper/dataset/tabledoc.py b/tripper/dataset/tabledoc.py
index 1dc37098..46ad4313 100644
--- a/tripper/dataset/tabledoc.py
+++ b/tripper/dataset/tabledoc.py
@@ -75,6 +75,7 @@ def parse_csv(
         type: "Optional[str]" = "dataset",
         prefixes: "Optional[dict]" = None,
         context: "Optional[Union[dict, list]]" = None,
+        encoding: str = "utf-8",
         dialect: "Union[csv.Dialect, str]" = "excel",
         **kwargs,
     ) -> "TableDoc":
@@ -91,6 +92,8 @@ def parse_csv(
             prefixes: Dict with prefixes in addition to those included in the
                 JSON-LD context.  Should map namespace prefixes to IRIs.
             context: Dict with user-defined JSON-LD context.
+            encoding: The encoding of the csv file.  Note that Excel may
+                encode as "ISO-8859" (commonly used in 1990th).
             dialect: A subclass of csv.Dialect, or the name of the dialect,
                 specifying how the `csvfile` is formatted.  For more details,
                 see [Dialects and Formatting Parameters].
@@ -101,7 +104,7 @@ def parse_csv(
         References:
         [Dialects and Formatting Parameters]: https://docs.python.org/3/library/csv.html#dialects-and-formatting-parameters
         """
-        with open(csvfile, encoding="utf-8") as f:
+        with open(csvfile, encoding=encoding) as f:
             reader = csv.reader(f, dialect=dialect, **kwargs)
             header = next(reader)[0].split(reader.dialect.delimiter)
             data = list(reader)

From 80048677f0c4612154dcca687565c90423a56eb0 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Fri, 20 Dec 2024 15:30:39 +0100
Subject: [PATCH 16/59] Strip off blanks when parsing a table.

---
 tripper/dataset/tabledoc.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/tripper/dataset/tabledoc.py b/tripper/dataset/tabledoc.py
index 46ad4313..75edb181 100644
--- a/tripper/dataset/tabledoc.py
+++ b/tripper/dataset/tabledoc.py
@@ -28,6 +28,7 @@ class TableDoc:
         prefixes: Dict with prefixes in addition to those included in the
             JSON-LD context.  Should map namespace prefixes to IRIs.
         context: Dict with user-defined JSON-LD context.
+        strip: Whether to strip leading and trailing whitespaces from cells.
 
     """
 
@@ -40,12 +41,14 @@ def __init__(
         type: "Optional[str]" = "dataset",
         prefixes: "Optional[dict]" = None,
         context: "Optional[Union[dict, list]]" = None,
+        strip: bool = True,
     ):
         self.header = header
         self.data = data
         self.type = type
         self.prefixes = prefixes
         self.context = context
+        self.strip = strip
 
     def asdicts(self) -> "List[dict]":
         """Return the table as a list of dicts."""
@@ -55,9 +58,11 @@ def asdicts(self) -> "List[dict]":
         for row in self.data:
             d = AttrDict()
             for i, colname in enumerate(self.header):
-                cell = row[i]
+                cell = row[i].strip() if self.strip else row[i]
                 if cell:
-                    addnested(d, colname, cell)
+                    addnested(
+                        d, colname.strip() if self.strip else colname, cell
+                    )
             jsonld = as_jsonld(
                 d, type=self.type, prefixes=self.prefixes, **kw  # type: ignore
             )
@@ -106,8 +111,9 @@ def parse_csv(
         """
         with open(csvfile, encoding=encoding) as f:
             reader = csv.reader(f, dialect=dialect, **kwargs)
-            header = next(reader)[0].split(reader.dialect.delimiter)
+            header = next(reader)
             data = list(reader)
+
         return TableDoc(
             header=header,
             data=data,

From 731253cd16ba58525b739166892251a0d88ca8af Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Fri, 20 Dec 2024 15:39:14 +0100
Subject: [PATCH 17/59] Added extra test to ensure that all properties are
 parsed correctly

---
 tests/dataset/test_tabledoc.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/dataset/test_tabledoc.py b/tests/dataset/test_tabledoc.py
index f1640dbc..e9fff0c1 100644
--- a/tests/dataset/test_tabledoc.py
+++ b/tests/dataset/test_tabledoc.py
@@ -112,6 +112,10 @@ def test_parse_csv():
         "https://he-matchmaker.eu/data/sem/SEM_cement_batch2/"
         "77600-23-001/77600-23-001_5kV_400x_m001"
     )
+    assert img.distribution.downloadURL == (
+        "https://github.com/EMMC-ASBL/tripper/raw/refs/heads/dataset/"
+        "tests/input/77600-23-001_5kV_400x_m001.tif"
+    )
 
     ts = Triplestore(backend="rdflib")
     td.save(ts)

From 60b0c6d2657242d36c5cac1f979ba7172783fba6 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Fri, 20 Dec 2024 15:57:11 +0100
Subject: [PATCH 18/59] Added write_csv() method to TableDoc

---
 tests/dataset/test_tabledoc.py |  9 +++++++--
 tripper/dataset/tabledoc.py    | 31 ++++++++++++++++++++++++++++++-
 2 files changed, 37 insertions(+), 3 deletions(-)

diff --git a/tests/dataset/test_tabledoc.py b/tests/dataset/test_tabledoc.py
index e9fff0c1..5020989c 100644
--- a/tests/dataset/test_tabledoc.py
+++ b/tests/dataset/test_tabledoc.py
@@ -82,15 +82,16 @@ def test_as_dicts():
 
 
 # if True:
-def test_parse_csv():
+def test_csv():
     """Test parsing a csv file."""
-    from dataset_paths import indir  # pylint: disable=import-error
+    from dataset_paths import indir, outdir  # pylint: disable=import-error
 
     pytest.importorskip("rdflib")
 
     from tripper import Triplestore
     from tripper.dataset import TableDoc
 
+    # Read csv file
     td = TableDoc.parse_csv(
         indir / "semdata.csv",
         delimiter=";",
@@ -117,6 +118,10 @@ def test_parse_csv():
         "tests/input/77600-23-001_5kV_400x_m001.tif"
     )
 
+    # Write the table to a new csv file
+    td.write_csv(outdir / "semdata.csv")
+
+    # Print serialised KB
     ts = Triplestore(backend="rdflib")
     td.save(ts)
     print(ts.serialize())
diff --git a/tripper/dataset/tabledoc.py b/tripper/dataset/tabledoc.py
index 75edb181..65337d83 100644
--- a/tripper/dataset/tabledoc.py
+++ b/tripper/dataset/tabledoc.py
@@ -109,7 +109,7 @@ def parse_csv(
         References:
         [Dialects and Formatting Parameters]: https://docs.python.org/3/library/csv.html#dialects-and-formatting-parameters
         """
-        with open(csvfile, encoding=encoding) as f:
+        with open(csvfile, mode="rt", encoding=encoding) as f:
             reader = csv.reader(f, dialect=dialect, **kwargs)
             header = next(reader)
             data = list(reader)
@@ -121,3 +121,32 @@ def parse_csv(
             prefixes=prefixes,
             context=context,
         )
+
+    def write_csv(
+        self,
+        csvfile: "Union[Path, str]",
+        encoding: str = "utf-8",
+        dialect: "Union[csv.Dialect, str]" = "excel",
+        **kwargs,
+    ) -> None:
+        # pylint: disable=line-too-long
+        """Write the table to a csv file using the standard library csv module.
+
+        Arguments:
+            csvfile: CSV file to parse.
+            encoding: The encoding of the csv file.
+            dialect: A subclass of csv.Dialect, or the name of the dialect,
+                specifying how the `csvfile` is formatted.  For more details,
+                see [Dialects and Formatting Parameters].
+            kwargs: Additional keyword arguments overriding individual
+                formatting parameters.  For more details, see
+                [Dialects and Formatting Parameters].
+
+        References:
+        [Dialects and Formatting Parameters]: https://docs.python.org/3/library/csv.html#dialects-and-formatting-parameters
+        """
+        with open(csvfile, mode="wt", encoding=encoding) as f:
+            writer = csv.writer(f, dialect=dialect, **kwargs)
+            writer.writerow(self.header)
+            for row in self.data:
+                writer.writerow(row)

From d26d92fdabfc27090558a66ed5c9362de026bb11 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 30 Dec 2024 12:14:49 +0100
Subject: [PATCH 19/59] Save serialised documentation to turtle file.

---
 tests/dataset/test_tabledoc.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/dataset/test_tabledoc.py b/tests/dataset/test_tabledoc.py
index 5020989c..2d3c8779 100644
--- a/tests/dataset/test_tabledoc.py
+++ b/tests/dataset/test_tabledoc.py
@@ -124,4 +124,5 @@ def test_csv():
     # Print serialised KB
     ts = Triplestore(backend="rdflib")
     td.save(ts)
+    ts.serialize(outdir / "semdata.ttl")
     print(ts.serialize())

From 66b9dd75d0291359f9507033b9a8159cf0a8d320 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper-friis@users.noreply.github.com>
Date: Mon, 30 Dec 2024 12:23:13 +0100
Subject: [PATCH 20/59] Apply suggestions from code review

Co-authored-by: Tor S. Haugland <torshaugland@gmail.com>
---
 pyproject.toml                 | 1 -
 tests/dataset/test_tabledoc.py | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 21196860..0398f0a0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -105,7 +105,6 @@ max-locals = 20
 disable = [
     "fixme",
     "invalid-name",
-    #"too-many-positional-arguments",
 ]
 good-names = [
     # Default
diff --git a/tests/dataset/test_tabledoc.py b/tests/dataset/test_tabledoc.py
index 4a1c0613..da74203c 100644
--- a/tests/dataset/test_tabledoc.py
+++ b/tests/dataset/test_tabledoc.py
@@ -1,4 +1,4 @@
-"""Test the dataset module."""
+"""Test the TableDoc class."""
 
 import pytest
 

From 575f09d2b13deb60ce8ae9addeb734650223ca31 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper-friis@users.noreply.github.com>
Date: Mon, 30 Dec 2024 12:30:22 +0100
Subject: [PATCH 21/59] Apply suggestions from code review

Co-authored-by: Tor S. Haugland <torshaugland@gmail.com>
---
 tripper/dataset/tabledoc.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tripper/dataset/tabledoc.py b/tripper/dataset/tabledoc.py
index b1a8ef51..9fd5d988 100644
--- a/tripper/dataset/tabledoc.py
+++ b/tripper/dataset/tabledoc.py
@@ -47,7 +47,7 @@ def __init__(
 
     def asdicts(self) -> "List[dict]":
         """Return the table as a list of dicts."""
-        kw = {"_context": self.context} if self.context else {}
+        kw = {"@context": self.context} if self.context else {}
 
         results = []
         for row in self.data:

From f45376db770b151d6ea7eb4de901fb646ef3dc43 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 30 Dec 2024 12:49:06 +0100
Subject: [PATCH 22/59] Added a clarifying comment as a responce to review
 comment by @torhaugl.

---
 tests/dataset/test_tabledoc.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/dataset/test_tabledoc.py b/tests/dataset/test_tabledoc.py
index da74203c..278e7881 100644
--- a/tests/dataset/test_tabledoc.py
+++ b/tests/dataset/test_tabledoc.py
@@ -32,6 +32,8 @@ def test_as_dicts():
             "onto": "http:/example.com/onto#",
             "ds": "http:/example.com/datasets#",
         },
+        # Replace the "ds" prefix above with this, once the "context" keyword
+        # argument is fully implemented.
         # context={
         #    "ds": "http:/example.com/datasets#",
         # },

From 1752db0016a521ad6f0b3e9a2bd4ab5997482181 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 30 Dec 2024 15:43:00 +0100
Subject: [PATCH 23/59] Fix test failure

---
 tripper/dataset/tabledoc.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tripper/dataset/tabledoc.py b/tripper/dataset/tabledoc.py
index 0711565b..6dbf8b32 100644
--- a/tripper/dataset/tabledoc.py
+++ b/tripper/dataset/tabledoc.py
@@ -58,7 +58,7 @@ def asdicts(self) -> "List[dict]":
         for row in self.data:
             d = AttrDict()
             for i, colname in enumerate(self.header):
-                cell = row[i].strip() if self.strip else row[i]
+                cell = row[i].strip() if row[i] and self.strip else row[i]
                 if cell:
                     addnested(
                         d, colname.strip() if self.strip else colname, cell

From 9b53f5e3eccfe6c7c326b18207a49dd53fdd4c15 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 30 Dec 2024 18:30:53 +0100
Subject: [PATCH 24/59] Added `context` argument to get_jsonld_context()

---
 tests/dataset/test_dataset.py |  9 +++++++
 tripper/dataset/dataset.py    | 48 ++++++++++++++++++++++-------------
 2 files changed, 39 insertions(+), 18 deletions(-)

diff --git a/tests/dataset/test_dataset.py b/tests/dataset/test_dataset.py
index 9bdec2c6..240d1bf7 100644
--- a/tests/dataset/test_dataset.py
+++ b/tests/dataset/test_dataset.py
@@ -11,6 +11,7 @@
 def test_get_jsonld_context():
     """Test get_jsonld_context()."""
     from tripper.dataset import get_jsonld_context
+    from tripper.dataset.dataset import CONTEXT_URL
 
     context = get_jsonld_context()
     assert isinstance(context, dict)
@@ -21,6 +22,14 @@ def test_get_jsonld_context():
     online_context = get_jsonld_context(fromfile=False)
     assert online_context == context
 
+    # Test context argument
+    context2 = get_jsonld_context(context=CONTEXT_URL)
+    assert context2 == context
+
+    assert "newkey" not in context
+    context3 = get_jsonld_context(context={"newkey": "onto:newkey"})
+    assert context3["newkey"] == "onto:newkey"
+
 
 def test_get_prefixes():
     """Test get_prefixes()."""
diff --git a/tripper/dataset/dataset.py b/tripper/dataset/dataset.py
index bbb4a178..4e779170 100644
--- a/tripper/dataset/dataset.py
+++ b/tripper/dataset/dataset.py
@@ -26,15 +26,12 @@
 
 ---
 
-__TODO__: Update the URL to the JSON-LD context when merged to master
-
 [DCAT]: https://www.w3.org/TR/vocab-dcat-3/
 [JSON-LD context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/dataset/tripper/context/0.2/context.json
 
 """
 
 # pylint: disable=invalid-name,redefined-builtin,import-outside-toplevel
-import functools
 import io
 import json
 import re
@@ -50,18 +47,12 @@
 
     from tripper.utils import Triple
 
-# Cache decorator
-cache = (
-    functools.cache  # new in Python 3.9, smaller and faster than lru_cache()
-    if hasattr(functools, "cache")
-    else functools.lru_cache(maxsize=1)
-)
 
 # Local path (for fast loading) and URL to the JSON-LD context
 CONTEXT_PATH = (
     Path(__file__).parent.parent / "context" / "0.2" / "context.json"
 ).as_uri()
-CONTEXT_URL = (  # __TODO__: Update URL when merged to master
+CONTEXT_URL = (
     "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/"
     "master/tripper/context/0.2/context.json"
 )
@@ -339,11 +330,11 @@ def get_values(
     return values
 
 
-# TODO: update this function to take an initial argument `context`,
-# which can be an URL (string), dict with raw context or a list of
-# strings or dicts.
-@cache  # type: ignore
-def get_jsonld_context(timeout: float = 5, fromfile: bool = True) -> dict:
+def get_jsonld_context(
+    context: "Optional[Union[str, dict, Sequence[Union[str, dict]]]]" = None,
+    timeout: float = 5,
+    fromfile: bool = True,
+) -> dict:
     """Returns the JSON-LD context as a dict.
 
     The JSON-LD context maps all the keywords that can be used as keys
@@ -351,6 +342,10 @@ def get_jsonld_context(timeout: float = 5, fromfile: bool = True) -> dict:
     common vocabularies and ontologies.
 
     Arguments:
+        context: Additional user-defined context that should be returned
+            on top of the default context.  It may be a string with an URL
+            to the user-defined context, a dict with the user-defined context
+            or a sequence of strings and dicts.
         timeout: Number of seconds before timing out.
         fromfile: Whether to load the context from local file.
 
@@ -359,11 +354,28 @@ def get_jsonld_context(timeout: float = 5, fromfile: bool = True) -> dict:
 
     if fromfile:
         with open(CONTEXT_PATH[7:], "r", encoding="utf-8") as f:
-            context = json.load(f)["@context"]
+            ctx = json.load(f)["@context"]
     else:
         r = requests.get(CONTEXT_URL, allow_redirects=True, timeout=timeout)
-        context = json.loads(r.content)["@context"]
-    return context
+        ctx = json.loads(r.content)["@context"]
+
+    if isinstance(context, (str, dict)):
+        context = [context]
+
+    if context:
+        for token in context:
+            if isinstance(token, str):
+                r = requests.get(token, allow_redirects=True, timeout=timeout)
+                ctx.update(json.loads(r.content)["@context"])
+            elif isinstance(token, dict):
+                ctx.update(token)
+            else:
+                raise TypeError(
+                    "`context` must be a string (URL), dict or a sequence of "
+                    f"strings and dicts.  Not '{type(token)}'"
+                )
+
+    return ctx
 
 
 # TODO: update this to take an initial argument `context`.

From 26ee5188d73577455014de06dbff96a8fc115bdc Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 30 Dec 2024 18:41:01 +0100
Subject: [PATCH 25/59] Added `context` argument to get_prefixes()

---
 tests/dataset/test_dataset.py |  4 ++++
 tripper/dataset/dataset.py    | 19 +++++++++++++------
 2 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/tests/dataset/test_dataset.py b/tests/dataset/test_dataset.py
index 240d1bf7..4d833a9b 100644
--- a/tests/dataset/test_dataset.py
+++ b/tests/dataset/test_dataset.py
@@ -39,6 +39,10 @@ def test_get_prefixes():
     assert prefixes["dcat"] == "http://www.w3.org/ns/dcat#"
     assert prefixes["emmo"] == "https://w3id.org/emmo#"
 
+    # Test context argument
+    prefixes2 = get_prefixes(context={"onto": "http://example.com/onto#"})
+    assert prefixes2["onto"] == "http://example.com/onto#"
+
 
 def test_get_shortnames():
     """Test get_shortnames()."""
diff --git a/tripper/dataset/dataset.py b/tripper/dataset/dataset.py
index 4e779170..2e4a3398 100644
--- a/tripper/dataset/dataset.py
+++ b/tripper/dataset/dataset.py
@@ -378,15 +378,22 @@ def get_jsonld_context(
     return ctx
 
 
-# TODO: update this to take an initial argument `context`.
-# See get_jsonld_context()
-def get_prefixes(timeout: float = 5) -> dict:
+def get_prefixes(
+    context: "Optional[Union[str, dict, Sequence[Union[str, dict]]]]" = None,
+    timeout: float = 5,
+    fromfile: bool = True,
+) -> dict:
     """Loads the JSON-LD context and returns a dict mapping prefixes to
-    their namespace URL."""
-    context = get_jsonld_context(timeout=timeout)
+    their namespace URL.
+
+    For arguments, see get_jsonld_context().
+    """
+    ctx = get_jsonld_context(
+        context=context, timeout=timeout, fromfile=fromfile
+    )
     prefixes = {
         k: v
-        for k, v in context.items()
+        for k, v in ctx.items()
         if isinstance(v, str) and v.endswith(("#", "/"))
     }
     return prefixes

From 568abd79517bd9147f7f01bbb07a4ad65db535ea Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 30 Dec 2024 18:47:49 +0100
Subject: [PATCH 26/59] Added `context?  argument to get_shortnames()

---
 tripper/dataset/dataset.py | 23 +++++++++++++++--------
 1 file changed, 15 insertions(+), 8 deletions(-)

diff --git a/tripper/dataset/dataset.py b/tripper/dataset/dataset.py
index 2e4a3398..022bcc3e 100644
--- a/tripper/dataset/dataset.py
+++ b/tripper/dataset/dataset.py
@@ -386,7 +386,7 @@ def get_prefixes(
     """Loads the JSON-LD context and returns a dict mapping prefixes to
     their namespace URL.
 
-    For arguments, see get_jsonld_context().
+    Arguments are passed to `get_jsonld_context()`.
     """
     ctx = get_jsonld_context(
         context=context, timeout=timeout, fromfile=fromfile
@@ -399,16 +399,23 @@ def get_prefixes(
     return prefixes
 
 
-# TODO: update this to take an initial argument `context`.
-# See get_jsonld_context()
-def get_shortnames(timeout: float = 5) -> dict:
+def get_shortnames(
+    context: "Optional[Union[str, dict, Sequence[Union[str, dict]]]]" = None,
+    timeout: float = 5,
+    fromfile: bool = True,
+) -> dict:
     """Loads the JSON-LD context and returns a dict mapping IRIs to their
-    short names defined in the context."""
-    context = get_jsonld_context(timeout=timeout)
-    prefixes = get_prefixes()
+    short names defined in the context.
+
+    Arguments are passed to `get_jsonld_context()`.
+    """
+    ctx = get_jsonld_context(
+        context=context, timeout=timeout, fromfile=fromfile
+    )
+    prefixes = get_prefixes(context=ctx)
     shortnames = {
         expand_iri(v["@id"] if isinstance(v, dict) else v, prefixes): k
-        for k, v in context.items()
+        for k, v in ctx.items()
         if (
             (isinstance(v, str) and not v.endswith(("#", "/")))
             or isinstance(v, dict)

From 2988a324bc612691a7462a912f9a94ef2806c1f0 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 30 Dec 2024 18:52:44 +0100
Subject: [PATCH 27/59] Updated .gitignore files

---
 .gitignore              | 1 +
 tests/output/.gitignore | 1 +
 2 files changed, 2 insertions(+)

diff --git a/.gitignore b/.gitignore
index c872f80e..9a0e7df5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -18,3 +18,4 @@ dist/
 
 # Test output
 route.svg
+coverage.xml
diff --git a/tests/output/.gitignore b/tests/output/.gitignore
index c26b5163..613dbf65 100644
--- a/tests/output/.gitignore
+++ b/tests/output/.gitignore
@@ -3,3 +3,4 @@
 *.ttl
 *.png
 *.tiff
+*.csv

From 841a74d05faa846a5676c1dc689232fcf9844529 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Thu, 2 Jan 2025 11:34:15 +0100
Subject: [PATCH 28/59] Added documentation for the dataset sub-package

---
 README.md                        |  15 +-
 docs/dataset/datadoc-keywords.md | 222 ++++++++++++++++++++++++++++
 docs/dataset/datadoc-prefixes.md |  26 ++++
 docs/dataset/datadoc.md          | 241 +++++++++++++++++++++++++++++++
 docs/index.md                    |  15 +-
 mkdocs.yml                       |   4 +
 pyproject.toml                   |   2 +-
 tests/dataset/test_dataset.py    |  19 ++-
 tests/input/openfile.txt         |   1 +
 tests/input/semdata.yaml         |   2 +-
 tests/test_utils.py              |  81 ++++++++---
 tripper/context/0.2/context.json |  44 ++++--
 tripper/convert/convert.py       |   2 +
 tripper/dataset/dataset.py       |  14 +-
 tripper/dataset/tabledoc.py      |   4 +-
 tripper/utils.py                 |  49 ++++++-
 16 files changed, 679 insertions(+), 62 deletions(-)
 create mode 100644 docs/dataset/datadoc-keywords.md
 create mode 100644 docs/dataset/datadoc-prefixes.md
 create mode 100644 docs/dataset/datadoc.md
 create mode 100644 tests/input/openfile.txt

diff --git a/README.md b/README.md
index 61e9828f..8c791e31 100644
--- a/README.md
+++ b/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/api_reference/dataset/dataset
+[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/
diff --git a/docs/dataset/datadoc-keywords.md b/docs/dataset/datadoc-keywords.md
new file mode 100644
index 00000000..f8a27852
--- /dev/null
+++ b/docs/dataset/datadoc-keywords.md
@@ -0,0 +1,222 @@
+Predefined keywords
+===================
+All keywords listed on this page (except for the special "@"-prefixed keywords) are defined in the [default JSON-LD context].
+
+
+Special keywords for JSON-LD
+----------------------------
+See the [JSON-LD documentation] for a complete list of "@"-prefixed keywords.
+Here we only list those that are commonly used for data documentation with Tripper.
+
+- **@context**: URL to or dict with user-defined JSON-LD context.
+      Used to extend the keywords listed on this page with domain- or application-specific keywords.
+- **@id**: IRI of the documented resource.
+- **@type**: IRI of ontological class that the resource is an individual of.
+
+
+General properties on resources used by DCAT
+--------------------------------------------
+These can also be used on datasets and distributions.
+See the DCAT documentation for [dcat:Dataset] and [dcat:Distribution] for recommendations.
+
+- **[accessRights]**: Information about who can access the resource or an indication of its security status.
+- **[conformsTo]**: An established standard to which the described resource conforms.
+- **[contactPoint]**: Relevant contact information for the cataloged resource. Use of [vCard] is recommended.
+- **[creator]**: The entity responsible for producing the resource.
+- **[description]**: A free-text account of the resource.
+- **[hasCurrentVersion]**: This resource has a more specific, versioned resource with equivalent content.
+- **[hasPart]**: A related resource that is included either physically or logically in the described resource.
+- **[hasPolicy]**: An ODRL conformant policy expressing the rights associated with the resource.
+- **[hasVersion]**: This resource has a more specific, versioned resource.
+- **[identifier]**: A unique identifier of the resource being described or cataloged.
+- **[isReferencedBy]**: A related resource, such as a publication, that references, cites, or otherwise points to the cataloged resource.
+- **[issued]**: Date of formal issuance (e.g., publication) of the resource.
+- **[keyword]**: A keyword or tag describing the resource.
+- **[landingPage]**: A Web page that can be navigated to in a Web browser to gain access to the catalog, a dataset, its distributions and/or additional information.
+- **[language]**: A language of the resource. This refers to the natural language used for textual metadata (i.e., titles, descriptions, etc.) of a cataloged resource (i.e., dataset or service) or the textual values of a dataset distribution.
+- **[license]**: A legal document under which the resource is made available.
+- **[modified]**: Most recent date on which the resource was changed, updated or modified.
+- **[publisher]**: The entity responsible for making the resource available.
+- **[qualifiedAttribution]**: Link to an Agent having some form of responsibility for the resource.
+- **[qualifiedRelation]**: Link to a description of a relationship with another resource.
+- **[relation]**: A resource with an unspecified relationship to the cataloged resource.
+- **[replaces]**: A related resource that is supplanted, displaced, or superseded by the described resource.
+- **[rights]**: A statement that concerns all rights not addressed with `license` or `accessRights`, such as copyright statements.
+- **[status]**: The status of the resource in the context of a particular workflow process.
+- **[theme]**: A main category of the resource. A resource can have multiple themes.
+- **[title]**: A name given to the resource.
+- **[type]**: The nature or genre of the resource.
+- **[version]**: The version indicator (name or identifier) of a resource.
+- **[versionNotes]**: A description of changes between this version and the previous version of the resource.
+
+
+Other general properties on resources
+-------------------------------------
+
+- **[abstract]**: A summary of the resource.
+- **[bibliographicCitation]**: A bibliographic reference for the resource. Recommended practice is to include sufficient bibliographic detail to identify the resource as unambiguously as possible.
+- **[deprecated]**: The annotation property that indicates that a given entity has been deprecated.  It should equal to `"true"^^xsd:boolean`.
+- **[isDefinedBy]**: Indicate a resource defining the subject resource. This property may be used to indicate an RDF vocabulary in which a resource is described.
+- **[label]**: Provides a human-readable version of a resource's name.
+- **[seeAlso]**: Indicates a resource that might provide additional information about the subject resource.
+- **[source]**: A related resource from which the described resource is derived.
+- **[statements]**: A list of subject-predicate-object triples with additional RDF statements documenting the resource.
+
+
+Properties specific for datasets
+--------------------------------
+
+- **[datamodel]**: URI of DLite datamodel for the dataset.
+- **[datamodelStorage]**: URL to DLite storage plugin where the datamodel is stored.
+- **[distribution]**: An available distribution of the dataset.
+- **[hasDatum]**: Relates a dataset to its datum parts. `hasDatum` relations are normally specified manually, since they are generated from the DLite data model.
+- **[inSeries]**: A dataset series of which the dataset is part.
+- **[isInputOf]**: A process that this dataset is the input to.
+- **[isOutputOf]**: A process that this dataset is the output of.
+- **[mappings]**: A list of subject-predicate-object triples mapping the datamodel to ontological concepts.
+- **[mappingURL]**: URL to a document defining the mappings of the datamodel.
+      The file format is given by `mappingFormat`.
+      Defaults to turtle.
+- **[mappingFormat]**: File format for `mappingURL`. Defaults to turtle.
+- **[spatial]**: The geographical area covered by the dataset.
+- **[spatialResolutionMeters]**: Minimum spatial separation resolvable in a dataset, measured in meters.
+- **[temporal]**: The temporal period that the dataset covers.
+- **[temporalResolution]**: Minimum time period resolvable in the dataset.
+- **[wasGeneratedBy]**: An activity that generated, or provides the business context for, the creation of the dataset.
+
+
+
+Properties specific for distributions
+-------------------------------------
+- **[accessService]**: A data service that gives access to the distribution of the dataset.
+- **[accessURL]**: A URL of the resource that gives access to a distribution of the dataset. E.g., landing page, feed, SPARQL endpoint.
+- **[byteSize]**: The size of a distribution in bytes.
+- **[checksum]**: The checksum property provides a mechanism that can be used to verify that the contents of a file or package have not changed.
+- **[compressFormat]**: The compression format of the distribution in which the data is contained in a compressed form, e.g., to reduce the size of the downloadable file.
+- **[downloadURL]**: The URL of the downloadable file in a given format. E.g., CSV file or RDF file. The format is indicated by the distribution's `format` and/or `mediaType`.
+- **[format]**: The file format of the distribution.
+      Use `mediaType` instead if the type of the distribution is defined by [IANA].
+- **[generator]**: A generator that can create the distribution.
+- **[mediaType]**: The media type of the distribution as defined by [IANA].
+- **[packageFormat]**: The package format of the distribution in which one or more data files are grouped together, e.g., to enable a set of related files to be downloaded together.
+- **[parser]**: A parser that can parse the distribution.
+
+
+Properties for parsers and generators
+-------------------------------------
+- **[configuration]**: A JSON string with configurations specific to the parser or generator.
+- **[generatorType]**: Generator type. Ex: `application/vnd.dlite-generate`.
+- **[parserType]**: Parser type. Ex: `application/vnd.dlite-parse`.
+
+<!--
+- **[functionType]**:
+- **[filterType]**:
+
+- **[hasDataSink]**:
+- **[storeURL]**:
+
+- **[subject]**:
+- **[predicate]**:
+- **[object]**:
+
+- **[prefixes]**:
+-->
+
+[default JSON-LD context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json
+[JSON-LD documentation]: https://www.w3.org/TR/json-ld/#syntax-tokens-and-keywords
+
+[accessRights]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_access_rights
+[conformsTo]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_conforms_to
+[contactPoint]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_contact_point
+[creator]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_creator
+[description]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_description
+[hasCurrentVersion]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_has_current_version
+[hasPart]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_has_part
+[hasPolicy]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_has_policy
+[hasVersion]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_has_version
+[identifier]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_identifier
+[isReferencedBy]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_is_referenced_by
+[issued]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_release_date
+[keyword]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_keyword
+[landingPage]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_landing_page
+[language]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_language
+[license]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_license
+[modified]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_update_date
+[publisher]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_publisher
+[qualifiedAttribution]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_qualified_attribution
+[qualifiedRelation]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_qualified_relation
+[relation]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_relation
+[replaces]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_replaces
+[rights]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_rights
+[status]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_status
+[theme]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_theme
+[title]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_title
+[type]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_type
+[version]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_version
+[versionNotes]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_version_notes
+
+
+[abstract]: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/abstract
+[bibliographicCitation]: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/bibliographicCitation
+[deprecated]: https://www.w3.org/TR/owl2-quick-reference/
+[isDefinedBy]: https://www.w3.org/TR/rdf12-schema/#ch_isdefinedby
+[label]: https://www.w3.org/TR/rdf12-schema/#ch_label
+[seeAlso]: https://www.w3.org/TR/rdf12-schema/#ch_seealso
+[source]: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/source
+
+
+[datamodel]: https://w3id.org/emmo/domain/oteio#hasDatamodel
+[datamodelStorage]: https://w3id.org/emmo/domain/oteio#hasDatamodelStorage
+[distribution]: https://www.w3.org/TR/vocab-dcat-3/#Property:dataset_distribution
+[hasDatum]: https://w3id.org/emmo#EMMO_b19aacfc_5f73_4c33_9456_469c1e89a53e
+[inSeries]: https://www.w3.org/TR/vocab-dcat-3/#Property:dataset_in_series
+[isInputOf]: https://w3id.org/emmo#EMMO_1494c1a9_00e1_40c2_a9cc_9bbf302a1cac
+[isOutputOf]: https://w3id.org/emmo#EMMO_2bb50428_568d_46e8_b8bf_59a4c5656461
+[mappings]: https://w3id.org/emmo/domain/oteio#mapping
+[mappingFormat]: https://w3id.org/emmo/domain/oteio#mappingFormat
+[mappingURL]: https://w3id.org/emmo/domain/oteio#mappingURL
+[spatial]: https://www.w3.org/TR/vocab-dcat-3/#Property:dataset_spatial
+[spatialResolutionMeters]: https://www.w3.org/TR/vocab-dcat-3/#Property:dataset_spatial_resolution
+[temporal]: https://www.w3.org/TR/vocab-dcat-3/#Property:dataset_temporal
+[temporalResolution]: https://www.w3.org/TR/vocab-dcat-3/#Property:dataset_temporal_resolution
+[wasGeneratedBy]: https://www.w3.org/TR/vocab-dcat-3/#Property:dataset_was_generated_by
+[statements]: https://w3id.org/emmo/domain/oteio#statement
+
+
+[accessService]: https://www.w3.org/TR/vocab-dcat-3/#Property:distribution_access_service
+[accessURL]: https://www.w3.org/TR/vocab-dcat-3/#Property:distribution_access_url
+[byteSize]: https://www.w3.org/TR/vocab-dcat-3/#Property:distribution_size
+[checksum]: https://www.w3.org/TR/vocab-dcat-3/#Property:distribution_checksum
+[compressFormat]: https://www.w3.org/TR/vocab-dcat-3/#Property:distribution_compression_format
+[downloadURL]: https://www.w3.org/TR/vocab-dcat-3/#Property:distribution_download_url
+[format]: https://www.w3.org/TR/vocab-dcat-3/#Property:distribution_format
+[mediaType]: https://www.w3.org/TR/vocab-dcat-3/#Property:distribution_media_type
+[packageFormat]: https://www.w3.org/TR/vocab-dcat-3/#Property:distribution_packaging_format
+[generator]: https://w3id.org/emmo/domain/oteio#generator
+[parser]: https://w3id.org/emmo/domain/oteio#parser
+
+
+[configuration]: https://w3id.org/emmo/domain/oteio#configuration
+[generatorType]: https://w3id.org/emmo/domain/oteio#generatorType
+[parserType]: https://w3id.org/emmo/domain/oteio#parserType
+
+<!--
+[functionType]:
+[filterType]:
+
+[hasDataSink]:
+[storeURL]:
+
+[subject]:
+[predicate]:
+[object]:
+
+[prefixes]:
+-->
+
+
+[DCAT]: https://www.w3.org/TR/vocab-dcat-3/
+[dcat:Dataset]: https://www.w3.org/TR/vocab-dcat-3/#Class:Dataset
+[dcat:Distribution]: https://www.w3.org/TR/vocab-dcat-3/#Class:Distribution
+[vCard]: https://www.w3.org/TR/vcard-rdf/
+[IANA]: https://www.iana.org/assignments/media-types/media-types.xhtml
diff --git a/docs/dataset/datadoc-prefixes.md b/docs/dataset/datadoc-prefixes.md
new file mode 100644
index 00000000..d5d3e538
--- /dev/null
+++ b/docs/dataset/datadoc-prefixes.md
@@ -0,0 +1,26 @@
+Predefined prefixes
+===================
+All prefixes listed on this page are defined in the [default JSON-LD context].
+
+* adms: http://www.w3.org/ns/adms#
+* dcat: http://www.w3.org/ns/dcat#
+* dcterms: http://purl.org/dc/terms/
+* dctype: http://purl.org/dc/dcmitype/
+* foaf: http://xmlns.com/foaf/0.1/
+* odrl: http://www.w3.org/ns/odrl/2/
+* owl: http://www.w3.org/2002/07/owl#
+* prov: http://www.w3.org/ns/prov#
+* rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
+* rdfs: http://www.w3.org/2000/01/rdf-schema#
+* schema: http://schema.org/
+* skos: http://www.w3.org/2004/02/skos/core#
+* spdx: http://spdx.org/rdf/terms#
+* vcard: http://www.w3.org/2006/vcard/ns#
+* xsd: http://www.w3.org/2001/XMLSchema#
+
+* emmo: https://w3id.org/emmo#
+* oteio: https://w3id.org/emmo/domain/oteio#
+* chameo: https://w3id.org/emmo/domain/characterisation-methodology/chameo#
+
+
+[default JSON-LD context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json
diff --git a/docs/dataset/datadoc.md b/docs/dataset/datadoc.md
new file mode 100644
index 00000000..6c343ff1
--- /dev/null
+++ b/docs/dataset/datadoc.md
@@ -0,0 +1,241 @@
+Data documentation
+==================
+<!-- markdownlint-disable MD007 -->
+
+
+Introduction
+------------
+The data documentation is based on small [JSON-LD documents], each documenting a single resource.
+Examples of resources can be a dataset, an instrument, a sample, etc.
+All resources are uniquely identified by their IRI.
+
+The primary focus of the [tripper.dataset] module is to document datasets such that they are consistent with the [DCAT vocabulary], but at the same time easily extended additional semantic meaning provided by other ontologies.
+It is also easy to add and relate the datasets to other types of documents, like people, instruments and samples.
+
+The [tripper.dataset] module provides a Python API for documenting resources at all four levels of data documentation, including:
+
+- **Cataloguing**: Storing and accessing *documents* based on their IRI and data properties.
+  (Addressed FAIR aspects: *findability* and *accessibility*).
+- **Structural documentation**: The structure of a dataset. Provided via [DLite] data models.
+  (Addressed FAIR aspects: *interoperability*).
+- **Contextual documentation**: Relations between resources, i.e. *linked data*. Enables contextual search.
+  (Addressed FAIR aspects: *findability* and *reusability*).
+- **Semantic documentation**: Describe what the resource *is* using ontologies. In combination with structural documentation, maps the properties of a data model to ontological concepts.
+  (Addressed FAIR aspects: *findability*, *interoperability* and *reusability*).
+
+The figure below shows illustrates how a dataset is documented in a triplestore.
+
+![Documentation of a dataset](https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/docs/figs/dataset-Dataset.png)
+
+
+Resource types
+--------------
+The [tripper.dataset] module include the following set of predefined resource types:
+
+- **dataset**: Individual of [dcat:Dataset] and [emmo:DataSet].
+- **distribution**: Individual of [dcat:Distribution].
+- **accessService**: Individual of [dcat:AccessService].
+- **generator**: Individual of [oteio:Generator].
+- **parser**: Individual of [oteio:Parser].
+- **resource**: Any other documented resource, with no implicit type.
+
+Future releases will support adding custom resource types.
+
+
+Documenting a resource
+----------------------
+In the Python API are the JSON-LD documents describing the resources internally represented as Python dicts.
+However, the [tripper.dataset] module tries to hide away the complexities of  [JSON-LD] behind a simple interface.
+
+
+### Documenting as a Python dict
+The API supports two Python dict representations, one for documenting a single resource and one for documenting multiple resources.
+
+
+#### Single-resource dict
+Below is a simple example of how to document a SEM image dataset as a Python dict:
+
+```python
+>>> dataset = {
+...     "@id": "kb:image1",
+...     "@type": "sem:SEMImage",
+...     "creator": "Sigurd Wenner",
+...     "description": "Back-scattered SEM image of cement, polished with 1 µm diamond compound.",
+...     "distribution": {
+...         "downloadURL": "https://github.com/EMMC-ASBL/tripper/raw/refs/heads/master/tests/input/77600-23-001_5kV_400x_m001.tif",
+...         "mediaType": "image/tiff"
+...     }
+... }
+
+```
+
+The keywords are defined in the [default JSON-LD context] and documented under [Predefined keywords].
+
+This example uses two namespace prefixes not included in the [predefined prefixes].
+We therefore have to define them explicitly
+
+```python
+>>> prefixes = {
+...     "sem": "https://w3id.com/emmo/domain/sem/0.1#",
+...     "kb": "http://example.com/kb/"
+... }
+
+```
+
+!!! note "Side note"
+
+    This dict is actually a [JSON-LD] document with an implicit context.
+    You can use [as_jsonld()] to create a valid JSON-LD document from it.
+    In addition to add a `@context` field, this function also adds some implicit `@type` declarations.
+
+    ```python
+    >>> import json
+    >>> from tripper.dataset import as_jsonld
+    >>> d = as_jsonld(dataset, prefixes=prefixes)
+    >>> print(json.dumps(d, indent=2))
+    {
+      "@context": "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json",
+      "@type": [
+        "http://www.w3.org/ns/dcat#Dataset",
+        "https://w3id.org/emmo#EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a",
+        "https://w3id.com/emmo/domain/sem/0.1#SEMImage"
+      ],
+      "@id": "http://example.com/kb/image1",
+      "creator": "Sigurd Wenner",
+      "description": "Back-scattered SEM image of cement, polished with 1 \u00b5m diamond compound.",
+      "distribution": {
+        "@type": "http://www.w3.org/ns/dcat#Distribution",
+        "downloadURL": "https://github.com/EMMC-ASBL/tripper/raw/refs/heads/master/tests/input/77600-23-001_5kV_400x_m001.tif",
+        "mediaType": "image/tiff"
+      }
+    }
+
+    ```
+
+You can use [save_dict()] to save this documentation to a triplestore.
+Since the prefixes "sem" and "kb" are not included in the [Predefined prefixes], they are have to be provided explicitly.
+
+```python
+>>> from tripper import Triplestore
+>>> from tripper.dataset import save_dict
+>>> ts = Triplestore(backend="rdflib")
+>>> save_dict(ts, dataset, prefixes=prefixes)  # doctest: +ELLIPSIS
+AttrDict(...)
+
+```
+
+You can use `ts.serialize()` to list the content of the triplestore (defaults to turtle):
+
+```python
+>>> print(ts.serialize())
+@prefix dcat: <http://www.w3.org/ns/dcat#> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix emmo: <https://w3id.org/emmo#> .
+@prefix kb: <http://example.com/kb/> .
+@prefix sem: <https://w3id.com/emmo/domain/sem/0.1#> .
+<BLANKLINE>
+kb:image1 a dcat:Dataset,
+        sem:SEMImage,
+        emmo:EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a ;
+    dcterms:creator "Sigurd Wenner" ;
+    dcterms:description "Back-scattered SEM image of cement, polished with 1 µm diamond compound." ;
+    dcat:distribution [ a dcat:Distribution ;
+            dcat:downloadURL "https://github.com/EMMC-ASBL/tripper/raw/refs/heads/master/tests/input/77600-23-001_5kV_400x_m001.tif" ;
+            dcat:mediaType "image/tiff" ] .
+<BLANKLINE>
+<BLANKLINE>
+
+```
+
+Note that the image implicitly has been declared to be an individual of the classes `dcat:Dataset` and `emmo:DataSet`.
+This is because the `type` argument of [save_dict()] defaults to "dataset".
+
+
+#### Multi-resource dict
+It is also possible to document multiple resources as a Python dict.
+
+!!! note
+
+    Unlike the single-resource dict representation, the multi-resource dict representation is not valid (possible incomplete) JSON-LD.
+
+This dict representation accepts the following keywords:
+
+- **@context**: Optional user-defined context to be appended to the documentation of all resources.
+- **prefixes**: A dict mapping namespace prefixes to their corresponding URLs.
+- **datasets**/**distributions**/**accessServices**/**generators**/**parsers**/**resources**: A list of valid [single-resource](#single-resource-dict) dict of the given [resource type](#resource-types).
+
+See [semdata.yaml] for an example of a [YAML] representation of a multi-resource dict documentation.
+
+
+### Documenting as a YAML file
+The [save_datadoc()] function allow to save a [YAML] file in [multi-resource](#multi-resource-dict) format to a triplestore.
+
+See [semdata.yaml] for an example.
+
+
+### Documenting as table
+The [TableDoc] class can be used to document multiple resources as rows in a table.
+
+The table must have a header row with defined keywords (either [predefined][predefined keywords] or provided with a custom context).
+Nested fields may be specified as dot-separated keywords. For example, the table
+
+| @id | distribution.downloadURL |
+| --- | ------------------------ |
+| :a  | http://example.com/a.txt |
+| :b  | http://example.com/b.txt |
+
+correspond to the following turtle representation:
+
+```turtle
+:a dcat:distribution [
+    a dcat:Distribution ;
+    downloadURL "http://example.com/a.txt" ] .
+
+:b dcat:distribution [
+    a dcat:Distribution ;
+    downloadURL "http://example.com/b.txt" ] .
+```
+
+The below example shows how to save all datasets listed in the CSV file [semdata.csv] to a triplestore.
+
+```python
+>>> from tripper.dataset import TableDoc
+
+>>> td = TableDoc.parse_csv(
+...     "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/tabledoc-csv/tests/input/semdata.csv",
+...     delimiter=";",
+...     prefixes={
+...         "sem": "https://w3id.com/emmo/domain/sem/0.1#",
+...         "semdata": "https://he-matchmaker.eu/data/sem/",
+...         "sample": "https://he-matchmaker.eu/sample/",
+...         "mat": "https://he-matchmaker.eu/material/",
+...         "dm": "http://onto-ns.com/meta/characterisation/0.1/SEMImage#",
+...         "parser": "http://sintef.no/dlite/parser#",
+...         "gen": "http://sintef.no/dlite/generator#",
+...     },
+... )
+>>> td.save(ts)
+
+```
+
+
+[tripper.dataset]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset
+[DCAT vocabulary]: https://www.w3.org/TR/vocab-dcat-3/
+[DLite]: https://github.com/SINTEF/dlite
+[YAML]: https://yaml.org/
+[JSON-LD documents]: https://json-ld.org/
+[JSON-LD]: https://www.w3.org/TR/json-ld/
+[default JSON-LD context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json
+[predefined prefixes]: datadoc-prefixes.md
+[predefined keywords]: datadoc-keywords.md
+[dcat:Dataset]: https://www.w3.org/TR/vocab-dcat-3/#Class:Dataset
+[dcat:Distribution]: https://www.w3.org/TR/vocab-dcat-3/#Class:Distribution
+[dcat:AccessService]: https://www.w3.org/TR/vocab-dcat-3/#Class:AccessService
+[emmo:DataSet]: https://w3id.org/emmo#EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a
+[oteio:Generator]: https://w3id.org/emmo/domain/oteio/Generator
+[oteio:Parser]: https://w3id.org/emmo/domain/oteio/Parser
+[save_dict()]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.dataset.save_dict
+[save_datadoc()]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.dataset.save_datadoc
+[semdata.yaml]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.yaml
+[semdata.csv]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/tabledoc-csv/tests/input/semdata.csv
+[TableDoc]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.tabledoc.TableDoc
diff --git a/docs/index.md b/docs/index.md
index 61e9828f..8c791e31 100644
--- a/docs/index.md
+++ b/docs/index.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/api_reference/dataset/dataset
+[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/
diff --git a/mkdocs.yml b/mkdocs.yml
index cf56fbff..117bec6b 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -81,6 +81,10 @@ nav:
   - Home: index.md
   - Tutorial: tutorial.md
   - Backend discovery: backend_discovery.md
+  - Data documentation:
+    - Introduction: dataset/datadoc.md
+    - Predefined prefixes: dataset/datadoc-prefixes.md
+    - Predefined keywords: dataset/datadoc-keywords.md
   - ... | api_reference/**
   - Known issues: known-issues.md
   - For developers: developers.md
diff --git a/pyproject.toml b/pyproject.toml
index 0398f0a0..58304083 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -121,7 +121,7 @@ good-names = [
 
 [tool.pytest.ini_options]
 minversion = "7.0"
-addopts = "-rs --cov=tripper --cov-report=term --doctest-modules --doctest-ignore-import-errors"
+addopts = "-rs --cov=tripper --cov-report=term --doctest-modules --doctest-ignore-import-errors --ignore=examples"
 filterwarnings = [
     "ignore:.*imp module.*:DeprecationWarning",
     "ignore:::tripper.literal:243",  # Ignore warning in doctest
diff --git a/tests/dataset/test_dataset.py b/tests/dataset/test_dataset.py
index 4d833a9b..0352d4e3 100644
--- a/tests/dataset/test_dataset.py
+++ b/tests/dataset/test_dataset.py
@@ -15,21 +15,30 @@ def test_get_jsonld_context():
 
     context = get_jsonld_context()
     assert isinstance(context, dict)
-    assert "@version" in context
-    assert len(context) > 20
+    assert len(context) > 80
+    assert context["@version"] == 1.1
+    assert context["status"] == "adms:status"
 
-    # Check for consistency between context online and on disk
+    # Test online context. It should equal context on disk.
+    # However, since they are updated asynchronously, we do not test for
+    # equality.
     online_context = get_jsonld_context(fromfile=False)
-    assert online_context == context
+    assert isinstance(online_context, dict)
+    assert len(online_context) > 80
+    assert online_context["@version"] == 1.1
+    assert online_context["status"] == "adms:status"
 
     # Test context argument
     context2 = get_jsonld_context(context=CONTEXT_URL)
-    assert context2 == context
+    assert context2 == online_context
 
     assert "newkey" not in context
     context3 = get_jsonld_context(context={"newkey": "onto:newkey"})
     assert context3["newkey"] == "onto:newkey"
 
+    with pytest.raises(TypeError):
+        get_jsonld_context(context=[None])
+
 
 def test_get_prefixes():
     """Test get_prefixes()."""
diff --git a/tests/input/openfile.txt b/tests/input/openfile.txt
new file mode 100644
index 00000000..6946578d
--- /dev/null
+++ b/tests/input/openfile.txt
@@ -0,0 +1 @@
+Example file.
diff --git a/tests/input/semdata.yaml b/tests/input/semdata.yaml
index 2d1da201..e1d1918d 100644
--- a/tests/input/semdata.yaml
+++ b/tests/input/semdata.yaml
@@ -81,7 +81,7 @@ generators:
 
 
 # Other entities, like samples, instruments, persons, models etc...
-other_entries:
+resources:
   - "@id": sample:SEM_cement_batch2/77600-23-001
     "@type": chameo:Sample
     title: Series for SEM images for sample 77600-23-001.
diff --git a/tests/test_utils.py b/tests/test_utils.py
index fe8e125f..04e8f324 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -5,6 +5,63 @@
 import pytest
 
 
+def test_AttrDict():
+    """Test AttrDict."""
+    from tripper.utils import AttrDict
+
+    d = AttrDict(a=1, b=2)
+    assert d.a == 1
+
+    with pytest.raises(KeyError):
+        d.c  # pylint: disable=pointless-statement
+
+    d.c = 3
+    assert d.c == 3
+
+    d.get = 4
+    assert d["get"] == 4
+    assert d.get("get") == 4  # pylint: disable=not-callable
+
+    d2 = AttrDict({"a": "A"})
+    assert d2.a == "A"
+    assert d2 == {"a": "A"}
+    assert repr(d2) == "AttrDict({'a': 'A'})"
+    assert "a" in dir(d2)
+
+
+def test_openfile():
+    """Test openfile()."""
+    from paths import indir
+
+    from tripper.utils import openfile
+
+    with openfile(indir / "openfile.txt") as f:
+        assert f.read().strip() == "Example file."
+
+    with openfile(f"file:{indir}/openfile.txt") as f:
+        assert f.read().strip() == "Example file."
+
+    with openfile(f"file://{indir}/openfile.txt") as f:
+        assert f.read().strip() == "Example file."
+
+    with pytest.raises(IOError):
+        with openfile("xxx://unknown_scheme"):
+            pass
+
+
+def test_openfile_http():
+    """Test openfile()."""
+    from tripper.utils import openfile
+
+    pytest.importorskip("requests")
+
+    with openfile(
+        "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/"
+        "dataset-docs/tests/input/openfile.txt"
+    ) as f:
+        assert f.read().strip() == "Example file."
+
+
 def infer_IRIs():
     """Test infer_IRIs"""
     from tripper import RDFS
@@ -328,27 +385,3 @@ def test_extend_namespace():
     EX = Namespace("http://example.com#")
     with pytest.raises(TypeError):
         extend_namespace(EX, {"Item": EX + "Item"})
-
-
-def test_AttrDict():
-    """Test AttrDict."""
-    from tripper.utils import AttrDict
-
-    d = AttrDict(a=1, b=2)
-    assert d.a == 1
-
-    with pytest.raises(KeyError):
-        d.c  # pylint: disable=pointless-statement
-
-    d.c = 3
-    assert d.c == 3
-
-    d.get = 4
-    assert d["get"] == 4
-    assert d.get("get") == 4  # pylint: disable=not-callable
-
-    d2 = AttrDict({"a": "A"})
-    assert d2.a == "A"
-    assert d2 == {"a": "A"}
-    assert repr(d2) == "AttrDict({'a': 'A'})"
-    assert "a" in dir(d2)
diff --git a/tripper/context/0.2/context.json b/tripper/context/0.2/context.json
index 3f658c0d..409e1117 100644
--- a/tripper/context/0.2/context.json
+++ b/tripper/context/0.2/context.json
@@ -24,10 +24,7 @@
 
     "status": "adms:status",
     "versionNotes": "adms:versionNotes",
-    "distribution": {
-      "@id": "dcat:distribution",
-      "@type": "@id"
-    },
+
     "contactPoint": "dcat:contactPoint",
     "hasCurrentVersion": "dcat:hasCurrentVersion",
     "hasVersion": "dcat:hasVersion",
@@ -37,14 +34,20 @@
     },
     "keyword": "dcat:keyword",
     "landingPage": "dcat:landingPage",
-    "qualifiedRelation": "dcat:qualifiedRelation",
+    "qualifiedRelation": {
+      "@id": "dcat:qualifiedRelation",
+      "@type": "@id"
+    },
     "theme": "dcat:theme",
     "version": "dcat:version",
     "accessRights": "dcterms:accessRights",
     "conformsTo": "dcterms:conformsTo",
     "creator": "dcterms:creator",
     "description": "dcterms:description",
-    "hasPart": "dcterms:hasPart",
+    "hasPart": {
+      "@id": "dcterms:hasPart",
+      "@type": "@id"
+    },
     "identifier": "dcterms:identifier",
     "isReferencedBy": "dcterms:isReferencedBy",
     "issued": "dcterms:issued",
@@ -52,13 +55,29 @@
     "license": "dcterms:license",
     "modified": "dcterms:modified",
     "publisher": "dcterms:publisher",
-    "relation": "dcterms:relation",
-    "replaces": "dcterms:replaces",
+    "relation": {
+      "@id": "dcterms:relation",
+      "@type": "@id"
+    },
+
+    "replaces": {
+      "@id": "dcterms:replaces",
+      "@type": "@id"
+    },
+
     "rights": "dcterms:rights",
     "title": "dcterms:title",
     "type": "dcterms:type",
     "hasPolicy": "odrl:hasPolicy",
-    "qualifiedAttribution": "prov:qualifiedAttribution",
+    "qualifiedAttribution": {
+      "@id": "prov:qualifiedAttribution",
+      "@type": "@id"
+    },
+
+    "distribution": {
+      "@id": "dcat:distribution",
+      "@type": "@id"
+    },
 
     "accessService": {
       "@id": "dcat:accessService",
@@ -76,16 +95,19 @@
     "temporalResolution": "dcat:temporalResolution",
     "wasGeneratedBy": "prov:wasGeneratedBy",
     "format": "dcterms:format",
-    "checksum": "spdx:checksum",
+    "checksum": {
+      "@id": "spdx:checksum",
+      "@type": "@id"
+    },
 
     "abstract": "dcterms:abstract",
     "bibliographicCitation": "dcterms:bibliographicCitation",
-    "source": "dcterms:source",
     "deprecated": "owl:deprecated",
     "comment": "rdfs:comment",
     "isDefinedBy": "rdfs:isDefinedBy",
     "label": "rdfs:label",
     "seeAlso": "rdfs:seeAlso",
+    "source": "dcterms:source",
 
     "hasDatum": {
       "@id": "emmo:EMMO_b19aacfc_5f73_4c33_9456_469c1e89a53e",
diff --git a/tripper/convert/convert.py b/tripper/convert/convert.py
index 8f420f5a..2efaa1af 100644
--- a/tripper/convert/convert.py
+++ b/tripper/convert/convert.py
@@ -3,6 +3,7 @@
 
 Example use:
 
+```python
 >>> from tripper import DCTERMS, Literal, Triplestore
 >>> from tripper.convert import load_container, save_container
 
@@ -22,6 +23,7 @@
 >>> load_container(ts, ":data_indv", ignore_unrecognised=True)
 {'a': 1, 'b': 2}
 
+```
 """
 
 # pylint: disable=invalid-name,redefined-builtin
diff --git a/tripper/dataset/dataset.py b/tripper/dataset/dataset.py
index 022bcc3e..5052169b 100644
--- a/tripper/dataset/dataset.py
+++ b/tripper/dataset/dataset.py
@@ -82,10 +82,10 @@
         "datadoc_label": "datasets",
         "@type": [DCAT.Dataset, EMMO.DataSet],
     },
-    "entry": {
-        # General datacatalog entry that is not one of the above
+    "resource": {
+        # General data resource
         # Ex: samples, instruments, models, people, projects, ...
-        "datadoc_label": "other_entries",  # XXX better label?
+        "datadoc_label": "resources",
         "@type": OWL.NamedIndividual,
     },
 }
@@ -620,7 +620,6 @@ def as_jsonld(
     dct: dict,
     type: "Optional[str]" = "dataset",
     prefixes: "Optional[dict]" = None,
-    _entryid: "Optional[str]" = None,
     **kwargs,
 ) -> dict:
     """Return an updated copy of dict `dct` as valid JSON-LD.
@@ -633,18 +632,19 @@ def as_jsonld(
             Defaults to "dataset".
         prefixes: Dict with prefixes in addition to those included in the
             JSON-LD context.  Should map namespace prefixes to IRIs.
-        _entryid: Id of base entry that is documented. Intended for
-            internal use only.
         kwargs: Additional keyword arguments to add to the returned dict.
             A leading underscore in a key will be translated to a
             leading "@"-sign.  For example, "@id" or "@context" may be
             provided as "_id" or "_context", respectively.
 
-
     Returns:
         An updated copy of `dct` as valid JSON-LD.
     """
     # pylint: disable=too-many-branches
+
+    # Id of base entry that is documented
+    _entryid = kwargs.pop("_entryid", None)
+
     d = AttrDict()
     if not _entryid:
         d["@context"] = CONTEXT_URL
diff --git a/tripper/dataset/tabledoc.py b/tripper/dataset/tabledoc.py
index 6dbf8b32..609fdd3d 100644
--- a/tripper/dataset/tabledoc.py
+++ b/tripper/dataset/tabledoc.py
@@ -6,7 +6,7 @@
 
 from tripper import Triplestore
 from tripper.dataset.dataset import addnested, as_jsonld, save_dict
-from tripper.utils import AttrDict
+from tripper.utils import AttrDict, openfile
 
 if TYPE_CHECKING:  # pragma: no cover
     from typing import List, Optional, Sequence, Union
@@ -109,7 +109,7 @@ def parse_csv(
         References:
         [Dialects and Formatting Parameters]: https://docs.python.org/3/library/csv.html#dialects-and-formatting-parameters
         """
-        with open(csvfile, mode="rt", encoding=encoding) as f:
+        with openfile(csvfile, mode="rt", encoding=encoding) as f:
             reader = csv.reader(f, dialect=dialect, **kwargs)
             header = next(reader)
             data = list(reader)
diff --git a/tripper/utils.py b/tripper/utils.py
index 41525269..4c6cc6d6 100644
--- a/tripper/utils.py
+++ b/tripper/utils.py
@@ -7,13 +7,15 @@
 import random
 import re
 import string
+import tempfile
+from contextlib import contextmanager
+from pathlib import Path
 from typing import TYPE_CHECKING
 
 from tripper.literal import Literal
 from tripper.namespace import XSD, Namespace
 
 if TYPE_CHECKING:  # pragma: no cover
-    from pathlib import Path
     from typing import (
         Any,
         Callable,
@@ -65,6 +67,51 @@ def __dir__(self):
         return dict.__dir__(self) + list(self.keys())
 
 
+@contextmanager
+def openfile(url: "Union[str, Path]", timeout: float = 3, **kwargs):
+    """Like open(), but allows opening remote files using http requests.
+
+    Should always be used in a with-statement.
+
+    Arguments:
+        url: File path or URL to open.
+        timeout: Timeout for accessing the file in seconds.
+        kwargs: Additional passed to open().
+
+    Returns:
+        A stream object returned by open().
+
+    """
+    url = str(url)
+    u = url.lower()
+    tmpfile = False
+
+    if u.startswith("file:"):
+        fname = url[7:] if u.startswith("file://") else url[5:]
+
+    elif u.startswith("http://") or u.startswith("https://"):
+        import requests  # pylint: disable=import-outside-toplevel
+
+        tmpfile = True
+        r = requests.get(url, timeout=timeout)
+        r.raise_for_status()
+        with tempfile.NamedTemporaryFile(delete=False) as f:
+            fname = f.name
+            f.write(r.content)
+
+    elif re.match(r"[a-zA-Z][a-zA-Z0-9+.-]*://", url):
+        raise IOError(f"unknown scheme: {url.split(':', 1)[0]}")
+
+    else:
+        fname = url
+
+    try:
+        yield open(fname, **kwargs)  # pylint: disable=unspecified-encoding
+    finally:
+        if tmpfile:
+            Path(fname).unlink()
+
+
 def infer_iri(obj):
     """Return IRI of the individual that stands for Python object `obj`.
 

From 39c9c1a3a6f15870a640a1bd10bef60cbfe0051e Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Thu, 2 Jan 2025 12:59:03 +0100
Subject: [PATCH 29/59] Added return annotation to utils.openfile()

---
 README.md                     | 4 ++--
 docs/index.md                 | 4 ++--
 tripper/convert/convert.py    | 1 +
 tripper/dataset/dataaccess.py | 6 ++++--
 tripper/utils.py              | 4 +++-
 5 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 8c791e31..b494f1b6 100644
--- a/README.md
+++ b/README.md
@@ -106,8 +106,8 @@ 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/api_reference/dataset/dataset
-[tripper.mappings]: https://emmc-asbl.github.io/tripper/latest/api_reference/mappings/mappings
+[tripper.dataset]: https://emmc-asbl.github.io/tripper/latest/dataset/datadoc/
+[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/
diff --git a/docs/index.md b/docs/index.md
index 8c791e31..b494f1b6 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -106,8 +106,8 @@ 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/api_reference/dataset/dataset
-[tripper.mappings]: https://emmc-asbl.github.io/tripper/latest/api_reference/mappings/mappings
+[tripper.dataset]: https://emmc-asbl.github.io/tripper/latest/dataset/datadoc/
+[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/
diff --git a/tripper/convert/convert.py b/tripper/convert/convert.py
index 2efaa1af..cf949f59 100644
--- a/tripper/convert/convert.py
+++ b/tripper/convert/convert.py
@@ -24,6 +24,7 @@
 {'a': 1, 'b': 2}
 
 ```
+
 """
 
 # pylint: disable=invalid-name,redefined-builtin
diff --git a/tripper/dataset/dataaccess.py b/tripper/dataset/dataaccess.py
index 3e248e36..dbe0ee25 100644
--- a/tripper/dataset/dataaccess.py
+++ b/tripper/dataset/dataaccess.py
@@ -3,11 +3,13 @@
 from the datasets module.
 
 High-level functions for accessing and storing actual data:
+
   - `load()`: Load documented dataset from its source.
   - `save()`: Save documented dataset to a data resource.
 
-Note: This module may eventually be moved out of tripper into a
-separate package.
+Note:
+    This module may eventually be moved out of tripper into a separate
+    package.
 
 """
 import secrets  # From Python 3.9 we could use random.randbytes(16).hex()
diff --git a/tripper/utils.py b/tripper/utils.py
index 4c6cc6d6..94850280 100644
--- a/tripper/utils.py
+++ b/tripper/utils.py
@@ -68,7 +68,9 @@ def __dir__(self):
 
 
 @contextmanager
-def openfile(url: "Union[str, Path]", timeout: float = 3, **kwargs):
+def openfile(
+    url: "Union[str, Path]", timeout: float = 3, **kwargs
+) -> "Generator":
     """Like open(), but allows opening remote files using http requests.
 
     Should always be used in a with-statement.

From 4302ddeae24362c418a3cafdbaa771b53764d963 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Thu, 2 Jan 2025 14:23:53 +0100
Subject: [PATCH 30/59] Try to avoid pytest failure during collection phase.

---
 docs/api_reference/triplestore_extend.md      | 3 +++
 docs/api_reference/tripper.md                 | 3 ---
 tripper/__init__.py                           | 2 +-
 tripper/{tripper.py => triplestore_extend.py} | 0
 tripper/utils.py                              | 5 +++++
 5 files changed, 9 insertions(+), 4 deletions(-)
 create mode 100644 docs/api_reference/triplestore_extend.md
 delete mode 100644 docs/api_reference/tripper.md
 rename tripper/{tripper.py => triplestore_extend.py} (100%)

diff --git a/docs/api_reference/triplestore_extend.md b/docs/api_reference/triplestore_extend.md
new file mode 100644
index 00000000..03c1fbbd
--- /dev/null
+++ b/docs/api_reference/triplestore_extend.md
@@ -0,0 +1,3 @@
+# triplestore_extend
+
+::: tripper.triplestore_extend
diff --git a/docs/api_reference/tripper.md b/docs/api_reference/tripper.md
deleted file mode 100644
index 57f90b06..00000000
--- a/docs/api_reference/tripper.md
+++ /dev/null
@@ -1,3 +0,0 @@
-# tripper
-
-::: tripper.tripper
diff --git a/tripper/__init__.py b/tripper/__init__.py
index 0d9197d3..af17dac1 100644
--- a/tripper/__init__.py
+++ b/tripper/__init__.py
@@ -24,7 +24,7 @@
     Namespace,
 )
 from .triplestore import Triplestore, backend_packages
-from .tripper import Tripper
+from .triplestore_extend import Tripper
 
 __version__ = "0.3.4"
 
diff --git a/tripper/tripper.py b/tripper/triplestore_extend.py
similarity index 100%
rename from tripper/tripper.py
rename to tripper/triplestore_extend.py
diff --git a/tripper/utils.py b/tripper/utils.py
index 94850280..7c2289b1 100644
--- a/tripper/utils.py
+++ b/tripper/utils.py
@@ -55,6 +55,11 @@ class AttrDict(dict):
     def __getattr__(self, name):
         if name in self:
             return self[name]
+        if name == "__wrapped__":
+            # Hack to work around a pytest bug.  During its collection
+            # phase pytest tries to mock namespace objects with an
+            # attribute `__wrapped__`.
+            return None
         raise KeyError(name)
 
     def __setattr__(self, name, value):

From 8f727c7d74e7dc87250250745655ddfaedf690ba Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Thu, 2 Jan 2025 15:25:23 +0100
Subject: [PATCH 31/59] Remove --ignore=examples from pytest options in
 pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 58304083..0398f0a0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -121,7 +121,7 @@ good-names = [
 
 [tool.pytest.ini_options]
 minversion = "7.0"
-addopts = "-rs --cov=tripper --cov-report=term --doctest-modules --doctest-ignore-import-errors --ignore=examples"
+addopts = "-rs --cov=tripper --cov-report=term --doctest-modules --doctest-ignore-import-errors"
 filterwarnings = [
     "ignore:.*imp module.*:DeprecationWarning",
     "ignore:::tripper.literal:243",  # Ignore warning in doctest

From 065e8935441594b28b75d56df29d1cadd281d572 Mon Sep 17 00:00:00 2001
From: "Tor S. Haugland" <tor.haugland@sintef.no>
Date: Thu, 2 Jan 2025 15:35:38 +0100
Subject: [PATCH 32/59] Fix CI doctest bug

---
 tripper/__init__.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tripper/__init__.py b/tripper/__init__.py
index af17dac1..5cbe0da0 100644
--- a/tripper/__init__.py
+++ b/tripper/__init__.py
@@ -26,6 +26,10 @@
 from .triplestore import Triplestore, backend_packages
 from .triplestore_extend import Tripper
 
+# Import backends here to avoid defining new globals later
+# Needed for pytest+doctest to pass
+import tripper.backends # pylint: disable=unused-import
+
 __version__ = "0.3.4"
 
 # Pre-defined namespaces

From dd92304e7ffec8ce2c80def5915a25d2f954b6e1 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 2 Jan 2025 14:35:53 +0000
Subject: [PATCH 33/59] [pre-commit.ci] auto fixes from pre-commit hooks

For more information, see https://pre-commit.ci
---
 tripper/__init__.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tripper/__init__.py b/tripper/__init__.py
index 5cbe0da0..c5561c62 100644
--- a/tripper/__init__.py
+++ b/tripper/__init__.py
@@ -4,6 +4,10 @@
 See the README.md file for a description for how to use this package.
 """
 
+# Import backends here to avoid defining new globals later
+# Needed for pytest+doctest to pass
+import tripper.backends  # pylint: disable=unused-import
+
 from .literal import Literal
 from .namespace import (
     DC,
@@ -26,10 +30,6 @@
 from .triplestore import Triplestore, backend_packages
 from .triplestore_extend import Tripper
 
-# Import backends here to avoid defining new globals later
-# Needed for pytest+doctest to pass
-import tripper.backends # pylint: disable=unused-import
-
 __version__ = "0.3.4"
 
 # Pre-defined namespaces

From 4241295c357016900293e62247d4bf51fd258d3d Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Thu, 2 Jan 2025 15:51:08 +0100
Subject: [PATCH 34/59] Use relative import from __init__.py file

---
 tripper/__init__.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tripper/__init__.py b/tripper/__init__.py
index c5561c62..e880db91 100644
--- a/tripper/__init__.py
+++ b/tripper/__init__.py
@@ -6,8 +6,7 @@
 
 # Import backends here to avoid defining new globals later
 # Needed for pytest+doctest to pass
-import tripper.backends  # pylint: disable=unused-import
-
+from . import backends  # pylint: disable=unused-import
 from .literal import Literal
 from .namespace import (
     DC,

From 38e0483d93665dffa349222e15dd61a391a9e431 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Thu, 2 Jan 2025 16:28:59 +0100
Subject: [PATCH 35/59] Updated documentation

---
 docs/dataset/datadoc.md    | 15 ++++++++++++++-
 tripper/dataset/dataset.py | 12 ++++++++----
 tripper/utils.py           |  2 +-
 3 files changed, 23 insertions(+), 6 deletions(-)

diff --git a/docs/dataset/datadoc.md b/docs/dataset/datadoc.md
index 6c343ff1..0afb16f5 100644
--- a/docs/dataset/datadoc.md
+++ b/docs/dataset/datadoc.md
@@ -124,6 +124,9 @@ AttrDict(...)
 
 ```
 
+The returned `AttrDict` instance is an updated copy of `dataset` (casted to a dict subclass with attribute access).
+It correspond to a valid JSON-LD document and is the same as returned by [as_jsonld()].
+
 You can use `ts.serialize()` to list the content of the triplestore (defaults to turtle):
 
 ```python
@@ -169,8 +172,17 @@ See [semdata.yaml] for an example of a [YAML] representation of a multi-resource
 
 ### Documenting as a YAML file
 The [save_datadoc()] function allow to save a [YAML] file in [multi-resource](#multi-resource-dict) format to a triplestore.
+Saving [semdata.yaml] to a triplestore can e.g. be done with
+
+```python
+>>> from tripper.dataset import save_datadoc
+>>> save_datadoc(  # doctest: +ELLIPSIS
+...    ts,
+...    "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.yaml"
+... )
+AttrDict(...)
 
-See [semdata.yaml] for an example.
+```
 
 
 ### Documenting as table
@@ -235,6 +247,7 @@ The below example shows how to save all datasets listed in the CSV file [semdata
 [oteio:Generator]: https://w3id.org/emmo/domain/oteio/Generator
 [oteio:Parser]: https://w3id.org/emmo/domain/oteio/Parser
 [save_dict()]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.dataset.save_dict
+[as_jsonld()]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.dataset.as_jsonld
 [save_datadoc()]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.dataset.save_datadoc
 [semdata.yaml]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.yaml
 [semdata.csv]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/tabledoc-csv/tests/input/semdata.csv
diff --git a/tripper/dataset/dataset.py b/tripper/dataset/dataset.py
index 5052169b..dd967521 100644
--- a/tripper/dataset/dataset.py
+++ b/tripper/dataset/dataset.py
@@ -40,7 +40,7 @@
 from typing import TYPE_CHECKING
 
 from tripper import DCAT, EMMO, OTEIO, OWL, RDF, Triplestore
-from tripper.utils import AttrDict, as_python
+from tripper.utils import AttrDict, as_python, openfile
 
 if TYPE_CHECKING:  # pragma: no cover
     from typing import Any, Iterable, List, Mapping, Optional, Sequence, Union
@@ -541,10 +541,13 @@ def expand_iri(iri: str, prefixes: dict) -> str:
 
 
 def read_datadoc(filename: "Union[str, Path]") -> dict:
-    """Read YAML data documentation and return it as a dict."""
+    """Read YAML data documentation and return it as a dict.
+
+    The filename may also be an URL to a file accessible with HTTP GET.
+    """
     import yaml  # type: ignore
 
-    with open(filename, "r", encoding="utf-8") as f:
+    with openfile(filename, mode="rt", encoding="utf-8") as f:
         d = yaml.safe_load(f)
     return prepare_datadoc(d)
 
@@ -557,7 +560,8 @@ def save_datadoc(
     Arguments:
         ts: Triplestore to save dataset documentation to.
         file_or_dict: Data documentation dict or name of a YAML file to read
-            the data documentation from.
+            the data documentation from.  It may also be an URL to a file
+            accessible with HTTP GET.
 
     Returns:
         Dict-representation of the loaded dataset.
diff --git a/tripper/utils.py b/tripper/utils.py
index 7c2289b1..76e9cc0f 100644
--- a/tripper/utils.py
+++ b/tripper/utils.py
@@ -76,7 +76,7 @@ def __dir__(self):
 def openfile(
     url: "Union[str, Path]", timeout: float = 3, **kwargs
 ) -> "Generator":
-    """Like open(), but allows opening remote files using http requests.
+    """Like open(), but allows opening remote files using HTTP GET requests.
 
     Should always be used in a with-statement.
 

From 8756727cdd04d2c05a6620e96af944250647d222 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Thu, 2 Jan 2025 20:36:02 +0100
Subject: [PATCH 36/59] Added types (literal/iri) to datadoc-keywords.md and
 reordered context.json to match the order in datadoc-keywords.md

---
 docs/dataset/datadoc-keywords.md | 140 +++++++++++++++--------------
 tripper/context/0.2/context.json | 150 ++++++++++++++++---------------
 2 files changed, 147 insertions(+), 143 deletions(-)

diff --git a/docs/dataset/datadoc-keywords.md b/docs/dataset/datadoc-keywords.md
index f8a27852..68a34fc5 100644
--- a/docs/dataset/datadoc-keywords.md
+++ b/docs/dataset/datadoc-keywords.md
@@ -8,10 +8,10 @@ Special keywords for JSON-LD
 See the [JSON-LD documentation] for a complete list of "@"-prefixed keywords.
 Here we only list those that are commonly used for data documentation with Tripper.
 
-- **@context**: URL to or dict with user-defined JSON-LD context.
+- **@context** (*IRI*): URL to or dict with user-defined JSON-LD context.
       Used to extend the keywords listed on this page with domain- or application-specific keywords.
-- **@id**: IRI of the documented resource.
-- **@type**: IRI of ontological class that the resource is an individual of.
+- **@id** (*IRI*): IRI of the documented resource.
+- **@type** (*IRI*): IRI of ontological class that the resource is an individual of.
 
 
 General properties on resources used by DCAT
@@ -19,94 +19,95 @@ General properties on resources used by DCAT
 These can also be used on datasets and distributions.
 See the DCAT documentation for [dcat:Dataset] and [dcat:Distribution] for recommendations.
 
-- **[accessRights]**: Information about who can access the resource or an indication of its security status.
-- **[conformsTo]**: An established standard to which the described resource conforms.
-- **[contactPoint]**: Relevant contact information for the cataloged resource. Use of [vCard] is recommended.
-- **[creator]**: The entity responsible for producing the resource.
-- **[description]**: A free-text account of the resource.
-- **[hasCurrentVersion]**: This resource has a more specific, versioned resource with equivalent content.
-- **[hasPart]**: A related resource that is included either physically or logically in the described resource.
-- **[hasPolicy]**: An ODRL conformant policy expressing the rights associated with the resource.
-- **[hasVersion]**: This resource has a more specific, versioned resource.
-- **[identifier]**: A unique identifier of the resource being described or cataloged.
-- **[isReferencedBy]**: A related resource, such as a publication, that references, cites, or otherwise points to the cataloged resource.
-- **[issued]**: Date of formal issuance (e.g., publication) of the resource.
-- **[keyword]**: A keyword or tag describing the resource.
-- **[landingPage]**: A Web page that can be navigated to in a Web browser to gain access to the catalog, a dataset, its distributions and/or additional information.
-- **[language]**: A language of the resource. This refers to the natural language used for textual metadata (i.e., titles, descriptions, etc.) of a cataloged resource (i.e., dataset or service) or the textual values of a dataset distribution.
-- **[license]**: A legal document under which the resource is made available.
-- **[modified]**: Most recent date on which the resource was changed, updated or modified.
-- **[publisher]**: The entity responsible for making the resource available.
-- **[qualifiedAttribution]**: Link to an Agent having some form of responsibility for the resource.
-- **[qualifiedRelation]**: Link to a description of a relationship with another resource.
-- **[relation]**: A resource with an unspecified relationship to the cataloged resource.
-- **[replaces]**: A related resource that is supplanted, displaced, or superseded by the described resource.
-- **[rights]**: A statement that concerns all rights not addressed with `license` or `accessRights`, such as copyright statements.
-- **[status]**: The status of the resource in the context of a particular workflow process.
-- **[theme]**: A main category of the resource. A resource can have multiple themes.
-- **[title]**: A name given to the resource.
-- **[type]**: The nature or genre of the resource.
-- **[version]**: The version indicator (name or identifier) of a resource.
-- **[versionNotes]**: A description of changes between this version and the previous version of the resource.
+- **[accessRights]** (*Literal*): Information about who can access the resource or an indication of its security status.
+- **[conformsTo]** (*Literal*): An established standard to which the described resource conforms.
+- **[contactPoint]** (*Literal*): Relevant contact information for the cataloged resource. Use of [vCard] is recommended.
+- **[creator]** (*Literal*): The entity responsible for producing the resource.
+- **[description]** (*Literal*): A free-text account of the resource.
+- **[hasCurrentVersion]** (*Literal*): This resource has a more specific, versioned resource with equivalent content.
+- **[hasPart]** (*IRI*): A related resource that is included either physically or logically in the described resource.
+- **[hasPolicy]** (*Literal*): An ODRL conformant policy expressing the rights associated with the resource.
+- **[hasVersion]** (*Literal*): This resource has a more specific, versioned resource.
+- **[identifier]** (*Literal*): A unique identifier of the resource being described or cataloged.
+- **[isReferencedBy]** (*Literal*): A related resource, such as a publication, that references, cites, or otherwise points to the cataloged resource.
+- **[issued]** (*Literal*): Date of formal issuance (e.g., publication) of the resource.
+- **[keyword]** (*Literal*): A keyword or tag describing the resource.
+- **[landingPage]** (*Literal*): A Web page that can be navigated to in a Web browser to gain access to the catalog, a dataset, its distributions and/or additional information.
+- **[language]** (*Literal*): A language of the resource. This refers to the natural language used for textual metadata (i.e., titles, descriptions, etc.) of a cataloged resource (i.e., dataset or service) or the textual values of a dataset distribution.
+- **[license]** (*Literal*): A legal document under which the resource is made available.
+- **[modified]** (*Literal*): Most recent date on which the resource was changed, updated or modified.
+- **[publisher]** (*Literal*): The entity responsible for making the resource available.
+- **[qualifiedAttribution]** (*IRI*): Link to an Agent having some form of responsibility for the resource.
+- **[qualifiedRelation]** (*IRI*): Link to a description of a relationship with another resource.
+- **[relation]** (*IRI*): A resource with an unspecified relationship to the cataloged resource.
+- **[replaces]** (*IRI*): A related resource that is supplanted, displaced, or superseded by the described resource.
+- **[rights]** (*Literal*): A statement that concerns all rights not addressed with `license` or `accessRights`, such as copyright statements.
+- **[status]** (*Literal*): The status of the resource in the context of a particular workflow process.
+- **[theme]** (*Literal*): A main category of the resource. A resource can have multiple themes.
+- **[title]** (*Literal*): A name given to the resource.
+- **[type]** (*Literal*): The nature or genre of the resource.
+- **[version]** (*Literal*): The version indicator (name or identifier) of a resource.
+- **[versionNotes]** (*Literal*): A description of changes between this version and the previous version of the resource.
 
 
 Other general properties on resources
 -------------------------------------
 
-- **[abstract]**: A summary of the resource.
-- **[bibliographicCitation]**: A bibliographic reference for the resource. Recommended practice is to include sufficient bibliographic detail to identify the resource as unambiguously as possible.
-- **[deprecated]**: The annotation property that indicates that a given entity has been deprecated.  It should equal to `"true"^^xsd:boolean`.
-- **[isDefinedBy]**: Indicate a resource defining the subject resource. This property may be used to indicate an RDF vocabulary in which a resource is described.
-- **[label]**: Provides a human-readable version of a resource's name.
-- **[seeAlso]**: Indicates a resource that might provide additional information about the subject resource.
-- **[source]**: A related resource from which the described resource is derived.
-- **[statements]**: A list of subject-predicate-object triples with additional RDF statements documenting the resource.
+- **[abstract]** (*Literal*): A summary of the resource.
+- **[bibliographicCitation]** (*Literal*): A bibliographic reference for the resource. Recommended practice is to include sufficient bibliographic detail to identify the resource as unambiguously as possible.
+- **[comment]** (*Literal*): A description of the subject resource.
+- **[deprecated]** (*Literal*): The annotation property that indicates that a given entity has been deprecated.  It should equal to `"true"^^xsd:boolean`.
+- **[isDefinedBy]** (*Literal*): Indicate a resource defining the subject resource. This property may be used to indicate an RDF vocabulary in which a resource is described.
+- **[label]** (*Literal*): Provides a human-readable version of a resource's name.
+- **[seeAlso]** (*Literal*): Indicates a resource that might provide additional information about the subject resource.
+- **[source]** (*Literal*): A related resource from which the described resource is derived.
+- **[statements]** (*Literal*): A list of subject-predicate-object triples with additional RDF statements documenting the resource.
 
 
 Properties specific for datasets
 --------------------------------
 
-- **[datamodel]**: URI of DLite datamodel for the dataset.
-- **[datamodelStorage]**: URL to DLite storage plugin where the datamodel is stored.
-- **[distribution]**: An available distribution of the dataset.
-- **[hasDatum]**: Relates a dataset to its datum parts. `hasDatum` relations are normally specified manually, since they are generated from the DLite data model.
-- **[inSeries]**: A dataset series of which the dataset is part.
-- **[isInputOf]**: A process that this dataset is the input to.
-- **[isOutputOf]**: A process that this dataset is the output of.
-- **[mappings]**: A list of subject-predicate-object triples mapping the datamodel to ontological concepts.
-- **[mappingURL]**: URL to a document defining the mappings of the datamodel.
+- **[datamodel]** (*Literal*): URI of DLite datamodel for the dataset.
+- **[datamodelStorage]** (*Literal*): URL to DLite storage plugin where the datamodel is stored.
+- **[distribution]** (*IRI*): An available distribution of the dataset.
+- **[hasDatum]** (*IRI*): Relates a dataset to its datum parts. `hasDatum` relations are normally specified manually, since they are generated from the DLite data model.
+- **[inSeries]** (*IRI*): A dataset series of which the dataset is part.
+- **[isInputOf]** (*IRI*): A process that this dataset is the input to.
+- **[isOutputOf]** (*IRI*): A process that this dataset is the output of.
+- **[mappings]** (*Literal*): A list of subject-predicate-object triples mapping the datamodel to ontological concepts.
+- **[mappingURL]** (*Literal*): URL to a document defining the mappings of the datamodel.
       The file format is given by `mappingFormat`.
       Defaults to turtle.
-- **[mappingFormat]**: File format for `mappingURL`. Defaults to turtle.
-- **[spatial]**: The geographical area covered by the dataset.
-- **[spatialResolutionMeters]**: Minimum spatial separation resolvable in a dataset, measured in meters.
-- **[temporal]**: The temporal period that the dataset covers.
-- **[temporalResolution]**: Minimum time period resolvable in the dataset.
-- **[wasGeneratedBy]**: An activity that generated, or provides the business context for, the creation of the dataset.
+- **[mappingFormat]** (*Literal*): File format for `mappingURL`. Defaults to turtle.
+- **[spatial]** (*Literal*): The geographical area covered by the dataset.
+- **[spatialResolutionMeters]** (*Literal*): Minimum spatial separation resolvable in a dataset, measured in meters.
+- **[temporal]** (*Literal*): The temporal period that the dataset covers.
+- **[temporalResolution]** (*Literal*): Minimum time period resolvable in the dataset.
+- **[wasGeneratedBy]** (*Literal*): An activity that generated, or provides the business context for, the creation of the dataset.
 
 
 
 Properties specific for distributions
 -------------------------------------
-- **[accessService]**: A data service that gives access to the distribution of the dataset.
-- **[accessURL]**: A URL of the resource that gives access to a distribution of the dataset. E.g., landing page, feed, SPARQL endpoint.
-- **[byteSize]**: The size of a distribution in bytes.
-- **[checksum]**: The checksum property provides a mechanism that can be used to verify that the contents of a file or package have not changed.
-- **[compressFormat]**: The compression format of the distribution in which the data is contained in a compressed form, e.g., to reduce the size of the downloadable file.
-- **[downloadURL]**: The URL of the downloadable file in a given format. E.g., CSV file or RDF file. The format is indicated by the distribution's `format` and/or `mediaType`.
-- **[format]**: The file format of the distribution.
+- **[accessService]** (*IRI*): A data service that gives access to the distribution of the dataset.
+- **[accessURL]** (*Literal*): A URL of the resource that gives access to a distribution of the dataset. E.g., landing page, feed, SPARQL endpoint.
+- **[byteSize]** (*Literal*): The size of a distribution in bytes.
+- **[checksum]** (*IRI*): The checksum property provides a mechanism that can be used to verify that the contents of a file or package have not changed.
+- **[compressFormat]** (*Literal*): The compression format of the distribution in which the data is contained in a compressed form, e.g., to reduce the size of the downloadable file.
+- **[downloadURL]** (*Literal*): The URL of the downloadable file in a given format. E.g., CSV file or RDF file. The format is indicated by the distribution's `format` and/or `mediaType`.
+- **[format]** (*Literal*): The file format of the distribution.
       Use `mediaType` instead if the type of the distribution is defined by [IANA].
-- **[generator]**: A generator that can create the distribution.
-- **[mediaType]**: The media type of the distribution as defined by [IANA].
-- **[packageFormat]**: The package format of the distribution in which one or more data files are grouped together, e.g., to enable a set of related files to be downloaded together.
-- **[parser]**: A parser that can parse the distribution.
+- **[generator]** (*IRI*): A generator that can create the distribution.
+- **[mediaType]** (*Literal*): The media type of the distribution as defined by [IANA].
+- **[packageFormat]** (*Literal*): The package format of the distribution in which one or more data files are grouped together, e.g., to enable a set of related files to be downloaded together.
+- **[parser]** (*IRI*): A parser that can parse the distribution.
 
 
 Properties for parsers and generators
 -------------------------------------
-- **[configuration]**: A JSON string with configurations specific to the parser or generator.
-- **[generatorType]**: Generator type. Ex: `application/vnd.dlite-generate`.
-- **[parserType]**: Parser type. Ex: `application/vnd.dlite-parse`.
+- **[configuration]** (*Literal*): A JSON string with configurations specific to the parser or generator.
+- **[generatorType]** (*Literal*): Generator type. Ex: `application/vnd.dlite-generate`.
+- **[parserType]** (*Literal*): Parser type. Ex: `application/vnd.dlite-parse`.
 
 <!--
 - **[functionType]**:
@@ -158,6 +159,7 @@ Properties for parsers and generators
 
 [abstract]: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/abstract
 [bibliographicCitation]: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/bibliographicCitation
+[comment]: https://www.w3.org/TR/rdf12-schema/#ch_comment
 [deprecated]: https://www.w3.org/TR/owl2-quick-reference/
 [isDefinedBy]: https://www.w3.org/TR/rdf12-schema/#ch_isdefinedby
 [label]: https://www.w3.org/TR/rdf12-schema/#ch_label
diff --git a/tripper/context/0.2/context.json b/tripper/context/0.2/context.json
index 409e1117..b2837617 100644
--- a/tripper/context/0.2/context.json
+++ b/tripper/context/0.2/context.json
@@ -22,97 +22,80 @@
     "oteio": "https://w3id.org/emmo/domain/oteio#",
     "chameo": "https://w3id.org/emmo/domain/characterisation-methodology/chameo#",
 
-    "status": "adms:status",
-    "versionNotes": "adms:versionNotes",
 
-    "contactPoint": "dcat:contactPoint",
-    "hasCurrentVersion": "dcat:hasCurrentVersion",
-    "hasVersion": "dcat:hasVersion",
-    "inSeries": {
-      "@id": "dcat:inSeries",
-      "@type": "@id"
-    },
-    "keyword": "dcat:keyword",
-    "landingPage": "dcat:landingPage",
-    "qualifiedRelation": {
-      "@id": "dcat:qualifiedRelation",
-      "@type": "@id"
-    },
-    "theme": "dcat:theme",
-    "version": "dcat:version",
     "accessRights": "dcterms:accessRights",
     "conformsTo": "dcterms:conformsTo",
+    "contactPoint": "dcat:contactPoint",
     "creator": "dcterms:creator",
     "description": "dcterms:description",
+    "hasCurrentVersion": "dcat:hasCurrentVersion",
     "hasPart": {
       "@id": "dcterms:hasPart",
       "@type": "@id"
     },
+    "hasPolicy": "odrl:hasPolicy",
+    "hasVersion": "dcat:hasVersion",
     "identifier": "dcterms:identifier",
     "isReferencedBy": "dcterms:isReferencedBy",
     "issued": "dcterms:issued",
+    "keyword": "dcat:keyword",
+    "landingPage": "dcat:landingPage",
     "language": "dcterms:language",
     "license": "dcterms:license",
     "modified": "dcterms:modified",
     "publisher": "dcterms:publisher",
+    "qualifiedAttribution": {
+      "@id": "prov:qualifiedAttribution",
+      "@type": "@id"
+    },
+    "qualifiedRelation": {
+      "@id": "dcat:qualifiedRelation",
+      "@type": "@id"
+    },
     "relation": {
       "@id": "dcterms:relation",
       "@type": "@id"
     },
-
     "replaces": {
       "@id": "dcterms:replaces",
       "@type": "@id"
     },
-
     "rights": "dcterms:rights",
+    "status": "adms:status",
+    "theme": "dcat:theme",
     "title": "dcterms:title",
     "type": "dcterms:type",
-    "hasPolicy": "odrl:hasPolicy",
-    "qualifiedAttribution": {
-      "@id": "prov:qualifiedAttribution",
-      "@type": "@id"
-    },
-
-    "distribution": {
-      "@id": "dcat:distribution",
-      "@type": "@id"
-    },
-
-    "accessService": {
-      "@id": "dcat:accessService",
-      "@type": "@id"
-    },
-    "accessURL": "dcat:accessURL",
-    "byteSize": "dcat:byteSize",
-    "compressFormat": "dcat:compressFormat",
-    "downloadURL": "dcat:downloadURL",
-    "mediaType": "dcat:mediaType",
-    "packageFormat": "dcat:packageFormat",
-    "spatial": "dcterms:spatial",
-    "spatialResolutionInMeters": "dcat:spatialResolutionInMeters",
-    "temporal": "dcterms:temporal",
-    "temporalResolution": "dcat:temporalResolution",
-    "wasGeneratedBy": "prov:wasGeneratedBy",
-    "format": "dcterms:format",
-    "checksum": {
-      "@id": "spdx:checksum",
-      "@type": "@id"
-    },
+    "version": "dcat:version",
+    "versionNotes": "adms:versionNotes",
 
     "abstract": "dcterms:abstract",
     "bibliographicCitation": "dcterms:bibliographicCitation",
-    "deprecated": "owl:deprecated",
     "comment": "rdfs:comment",
+    "deprecated": "owl:deprecated",
     "isDefinedBy": "rdfs:isDefinedBy",
     "label": "rdfs:label",
     "seeAlso": "rdfs:seeAlso",
     "source": "dcterms:source",
+    "statements": {
+      "@id": "oteio:statement",
+      "@type": "@json"
+    },
+
 
+    "datamodel": "oteio:hasDatamodel",
+    "datamodelStorage": "oteio:hasDatamodelStorage",
+    "distribution": {
+      "@id": "dcat:distribution",
+      "@type": "@id"
+    },
     "hasDatum": {
       "@id": "emmo:EMMO_b19aacfc_5f73_4c33_9456_469c1e89a53e",
       "@type": "@id"
     },
+    "inSeries": {
+      "@id": "dcat:inSeries",
+      "@type": "@id"
+    },
     "isInputOf": {
       "@id": "emmo:EMMO_1494c1a9_00e1_40c2_a9cc_9bbf302a1cac",
       "@type": "@id"
@@ -121,26 +104,59 @@
       "@id": "emmo:EMMO_2bb50428_568d_46e8_b8bf_59a4c5656461",
       "@type": "@id"
     },
+    "mappings": {
+      "@id": "oteio:mapping",
+      "@type": "@json"
+    },
+    "mappingURL": "oteio:mappingURL",
+    "mappingFormat": "oteio:mappingFormat",
+    "spatial": "dcterms:spatial",
+    "spatialResolutionInMeters": "dcat:spatialResolutionInMeters",
+    "temporal": "dcterms:temporal",
+    "temporalResolution": "dcat:temporalResolution",
+    "wasGeneratedBy": "prov:wasGeneratedBy",
 
-    "parser": {
-      "@id": "oteio:parser",
+
+    "accessService": {
+      "@id": "dcat:accessService",
       "@type": "@id"
     },
+    "accessURL": "dcat:accessURL",
+    "byteSize": "dcat:byteSize",
+    "checksum": {
+      "@id": "spdx:checksum",
+      "@type": "@id"
+    },
+    "compressFormat": "dcat:compressFormat",
+    "downloadURL": "dcat:downloadURL",
+    "format": "dcterms:format",
     "generator": {
       "@id": "oteio:generator",
       "@type": "@id"
     },
-    "parserType": "oteio:parserType",
+    "mediaType": "dcat:mediaType",
+    "packageFormat": "dcat:packageFormat",
+    "parser": {
+      "@id": "oteio:parser",
+      "@type": "@id"
+    },
+
+    "configuration": {
+      "@id": "oteio:hasConfiguration",
+      "@type": "@json"
+    },
     "generatorType": "oteio:generatorType",
-    "functionType": "oteio:functionType",
+    "parserType": "oteio:parserType",
+
+
+
+
+
     "filterType": "oteio:filterType",
+    "functionType": "oteio:functionType",
 
-    "datamodel": "oteio:hasDatamodel",
-    "datamodelStorage": "oteio:hasDatamodelStorage",
     "hasDataSink": "oteio:hasDataSink",
     "storeURL": "oteio:storeURL",
-    "mappingURL": "oteio:mappingURL",
-    "mappingFormat": "oteio:mappingFormat",
 
     "subject": "rdf:subject",
     "predicate": "rdf:predicate",
@@ -149,21 +165,7 @@
     "prefixes": {
       "@id": "oteio:prefix",
       "@type": "@json"
-    },
-
-    "configuration": {
-      "@id": "oteio:hasConfiguration",
-      "@type": "@json"
-    },
-
-    "mappings": {
-      "@id": "oteio:mapping",
-      "@type": "@json"
-    },
-
-    "statements": {
-      "@id": "oteio:statement",
-      "@type": "@json"
     }
+
   }
 }

From ff4d0774e637de48e229a906ce81a8a661106ff4 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Fri, 3 Jan 2025 09:51:33 +0100
Subject: [PATCH 37/59] Separated the data documentation introduction into an
 own page.

---
 README.md                                     |  2 +-
 .../{datadoc.md => documenting-a-resource.md} | 63 ++++--------------
 docs/dataset/introduction.md                  | 66 +++++++++++++++++++
 .../{datadoc-keywords.md => keywords.md}      |  0
 .../{datadoc-prefixes.md => prefixes.md}      |  0
 docs/index.md                                 |  2 +-
 mkdocs.yml                                    |  7 +-
 7 files changed, 83 insertions(+), 57 deletions(-)
 rename docs/dataset/{datadoc.md => documenting-a-resource.md} (77%)
 create mode 100644 docs/dataset/introduction.md
 rename docs/dataset/{datadoc-keywords.md => keywords.md} (100%)
 rename docs/dataset/{datadoc-prefixes.md => prefixes.md} (100%)

diff --git a/README.md b/README.md
index b494f1b6..5ad9f7e0 100644
--- a/README.md
+++ b/README.md
@@ -106,7 +106,7 @@ 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/datadoc/
+[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/
diff --git a/docs/dataset/datadoc.md b/docs/dataset/documenting-a-resource.md
similarity index 77%
rename from docs/dataset/datadoc.md
rename to docs/dataset/documenting-a-resource.md
index 0afb16f5..495ba3fc 100644
--- a/docs/dataset/datadoc.md
+++ b/docs/dataset/documenting-a-resource.md
@@ -1,58 +1,15 @@
-Data documentation
-==================
-<!-- markdownlint-disable MD007 -->
-
-
-Introduction
-------------
-The data documentation is based on small [JSON-LD documents], each documenting a single resource.
-Examples of resources can be a dataset, an instrument, a sample, etc.
-All resources are uniquely identified by their IRI.
-
-The primary focus of the [tripper.dataset] module is to document datasets such that they are consistent with the [DCAT vocabulary], but at the same time easily extended additional semantic meaning provided by other ontologies.
-It is also easy to add and relate the datasets to other types of documents, like people, instruments and samples.
-
-The [tripper.dataset] module provides a Python API for documenting resources at all four levels of data documentation, including:
-
-- **Cataloguing**: Storing and accessing *documents* based on their IRI and data properties.
-  (Addressed FAIR aspects: *findability* and *accessibility*).
-- **Structural documentation**: The structure of a dataset. Provided via [DLite] data models.
-  (Addressed FAIR aspects: *interoperability*).
-- **Contextual documentation**: Relations between resources, i.e. *linked data*. Enables contextual search.
-  (Addressed FAIR aspects: *findability* and *reusability*).
-- **Semantic documentation**: Describe what the resource *is* using ontologies. In combination with structural documentation, maps the properties of a data model to ontological concepts.
-  (Addressed FAIR aspects: *findability*, *interoperability* and *reusability*).
-
-The figure below shows illustrates how a dataset is documented in a triplestore.
-
-![Documentation of a dataset](https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/docs/figs/dataset-Dataset.png)
-
-
-Resource types
---------------
-The [tripper.dataset] module include the following set of predefined resource types:
-
-- **dataset**: Individual of [dcat:Dataset] and [emmo:DataSet].
-- **distribution**: Individual of [dcat:Distribution].
-- **accessService**: Individual of [dcat:AccessService].
-- **generator**: Individual of [oteio:Generator].
-- **parser**: Individual of [oteio:Parser].
-- **resource**: Any other documented resource, with no implicit type.
-
-Future releases will support adding custom resource types.
-
-
 Documenting a resource
-----------------------
+======================
 In the Python API are the JSON-LD documents describing the resources internally represented as Python dicts.
 However, the [tripper.dataset] module tries to hide away the complexities of  [JSON-LD] behind a simple interface.
 
 
-### Documenting as a Python dict
+Documenting as a Python dict
+----------------------------
 The API supports two Python dict representations, one for documenting a single resource and one for documenting multiple resources.
 
 
-#### Single-resource dict
+### Single-resource dict
 Below is a simple example of how to document a SEM image dataset as a Python dict:
 
 ```python
@@ -154,7 +111,7 @@ Note that the image implicitly has been declared to be an individual of the clas
 This is because the `type` argument of [save_dict()] defaults to "dataset".
 
 
-#### Multi-resource dict
+### Multi-resource dict
 It is also possible to document multiple resources as a Python dict.
 
 !!! note
@@ -170,7 +127,8 @@ This dict representation accepts the following keywords:
 See [semdata.yaml] for an example of a [YAML] representation of a multi-resource dict documentation.
 
 
-### Documenting as a YAML file
+Documenting as a YAML file
+--------------------------
 The [save_datadoc()] function allow to save a [YAML] file in [multi-resource](#multi-resource-dict) format to a triplestore.
 Saving [semdata.yaml] to a triplestore can e.g. be done with
 
@@ -185,7 +143,8 @@ AttrDict(...)
 ```
 
 
-### Documenting as table
+Documenting as table
+--------------------
 The [TableDoc] class can be used to document multiple resources as rows in a table.
 
 The table must have a header row with defined keywords (either [predefined][predefined keywords] or provided with a custom context).
@@ -238,8 +197,8 @@ The below example shows how to save all datasets listed in the CSV file [semdata
 [JSON-LD documents]: https://json-ld.org/
 [JSON-LD]: https://www.w3.org/TR/json-ld/
 [default JSON-LD context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json
-[predefined prefixes]: datadoc-prefixes.md
-[predefined keywords]: datadoc-keywords.md
+[predefined prefixes]: prefixes.md
+[predefined keywords]: keywords.md
 [dcat:Dataset]: https://www.w3.org/TR/vocab-dcat-3/#Class:Dataset
 [dcat:Distribution]: https://www.w3.org/TR/vocab-dcat-3/#Class:Distribution
 [dcat:AccessService]: https://www.w3.org/TR/vocab-dcat-3/#Class:AccessService
diff --git a/docs/dataset/introduction.md b/docs/dataset/introduction.md
new file mode 100644
index 00000000..0be53abf
--- /dev/null
+++ b/docs/dataset/introduction.md
@@ -0,0 +1,66 @@
+Data documentation
+==================
+<!-- markdownlint-disable MD007 -->
+
+
+Introduction
+------------
+The data documentation is based on small [JSON-LD documents], each documenting a single resource.
+Examples of resources can be a dataset, an instrument, a sample, etc.
+All resources are uniquely identified by their IRI.
+
+The primary focus of the [tripper.dataset] module is to document datasets such that they are consistent with the [DCAT vocabulary], but at the same time easily extended additional semantic meaning provided by other ontologies.
+It is also easy to add and relate the datasets to other types of documents, like people, instruments and samples.
+
+The [tripper.dataset] module provides a Python API for documenting resources at all four levels of data documentation, including:
+
+- **Cataloguing**: Storing and accessing *documents* based on their IRI and data properties.
+  (Addressed FAIR aspects: *findability* and *accessibility*).
+- **Structural documentation**: The structure of a dataset. Provided via [DLite] data models.
+  (Addressed FAIR aspects: *interoperability*).
+- **Contextual documentation**: Relations between resources, i.e. *linked data*. Enables contextual search.
+  (Addressed FAIR aspects: *findability* and *reusability*).
+- **Semantic documentation**: Describe what the resource *is* using ontologies. In combination with structural documentation, maps the properties of a data model to ontological concepts.
+  (Addressed FAIR aspects: *findability*, *interoperability* and *reusability*).
+
+The figure below shows illustrates how a dataset is documented in a triplestore.
+
+![Documentation of a dataset](https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/docs/figs/dataset-Dataset.png)
+
+
+Resource types
+--------------
+The [tripper.dataset] module include the following set of predefined resource types:
+
+- **dataset**: Individual of [dcat:Dataset] and [emmo:DataSet].
+- **distribution**: Individual of [dcat:Distribution].
+- **accessService**: Individual of [dcat:AccessService].
+- **generator**: Individual of [oteio:Generator].
+- **parser**: Individual of [oteio:Parser].
+- **resource**: Any other documented resource, with no implicit type.
+
+Future releases will support adding custom resource types.
+
+
+
+[tripper.dataset]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset
+[DCAT vocabulary]: https://www.w3.org/TR/vocab-dcat-3/
+[DLite]: https://github.com/SINTEF/dlite
+[YAML]: https://yaml.org/
+[JSON-LD documents]: https://json-ld.org/
+[JSON-LD]: https://www.w3.org/TR/json-ld/
+[default JSON-LD context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json
+[predefined prefixes]: prefixes.md
+[predefined keywords]: keywords.md
+[dcat:Dataset]: https://www.w3.org/TR/vocab-dcat-3/#Class:Dataset
+[dcat:Distribution]: https://www.w3.org/TR/vocab-dcat-3/#Class:Distribution
+[dcat:AccessService]: https://www.w3.org/TR/vocab-dcat-3/#Class:AccessService
+[emmo:DataSet]: https://w3id.org/emmo#EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a
+[oteio:Generator]: https://w3id.org/emmo/domain/oteio/Generator
+[oteio:Parser]: https://w3id.org/emmo/domain/oteio/Parser
+[save_dict()]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.dataset.save_dict
+[as_jsonld()]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.dataset.as_jsonld
+[save_datadoc()]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.dataset.save_datadoc
+[semdata.yaml]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.yaml
+[semdata.csv]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/tabledoc-csv/tests/input/semdata.csv
+[TableDoc]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.tabledoc.TableDoc
diff --git a/docs/dataset/datadoc-keywords.md b/docs/dataset/keywords.md
similarity index 100%
rename from docs/dataset/datadoc-keywords.md
rename to docs/dataset/keywords.md
diff --git a/docs/dataset/datadoc-prefixes.md b/docs/dataset/prefixes.md
similarity index 100%
rename from docs/dataset/datadoc-prefixes.md
rename to docs/dataset/prefixes.md
diff --git a/docs/index.md b/docs/index.md
index b494f1b6..5ad9f7e0 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -106,7 +106,7 @@ 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/datadoc/
+[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/
diff --git a/mkdocs.yml b/mkdocs.yml
index 117bec6b..f666b395 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -82,9 +82,10 @@ nav:
   - Tutorial: tutorial.md
   - Backend discovery: backend_discovery.md
   - Data documentation:
-    - Introduction: dataset/datadoc.md
-    - Predefined prefixes: dataset/datadoc-prefixes.md
-    - Predefined keywords: dataset/datadoc-keywords.md
+    - Introduction: dataset/introduction.md
+    - Documenting a resource: dataset/documenting-a-resource.md
+    - Predefined prefixes: dataset/prefixes.md
+    - Predefined keywords: dataset/keywords.md
   - ... | api_reference/**
   - Known issues: known-issues.md
   - For developers: developers.md

From c7709ae5ec683e2e37462c8bbea434008dce808c Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Fri, 3 Jan 2025 12:24:59 +0100
Subject: [PATCH 38/59] Added a section about customisation to the
 documentation

---
 docs/dataset/customisation.md          | 100 +++++++++++++++++++++++++
 docs/dataset/documenting-a-resource.md |   7 +-
 docs/dataset/introduction.md           |   7 +-
 docs/dataset/keywords.md               |   9 ++-
 docs/dataset/prefixes.md               |   4 +-
 mkdocs.yml                             |   1 +
 6 files changed, 118 insertions(+), 10 deletions(-)
 create mode 100644 docs/dataset/customisation.md

diff --git a/docs/dataset/customisation.md b/docs/dataset/customisation.md
new file mode 100644
index 00000000..4cfeddb2
--- /dev/null
+++ b/docs/dataset/customisation.md
@@ -0,0 +1,100 @@
+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 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 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
+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.
+
+
+
+[With custom context]: #with-custom-context
+[User-defined keywords]: #user-defined-keywords
+[resource types]: introduction.md#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://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json
diff --git a/docs/dataset/documenting-a-resource.md b/docs/dataset/documenting-a-resource.md
index 495ba3fc..3e838ce8 100644
--- a/docs/dataset/documenting-a-resource.md
+++ b/docs/dataset/documenting-a-resource.md
@@ -205,9 +205,10 @@ The below example shows how to save all datasets listed in the CSV file [semdata
 [emmo:DataSet]: https://w3id.org/emmo#EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a
 [oteio:Generator]: https://w3id.org/emmo/domain/oteio/Generator
 [oteio:Parser]: https://w3id.org/emmo/domain/oteio/Parser
-[save_dict()]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.dataset.save_dict
-[as_jsonld()]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.dataset.as_jsonld
-[save_datadoc()]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.dataset.save_datadoc
+[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
 [semdata.yaml]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.yaml
 [semdata.csv]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/tabledoc-csv/tests/input/semdata.csv
 [TableDoc]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.tabledoc.TableDoc
diff --git a/docs/dataset/introduction.md b/docs/dataset/introduction.md
index 0be53abf..b6431bac 100644
--- a/docs/dataset/introduction.md
+++ b/docs/dataset/introduction.md
@@ -58,9 +58,10 @@ Future releases will support adding custom resource types.
 [emmo:DataSet]: https://w3id.org/emmo#EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a
 [oteio:Generator]: https://w3id.org/emmo/domain/oteio/Generator
 [oteio:Parser]: https://w3id.org/emmo/domain/oteio/Parser
-[save_dict()]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.dataset.save_dict
-[as_jsonld()]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.dataset.as_jsonld
-[save_datadoc()]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.dataset.save_datadoc
+[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
 [semdata.yaml]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.yaml
 [semdata.csv]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/tabledoc-csv/tests/input/semdata.csv
 [TableDoc]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.tabledoc.TableDoc
diff --git a/docs/dataset/keywords.md b/docs/dataset/keywords.md
index 68a34fc5..3739cb7e 100644
--- a/docs/dataset/keywords.md
+++ b/docs/dataset/keywords.md
@@ -1,6 +1,7 @@
 Predefined keywords
 ===================
 All keywords listed on this page (except for the special "@"-prefixed keywords) are defined in the [default JSON-LD context].
+See [User-defined keywords] for how to extend this list with additional namespace prefixes.
 
 
 Special keywords for JSON-LD
@@ -61,7 +62,7 @@ Other general properties on resources
 - **[label]** (*Literal*): Provides a human-readable version of a resource's name.
 - **[seeAlso]** (*Literal*): Indicates a resource that might provide additional information about the subject resource.
 - **[source]** (*Literal*): A related resource from which the described resource is derived.
-- **[statements]** (*Literal*): A list of subject-predicate-object triples with additional RDF statements documenting the resource.
+- **[statements]** (*Literal JSON*): A list of subject-predicate-object triples with additional RDF statements documenting the resource.
 
 
 Properties specific for datasets
@@ -74,7 +75,7 @@ Properties specific for datasets
 - **[inSeries]** (*IRI*): A dataset series of which the dataset is part.
 - **[isInputOf]** (*IRI*): A process that this dataset is the input to.
 - **[isOutputOf]** (*IRI*): A process that this dataset is the output of.
-- **[mappings]** (*Literal*): A list of subject-predicate-object triples mapping the datamodel to ontological concepts.
+- **[mappings]** (*Literal JSON*): A list of subject-predicate-object triples mapping the datamodel to ontological concepts.
 - **[mappingURL]** (*Literal*): URL to a document defining the mappings of the datamodel.
       The file format is given by `mappingFormat`.
       Defaults to turtle.
@@ -105,7 +106,7 @@ Properties specific for distributions
 
 Properties for parsers and generators
 -------------------------------------
-- **[configuration]** (*Literal*): A JSON string with configurations specific to the parser or generator.
+- **[configuration]** (*Literal JSON*): A JSON string with configurations specific to the parser or generator.
 - **[generatorType]** (*Literal*): Generator type. Ex: `application/vnd.dlite-generate`.
 - **[parserType]** (*Literal*): Parser type. Ex: `application/vnd.dlite-parse`.
 
@@ -222,3 +223,5 @@ Properties for parsers and generators
 [dcat:Distribution]: https://www.w3.org/TR/vocab-dcat-3/#Class:Distribution
 [vCard]: https://www.w3.org/TR/vcard-rdf/
 [IANA]: https://www.iana.org/assignments/media-types/media-types.xhtml
+
+[User-defined keywords]: ../customisation/#user-defined-keywords
diff --git a/docs/dataset/prefixes.md b/docs/dataset/prefixes.md
index d5d3e538..5af69c85 100644
--- a/docs/dataset/prefixes.md
+++ b/docs/dataset/prefixes.md
@@ -1,6 +1,7 @@
 Predefined prefixes
 ===================
-All prefixes listed on this page are defined in the [default JSON-LD context].
+All namespace prefixes listed on this page are defined in the [default JSON-LD context].
+See [User-defined prefixes] for how to extend this list with additional namespace prefixes.
 
 * adms: http://www.w3.org/ns/adms#
 * dcat: http://www.w3.org/ns/dcat#
@@ -24,3 +25,4 @@ All prefixes listed on this page are defined in the [default JSON-LD context].
 
 
 [default JSON-LD context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json
+[User-defined prefixes]: ../customisation/#user-defined-prefixes
diff --git a/mkdocs.yml b/mkdocs.yml
index f666b395..db90385f 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -84,6 +84,7 @@ nav:
   - Data documentation:
     - Introduction: dataset/introduction.md
     - Documenting a resource: dataset/documenting-a-resource.md
+    - Customisation: dataset/customisation.md
     - Predefined prefixes: dataset/prefixes.md
     - Predefined keywords: dataset/keywords.md
   - ... | api_reference/**

From 1a1cbad4806a9b5ec09ce320f7473f2bc1970e6c Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper-friis@users.noreply.github.com>
Date: Fri, 3 Jan 2025 14:53:19 +0100
Subject: [PATCH 39/59] Update docs/dataset/customisation.md

Co-authored-by: Tor S. Haugland <torshaugland@gmail.com>
---
 docs/dataset/customisation.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/dataset/customisation.md b/docs/dataset/customisation.md
index 4cfeddb2..ad176916 100644
--- a/docs/dataset/customisation.md
+++ b/docs/dataset/customisation.md
@@ -15,7 +15,7 @@ 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 from the Python API.
+This may be handy when used from the Python API.
 
 
 ### With custom context

From 3f30c0072ee890148789e0ebbcddf875f4d84531 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper-friis@users.noreply.github.com>
Date: Fri, 3 Jan 2025 14:54:20 +0100
Subject: [PATCH 40/59] Update docs/dataset/customisation.md

Co-authored-by: Tor S. Haugland <torshaugland@gmail.com>
---
 docs/dataset/customisation.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/dataset/customisation.md b/docs/dataset/customisation.md
index ad176916..f52cf0a6 100644
--- a/docs/dataset/customisation.md
+++ b/docs/dataset/customisation.md
@@ -27,6 +27,7 @@ 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.
 

From c69dd23409d18f86c922e32a885864fdb338e67c Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Fri, 3 Jan 2025 14:55:49 +0100
Subject: [PATCH 41/59] Documented custum context

---
 docs/dataset/customisation.md          | 11 ++--
 docs/dataset/documenting-a-resource.md |  6 ++-
 tests/dataset/test_dataset.py          | 71 ++++++++++++++++++++++++++
 tests/input/custom_context.yaml        | 40 +++++++++++++++
 tripper/dataset/dataset.py             | 40 +++++++++------
 5 files changed, 148 insertions(+), 20 deletions(-)
 create mode 100644 tests/input/custom_context.yaml

diff --git a/docs/dataset/customisation.md b/docs/dataset/customisation.md
index 4cfeddb2..7f12bf06 100644
--- a/docs/dataset/customisation.md
+++ b/docs/dataset/customisation.md
@@ -72,8 +72,12 @@ In your ontology you may define `fromBatch` as a object property with IRI: http:
 
 Here the special value "@id" for the "@type" means that the value of `fromBatch` must be an IRI.
 
-### Providing a custom context
-TODO
+
+Providing a custom context
+--------------------------
+Custom context can be provided for all the interfaces described in the section [Documenting a resource].
+
+In the YAML documentation, Custom context can be provided with the "@context"
 
 
 User-defined resource types
@@ -87,9 +91,10 @@ Instead, the list of available resource types should be stored and retrieved fro
 
 
 
+[Documenting a resource]: ../documenting-a-resource
 [With custom context]: #with-custom-context
 [User-defined keywords]: #user-defined-keywords
-[resource types]: introduction.md#resource-types
+[resource types]: ../introduction#resource-types
 [predefined prefixes]: ../prefixes
 [predefined keywords]: ../keywords
 [save_dict()]: ../../api_reference/dataset/dataset/#tripper.dataset.dataset.save_dict
diff --git a/docs/dataset/documenting-a-resource.md b/docs/dataset/documenting-a-resource.md
index 3e838ce8..a85342dd 100644
--- a/docs/dataset/documenting-a-resource.md
+++ b/docs/dataset/documenting-a-resource.md
@@ -1,7 +1,9 @@
 Documenting a resource
 ======================
-In the Python API are the JSON-LD documents describing the resources internally represented as Python dicts.
-However, the [tripper.dataset] module tries to hide away the complexities of  [JSON-LD] behind a simple interface.
+In the [tripper.dataset] sub-package are the documents documenting the resources internally represented as [JSON-LD] documents stored as Python dicts.
+However, the API tries to hide away the complexities of JSON-LD behind simple interfaces.
+To support different use cases, the sub-package provide several interfaces for data documentation, including Python dicts, YAML files and tables.
+These are further described below.
 
 
 Documenting as a Python dict
diff --git a/tests/dataset/test_dataset.py b/tests/dataset/test_dataset.py
index 0352d4e3..2bd94cb6 100644
--- a/tests/dataset/test_dataset.py
+++ b/tests/dataset/test_dataset.py
@@ -144,6 +144,50 @@ def test_expand_iri():
         assert expand_iri("xxx:type", prefixes) == "xxx:type"
 
 
+def test_as_jsonld():
+    """Test as_jsonld()."""
+    from tripper import DCAT, EMMO, OWL, Namespace
+    from tripper.dataset import as_jsonld
+    from tripper.dataset.dataset import CONTEXT_URL
+
+    with pytest.raises(ValueError):
+        as_jsonld({})
+
+    EX = Namespace("http://example.com/ex#")
+    SER = Namespace("http://example.com/series#")
+    dct = {"@id": "ex:indv", "a": "val"}
+    context = {"ex": EX, "a": "ex:a"}
+
+    d = as_jsonld(dct, _context=context)
+    assert len(d["@context"]) == 2
+    assert d["@context"][0] == CONTEXT_URL
+    assert d["@context"][1] == context
+    assert d["@id"] == EX.indv
+    assert len(d["@type"]) == 2
+    assert set(d["@type"]) == {DCAT.Dataset, EMMO.DataSet}
+    assert d.a == "val"
+
+    d2 = as_jsonld(dct, type="resource", _context=context)
+    assert d2["@context"] == d["@context"]
+    assert d2["@id"] == d["@id"]
+    assert d2["@type"] == OWL.NamedIndividual
+    assert d2.a == "val"
+
+    d3 = as_jsonld(
+        {"inSeries": "ser:main"},
+        prefixes={"ser": SER},
+        a="value",
+        _id="ex:indv2",
+        _type="ex:Item",
+        _context=context,
+    )
+    assert d3["@context"] == d["@context"]
+    assert d3["@id"] == EX.indv2
+    assert set(d3["@type"]) == {DCAT.Dataset, EMMO.DataSet, EX.Item}
+    assert d3.a == "value"
+    assert d3.inSeries == SER.main
+
+
 # if True:
 def test_datadoc():
     """Test save_datadoc() and load_dict()/save_dict()."""
@@ -236,6 +280,33 @@ def test_datadoc():
     }
 
 
+def test_custom_context():
+    """Test saving YAML file with custom context to triplestore."""
+    from dataset_paths import indir  # pylint: disable=import-error
+
+    from tripper import Triplestore
+    from tripper.dataset import save_datadoc
+
+    ts = Triplestore("rdflib")
+    d = save_datadoc(ts, indir / "custom_context.yaml")
+
+    KB = ts.namespaces["kb"]
+    assert d.resources[0]["@id"] == KB.sampleA
+    assert d.resources[0].fromBatch == KB.batch1
+
+    assert d.resources[1]["@id"] == KB.sampleB
+    assert d.resources[1].fromBatch == KB.batch1
+
+    assert d.resources[2]["@id"] == KB.sampleC
+    assert d.resources[2].fromBatch == KB.batch2
+
+    assert d.resources[3]["@id"] == KB.batch1
+    assert d.resources[3].batchNumber == 1
+
+    assert d.resources[4]["@id"] == KB.batch2
+    assert d.resources[4].batchNumber == 2
+
+
 # if True:
 def test_pipeline():
     """Test creating OTEAPI pipeline."""
diff --git a/tests/input/custom_context.yaml b/tests/input/custom_context.yaml
new file mode 100644
index 00000000..f2270f0d
--- /dev/null
+++ b/tests/input/custom_context.yaml
@@ -0,0 +1,40 @@
+# 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
diff --git a/tripper/dataset/dataset.py b/tripper/dataset/dataset.py
index dd967521..c7fbb16f 100644
--- a/tripper/dataset/dataset.py
+++ b/tripper/dataset/dataset.py
@@ -39,7 +39,7 @@
 from pathlib import Path
 from typing import TYPE_CHECKING
 
-from tripper import DCAT, EMMO, OTEIO, OWL, RDF, Triplestore
+from tripper import DCAT, EMMO, OTEIO, OWL, RDF, Namespace, Triplestore
 from tripper.utils import AttrDict, as_python, openfile
 
 if TYPE_CHECKING:  # pragma: no cover
@@ -392,9 +392,9 @@ def get_prefixes(
         context=context, timeout=timeout, fromfile=fromfile
     )
     prefixes = {
-        k: v
+        k: str(v)
         for k, v in ctx.items()
-        if isinstance(v, str) and v.endswith(("#", "/"))
+        if isinstance(v, (str, Namespace)) and str(v).endswith(("#", "/"))
     }
     return prefixes
 
@@ -572,7 +572,8 @@ def save_datadoc(
         d = read_datadoc(file_or_dict)
 
     # Bind prefixes
-    prefixes = get_prefixes()
+    context = d.get("@context")
+    prefixes = get_prefixes(context=context)
     prefixes.update(d.get("prefixes", {}))
     for prefix, ns in prefixes.items():  # type: ignore
         ts.bind(prefix, ns)
@@ -584,7 +585,9 @@ def save_datadoc(
     for spec in dicttypes.values():
         label = spec["datadoc_label"]
         for dct in get(d, label):
-            dct = as_jsonld(dct=dct, type=types[label], prefixes=prefixes)
+            dct = as_jsonld(
+                dct=dct, type=types[label], prefixes=prefixes, _context=context
+            )
             f = io.StringIO(json.dumps(dct))
             with Triplestore(backend="rdflib") as ts2:
                 ts2.parse(f, format="json-ld")
@@ -604,7 +607,8 @@ def prepare_datadoc(datadoc: dict) -> dict:
     d = AttrDict({"@context": CONTEXT_URL})
     d.update(datadoc)
 
-    prefixes = get_prefixes()
+    context = datadoc.get("@context")
+    prefixes = get_prefixes(context=context)
     if "prefixes" in d:
         d.prefixes.update(prefixes)
     else:
@@ -613,13 +617,13 @@ def prepare_datadoc(datadoc: dict) -> dict:
     for type, spec in dicttypes.items():
         label = spec["datadoc_label"]
         for i, dct in enumerate(get(d, label)):
-            d[label][i] = as_jsonld(dct=dct, type=type, prefixes=d.prefixes)
+            d[label][i] = as_jsonld(
+                dct=dct, type=type, prefixes=d.prefixes, _context=context
+            )
 
     return d
 
 
-# TODO: update this function to correctly handle multiple contexts
-# provided with the `_context` keyword argument.
 def as_jsonld(
     dct: dict,
     type: "Optional[str]" = "dataset",
@@ -629,29 +633,35 @@ def as_jsonld(
     """Return an updated copy of dict `dct` as valid JSON-LD.
 
     Arguments:
-        dct: Dict with data documentation to represent as JSON-LD.
+        dct: Dict documenting a resource to be represented as JSON-LD.
         type: Type of data to document.  Should either be one of the
             pre-defined names: "dataset", "distribution", "accessService",
             "parser" and "generator" or an IRI to a class in an ontology.
             Defaults to "dataset".
         prefixes: Dict with prefixes in addition to those included in the
             JSON-LD context.  Should map namespace prefixes to IRIs.
-        kwargs: Additional keyword arguments to add to the returned dict.
-            A leading underscore in a key will be translated to a
-            leading "@"-sign.  For example, "@id" or "@context" may be
-            provided as "_id" or "_context", respectively.
+        kwargs: Additional keyword arguments to add to the returned
+            dict.  A leading underscore in a key will be translated to
+            a leading "@"-sign.  For example, "@id", "@type" or
+            "@context" may be provided as "_id" "_type" or "_context",
+            respectively.
 
     Returns:
         An updated copy of `dct` as valid JSON-LD.
+
     """
     # pylint: disable=too-many-branches
 
     # Id of base entry that is documented
     _entryid = kwargs.pop("_entryid", None)
 
+    context = kwargs.pop("_context", None)
+
     d = AttrDict()
     if not _entryid:
         d["@context"] = CONTEXT_URL
+        if context:
+            add(d, "@context", context)
 
     if type:
         t = dicttypes[type]["@type"] if type in dicttypes else type
@@ -674,7 +684,7 @@ def as_jsonld(
     if "@type" not in d:
         warnings.warn(f"Missing '@type' in dict to document: {_entryid}")
 
-    all_prefixes = get_prefixes()
+    all_prefixes = get_prefixes(context=context)
     if prefixes:
         all_prefixes.update(prefixes)
 

From 5686804769516e67c314232435b8bb199a8c012c Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Fri, 3 Jan 2025 15:29:24 +0100
Subject: [PATCH 42/59] Added example with custom context

---
 docs/dataset/customisation.md   | 111 +++++++++++++++++++++++++++++++-
 tests/input/custom_context.yaml |   2 +
 2 files changed, 112 insertions(+), 1 deletion(-)

diff --git a/docs/dataset/customisation.md b/docs/dataset/customisation.md
index 31503035..3691e187 100644
--- a/docs/dataset/customisation.md
+++ b/docs/dataset/customisation.md
@@ -78,7 +78,116 @@ Providing a custom context
 --------------------------
 Custom context can be provided for all the interfaces described in the section [Documenting a resource].
 
-In the YAML documentation, Custom context can be provided with the "@context"
+### 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://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.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
diff --git a/tests/input/custom_context.yaml b/tests/input/custom_context.yaml
index f2270f0d..5e647afa 100644
--- a/tests/input/custom_context.yaml
+++ b/tests/input/custom_context.yaml
@@ -1,3 +1,5 @@
+---
+
 # Custom context
 "@context":
   myonto: http://example.com/myonto#

From abbef4b78e2276c9ab0e439812d4a5caf8e2a9f6 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Fri, 3 Jan 2025 15:34:58 +0100
Subject: [PATCH 43/59] Correct example

---
 docs/dataset/customisation.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/dataset/customisation.md b/docs/dataset/customisation.md
index 3691e187..70db2b0a 100644
--- a/docs/dataset/customisation.md
+++ b/docs/dataset/customisation.md
@@ -144,7 +144,7 @@ You can save this context to a triplestore with
 >>> ts = Triplestore("rdflib")
 >>> save_datadoc(  # doctest: +ELLIPSIS
 ...     ts,
-...      "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.yaml",
+...      "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/dataset-docs/tests/input/custom_context.yaml",
 ... )
 AttrDict(...)
 

From 85a51ae24c7531b370a94946b62644fcae94d71c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 3 Jan 2025 22:29:16 +0000
Subject: [PATCH 44/59] [pre-commit.ci] auto fixes from pre-commit hooks

For more information, see https://pre-commit.ci
---
 tripper/dataset/tabledoc.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tripper/dataset/tabledoc.py b/tripper/dataset/tabledoc.py
index c4f14567..6dbf8b32 100644
--- a/tripper/dataset/tabledoc.py
+++ b/tripper/dataset/tabledoc.py
@@ -150,4 +150,3 @@ def write_csv(
             writer.writerow(self.header)
             for row in self.data:
                 writer.writerow(row)
-

From aa99eecf1b89dd1ea196c9cc6affc4eb1466e3aa Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Fri, 3 Jan 2025 23:37:43 +0100
Subject: [PATCH 45/59] Added datadoc tool

---
 docs/api_reference/dataset/datadoc.md |   3 +
 docs/dataset/customisation.md         |   4 +-
 mkdocs.yml                            |   4 +
 pyproject.toml                        |   3 +
 tests/dataset/test_dataset.py         |   2 +-
 tests/dataset/test_tabledoc.py        |  51 ++++++-
 tripper/dataset/datadoc.py            | 184 ++++++++++++++++++++++++++
 tripper/dataset/dataset.py            |  37 +++++-
 tripper/dataset/tabledoc.py           | 118 ++++++++++++++---
 9 files changed, 379 insertions(+), 27 deletions(-)
 create mode 100644 docs/api_reference/dataset/datadoc.md
 create mode 100644 tripper/dataset/datadoc.py

diff --git a/docs/api_reference/dataset/datadoc.md b/docs/api_reference/dataset/datadoc.md
new file mode 100644
index 00000000..b601d56d
--- /dev/null
+++ b/docs/api_reference/dataset/datadoc.md
@@ -0,0 +1,3 @@
+# datadoc
+
+::: tripper.dataset.datadoc
diff --git a/docs/dataset/customisation.md b/docs/dataset/customisation.md
index 70db2b0a..197b7fb9 100644
--- a/docs/dataset/customisation.md
+++ b/docs/dataset/customisation.md
@@ -205,8 +205,8 @@ Instead, the list of available resource types should be stored and retrieved fro
 [With custom context]: #with-custom-context
 [User-defined keywords]: #user-defined-keywords
 [resource types]: ../introduction#resource-types
-[predefined prefixes]: ../prefixes
-[predefined keywords]: ../keywords
+[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()]:
diff --git a/mkdocs.yml b/mkdocs.yml
index db90385f..815211d4 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -49,6 +49,10 @@ markdown_extensions:
   - toc:
       permalink: true
 
+exclude_docs: |
+  ../dataset/datadoc.py
+
+
 plugins:
   - search:
       lang: en
diff --git a/pyproject.toml b/pyproject.toml
index 0398f0a0..1e871728 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -83,6 +83,9 @@ Source = "https://github.com/EMMC-ASBL/tripper"
 Changelog = "https://github.com/EMMC-ASBL/tripper/blob/master/CHANGELOG.md"
 Package = "https://pypi.org/project/tripper"
 
+[project.scripts]
+datadoc = "tripper.dataset.datadoc:main"
+
 [tool.isort]
 line_length = 79  # PEP8
 
diff --git a/tests/dataset/test_dataset.py b/tests/dataset/test_dataset.py
index 2bd94cb6..01a90c57 100644
--- a/tests/dataset/test_dataset.py
+++ b/tests/dataset/test_dataset.py
@@ -263,7 +263,7 @@ def test_datadoc():
 
     # Test searching the triplestore
     SAMPLE = ts.namespaces["sample"]
-    datasets = search_iris(ts)
+    datasets = search_iris(ts, type="dcat:Dataset")
     named_datasets = {
         SEMDATA["SEM_cement_batch2/77600-23-001/77600-23-001_5kV_400x_m001"],
         SEMDATA["SEM_cement_batch2/77600-23-001"],
diff --git a/tests/dataset/test_tabledoc.py b/tests/dataset/test_tabledoc.py
index 67ce74ed..0df11e53 100644
--- a/tests/dataset/test_tabledoc.py
+++ b/tests/dataset/test_tabledoc.py
@@ -4,8 +4,8 @@
 
 
 # if True:
-def test_as_dicts():
-    """Test the as_dicts() method."""
+def test_asdicts():
+    """Test the asdicts() method."""
 
     pytest.importorskip("rdflib")
 
@@ -83,9 +83,33 @@ def test_as_dicts():
     print(ts.serialize())
 
 
+def test_fromdicts():
+    """Test the fromdicts() method."""
+    from tripper import Namespace
+    from tripper.dataset import TableDoc
+
+    EX = Namespace("http://example.com/ex#")
+    dicts = [
+        {"@id": EX.data1, "label": "data1"},
+        {
+            "@id": EX.data2,
+            "distribution": {"downloadURL": "http://example.com/data2"},
+        },
+    ]
+    td = TableDoc.fromdicts(dicts)
+
+    assert td.header == ["@id", "label", "distribution.downloadURL"]
+    assert td.data == [
+        [EX.data1, "data1", None],
+        [EX.data2, None, "http://example.com/data2"],
+    ]
+
+
 # if True:
 def test_csv():
     """Test parsing a csv file."""
+    import io
+
     from dataset_paths import indir, outdir  # pylint: disable=import-error
 
     pytest.importorskip("rdflib")
@@ -123,6 +147,29 @@ def test_csv():
     # Write the table to a new csv file
     td.write_csv(outdir / "semdata.csv")
 
+    # Write table to string
+    with io.StringIO() as f:
+        td.write_csv(f)
+        s = f.getvalue()
+
+    # Re-read the csv file from the string
+    with io.StringIO(s) as f:
+        td2 = TableDoc.parse_csv(
+            indir / "semdata.csv",
+            delimiter=";",
+            prefixes={
+                "sem": "https://w3id.com/emmo/domain/sem/0.1#",
+                "semdata": "https://he-matchmaker.eu/data/sem/",
+                "sample": "https://he-matchmaker.eu/sample/",
+                "mat": "https://he-matchmaker.eu/material/",
+                "dm": "http://onto-ns.com/meta/characterisation/0.1/SEMImage#",
+                "parser": "http://sintef.no/dlite/parser#",
+                "gen": "http://sintef.no/dlite/generator#",
+            },
+        )
+    assert td2.header == td.header
+    assert td2.data == td.data
+
     # Print serialised KB
     ts = Triplestore(backend="rdflib")
     td.save(ts)
diff --git a/tripper/dataset/datadoc.py b/tripper/dataset/datadoc.py
new file mode 100644
index 00000000..8b7b0eec
--- /dev/null
+++ b/tripper/dataset/datadoc.py
@@ -0,0 +1,184 @@
+"""A script for data documentation."""
+
+import argparse
+import io
+import json
+
+from tripper import Triplestore
+from tripper.dataset import (
+    TableDoc,
+    get_jsonld_context,
+    load_dict,
+    save_datadoc,
+    save_dict,
+    search_iris,
+)
+
+
+def subcommand_add(ts, args):
+    """Subcommand for populating the triplestore"""
+    if args.yamlfile:
+        save_datadoc(ts, args.yamlfile)
+
+    if args.table:
+        td = TableDoc.parse_csv(
+            args.table, context=get_jsonld_context(args.context)
+        )
+        td.save(ts)
+
+        save_datadoc(ts, args.yamlfile)
+
+    if args.serialize:
+        ts.serialize(args.serialize, format=args.sformat)
+
+
+def subcommand_find(ts, args):
+    """Subcommand for finding IRIs in the triplestore."""
+    if args.criteria:
+        kwargs = dict(crit.split("=", 1) for crit in args.criteria)
+    else:
+        kwargs = {}
+    iris = search_iris(ts, type=args.type, **kwargs)
+
+    # Create output
+    if args.format == "iris":
+        s = "\n".join(iris)
+    elif args.format == "json":
+        s = json.dumps([load_dict(ts, iri) for iri in iris], indent=2)
+    elif args.format == "turtle":
+        ts2 = Triplestore("rdflib")
+        for iri in iris:
+            d = load_dict(ts, iri)
+            save_dict(ts2, d)
+        s = ts2.serialize()
+    elif args.format == "csv":
+        dicts = [load_dict(ts, iri) for iri in iris]
+        td = TableDoc.fromdicts(dicts)
+        with io.StringIO() as f:
+            td.write_csv(f)
+            s = f.getvalue()
+    else:
+        raise ValueError(args.format)
+
+    print(s)
+
+
+def main():
+    """Main function."""
+    parser = argparse.ArgumentParser(
+        description=(
+            "Tool for data documentation.\n\n"
+            "It allows populating and searching a triplestore for existing "
+            "documentation."
+        ),
+    )
+
+    subparsers = parser.add_subparsers(required=True, help="subcommand help")
+
+    # Subcommand: add
+    parser_add = subparsers.add_parser("add", help="add help")
+    parser_add.set_defaults(func=subcommand_add)
+    parser_add.add_argument(
+        "--context",
+        help="Path or URL to custom JSON-LD context.  Used with `--table`.",
+    )
+    parser_add.add_argument(
+        "--yamlfile",
+        help="Path or URL to YAML file to add to the triplestore.",
+    )
+    parser_add.add_argument(
+        "--table", help="Path to table to populate the triplestore from."
+    )
+    parser_add.add_argument(
+        "--tformat",
+        help=(
+            "Used with `--table`. Format of the table to load. "
+            "Only csv is currently supported."
+        ),
+    )
+    parser_add.add_argument(
+        "--serialize",
+        metavar="FILENAME",
+        help="File to serialise the populated triplestore to.",
+    )
+    parser_add.add_argument(
+        "--sformat",
+        default="turtle",
+        help='Format to use with `--serialize`.  Default is "turtle".',
+    )
+
+    # Subcommand: find
+    parser_find = subparsers.add_parser(
+        "find", help="Find IRIs of resources in the triplestore."
+    )
+    parser_find.set_defaults(func=subcommand_find)
+    parser_find.add_argument(
+        "--type",
+        "-t",
+        help="The type of resources to find.",
+    )
+    parser_find.add_argument(
+        "--criteria",
+        "-c",
+        action="extend",
+        nargs="+",
+        metavar="KEY=VALUE",
+        help=("Matching criteria for resources to find.  "),
+    )
+    parser_find.add_argument(
+        "--format",
+        "-f",
+        default="iris",
+        choices=["iris", "json", "turtle", "csv"],
+        help="Output format to list the matched resources.",
+    )
+
+    # General: options
+    parser.add_argument(
+        "--backend",
+        "-b",
+        default="rdflib",
+        help="Triplestore backend to use.",
+    )
+    parser.add_argument(
+        "--base_iri",
+        help="Base IRI of the triplestore (seldom needed).",
+    )
+    parser.add_argument(
+        "--database",
+        "-d",
+        help="Name of database to connect to (for backends supporting it).",
+    )
+    parser.add_argument(
+        "--package",
+        help="Only needed when `backend` is a relative module.",
+    )
+    parser.add_argument(
+        "--parse",
+        "-p",
+        metavar="LOCATION",
+        help="Load triplestore from this location.",
+    )
+    parser.add_argument(
+        "--pformat",
+        "-f",
+        help="Used with `--parse`. Format to use when parsing triplestore.",
+    )
+
+    args = parser.parse_args()
+
+    ts = Triplestore(
+        backend=args.backend,
+        base_iri=args.base_iri,
+        database=args.database,
+        package=args.package,
+    )
+    if args.parse:
+        ts.parse(args.parse, format=args.pformat)
+
+    # Call subcommand handler
+    args.func(ts, args)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/tripper/dataset/dataset.py b/tripper/dataset/dataset.py
index c7fbb16f..cc0a9bda 100644
--- a/tripper/dataset/dataset.py
+++ b/tripper/dataset/dataset.py
@@ -61,6 +61,7 @@
     r"^([a-z0-9]*):([a-zA-Z_]([a-zA-Z0-9_/+-]*[a-zA-Z0-9_+-])?)$"
 )
 
+# Resource types
 dicttypes = {
     "parser": {
         "datadoc_label": "parsers",
@@ -91,6 +92,10 @@
 }
 
 
+class InvalidKeywordError(KeyError):
+    """Keyword is not defined."""
+
+
 def save_dict(
     ts: Triplestore,
     dct: dict,
@@ -846,17 +851,19 @@ def get_partial_pipeline(
     return pipeline
 
 
-def search_iris(ts: Triplestore, type=DCAT.Dataset, **kwargs):
-    """Return a list of IRIs for all entries of the given type.
+def search_iris(ts: Triplestore, type=None, **kwargs):
+    """Return a list of IRIs for all matching resources.
     Additional matching criterias can be specified by `kwargs`.
 
-
     Arguments:
         ts: Triplestore to search.
         type: Search for entries that are individuals of the class with
-            this IRI.  The default is `dcat:Dataset`.
+            this IRI.
         kwargs: Match criterias.
 
+    Returns:
+        List of IRIs for matching resources.
+
     Examples:
         List all dataset IRIs:
 
@@ -880,11 +887,29 @@ def search_iris(ts: Triplestore, type=DCAT.Dataset, **kwargs):
     crit = []
 
     if type:
-        crit.append(f"  ?iri rdf:type <{type}> .")
+        if ":" in type:
+            expanded = ts.expand_iri(type)
+            crit.append(f"  ?iri rdf:type <{expanded}> .")
+        elif type in dicttypes:
+            types = dicttypes[type]["@type"]
+            if isinstance(types, str):
+                types = [types]
+            for t in types:
+                crit.append(f"  ?iri rdf:type <{t}> .")
+        else:
+            raise ValueError(
+                "`type` must either be an IRI or the name of one the "
+                f"resource types. Got: {type}"
+            )
+
+    else:
+        crit.append("  ?iri rdf:type ?o .")
 
     expanded = {v: k for k, v in get_shortnames().items()}
     for k, v in kwargs.items():
         key = f"@{k[1:]}" if k.startswith("_") else k
+        if key not in expanded:
+            raise InvalidKeywordError(key)
         predicate = expanded[key]
         if v in expanded:
             value = f"<{expanded[v]}>"
@@ -894,7 +919,7 @@ def search_iris(ts: Triplestore, type=DCAT.Dataset, **kwargs):
             )
         else:
             value = v
-        crit.append(f"  ?iri <{predicate}> {value} .")
+        crit.append(f"      ?iri <{predicate}> {value} .")
     criterias = "\n".join(crit)
     query = f"""
     PREFIX rdf: <{RDF}>
diff --git a/tripper/dataset/tabledoc.py b/tripper/dataset/tabledoc.py
index 609fdd3d..6624afe8 100644
--- a/tripper/dataset/tabledoc.py
+++ b/tripper/dataset/tabledoc.py
@@ -9,7 +9,14 @@
 from tripper.utils import AttrDict, openfile
 
 if TYPE_CHECKING:  # pragma: no cover
-    from typing import List, Optional, Sequence, Union
+    from typing import Iterable, List, Optional, Protocol, Sequence, Union
+
+    class Writer(Protocol):
+        """Prototype for a class with a write() method."""
+
+        # pylint: disable=too-few-public-methods,missing-function-docstring
+
+        def write(self, data: str) -> None: ...
 
 
 class TableDoc:
@@ -43,13 +50,18 @@ def __init__(
         context: "Optional[Union[dict, list]]" = None,
         strip: bool = True,
     ):
-        self.header = header
-        self.data = data
+        self.header = list(header)
+        self.data = [list(row) for row in data]
         self.type = type
         self.prefixes = prefixes
         self.context = context
         self.strip = strip
 
+    def save(self, ts: Triplestore) -> None:
+        """Save tabular datadocumentation to triplestore."""
+        for d in self.asdicts():
+            save_dict(ts, d)
+
     def asdicts(self) -> "List[dict]":
         """Return the table as a list of dicts."""
         kw = {"@context": self.context} if self.context else {}
@@ -69,14 +81,74 @@ def asdicts(self) -> "List[dict]":
             results.append(jsonld)
         return results
 
-    def save(self, ts: Triplestore) -> None:
-        """Save tabular datadocumentation to triplestore."""
-        for d in self.asdicts():
-            save_dict(ts, d)
+    @staticmethod
+    def fromdicts(
+        dicts: "Sequence[dict]",
+        type: "Optional[str]" = "dataset",
+        prefixes: "Optional[dict]" = None,
+        context: "Optional[Union[dict, list]]" = None,
+        strip: bool = True,
+    ) -> "TableDoc":
+        """Create new TableDoc instance from a sequence of dicts.
+
+        Arguments:
+            dicts: Sequence of single-resource dicts.
+            type: Type of data to save (applies to all rows).  Should
+                either be one of the pre-defined names: "dataset",
+                "distribution", "accessService", "parser" and "generator"
+                or an IRI to a class in an ontology.  Defaults to
+                "dataset".
+            prefixes: Dict with prefixes in addition to those included in
+                the JSON-LD context.  Should map namespace prefixes to IRIs.
+            context: Dict with user-defined JSON-LD context.
+            strip: Whether to strip leading and trailing whitespaces from
+                cells.
+
+        Returns:
+            New TableDoc instance.
+
+        """
+        # Store the header as keys in a dict to keep ordering
+        header = {}
+
+        def addheader(d, prefix=""):
+            """Add keys in `d` to header.
+
+            Nested dicts will result in dot-separated keys.
+            """
+            for k, v in d.items():
+                if isinstance(v, dict):
+                    addheader(v, k + ".")
+                else:
+                    header[prefix + k] = True
+
+        # Assign the header
+        for d in dicts:
+            addheader(d)
+
+        # Assign table data. Nested dicts are accounted for
+        data = []
+        for dct in dicts:
+            row = []
+            for head in header:
+                d = dct
+                for key in head.split("."):
+                    d = d.get(key, {})
+                row.append(d if d != {} else None)
+            data.append(row)
+
+        return TableDoc(
+            header=header.keys(),  # type: ignore
+            data=data,  # type: ignore
+            type=type,
+            prefixes=prefixes,
+            context=context,
+            strip=strip,
+        )
 
     @staticmethod
     def parse_csv(
-        csvfile: "Union[Path, str]",
+        csvfile: "Union[Iterable[str], Path, str]",
         type: "Optional[str]" = "dataset",
         prefixes: "Optional[dict]" = None,
         context: "Optional[Union[dict, list]]" = None,
@@ -88,7 +160,7 @@ def parse_csv(
         """Parse a csv file using the standard library csv module.
 
         Arguments:
-            csvfile: CSV file to parse.
+            csvfile: Name of CSV file to parse or an iterable of strings.
             type: Type of data to save (applies to all rows).  Should
                 either be one of the pre-defined names: "dataset",
                 "distribution", "accessService", "parser" and "generator"
@@ -106,13 +178,20 @@ def parse_csv(
                 formatting parameters.  For more details, see
                 [Dialects and Formatting Parameters].
 
+        Returns:
+            New TableDoc instance.
+
         References:
         [Dialects and Formatting Parameters]: https://docs.python.org/3/library/csv.html#dialects-and-formatting-parameters
         """
-        with openfile(csvfile, mode="rt", encoding=encoding) as f:
-            reader = csv.reader(f, dialect=dialect, **kwargs)
-            header = next(reader)
-            data = list(reader)
+        if isinstance(csvfile, (str, Path)):
+            with openfile(csvfile, mode="rt", encoding=encoding) as f:
+                reader = csv.reader(f, dialect=dialect, **kwargs)
+        else:
+            reader = csv.reader(csvfile, dialect=dialect, **kwargs)
+
+        header = next(reader)
+        data = list(reader)
 
         return TableDoc(
             header=header,
@@ -124,7 +203,7 @@ def parse_csv(
 
     def write_csv(
         self,
-        csvfile: "Union[Path, str]",
+        csvfile: "Union[Path, str, Writer]",
         encoding: str = "utf-8",
         dialect: "Union[csv.Dialect, str]" = "excel",
         **kwargs,
@@ -133,7 +212,7 @@ def write_csv(
         """Write the table to a csv file using the standard library csv module.
 
         Arguments:
-            csvfile: CSV file to parse.
+            csvfile: File-like object or name of CSV file to write.
             encoding: The encoding of the csv file.
             dialect: A subclass of csv.Dialect, or the name of the dialect,
                 specifying how the `csvfile` is formatted.  For more details,
@@ -145,8 +224,15 @@ def write_csv(
         References:
         [Dialects and Formatting Parameters]: https://docs.python.org/3/library/csv.html#dialects-and-formatting-parameters
         """
-        with open(csvfile, mode="wt", encoding=encoding) as f:
+
+        def write(f):
             writer = csv.writer(f, dialect=dialect, **kwargs)
             writer.writerow(self.header)
             for row in self.data:
                 writer.writerow(row)
+
+        if isinstance(csvfile, (str, Path)):
+            with open(csvfile, mode="wt", encoding=encoding) as f:
+                write(f)
+        else:
+            write(csvfile)

From 8dbe71ac4e3e0073863658b93707389290f9d602 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Sat, 4 Jan 2025 00:04:31 +0100
Subject: [PATCH 46/59] Removed duplicated tests

---
 tests/dataset/test_dataset.py | 8 --------
 tripper/dataset/dataset.py    | 2 +-
 2 files changed, 1 insertion(+), 9 deletions(-)

diff --git a/tests/dataset/test_dataset.py b/tests/dataset/test_dataset.py
index 678913b5..01a90c57 100644
--- a/tests/dataset/test_dataset.py
+++ b/tests/dataset/test_dataset.py
@@ -39,14 +39,6 @@ def test_get_jsonld_context():
     with pytest.raises(TypeError):
         get_jsonld_context(context=[None])
 
-    # Test context argument
-    context2 = get_jsonld_context(context=CONTEXT_URL)
-    assert context2 == context
-
-    assert "newkey" not in context
-    context3 = get_jsonld_context(context={"newkey": "onto:newkey"})
-    assert context3["newkey"] == "onto:newkey"
-
 
 def test_get_prefixes():
     """Test get_prefixes()."""
diff --git a/tripper/dataset/dataset.py b/tripper/dataset/dataset.py
index cc0a9bda..774b49b9 100644
--- a/tripper/dataset/dataset.py
+++ b/tripper/dataset/dataset.py
@@ -851,7 +851,7 @@ def get_partial_pipeline(
     return pipeline
 
 
-def search_iris(ts: Triplestore, type=None, **kwargs):
+def search_iris(ts: Triplestore, type=None, **kwargs) -> "List[str]":
     """Return a list of IRIs for all matching resources.
     Additional matching criterias can be specified by `kwargs`.
 

From e054557ed7a23605804088b82ecd02011086776f Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Sat, 4 Jan 2025 00:07:32 +0100
Subject: [PATCH 47/59] Removed duplicated test

---
 tests/dataset/test_dataset.py | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/tests/dataset/test_dataset.py b/tests/dataset/test_dataset.py
index ca539262..2bd94cb6 100644
--- a/tests/dataset/test_dataset.py
+++ b/tests/dataset/test_dataset.py
@@ -39,14 +39,6 @@ def test_get_jsonld_context():
     with pytest.raises(TypeError):
         get_jsonld_context(context=[None])
 
-    # Test context argument
-    context2 = get_jsonld_context(context=CONTEXT_URL)
-    assert context2 == context
-
-    assert "newkey" not in context
-    context3 = get_jsonld_context(context={"newkey": "onto:newkey"})
-    assert context3["newkey"] == "onto:newkey"
-
 
 def test_get_prefixes():
     """Test get_prefixes()."""

From 58974e8cf86d1fd7cae6b6fd495c4226a4a8b0aa Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Sat, 4 Jan 2025 00:11:20 +0100
Subject: [PATCH 48/59] Updated URL after branch dataset-docs has been merged
 to master.

---
 tests/test_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_utils.py b/tests/test_utils.py
index 04e8f324..5911ba1f 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -57,7 +57,7 @@ def test_openfile_http():
 
     with openfile(
         "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/"
-        "dataset-docs/tests/input/openfile.txt"
+        "master/tests/input/openfile.txt"
     ) as f:
         assert f.read().strip() == "Example file."
 

From 726e9ac548c3aeb7fd12f0a4c3181e4c29fd2d8f Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Sat, 4 Jan 2025 00:37:27 +0100
Subject: [PATCH 49/59] Updated tabledoc test

---
 tests/dataset/test_tabledoc.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/dataset/test_tabledoc.py b/tests/dataset/test_tabledoc.py
index 0df11e53..1c6aec35 100644
--- a/tests/dataset/test_tabledoc.py
+++ b/tests/dataset/test_tabledoc.py
@@ -155,8 +155,8 @@ def test_csv():
     # Re-read the csv file from the string
     with io.StringIO(s) as f:
         td2 = TableDoc.parse_csv(
-            indir / "semdata.csv",
-            delimiter=";",
+            f,
+            delimiter=",",
             prefixes={
                 "sem": "https://w3id.com/emmo/domain/sem/0.1#",
                 "semdata": "https://he-matchmaker.eu/data/sem/",

From 3d64b34117af6e61bc17f7a5616781c03e31e204 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Sat, 4 Jan 2025 00:50:01 +0100
Subject: [PATCH 50/59] Added more tests

---
 tests/dataset/test_dataset.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tests/dataset/test_dataset.py b/tests/dataset/test_dataset.py
index 01a90c57..93f57a47 100644
--- a/tests/dataset/test_dataset.py
+++ b/tests/dataset/test_dataset.py
@@ -263,7 +263,8 @@ def test_datadoc():
 
     # Test searching the triplestore
     SAMPLE = ts.namespaces["sample"]
-    datasets = search_iris(ts, type="dcat:Dataset")
+    datasets = search_iris(ts, type="dataset")
+    assert search_iris(ts, type="dcat:Dataset") == datasets
     named_datasets = {
         SEMDATA["SEM_cement_batch2/77600-23-001/77600-23-001_5kV_400x_m001"],
         SEMDATA["SEM_cement_batch2/77600-23-001"],
@@ -279,6 +280,9 @@ def test_datadoc():
         SAMPLE["SEM_cement_batch2/77600-23-001"],
     }
 
+    with pytest.raises(ValueError):
+        search_iris(ts, type="invalid-type")
+
 
 def test_custom_context():
     """Test saving YAML file with custom context to triplestore."""

From 2773d239cd1beb29a482d285bb254b79eddad92d Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Sat, 4 Jan 2025 00:54:12 +0100
Subject: [PATCH 51/59] Skip test_fromdicts() if rdflib isn't available

---
 tests/dataset/test_tabledoc.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/dataset/test_tabledoc.py b/tests/dataset/test_tabledoc.py
index 1c6aec35..4f9dfd93 100644
--- a/tests/dataset/test_tabledoc.py
+++ b/tests/dataset/test_tabledoc.py
@@ -85,6 +85,9 @@ def test_asdicts():
 
 def test_fromdicts():
     """Test the fromdicts() method."""
+
+    pytest.importorskip("rdflib")
+
     from tripper import Namespace
     from tripper.dataset import TableDoc
 

From 972cca4a6bd0e1390506395186882825af4fe686 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Sat, 4 Jan 2025 20:45:07 +0100
Subject: [PATCH 52/59] Documented the datadoc tool

---
 docs/dataset/customisation.md    |  66 ++++--
 docs/figs/semdata.png            | Bin 0 -> 54829 bytes
 docs/tools/datadoc.md            | 378 +++++++++++++++++++++++++++++++
 mkdocs.yml                       |   5 +-
 tests/input/semdata-context.json |  18 ++
 tests/input/semdata.csv          |   2 +-
 tripper/context/0.2/context.json |   4 +
 tripper/dataset/dataaccess.py    |   5 +
 tripper/dataset/datadoc.py       | 165 ++++++++++----
 tripper/dataset/dataset.py       |  25 +-
 tripper/dataset/tabledoc.py      |  55 +++--
 tripper/utils.py                 |   4 +-
 12 files changed, 637 insertions(+), 90 deletions(-)
 create mode 100644 docs/figs/semdata.png
 create mode 100644 docs/tools/datadoc.md
 create mode 100644 tests/input/semdata-context.json

diff --git a/docs/dataset/customisation.md b/docs/dataset/customisation.md
index 197b7fb9..71013c49 100644
--- a/docs/dataset/customisation.md
+++ b/docs/dataset/customisation.md
@@ -35,7 +35,9 @@ Lets assume that you already have a domain ontology with base IRI http://example
 
 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#",
+```json
+"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.
 
@@ -46,15 +48,19 @@ Assume you want to add the keyword `batchNumber` to relate documented samples to
 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",
+```json
+"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"
-    },
+```json
+"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.
 
@@ -65,11 +71,12 @@ If you want to say more about the batches, you may want to store them as individ
 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"
-    },
+```json
+"fromBatch": {
+    "@id": "myonto:fromBatch",
+    "@type": "@id"
+},
+```
 
 Here the special value "@id" for the "@type" means that the value of `fromBatch` must be an IRI.
 
@@ -80,10 +87,36 @@ Custom context can be provided for all the interfaces described in the section [
 
 ### 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.
 
+For example
+
+```json
+{
+    "@context": [
+        # URL to a JSON file, typically a domain-specific context
+        "https://json-ld.org/contexts/person.jsonld",
+
+        # Local context
+        {
+            "fromBatch": {
+                "@id": "myonto:fromBatch",
+                "@type": "@id"
+            }
+        }
+    ],
+
+    # Documenting of the resource using keywords defined in the context
+    ...
+}
+```
+
+Note that the [default context] is always included and doesn't need to be specified explicitly.
+
+
 ### 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.
 
@@ -144,7 +177,7 @@ You can save this context to a triplestore with
 >>> ts = Triplestore("rdflib")
 >>> save_datadoc(  # doctest: +ELLIPSIS
 ...     ts,
-...      "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/dataset-docs/tests/input/custom_context.yaml",
+...      "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/custom_context.yaml",
 ... )
 AttrDict(...)
 
@@ -186,8 +219,8 @@ kb:batch1 a myonto:Batch,
 
 
 ### Table
-TODO
-
+The `__init__()` method of the [TableDoc] class takes a `context` argument with witch user-defined context can be provided.
+The value of the `context` argument is the same as for the `@context` key of a [Python dict].
 
 
 User-defined resource types
@@ -201,15 +234,18 @@ Instead, the list of available resource types should be stored and retrieved fro
 
 
 
-[Documenting a resource]: ../documenting-a-resource
 [With custom context]: #with-custom-context
 [User-defined keywords]: #user-defined-keywords
+[Python dict]: #python-dict
 [resource types]: ../introduction#resource-types
+[Documenting a resource]: ../documenting-a-resource
 [predefined prefixes]: ../prefixes/
 [predefined keywords]: ../keywords/
+[default context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json
 [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]: ../../api_reference/dataset/tabledoc/#tripper.dataset.tabledoc.TableDoc
 [TableDoc.parse_csv()]: ../../api_reference/dataset/tabledoc/#tripper.dataset.tabledoc.TableDoc.parse_csv
 [default JSON-LD context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json
diff --git a/docs/figs/semdata.png b/docs/figs/semdata.png
new file mode 100644
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diff --git a/docs/tools/datadoc.md b/docs/tools/datadoc.md
new file mode 100644
index 00000000..9bd2fe5a
--- /dev/null
+++ b/docs/tools/datadoc.md
@@ -0,0 +1,378 @@
+Datadoc
+=======
+`datadoc` is a command-line tool for data documentation which comes with Tripper.
+It provides functionality for both populating a triplestore with data documentation and to search for and find the documentation at a later stage.
+
+Running `datadoc --help` from the shell will show the following help message:
+
+```
+usage: datadoc [-h] [--backend BACKEND] [--base-iri BASE_IRI]
+               [--database DATABASE] [--package PACKAGE] [--parse LOCATION]
+               [--parse-format PARSE_FORMAT]
+               [--prefixes PREFIX=URL [PREFIX=URL ...]]
+               {add,find} ...
+
+Tool for data documentation. It allows populating and searching a triplestore
+for existing documentation.
+
+positional arguments:
+  {add,find}            Subcommands:
+    add                 Populate the triplestore with data documentation.
+    find                Find documented resources in the triplestore.
+
+options:
+  -h, --help            show this help message and exit
+  --backend BACKEND, -b BACKEND
+                        Triplestore backend to use. Defaults to 'rdflib' - an
+                        in-memory rdflib triplestore, that can be pre-loaded
+                        with --parse.
+  --base-iri BASE_IRI, -B BASE_IRI
+                        Base IRI of the triplestore.
+  --database DATABASE, -d DATABASE
+                        Name of database to connect to (for backends
+                        supporting it).
+  --package PACKAGE     Only needed when `backend` is a relative module.
+  --parse LOCATION, -p LOCATION
+                        Load triplestore from this location.
+  --parse-format PARSE_FORMAT, -F PARSE_FORMAT
+                        Used with `--parse`. Format to use when parsing
+                        triplestore.
+  --prefixes PREFIX=URL [PREFIX=URL ...], -P PREFIX=URL [PREFIX=URL ...]
+                        Namespace prefixes to add to bind to the triplestore.
+```
+
+Currently, `datadoc` has two sub-commands, `add` and `find` for populating and searching the triplestore, respectively.
+
+### General options
+
+* The `--backend`, `--base-iri`, `--database` and `--package` options are all for connecting to a triplestore.
+
+* The `--parse`, `--parse-format` and `--prefixes` options are for pre-loading the triplestore with with triples from an external source, like a ntriples or turtle file, and for adding namespace prefixes.
+They are typically used with the default "rdflib" in-memory backend.
+
+
+Subcomands
+----------
+
+### add
+Populates the triplestore with data documentation.
+Running `datadoc add --help` will show the following help message:
+
+```
+usage: datadoc add [-h] [--input-format {yaml,csv}]
+                   [--csv-options OPTION=VALUE [OPTION=VALUE ...]]
+                   [--context CONTEXT] [--dump FILENAME] [--format FORMAT]
+                   input
+
+positional arguments:
+  input                 Path or URL to the input the triplestore should be
+                        populated from.
+
+options:
+  -h, --help            show this help message and exit
+  --input-format {yaml,csv}, -i {yaml,csv}
+                        Input format. By default it is inferred from the file
+                        extension of the `input` argument.
+  --csv-options OPTION=VALUE [OPTION=VALUE ...]
+                        Options describing the CSV dialect for --input-
+                        format=csv. Common options are 'dialect', 'delimiter'
+                        and 'quotechar'.
+  --context CONTEXT     Path or URL to custom JSON-LD context for the input.
+  --dump FILENAME, -d FILENAME
+                        File to dump the populated triplestore to.
+  --format FORMAT, -f FORMAT
+                        Format to use with `--dump`. Default is "turtle".
+```
+
+The positional `input` argument is the path or URL to the source from which to populate the triplestore.
+The `--input-format`, `--csv-options` and `--context` options provide more details about the input.
+
+The `--dump` and `--format` options allow to dump the populated triplestore to file.
+This is useful if you are working with an in-memory triplestore.
+
+!!! example
+
+    The `tests/input/` folder in the source code contain the `semdata.csv` CSV file documenting four datasets, a SEM image, two nested dataset series and the sample the image was acquired from.
+
+    [![semdata.csv](../../figs/semdata.png)](../../figs/semdata.png)
+
+    Running the following command from the root folder of the source code will populate an in-memory rdflib store with the data documented in the `semdata.csv` file.
+
+    ```shell
+    datadoc add tests/input/semdata.csv --csv-options delimiter=';' --context tests/input/semdata-context.json --dump kb.ttl
+    ```
+
+    The `--csv-options` tells that the csv file is delimited by semi-colon, which is the default delimiter used by excel in Scandinavia.
+
+    The `--context` option provides a user-defined context defining prefixes and keywords used by the input.
+
+    Finally the `--dump` option dumps the in-memory triplestore to the file `kb.ttl`.
+    If you open the file, you will notice that it in addition to the four datasets listed in the input, also include the `SEMImage` class and its properties, providing structural documentation of the `SEMImage` individuals.
+
+    ??? abstract "Generated turtle file"
+
+        ```turtle
+        @prefix chameo: <https://w3id.org/emmo/domain/characterisation-methodology/chameo#> .
+        @prefix dcat: <http://www.w3.org/ns/dcat#> .
+        @prefix dcterms: <http://purl.org/dc/terms/> .
+        @prefix emmo: <https://w3id.org/emmo#> .
+        @prefix oteio: <https://w3id.org/emmo/domain/oteio#> .
+        @prefix owl: <http://www.w3.org/2002/07/owl#> .
+        @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+        @prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+        @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+        <http://onto-ns.com/meta/matchmaker/0.2/SEMImage> a owl:Class ;
+            rdfs:subClassOf [ a owl:Restriction ;
+                    owl:onClass <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#data> ;
+                    owl:onProperty emmo:EMMO_b19aacfc_5f73_4c33_9456_469c1e89a53e ;
+                    owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ],
+                [ a owl:Restriction ;
+                    owl:onClass <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#labels> ;
+                    owl:onProperty emmo:EMMO_b19aacfc_5f73_4c33_9456_469c1e89a53e ;
+                    owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ],
+                [ a owl:Restriction ;
+                    owl:onClass <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#metadata> ;
+                    owl:onProperty emmo:EMMO_b19aacfc_5f73_4c33_9456_469c1e89a53e ;
+                    owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ],
+                [ a owl:Restriction ;
+                    owl:onClass <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#pixelheight> ;
+                    owl:onProperty emmo:EMMO_b19aacfc_5f73_4c33_9456_469c1e89a53e ;
+                    owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ],
+                [ a owl:Restriction ;
+                    owl:onClass <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#pixelwidth> ;
+                    owl:onProperty emmo:EMMO_b19aacfc_5f73_4c33_9456_469c1e89a53e ;
+                    owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ],
+                emmo:EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a ;
+            skos:prefLabel "SEMImage"@en ;
+            emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "SEM image with elemental mappings. Represented as a stack of elemental mapping\\nfollowed by the image formed by the back-scattered electrons (BSE).\\nSet `nelements=0` if you only have the back-scattered image.\\n"@en ;
+            oteio:hasURI "http://onto-ns.com/meta/matchmaker/0.2/SEMImage"^^xsd:anyURI .
+
+        <https://he-matchmaker.eu/data/sem/SEM_cement_batch2/77600-23-001/77600-23-001_5kV_400x_m001> a dcat:Dataset,
+                <https://w3id.com/emmo/domain/sem/0.1#SEMImage>,
+                emmo:EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a ;
+            dcterms:creator "Sigurd Wenner" ;
+            dcterms:description "Back-scattered SEM image of cement sample 77600 from Heidelberg, polished with 1 µm diamond compound." ;
+            dcterms:title "SEM image of cement" ;
+            dcat:contactPoint "Sigurd Wenner <Sigurd.Wenner@sintef.no>" ;
+            dcat:distribution [ a dcat:Distribution ;
+                    <http://sintef.no/dlite/parser#> "http://sintef.no/dlite/parser#sem_hitachi" ;
+                    dcat:downloadURL "https://github.com/EMMC-ASBL/tripper/raw/refs/heads/dataset/tests/input/77600-23-001_5kV_400x_m001.tif" ;
+                    dcat:mediaType "image/tiff" ] ;
+            dcat:inSeries <https://he-matchmaker.eu/data/sem/SEM_cement_batch2/77600-23-001> ;
+            emmo:EMMO_f702bad4_fc77_41f0_a26d_79f6444fd4f3 <https://he-matchmaker.eu/material/concrete1> ;
+            oteio:hasDatamodel "http://onto-ns.com/meta/matchmaker/0.2/SEMImage" ;
+            oteio:hasDatamodelStorage "https://github.com/HEU-MatCHMaker/DataDocumentation/blob/master/SEM/datamodels/SEMImage.yaml" .
+
+        <https://he-matchmaker.eu/sample/SEM_cement_batch2/77600-23-001> a dcat:Dataset,
+                emmo:EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a,
+                chameo:Sample ;
+            dcterms:title "Series for SEM images for sample 77600-23-001." .
+
+        <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#data> a owl:Class ;
+            rdfs:subClassOf [ a owl:Restriction ;
+                    owl:hasValue <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#data_dimension0> ;
+                    owl:onProperty emmo:EMMO_0a9ae0cb_526d_4377_9a11_63d1ce5b3499 ],
+                [ a owl:Restriction ;
+                    owl:onProperty emmo:EMMO_e5a34647_a955_40bc_8d81_9b784f0ac527 ;
+                    owl:someValuesFrom emmo:EMMO_ac9e518d_b403_4d8b_97e2_06f9d40bac01 ],
+                emmo:EMMO_28fbea28_2204_4613_87ff_6d877b855fcd,
+                emmo:EMMO_50d6236a_7667_4883_8ae1_9bb5d190423a ;
+            skos:prefLabel "Data"@en ;
+            emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "Image data - a stack of images for each channel"@en ;
+            oteio:datasize "4"^^xsd:nonNegativeInteger .
+
+        <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#data_dimension0> a emmo:EMMO_b4c97fa0_d82c_406a_bda7_597d6e190654 ;
+            skos:prefLabel "data_dimension0"@en ;
+            emmo:EMMO_23b579e1_8088_45b5_9975_064014026c42 "channels"^^xsd:string ;
+            emmo:EMMO_499e24a5_5072_4c83_8625_fe3f96ae4a8d <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#data_dimension1> ;
+            emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "Number of channels."@en .
+
+        <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#data_dimension1> a emmo:EMMO_b4c97fa0_d82c_406a_bda7_597d6e190654 ;
+            skos:prefLabel "data_dimension1"@en ;
+            emmo:EMMO_23b579e1_8088_45b5_9975_064014026c42 "height"^^xsd:string ;
+            emmo:EMMO_499e24a5_5072_4c83_8625_fe3f96ae4a8d <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#data_dimension2> ;
+            emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "Number of pixels along the image height."@en .
+
+        <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#data_dimension2> a emmo:EMMO_b4c97fa0_d82c_406a_bda7_597d6e190654 ;
+            skos:prefLabel "data_dimension2"@en ;
+            emmo:EMMO_23b579e1_8088_45b5_9975_064014026c42 "width"^^xsd:string ;
+            emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "Number of pixels along the image width."@en .
+
+        <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#labels> a owl:Class ;
+            rdfs:subClassOf [ a owl:Restriction ;
+                    owl:hasValue <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#labels_dimension0> ;
+                    owl:onProperty emmo:EMMO_0a9ae0cb_526d_4377_9a11_63d1ce5b3499 ],
+                [ a owl:Restriction ;
+                    owl:onProperty emmo:EMMO_e5a34647_a955_40bc_8d81_9b784f0ac527 ;
+                    owl:someValuesFrom emmo:EMMO_5f334606_f67d_4f0e_acb9_eeb21cb10c66 ],
+                emmo:EMMO_28fbea28_2204_4613_87ff_6d877b855fcd,
+                emmo:EMMO_50d6236a_7667_4883_8ae1_9bb5d190423a ;
+            skos:prefLabel "Labels"@en ;
+            emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "The label of each channel. For elemental mapping this should be the chemical symbol of the element or BSE for the back-scattered image."@en .
+
+        <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#labels_dimension0> a emmo:EMMO_b4c97fa0_d82c_406a_bda7_597d6e190654 ;
+            skos:prefLabel "labels_dimension0"@en ;
+            emmo:EMMO_23b579e1_8088_45b5_9975_064014026c42 "channels"^^xsd:string ;
+            emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "Number of channels."@en .
+
+        <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#metadata> a owl:Class ;
+            rdfs:subClassOf emmo:EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a,
+                emmo:EMMO_50d6236a_7667_4883_8ae1_9bb5d190423a ;
+            skos:prefLabel "Metadata"@en ;
+            emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "Reference to data model for SEM metadata."@en .
+
+        <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#pixelheight> a owl:Class ;
+            rdfs:subClassOf [ a owl:Restriction ;
+                    owl:onClass emmo:Metre ;
+                    owl:onProperty emmo:EMMO_bed1d005_b04e_4a90_94cf_02bc678a8569 ;
+                    owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ],
+                emmo:EMMO_50d6236a_7667_4883_8ae1_9bb5d190423a,
+                emmo:EMMO_52fa9c76_fc42_4eca_a5c1_6095a1c9caab ;
+            skos:prefLabel "Pixelheight"@en ;
+            emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "Height of each pixel."@en ;
+            oteio:datasize "8"^^xsd:nonNegativeInteger .
+
+        <http://onto-ns.com/meta/matchmaker/0.2/SEMImage#pixelwidth> a owl:Class ;
+            rdfs:subClassOf [ a owl:Restriction ;
+                    owl:onClass emmo:Metre ;
+                    owl:onProperty emmo:EMMO_bed1d005_b04e_4a90_94cf_02bc678a8569 ;
+                    owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ],
+                emmo:EMMO_50d6236a_7667_4883_8ae1_9bb5d190423a,
+                emmo:EMMO_52fa9c76_fc42_4eca_a5c1_6095a1c9caab ;
+            skos:prefLabel "Pixelwidth"@en ;
+            emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "Width of each pixel."@en ;
+            oteio:datasize "8"^^xsd:nonNegativeInteger .
+
+        <https://he-matchmaker.eu/data/sem/SEM_cement_batch2> a dcat:Dataset,
+                <https://w3id.com/emmo/domain/sem/0.1#SEMImageSeries>,
+                emmo:EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a ;
+            dcterms:creator "Sigurd Wenner" ;
+            dcterms:description "..." ;
+            dcterms:title "Nested series of SEM images of cement batch2" ;
+            dcat:contactPoint "Sigurd Wenner <Sigurd.Wenner@sintef.no>" ;
+            dcat:distribution [ a dcat:Distribution ;
+                    dcat:downloadURL "sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2" ;
+                    dcat:mediaType "inode/directory" ] .
+
+        <https://he-matchmaker.eu/data/sem/SEM_cement_batch2/77600-23-001> a dcat:Dataset,
+                <https://w3id.com/emmo/domain/sem/0.1#SEMImageSeries>,
+                emmo:EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a ;
+            dcterms:creator "Sigurd Wenner" ;
+            dcterms:description "Back-scattered SEM image of cement sample 77600, polished with 1 µm diamond compound." ;
+            dcterms:title "Series of SEM image of cement sample 77600" ;
+            dcat:contactPoint "Sigurd Wenner <Sigurd.Wenner@sintef.no>" ;
+            dcat:distribution [ a dcat:Distribution ;
+                    dcat:downloadURL "sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2/77600-23-001" ;
+                    dcat:mediaType "inode/directory" ] ;
+            dcat:inSeries <https://he-matchmaker.eu/data/sem/SEM_cement_batch2> .
+
+        ```
+
+
+### find
+Search the triplestore for documented resources.
+Running `datadoc find --help` will show the following help message:
+
+```
+usage: datadoc find [-h] [--type TYPE]
+                    [--criteria KEYWORD=VALUE [KEYWORD=VALUE ...]]
+                    [--output FILENAME] [--format {iris,json,turtle,csv}]
+
+options:
+  -h, --help            show this help message and exit
+  --type TYPE, -t TYPE  Either a resource type (ex: "dataset", "distribution",
+                        ...) or the IRI of a class to limit the search to.
+  --criteria KEYWORD=VALUE [KEYWORD=VALUE ...], -c KEYWORD=VALUE [KEYWORD=VALUE ...]
+                        One of more additional matching criteria for resources
+                        to find. Only resources with the given KEYWORD and
+                        VALUE will be matched. The match is exact.
+  --output FILENAME, -o FILENAME
+                        Write matching output to the given file. The default
+                        is to write to standard output.
+  --format {iris,json,turtle,csv}, -f {iris,json,turtle,csv}
+                        Output format to list the matched resources. The
+                        default is to infer from the file extension if
+                        --output is given. Otherwise it defaults to "iris".
+```
+
+The `--type` and `--criteria` options provide search criteria.
+The `--type` argument an be any of the recognised [resource types] to limit the search to.
+Alternatively, it may be the IRI of a class.
+This limits the search to only resources that are individuals of this class.
+
+The `--output` options allows to write the matching output to file instead of standard output.
+
+The `--format` option controls how the search result should be presented.
+The following formats are currently available:
+
+- **iris**: Return the IRIs of matching resources.
+- **json**: Return a JSON array with documentation of matching resources.
+- **turtle**: Return a turtle representation of matching resources.
+
+      *Note*: In case the matching resources are datasets with a `datamodel` keyword, the serialised data model will also be included in the turtle output.
+
+- **csv**: Return a CSV table with the matching resources.
+
+!!! example "Examples"
+
+    For all the examples below, we use `--parse` option to pre-load the triplestore from the `kb.ttl` file that we generated in the previous example.
+
+    **Ex 1**: List IRIs of all datasets:
+
+    ```shell
+    $ datadoc --parse=kb.ttl find --type=dataset
+    https://he-matchmaker.eu/data/sem/SEM_cement_batch2/77600-23-001/77600-23-001_5kV_400x_m001
+    https://he-matchmaker.eu/sample/SEM_cement_batch2/77600-23-001
+    https://he-matchmaker.eu/data/sem/SEM_cement_batch2
+    https://he-matchmaker.eu/data/sem/SEM_cement_batch2/77600-23-001
+    ```
+
+    **Ex 2**: List IRIs of all samples (individuals of `chameo:Sample`):
+
+    ```shell
+    $ datadoc --parse=kb.ttl find --type=chameo:Sample
+    https://he-matchmaker.eu/sample/SEM_cement_batch2/77600-23-001
+    ```
+
+    **Ex 3**: List IRIs of all resources with a given title:
+
+    ```shell
+    $ datadoc --parse=kb.ttl find --criteria title="Series of SEM image of cement sample 77600"
+    https://he-matchmaker.eu/data/sem/SEM_cement_batch2/77600-23-001
+    ```
+
+    **Ex 4**: List all sample individuals as JSON:
+
+    ```shell
+    $ datadoc --parse=kb.ttl find --type=chameo:Sample --format=json
+    ```
+
+    ```json
+    [
+      {
+        "@id": "https://he-matchmaker.eu/data/sem/SEM_cement_batch2/77600-23-001",
+        "@type": [
+          "http://www.w3.org/ns/dcat#Dataset",
+          "https://w3id.com/emmo/domain/sem/0.1#SEMImageSeries",
+          "https://w3id.org/emmo#EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a"
+        ],
+        "creator": "Sigurd Wenner",
+        "description": "Back-scattered SEM image of cement sample 77600, polished with 1 \u00b5m diamond compound.",
+        "title": "Series of SEM image of cement sample 77600",
+        "contactPoint": "Sigurd Wenner <Sigurd.Wenner@sintef.no>",
+        "distribution": {
+          "@id": "_:nac2552b949a94ef391080807ca2a02e4b14",
+          "@type": "http://www.w3.org/ns/dcat#Distribution",
+          "downloadURL": "sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2/77600-23-001",
+          "mediaType": "inode/directory"
+        },
+        "inSeries": "https://he-matchmaker.eu/data/sem/SEM_cement_batch2"
+      }
+    ]
+    ```
+
+
+
+
+[resource types]: ../../dataset/introduction/#resource-types
diff --git a/mkdocs.yml b/mkdocs.yml
index 815211d4..0212137c 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1,7 +1,7 @@
 site_name: "Tripper"
 site_description: Documentation for the Tripper package
 site_url: https://EMMC-ASBL.github.io/tripper
-copyright: Copyright &copy; 2022 SINTEF
+copyright: Copyright &copy; 2022-2025 SINTEF
 
 theme:
   name: material
@@ -39,6 +39,7 @@ markdown_extensions:
   - admonition
   - attr_list
   - pymdownx.highlight
+  - pymdownx.details
   - pymdownx.superfences
   - pymdownx.inlinehilite
   - pymdownx.tabbed:
@@ -85,6 +86,8 @@ nav:
   - Home: index.md
   - Tutorial: tutorial.md
   - Backend discovery: backend_discovery.md
+  - Tools:
+    - datadoc: tools/datadoc.md
   - Data documentation:
     - Introduction: dataset/introduction.md
     - Documenting a resource: dataset/documenting-a-resource.md
diff --git a/tests/input/semdata-context.json b/tests/input/semdata-context.json
new file mode 100644
index 00000000..74112f5f
--- /dev/null
+++ b/tests/input/semdata-context.json
@@ -0,0 +1,18 @@
+{
+  "@context": {
+    "sem": "https://w3id.com/emmo/domain/sem/0.1#",
+    "semdata": "https://he-matchmaker.eu/data/sem/",
+    "sample": "https://he-matchmaker.eu/sample/",
+    "mat": "https://he-matchmaker.eu/material/",
+    "dm": "http://onto-ns.com/meta/characterisation/0.1/SEMImage#",
+    "parser": "http://sintef.no/dlite/parser#",
+    "gen": "http://sintef.no/dlite/generator#",
+    "micro": "https://w3id.com/emmo/domain/microstructure/0.3#"
+  },
+
+  "fromSample": {
+    "@id": "micro:fromSample",
+    "@type": "@id"
+  }
+
+}
diff --git a/tests/input/semdata.csv b/tests/input/semdata.csv
index 4d7a78c6..3f764831 100644
--- a/tests/input/semdata.csv
+++ b/tests/input/semdata.csv
@@ -1,4 +1,4 @@
-@id;@type;title;description;creator;contactPoint;inSeries;datamodel;datamodelStorage;distribution.downloadURL;distribution.mediaType;distribution.parser;fromSample;isDescriptionOf
+@id;@type;title;description;creator;contactPoint;inSeries;datamodel;datamodelStorage;distribution.downloadURL;distribution.mediaType;distribution.parser;fromSample;isDescriptionFor
 semdata:SEM_cement_batch2/77600-23-001/77600-23-001_5kV_400x_m001;sem:SEMImage;SEM image of cement;Back-scattered SEM image of cement sample 77600 from Heidelberg, polished with 1 µm diamond compound.;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>;semdata:SEM_cement_batch2/77600-23-001;http://onto-ns.com/meta/matchmaker/0.2/SEMImage;https://github.com/HEU-MatCHMaker/DataDocumentation/blob/master/SEM/datamodels/SEMImage.yaml;https://github.com/EMMC-ASBL/tripper/raw/refs/heads/dataset/tests/input/77600-23-001_5kV_400x_m001.tif;image/tiff;parser:sem_hitachi;sample:SEM_cement_batch2/77600-23-001;mat:concrete1
 semdata:SEM_cement_batch2/77600-23-001;sem:SEMImageSeries;Series of SEM image of cement sample 77600;Back-scattered SEM image of cement sample 77600, polished with 1 µm diamond compound.;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>;semdata:SEM_cement_batch2; ;;sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2/77600-23-001;inode/directory;;;
 semdata:SEM_cement_batch2;sem:SEMImageSeries;Nested series of SEM images of cement batch2;...;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>; ;;;sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2;inode/directory;;;
diff --git a/tripper/context/0.2/context.json b/tripper/context/0.2/context.json
index b2837617..cf938e97 100644
--- a/tripper/context/0.2/context.json
+++ b/tripper/context/0.2/context.json
@@ -96,6 +96,10 @@
       "@id": "dcat:inSeries",
       "@type": "@id"
     },
+    "isDescriptionFor": {
+      "@id": "emmo:EMMO_f702bad4_fc77_41f0_a26d_79f6444fd4f3",
+      "@type": "@id"
+    },
     "isInputOf": {
       "@id": "emmo:EMMO_1494c1a9_00e1_40c2_a9cc_9bbf302a1cac",
       "@type": "@id"
diff --git a/tripper/dataset/dataaccess.py b/tripper/dataset/dataaccess.py
index dbe0ee25..78a3c923 100644
--- a/tripper/dataset/dataaccess.py
+++ b/tripper/dataset/dataaccess.py
@@ -248,5 +248,10 @@ def load(
                 # pylint: disable=no-member
             except (dlite.DLiteProtocolError, dlite.DLiteIOError):
                 pass
+            except Exception as exc:
+                raise IOError(
+                    f"cannot access dataset '{iri}' using scheme={scheme}, "
+                    f"location={location} and optins={p.query}"
+                ) from exc
 
     raise IOError(f"Cannot access dataset: {iri}")
diff --git a/tripper/dataset/datadoc.py b/tripper/dataset/datadoc.py
index 8b7b0eec..a241ccf8 100644
--- a/tripper/dataset/datadoc.py
+++ b/tripper/dataset/datadoc.py
@@ -1,8 +1,12 @@
 """A script for data documentation."""
 
+# pylint: disable=too-many-branches
+
 import argparse
 import io
 import json
+import os
+from pathlib import Path
 
 from tripper import Triplestore
 from tripper.dataset import (
@@ -17,19 +21,27 @@
 
 def subcommand_add(ts, args):
     """Subcommand for populating the triplestore"""
-    if args.yamlfile:
-        save_datadoc(ts, args.yamlfile)
+    infile = Path(args.input)
+    extension = args.input_format if args.input_format else infile.suffix
+    fmt = extension.lower().lstrip(".")
 
-    if args.table:
+    if fmt in ("yml", "yaml"):
+        save_datadoc(ts, infile)
+    elif fmt in ("csv",):
+        kw = {}
+        if args.csv_options:
+            for token in args.csv_options:
+                option, value = token.split("=", 1)
+                kw[option] = value
         td = TableDoc.parse_csv(
-            args.table, context=get_jsonld_context(args.context)
+            infile, context=get_jsonld_context(args.context), **kw
         )
         td.save(ts)
+    else:
+        raise ValueError(f"Unknown input format: {fmt}")
 
-        save_datadoc(ts, args.yamlfile)
-
-    if args.serialize:
-        ts.serialize(args.serialize, format=args.sformat)
+    if args.dump:
+        ts.serialize(args.dump, format=args.format)
 
 
 def subcommand_find(ts, args):
@@ -40,30 +52,42 @@ def subcommand_find(ts, args):
         kwargs = {}
     iris = search_iris(ts, type=args.type, **kwargs)
 
+    # Infer format
+    if args.format:
+        fmt = args.format.lower()
+    elif args.output:
+        fmt = Path(args.output).suffix.lower().lstrip(".")
+    else:
+        fmt = "iris"
+
     # Create output
-    if args.format == "iris":
+    if fmt in ("iris", "txt"):
         s = "\n".join(iris)
-    elif args.format == "json":
+    elif fmt == "json":
         s = json.dumps([load_dict(ts, iri) for iri in iris], indent=2)
-    elif args.format == "turtle":
+    elif fmt in ("turtle", "ttl"):
         ts2 = Triplestore("rdflib")
         for iri in iris:
             d = load_dict(ts, iri)
             save_dict(ts2, d)
         s = ts2.serialize()
-    elif args.format == "csv":
+    elif fmt == "csv":
         dicts = [load_dict(ts, iri) for iri in iris]
         td = TableDoc.fromdicts(dicts)
         with io.StringIO() as f:
             td.write_csv(f)
             s = f.getvalue()
     else:
-        raise ValueError(args.format)
+        raise ValueError(f"Unknown format: {fmt}")
 
-    print(s)
+    if args.output:
+        with open(args.output, "wt", encoding="utf-8") as f:
+            f.write(s + os.linesep)
+    else:
+        print(s)
 
 
-def main():
+def main(argv=None):
     """Main function."""
     parser = argparse.ArgumentParser(
         description=(
@@ -73,64 +97,101 @@ def main():
         ),
     )
 
-    subparsers = parser.add_subparsers(required=True, help="subcommand help")
+    subparsers = parser.add_subparsers(required=True, help="Subcommands:")
 
     # Subcommand: add
-    parser_add = subparsers.add_parser("add", help="add help")
-    parser_add.set_defaults(func=subcommand_add)
-    parser_add.add_argument(
-        "--context",
-        help="Path or URL to custom JSON-LD context.  Used with `--table`.",
+    parser_add = subparsers.add_parser(
+        "add",
+        help="Populate the triplestore with data documentation.",
     )
+    parser_add.set_defaults(func=subcommand_add)
     parser_add.add_argument(
-        "--yamlfile",
-        help="Path or URL to YAML file to add to the triplestore.",
+        "input",
+        help=(
+            "Path or URL to the input the triplestore should be populated "
+            "from."
+        ),
     )
     parser_add.add_argument(
-        "--table", help="Path to table to populate the triplestore from."
+        "--input-format",
+        "-i",
+        choices=["yaml", "csv"],
+        help=(
+            "Input format. By default it is inferred from the file "
+            "extension of the `input` argument."
+        ),
     )
     parser_add.add_argument(
-        "--tformat",
+        "--csv-options",
+        action="extend",
+        nargs="+",
+        metavar="OPTION=VALUE",
         help=(
-            "Used with `--table`. Format of the table to load. "
-            "Only csv is currently supported."
+            "Options describing the CSV dialect for --input-format=csv. "
+            "Common options are 'dialect', 'delimiter' and 'quotechar'."
         ),
     )
     parser_add.add_argument(
-        "--serialize",
+        "--context",
+        help="Path or URL to custom JSON-LD context for the input.",
+    )
+    parser_add.add_argument(
+        "--dump",
+        "-d",
         metavar="FILENAME",
-        help="File to serialise the populated triplestore to.",
+        help="File to dump the populated triplestore to.",
     )
     parser_add.add_argument(
-        "--sformat",
+        "--format",
+        "-f",
         default="turtle",
-        help='Format to use with `--serialize`.  Default is "turtle".',
+        help='Format to use with `--dump`.  Default is "turtle".',
     )
 
     # Subcommand: find
     parser_find = subparsers.add_parser(
-        "find", help="Find IRIs of resources in the triplestore."
+        "find", help="Find documented resources in the triplestore."
     )
     parser_find.set_defaults(func=subcommand_find)
     parser_find.add_argument(
         "--type",
         "-t",
-        help="The type of resources to find.",
+        help=(
+            'Either a resource type (ex: "dataset", "distribution", ...) '
+            "or the IRI of a class to limit the search to."
+        ),
     )
     parser_find.add_argument(
         "--criteria",
         "-c",
         action="extend",
         nargs="+",
-        metavar="KEY=VALUE",
-        help=("Matching criteria for resources to find.  "),
+        metavar="KEYWORD=VALUE",
+        help=(
+            "One of more additional matching criteria for resources to find. "
+            "Only resources with the given KEYWORD and VALUE will be matched. "
+            "The match is exact."
+        ),
+    )
+    parser_find.add_argument(
+        "--output",
+        "-o",
+        metavar="FILENAME",
+        help=(
+            "Write matching output to the given file. The default is to "
+            "write to standard output."
+        ),
     )
     parser_find.add_argument(
         "--format",
         "-f",
         default="iris",
         choices=["iris", "json", "turtle", "csv"],
-        help="Output format to list the matched resources.",
+        help=(
+            "Output format to list the matched resources. The default is "
+            "to infer from the file extension if --output is given. "
+            'Otherwise it defaults to "iris".'
+        ),
     )
 
     # General: options
@@ -138,11 +199,16 @@ def main():
         "--backend",
         "-b",
         default="rdflib",
-        help="Triplestore backend to use.",
+        help=(
+            'Triplestore backend to use. Defaults to "rdflib" - an '
+            "in-memory rdflib triplestore, that can be pre-loaded with "
+            "--parse."
+        ),
     )
     parser.add_argument(
-        "--base_iri",
-        help="Base IRI of the triplestore (seldom needed).",
+        "--base-iri",
+        "-B",
+        help="Base IRI of the triplestore.",
     )
     parser.add_argument(
         "--database",
@@ -160,12 +226,20 @@ def main():
         help="Load triplestore from this location.",
     )
     parser.add_argument(
-        "--pformat",
-        "-f",
+        "--parse-format",
+        "-F",
         help="Used with `--parse`. Format to use when parsing triplestore.",
     )
+    parser.add_argument(
+        "--prefixes",
+        "-P",
+        action="extend",
+        nargs="+",
+        metavar="PREFIX=URL",
+        help="Namespace prefixes to add to bind to the triplestore.",
+    )
 
-    args = parser.parse_args()
+    args = parser.parse_args(argv)
 
     ts = Triplestore(
         backend=args.backend,
@@ -174,7 +248,12 @@ def main():
         package=args.package,
     )
     if args.parse:
-        ts.parse(args.parse, format=args.pformat)
+        ts.parse(args.parse, format=args.parse_format)
+
+    if args.prefixes:
+        for token in args.prefixes:
+            prefix, ns = token.split("=", 1)
+            ts.bind(prefix, ns)
 
     # Call subcommand handler
     args.func(ts, args)
diff --git a/tripper/dataset/dataset.py b/tripper/dataset/dataset.py
index 774b49b9..7fd8b1c4 100644
--- a/tripper/dataset/dataset.py
+++ b/tripper/dataset/dataset.py
@@ -174,7 +174,8 @@ def save_extra_content(ts: Triplestore, dct: dict) -> None:
     # Save statements and mappings
     statements = get_values(dct, "statements")
     statements.extend(get_values(dct, "mappings"))
-    ts.add_triples(statements)
+    if statements:
+        ts.add_triples(statements)
 
     # Save data models
     datamodels = get_values(dct, "datamodel")
@@ -325,8 +326,8 @@ def get_values(
             values.extend(val)
         elif val:
             values.append(val)
-        for v in data.values():
-            if isinstance(v, (dict, list)):
+        for k, v in data.items():
+            if k != "@context" and isinstance(v, (dict, list)):
                 values.extend(get_values(v, key))
     elif isinstance(data, list):
         for ele in data:
@@ -370,8 +371,9 @@ def get_jsonld_context(
     if context:
         for token in context:
             if isinstance(token, str):
-                r = requests.get(token, allow_redirects=True, timeout=timeout)
-                ctx.update(json.loads(r.content)["@context"])
+                with openfile(token, timeout=timeout, mode="rt") as f:
+                    content = f.read()
+                ctx.update(json.loads(content)["@context"])
             elif isinstance(token, dict):
                 ctx.update(token)
             else:
@@ -723,10 +725,10 @@ def as_jsonld(
                     v[i] = expand_iri(e, all_prefixes)
                 elif isinstance(e, dict) and k in nested:
                     v[i] = as_jsonld(
-                        e, k, _entryid=_entryid, prefixes=prefixes
+                        e, k, _entryid=_entryid, prefixes=all_prefixes
                     )
         elif isinstance(v, dict) and k in nested:
-            d[k] = as_jsonld(v, k, _entryid=_entryid, prefixes=prefixes)
+            d[k] = as_jsonld(v, k, _entryid=_entryid, prefixes=all_prefixes)
 
     return d
 
@@ -857,8 +859,8 @@ def search_iris(ts: Triplestore, type=None, **kwargs) -> "List[str]":
 
     Arguments:
         ts: Triplestore to search.
-        type: Search for entries that are individuals of the class with
-            this IRI.
+        type: Either a [resource type] (ex: "dataset", "distribution", ...)
+            or the IRI of a class to limit the search to.
         kwargs: Match criterias.
 
     Returns:
@@ -883,6 +885,9 @@ def search_iris(ts: Triplestore, type=None, **kwargs) -> "List[str]":
             search_iris(
                 ts, contactPoint="John Doe", fromSample=SAMPLE.batch2/sample3
             )
+
+    SeeAlso:
+    [resource type]: https://emmc-asbl.github.io/tripper/latest/dataset/introduction/#resource-types
     """
     crit = []
 
@@ -923,7 +928,7 @@ def search_iris(ts: Triplestore, type=None, **kwargs) -> "List[str]":
     criterias = "\n".join(crit)
     query = f"""
     PREFIX rdf: <{RDF}>
-    SELECT ?iri
+    SELECT DISTINCT ?iri
     WHERE {{
     {criterias}
     }}
diff --git a/tripper/dataset/tabledoc.py b/tripper/dataset/tabledoc.py
index 6624afe8..4f4d676f 100644
--- a/tripper/dataset/tabledoc.py
+++ b/tripper/dataset/tabledoc.py
@@ -34,7 +34,11 @@ class TableDoc:
             "dataset".
         prefixes: Dict with prefixes in addition to those included in the
             JSON-LD context.  Should map namespace prefixes to IRIs.
-        context: Dict with user-defined JSON-LD context.
+        context: Additional user-defined context that should be
+            returned on top of the default context.  It may be a
+            string with an URL to the user-defined context, a dict
+            with the user-defined context or a sequence of strings and
+            dicts.
         strip: Whether to strip leading and trailing whitespaces from cells.
 
     """
@@ -47,7 +51,7 @@ def __init__(
         data: "Sequence[Sequence[str]]",
         type: "Optional[str]" = "dataset",
         prefixes: "Optional[dict]" = None,
-        context: "Optional[Union[dict, list]]" = None,
+        context: "Optional[Union[str, dict, list]]" = None,
         strip: bool = True,
     ):
         self.header = list(header)
@@ -64,7 +68,7 @@ def save(self, ts: Triplestore) -> None:
 
     def asdicts(self) -> "List[dict]":
         """Return the table as a list of dicts."""
-        kw = {"@context": self.context} if self.context else {}
+        kw = {"_context": self.context} if self.context else {}
 
         results = []
         for row in self.data:
@@ -86,7 +90,7 @@ def fromdicts(
         dicts: "Sequence[dict]",
         type: "Optional[str]" = "dataset",
         prefixes: "Optional[dict]" = None,
-        context: "Optional[Union[dict, list]]" = None,
+        context: "Optional[Union[str, dict, list]]" = None,
         strip: bool = True,
     ) -> "TableDoc":
         """Create new TableDoc instance from a sequence of dicts.
@@ -95,14 +99,19 @@ def fromdicts(
             dicts: Sequence of single-resource dicts.
             type: Type of data to save (applies to all rows).  Should
                 either be one of the pre-defined names: "dataset",
-                "distribution", "accessService", "parser" and "generator"
-                or an IRI to a class in an ontology.  Defaults to
-                "dataset".
-            prefixes: Dict with prefixes in addition to those included in
-                the JSON-LD context.  Should map namespace prefixes to IRIs.
-            context: Dict with user-defined JSON-LD context.
-            strip: Whether to strip leading and trailing whitespaces from
-                cells.
+                "distribution", "accessService", "parser" and
+                "generator" or an IRI to a class in an ontology.
+                Defaults to "dataset".
+            prefixes: Dict with prefixes in addition to those included
+                in the JSON-LD context.  Should map namespace prefixes
+                to IRIs.
+            context: Additional user-defined context that should be
+                returned on top of the default context.  It may be a
+                string with an URL to the user-defined context, a dict
+                with the user-defined context or a sequence of strings
+                and dicts.
+            strip: Whether to strip leading and trailing whitespaces
+                from cells.
 
         Returns:
             New TableDoc instance.
@@ -153,7 +162,7 @@ def parse_csv(
         prefixes: "Optional[dict]" = None,
         context: "Optional[Union[dict, list]]" = None,
         encoding: str = "utf-8",
-        dialect: "Union[csv.Dialect, str]" = "excel",
+        dialect: "Optional[Union[csv.Dialect, str]]" = None,
         **kwargs,
     ) -> "TableDoc":
         # pylint: disable=line-too-long
@@ -170,7 +179,7 @@ def parse_csv(
                 JSON-LD context.  Should map namespace prefixes to IRIs.
             context: Dict with user-defined JSON-LD context.
             encoding: The encoding of the csv file.  Note that Excel may
-                encode as "ISO-8859" (commonly used in 1990th).
+                encode as "ISO-8859" (which was commonly used in 1990th).
             dialect: A subclass of csv.Dialect, or the name of the dialect,
                 specifying how the `csvfile` is formatted.  For more details,
                 see [Dialects and Formatting Parameters].
@@ -184,14 +193,22 @@ def parse_csv(
         References:
         [Dialects and Formatting Parameters]: https://docs.python.org/3/library/csv.html#dialects-and-formatting-parameters
         """
+
+        def read(f, dialect):
+            """Return csv reader from file-like object `f`."""
+            if dialect is None and not kwargs:
+                dialect = csv.Sniffer().sniff(f.read(1024), delimiters=",;\t ")
+                f.seek(0)
+            reader = csv.reader(f, dialect=dialect, **kwargs)
+            header = next(reader)
+            data = list(reader)
+            return header, data
+
         if isinstance(csvfile, (str, Path)):
             with openfile(csvfile, mode="rt", encoding=encoding) as f:
-                reader = csv.reader(f, dialect=dialect, **kwargs)
+                header, data = read(f, dialect)
         else:
-            reader = csv.reader(csvfile, dialect=dialect, **kwargs)
-
-        header = next(reader)
-        data = list(reader)
+            header, data = read(csvfile, dialect)
 
         return TableDoc(
             header=header,
diff --git a/tripper/utils.py b/tripper/utils.py
index 76e9cc0f..e44650b1 100644
--- a/tripper/utils.py
+++ b/tripper/utils.py
@@ -113,8 +113,10 @@ def openfile(
         fname = url
 
     try:
-        yield open(fname, **kwargs)  # pylint: disable=unspecified-encoding
+        f = open(fname, **kwargs)  # pylint: disable=unspecified-encoding
+        yield f
     finally:
+        f.close()
         if tmpfile:
             Path(fname).unlink()
 

From 9851fa871f87d910e5194a03728aaf63d96e850e Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Sat, 4 Jan 2025 21:01:50 +0100
Subject: [PATCH 53/59] Added documentation of isDescriptionFor

---
 docs/dataset/keywords.md    | 2 ++
 tripper/dataset/tabledoc.py | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/docs/dataset/keywords.md b/docs/dataset/keywords.md
index 3739cb7e..8978af1e 100644
--- a/docs/dataset/keywords.md
+++ b/docs/dataset/keywords.md
@@ -73,6 +73,7 @@ Properties specific for datasets
 - **[distribution]** (*IRI*): An available distribution of the dataset.
 - **[hasDatum]** (*IRI*): Relates a dataset to its datum parts. `hasDatum` relations are normally specified manually, since they are generated from the DLite data model.
 - **[inSeries]** (*IRI*): A dataset series of which the dataset is part.
+- **[isDescriptionFor]** (*IRI*): An object (e.g. a material) that this dataset describes.
 - **[isInputOf]** (*IRI*): A process that this dataset is the input to.
 - **[isOutputOf]** (*IRI*): A process that this dataset is the output of.
 - **[mappings]** (*Literal JSON*): A list of subject-predicate-object triples mapping the datamodel to ontological concepts.
@@ -173,6 +174,7 @@ Properties for parsers and generators
 [distribution]: https://www.w3.org/TR/vocab-dcat-3/#Property:dataset_distribution
 [hasDatum]: https://w3id.org/emmo#EMMO_b19aacfc_5f73_4c33_9456_469c1e89a53e
 [inSeries]: https://www.w3.org/TR/vocab-dcat-3/#Property:dataset_in_series
+[isDescriptionFor]: https://w3id.org/emmo#EMMO_f702bad4_fc77_41f0_a26d_79f6444fd4f3
 [isInputOf]: https://w3id.org/emmo#EMMO_1494c1a9_00e1_40c2_a9cc_9bbf302a1cac
 [isOutputOf]: https://w3id.org/emmo#EMMO_2bb50428_568d_46e8_b8bf_59a4c5656461
 [mappings]: https://w3id.org/emmo/domain/oteio#mapping
diff --git a/tripper/dataset/tabledoc.py b/tripper/dataset/tabledoc.py
index 4f4d676f..532cbaa7 100644
--- a/tripper/dataset/tabledoc.py
+++ b/tripper/dataset/tabledoc.py
@@ -179,7 +179,7 @@ def parse_csv(
                 JSON-LD context.  Should map namespace prefixes to IRIs.
             context: Dict with user-defined JSON-LD context.
             encoding: The encoding of the csv file.  Note that Excel may
-                encode as "ISO-8859" (which was commonly used in 1990th).
+                encode as "ISO-8859" (which was commonly used in the 1990th).
             dialect: A subclass of csv.Dialect, or the name of the dialect,
                 specifying how the `csvfile` is formatted.  For more details,
                 see [Dialects and Formatting Parameters].

From 59c7f0966254b094554960c17fc512e53180cc51 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Sat, 4 Jan 2025 21:37:06 +0100
Subject: [PATCH 54/59] Updated mkdocs and fixed link warnings

---
 docs/dataset/customisation.md          | 19 +++++++++----------
 docs/dataset/documenting-a-resource.md |  8 ++++----
 docs/dataset/keywords.md               |  8 +++-----
 docs/dataset/prefixes.md               |  2 +-
 docs/tools/datadoc.md                  |  4 ++--
 mkdocs.yml                             | 12 ++++++++++++
 pyproject.toml                         | 14 +++++++-------
 7 files changed, 38 insertions(+), 29 deletions(-)

diff --git a/docs/dataset/customisation.md b/docs/dataset/customisation.md
index 71013c49..52f28660 100644
--- a/docs/dataset/customisation.md
+++ b/docs/dataset/customisation.md
@@ -237,15 +237,14 @@ Instead, the list of available resource types should be stored and retrieved fro
 [With custom context]: #with-custom-context
 [User-defined keywords]: #user-defined-keywords
 [Python dict]: #python-dict
-[resource types]: ../introduction#resource-types
-[Documenting a resource]: ../documenting-a-resource
-[predefined prefixes]: ../prefixes/
-[predefined keywords]: ../keywords/
+[resource types]: introduction.md#resource-types
+[Documenting a resource]: documenting-a-resource.md
+[predefined prefixes]: prefixes.md
+[predefined keywords]: keywords.md
 [default context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json
-[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]: ../../api_reference/dataset/tabledoc/#tripper.dataset.tabledoc.TableDoc
-[TableDoc.parse_csv()]: ../../api_reference/dataset/tabledoc/#tripper.dataset.tabledoc.TableDoc.parse_csv
+[save_dict()]: ../api_reference/dataset/dataset.md#tripper.dataset.dataset.save_dict
+[as_jsonld()]: ../api_reference/dataset/dataset.md#tripper.dataset.dataset.as_jsonld
+[save_datadoc()]: ../api_reference/dataset/dataset.md#tripper.dataset.dataset.save_datadoc
+[TableDoc]: ../api_reference/dataset/tabledoc.md/#tripper.dataset.tabledoc.TableDoc
+[TableDoc.parse_csv()]: ../api_reference/dataset/tabledoc.md/#tripper.dataset.tabledoc.TableDoc.parse_csv
 [default JSON-LD context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json
diff --git a/docs/dataset/documenting-a-resource.md b/docs/dataset/documenting-a-resource.md
index a85342dd..ad8b6c34 100644
--- a/docs/dataset/documenting-a-resource.md
+++ b/docs/dataset/documenting-a-resource.md
@@ -124,7 +124,7 @@ This dict representation accepts the following keywords:
 
 - **@context**: Optional user-defined context to be appended to the documentation of all resources.
 - **prefixes**: A dict mapping namespace prefixes to their corresponding URLs.
-- **datasets**/**distributions**/**accessServices**/**generators**/**parsers**/**resources**: A list of valid [single-resource](#single-resource-dict) dict of the given [resource type](#resource-types).
+- **datasets**/**distributions**/**accessServices**/**generators**/**parsers**/**resources**: A list of valid [single-resource](#single-resource-dict) dict of the given [resource type](introduction.md#resource-types).
 
 See [semdata.yaml] for an example of a [YAML] representation of a multi-resource dict documentation.
 
@@ -207,10 +207,10 @@ The below example shows how to save all datasets listed in the CSV file [semdata
 [emmo:DataSet]: https://w3id.org/emmo#EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a
 [oteio:Generator]: https://w3id.org/emmo/domain/oteio/Generator
 [oteio:Parser]: https://w3id.org/emmo/domain/oteio/Parser
-[save_dict()]: ../../api_reference/dataset/dataset/#tripper.dataset.dataset.save_dict
-[as_jsonld()]: ../../api_reference/dataset/dataset/#tripper.dataset.dataset.as_jsonld
+[save_dict()]: ../api_reference/dataset/dataset.md/#tripper.dataset.dataset.save_dict
+[as_jsonld()]: ../api_reference/dataset/dataset.md/#tripper.dataset.dataset.as_jsonld
 [save_datadoc()]:
-../../api_reference/dataset/dataset/#tripper.dataset.dataset.save_datadoc
+../api_reference/dataset/dataset.md/#tripper.dataset.dataset.save_datadoc
 [semdata.yaml]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.yaml
 [semdata.csv]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/tabledoc-csv/tests/input/semdata.csv
 [TableDoc]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.tabledoc.TableDoc
diff --git a/docs/dataset/keywords.md b/docs/dataset/keywords.md
index 8978af1e..de9f8b6c 100644
--- a/docs/dataset/keywords.md
+++ b/docs/dataset/keywords.md
@@ -125,9 +125,6 @@ Properties for parsers and generators
 - **[prefixes]**:
 -->
 
-[default JSON-LD context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json
-[JSON-LD documentation]: https://www.w3.org/TR/json-ld/#syntax-tokens-and-keywords
-
 [accessRights]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_access_rights
 [conformsTo]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_conforms_to
 [contactPoint]: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_contact_point
@@ -219,11 +216,12 @@ Properties for parsers and generators
 [prefixes]:
 -->
 
-
 [DCAT]: https://www.w3.org/TR/vocab-dcat-3/
 [dcat:Dataset]: https://www.w3.org/TR/vocab-dcat-3/#Class:Dataset
 [dcat:Distribution]: https://www.w3.org/TR/vocab-dcat-3/#Class:Distribution
 [vCard]: https://www.w3.org/TR/vcard-rdf/
 [IANA]: https://www.iana.org/assignments/media-types/media-types.xhtml
+[default JSON-LD context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json
+[JSON-LD documentation]: https://www.w3.org/TR/json-ld/#syntax-tokens-and-keywords
 
-[User-defined keywords]: ../customisation/#user-defined-keywords
+[User-defined keywords]: customisation.md/#user-defined-keywords
diff --git a/docs/dataset/prefixes.md b/docs/dataset/prefixes.md
index 5af69c85..2caaf8d4 100644
--- a/docs/dataset/prefixes.md
+++ b/docs/dataset/prefixes.md
@@ -25,4 +25,4 @@ See [User-defined prefixes] for how to extend this list with additional namespac
 
 
 [default JSON-LD context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json
-[User-defined prefixes]: ../customisation/#user-defined-prefixes
+[User-defined prefixes]: customisation.md/#user-defined-prefixes
diff --git a/docs/tools/datadoc.md b/docs/tools/datadoc.md
index 9bd2fe5a..3785a9fc 100644
--- a/docs/tools/datadoc.md
+++ b/docs/tools/datadoc.md
@@ -94,7 +94,7 @@ This is useful if you are working with an in-memory triplestore.
 
     The `tests/input/` folder in the source code contain the `semdata.csv` CSV file documenting four datasets, a SEM image, two nested dataset series and the sample the image was acquired from.
 
-    [![semdata.csv](../../figs/semdata.png)](../../figs/semdata.png)
+    [![semdata.csv](/figs/semdata.png)](/figs/semdata.png)
 
     Running the following command from the root folder of the source code will populate an in-memory rdflib store with the data documented in the `semdata.csv` file.
 
@@ -375,4 +375,4 @@ The following formats are currently available:
 
 
 
-[resource types]: ../../dataset/introduction/#resource-types
+[resource types]: ../dataset/introduction.md/#resource-types
diff --git a/mkdocs.yml b/mkdocs.yml
index 0212137c..e1ebbbd2 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -102,3 +102,15 @@ nav:
 
 watch:
   - tripper
+
+#validation:
+#  omitted_files: warn
+#  absolute_links: warn  # Or 'relative_to_docs' - new in MkDocs 1.6
+#  unrecognized_links: warn
+#  anchors: warn  # New in MkDocs 1.6
+
+validation:
+  links:
+    absolute_links: relative_to_docs
+    anchors: warn
+    unrecognized_links: warn
diff --git a/pyproject.toml b/pyproject.toml
index 1e871728..349636e7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -63,13 +63,13 @@ testing = [
 ]
 docs = [
     "tripper[testing]",
-    "mike==2.1.2",
-    "mkdocs==1.5.3",
-    "mkdocs-autorefs==0.4.1",
-    "mkdocs-awesome-pages-plugin==2.9.2",
-    "mkdocs-material==9.5.17",
-    "mkdocstrings==0.22.0",
-    "mkdocstrings-python-legacy==0.2.3",
+    "mike==2.1.3",
+    "mkdocs==1.6.1",
+    "mkdocs-autorefs==1.2.0",
+    "mkdocs-awesome-pages-plugin==2.10.1",
+    "mkdocs-material==9.5.49",
+    "mkdocstrings==0.27.0",
+    "mkdocstrings-python-legacy==0.2.4",
 ]
 dev = [
     "tripper[pre-commit,docs]",

From 462742f2782588fe2dbd9988c431e8902dae2f41 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Sat, 4 Jan 2025 21:39:33 +0100
Subject: [PATCH 55/59] Minor documentation update

---
 docs/tools/datadoc.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/tools/datadoc.md b/docs/tools/datadoc.md
index 3785a9fc..03ba1af2 100644
--- a/docs/tools/datadoc.md
+++ b/docs/tools/datadoc.md
@@ -92,7 +92,7 @@ This is useful if you are working with an in-memory triplestore.
 
 !!! example
 
-    The `tests/input/` folder in the source code contain the `semdata.csv` CSV file documenting four datasets, a SEM image, two nested dataset series and the sample the image was acquired from.
+    The `tests/input/` folder in the source code contain the `semdata.csv` CSV file documenting four datasets, a SEM image, two nested dataset series and the sample the image was acquired from as shown in the figure below (click on it to see it in full size).
 
     [![semdata.csv](/figs/semdata.png)](/figs/semdata.png)
 

From 2ec83716ba96518acb31d95450b6e8d654c058be Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Sat, 4 Jan 2025 21:45:30 +0100
Subject: [PATCH 56/59] Fix failing test

---
 tests/dataset/test_dataset.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/dataset/test_dataset.py b/tests/dataset/test_dataset.py
index 93f57a47..5fe34ba8 100644
--- a/tests/dataset/test_dataset.py
+++ b/tests/dataset/test_dataset.py
@@ -29,7 +29,7 @@ def test_get_jsonld_context():
     assert online_context["status"] == "adms:status"
 
     # Test context argument
-    context2 = get_jsonld_context(context=CONTEXT_URL)
+    context2 = get_jsonld_context(context=CONTEXT_URL, fromfile=False)
     assert context2 == online_context
 
     assert "newkey" not in context

From 883fe419edfec3cd0db6e174b1c3555b25319622 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Sat, 4 Jan 2025 21:45:30 +0100
Subject: [PATCH 57/59] Fix failing test

---
 tests/dataset/test_dataset.py | 2 +-
 tripper/dataset/datadoc.py    | 7 ++++++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/tests/dataset/test_dataset.py b/tests/dataset/test_dataset.py
index 93f57a47..5fe34ba8 100644
--- a/tests/dataset/test_dataset.py
+++ b/tests/dataset/test_dataset.py
@@ -29,7 +29,7 @@ def test_get_jsonld_context():
     assert online_context["status"] == "adms:status"
 
     # Test context argument
-    context2 = get_jsonld_context(context=CONTEXT_URL)
+    context2 = get_jsonld_context(context=CONTEXT_URL, fromfile=False)
     assert context2 == online_context
 
     assert "newkey" not in context
diff --git a/tripper/dataset/datadoc.py b/tripper/dataset/datadoc.py
index a241ccf8..89a98eb6 100644
--- a/tripper/dataset/datadoc.py
+++ b/tripper/dataset/datadoc.py
@@ -87,6 +87,11 @@ def subcommand_find(ts, args):
         print(s)
 
 
+def subcommand_load(ts, args):
+    """Subcommand for loading data from a documented storage."""
+    print(ts, args)
+
+
 def main(argv=None):
     """Main function."""
     parser = argparse.ArgumentParser(
@@ -236,7 +241,7 @@ def main(argv=None):
         action="extend",
         nargs="+",
         metavar="PREFIX=URL",
-        help="Namespace prefixes to add to bind to the triplestore.",
+        help="Namespace prefixes to bind to the triplestore.",
     )
 
     args = parser.parse_args(argv)

From 1c6ee69999de3d04e7a7eee866e642740e11a2d6 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 6 Jan 2025 00:25:43 +0100
Subject: [PATCH 58/59] Added load sub-command to tabledoc

---
 docs/dataset/documenting-a-resource.md |  5 +-
 docs/dataset/keywords.md               |  7 +--
 docs/tools/datadoc.md                  | 65 ++++++++++++++++++++++----
 tests/dataset/test_tabledoc.py         |  3 +-
 tests/input/semdata.csv                | 10 ++--
 tripper/dataset/datadoc.py             | 30 +++++++++++-
 tripper/dataset/dataset.py             |  6 ++-
 7 files changed, 99 insertions(+), 27 deletions(-)

diff --git a/docs/dataset/documenting-a-resource.md b/docs/dataset/documenting-a-resource.md
index ad8b6c34..c6b04a54 100644
--- a/docs/dataset/documenting-a-resource.md
+++ b/docs/dataset/documenting-a-resource.md
@@ -175,8 +175,7 @@ The below example shows how to save all datasets listed in the CSV file [semdata
 >>> from tripper.dataset import TableDoc
 
 >>> td = TableDoc.parse_csv(
-...     "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/tabledoc-csv/tests/input/semdata.csv",
-...     delimiter=";",
+...     "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.csv",
 ...     prefixes={
 ...         "sem": "https://w3id.com/emmo/domain/sem/0.1#",
 ...         "semdata": "https://he-matchmaker.eu/data/sem/",
@@ -212,5 +211,5 @@ The below example shows how to save all datasets listed in the CSV file [semdata
 [save_datadoc()]:
 ../api_reference/dataset/dataset.md/#tripper.dataset.dataset.save_datadoc
 [semdata.yaml]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.yaml
-[semdata.csv]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/tabledoc-csv/tests/input/semdata.csv
+[semdata.csv]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.csv
 [TableDoc]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.tabledoc.TableDoc
diff --git a/docs/dataset/keywords.md b/docs/dataset/keywords.md
index de9f8b6c..c8a6c366 100644
--- a/docs/dataset/keywords.md
+++ b/docs/dataset/keywords.md
@@ -11,8 +11,8 @@ Here we only list those that are commonly used for data documentation with Tripp
 
 - **@context** (*IRI*): URL to or dict with user-defined JSON-LD context.
       Used to extend the keywords listed on this page with domain- or application-specific keywords.
-- **@id** (*IRI*): IRI of the documented resource.
-- **@type** (*IRI*): IRI of ontological class that the resource is an individual of.
+- **@id** (*IRI*): IRI identifying the documented resource.
+- **@type** (*IRI*): IRI of ontological class that defines what the resource *is*.
 
 
 General properties on resources used by DCAT
@@ -56,10 +56,11 @@ Other general properties on resources
 
 - **[abstract]** (*Literal*): A summary of the resource.
 - **[bibliographicCitation]** (*Literal*): A bibliographic reference for the resource. Recommended practice is to include sufficient bibliographic detail to identify the resource as unambiguously as possible.
-- **[comment]** (*Literal*): A description of the subject resource.
+- **[comment]** (*Literal*): A description of the subject resource. Use `description` instead.
 - **[deprecated]** (*Literal*): The annotation property that indicates that a given entity has been deprecated.  It should equal to `"true"^^xsd:boolean`.
 - **[isDefinedBy]** (*Literal*): Indicate a resource defining the subject resource. This property may be used to indicate an RDF vocabulary in which a resource is described.
 - **[label]** (*Literal*): Provides a human-readable version of a resource's name.
+- **[scopeNote]** (*Literal*): A note that helps to clarify the meaning and/or the use of a concept.
 - **[seeAlso]** (*Literal*): Indicates a resource that might provide additional information about the subject resource.
 - **[source]** (*Literal*): A related resource from which the described resource is derived.
 - **[statements]** (*Literal JSON*): A list of subject-predicate-object triples with additional RDF statements documenting the resource.
diff --git a/docs/tools/datadoc.md b/docs/tools/datadoc.md
index 03ba1af2..950881a6 100644
--- a/docs/tools/datadoc.md
+++ b/docs/tools/datadoc.md
@@ -10,15 +10,16 @@ usage: datadoc [-h] [--backend BACKEND] [--base-iri BASE_IRI]
                [--database DATABASE] [--package PACKAGE] [--parse LOCATION]
                [--parse-format PARSE_FORMAT]
                [--prefixes PREFIX=URL [PREFIX=URL ...]]
-               {add,find} ...
+               {add,find,load} ...
 
 Tool for data documentation. It allows populating and searching a triplestore
 for existing documentation.
 
 positional arguments:
-  {add,find}            Subcommands:
+  {add,find,load}       Subcommands:
     add                 Populate the triplestore with data documentation.
     find                Find documented resources in the triplestore.
+    load                Load documented dataset from a storage.
 
 options:
   -h, --help            show this help message and exit
@@ -41,7 +42,7 @@ options:
                         Namespace prefixes to add to bind to the triplestore.
 ```
 
-Currently, `datadoc` has two sub-commands, `add` and `find` for populating and searching the triplestore, respectively.
+Currently, `datadoc` has currently three sub-commands, `add`, `find` and `load` for populating  the triplestore, searching  the triplestore and accessing a dataset documented the triplestore, respectively.
 
 ### General options
 
@@ -51,7 +52,7 @@ Currently, `datadoc` has two sub-commands, `add` and `find` for populating and s
 They are typically used with the default "rdflib" in-memory backend.
 
 
-Subcomands
+Subcommands
 ----------
 
 ### add
@@ -99,14 +100,12 @@ This is useful if you are working with an in-memory triplestore.
     Running the following command from the root folder of the source code will populate an in-memory rdflib store with the data documented in the `semdata.csv` file.
 
     ```shell
-    datadoc add tests/input/semdata.csv --csv-options delimiter=';' --context tests/input/semdata-context.json --dump kb.ttl
+    datadoc add tests/input/semdata.csv --context tests/input/semdata-context.json --dump kb.ttl
     ```
 
-    The `--csv-options` tells that the csv file is delimited by semi-colon, which is the default delimiter used by excel in Scandinavia.
-
     The `--context` option provides a user-defined context defining prefixes and keywords used by the input.
 
-    Finally the `--dump` option dumps the in-memory triplestore to the file `kb.ttl`.
+    The `--dump` option dumps the in-memory triplestore to the file `kb.ttl`.
     If you open the file, you will notice that it in addition to the four datasets listed in the input, also include the `SEMImage` class and its properties, providing structural documentation of the `SEMImage` individuals.
 
     ??? abstract "Generated turtle file"
@@ -157,7 +156,7 @@ This is useful if you are working with an in-memory triplestore.
             dcat:contactPoint "Sigurd Wenner <Sigurd.Wenner@sintef.no>" ;
             dcat:distribution [ a dcat:Distribution ;
                     <http://sintef.no/dlite/parser#> "http://sintef.no/dlite/parser#sem_hitachi" ;
-                    dcat:downloadURL "https://github.com/EMMC-ASBL/tripper/raw/refs/heads/dataset/tests/input/77600-23-001_5kV_400x_m001.tif" ;
+                    dcat:downloadURL "https://github.com/EMMC-ASBL/tripper/raw/refs/heads/master/tests/input/77600-23-001_5kV_400x_m001.tif" ;
                     dcat:mediaType "image/tiff" ] ;
             dcat:inSeries <https://he-matchmaker.eu/data/sem/SEM_cement_batch2/77600-23-001> ;
             emmo:EMMO_f702bad4_fc77_41f0_a26d_79f6444fd4f3 <https://he-matchmaker.eu/material/concrete1> ;
@@ -297,7 +296,7 @@ options:
 ```
 
 The `--type` and `--criteria` options provide search criteria.
-The `--type` argument an be any of the recognised [resource types] to limit the search to.
+The `--type` option an be any of the recognised [resource types] to limit the search to.
 Alternatively, it may be the IRI of a class.
 This limits the search to only resources that are individuals of this class.
 
@@ -372,6 +371,52 @@ The following formats are currently available:
     ]
     ```
 
+    **Ex 5**: Show the documentation of a resource with a given IRI as JSON:
+
+    ```shell
+    $ datadoc --parse=kb.ttl find --criteria @id=https://he-matchmaker.eu/data/sem/SEM_cement_batch2/77600-23-001 --format=json
+    ```
+
+    This will show the same output as in Ex 4.
+
+
+### load
+Loads documented dataset from a storage.
+Running `datadoc load --help` will show the following help message:
+
+```
+usage: datadoc load [-h] [--output FILENAME] iri
+
+positional arguments:
+  iri                   IRI of dataset to load.
+
+options:
+  -h, --help            show this help message and exit
+  --output FILENAME, -o FILENAME
+                        Write the dataset to the given file. The default is to
+                        write to standard output.
+```
+
+!!! note
+    The `load` subcommand is specific for datasets since it uses DCAT documentation of how to fetch the dataset.
+
+The positional `iri` argument is the IRI of the documented dataset to load.
+
+The `--output` option allows to write the dataset to a local file.
+
+
+!!! example
+
+    Save the dataset `https://he-matchmaker.eu/data/sem/SEM_cement_batch2/77600-23-001/77600-23-001_5kV_400x_m001` documented in `kb.ttl` to file:
+
+    ```shell
+    $ datadoc -p kb.ttl load https://he-matchmaker.eu/data/sem/SEM_cement_batch2/77600-23-001/77600-23-001_5kV_400x_m001 -o cement.tif
+    ```
+
+    This should create the file `cement.tif` containing the image data.
+
+
+
 
 
 
diff --git a/tests/dataset/test_tabledoc.py b/tests/dataset/test_tabledoc.py
index 4f9dfd93..56d66512 100644
--- a/tests/dataset/test_tabledoc.py
+++ b/tests/dataset/test_tabledoc.py
@@ -123,7 +123,6 @@ def test_csv():
     # Read csv file
     td = TableDoc.parse_csv(
         indir / "semdata.csv",
-        delimiter=";",
         prefixes={
             "sem": "https://w3id.com/emmo/domain/sem/0.1#",
             "semdata": "https://he-matchmaker.eu/data/sem/",
@@ -143,7 +142,7 @@ def test_csv():
         "77600-23-001/77600-23-001_5kV_400x_m001"
     )
     assert img.distribution.downloadURL == (
-        "https://github.com/EMMC-ASBL/tripper/raw/refs/heads/dataset/"
+        "https://github.com/EMMC-ASBL/tripper/raw/refs/heads/master/"
         "tests/input/77600-23-001_5kV_400x_m001.tif"
     )
 
diff --git a/tests/input/semdata.csv b/tests/input/semdata.csv
index 3f764831..9dca3036 100644
--- a/tests/input/semdata.csv
+++ b/tests/input/semdata.csv
@@ -1,5 +1,5 @@
-@id;@type;title;description;creator;contactPoint;inSeries;datamodel;datamodelStorage;distribution.downloadURL;distribution.mediaType;distribution.parser;fromSample;isDescriptionFor
-semdata:SEM_cement_batch2/77600-23-001/77600-23-001_5kV_400x_m001;sem:SEMImage;SEM image of cement;Back-scattered SEM image of cement sample 77600 from Heidelberg, polished with 1 µm diamond compound.;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>;semdata:SEM_cement_batch2/77600-23-001;http://onto-ns.com/meta/matchmaker/0.2/SEMImage;https://github.com/HEU-MatCHMaker/DataDocumentation/blob/master/SEM/datamodels/SEMImage.yaml;https://github.com/EMMC-ASBL/tripper/raw/refs/heads/dataset/tests/input/77600-23-001_5kV_400x_m001.tif;image/tiff;parser:sem_hitachi;sample:SEM_cement_batch2/77600-23-001;mat:concrete1
-semdata:SEM_cement_batch2/77600-23-001;sem:SEMImageSeries;Series of SEM image of cement sample 77600;Back-scattered SEM image of cement sample 77600, polished with 1 µm diamond compound.;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>;semdata:SEM_cement_batch2; ;;sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2/77600-23-001;inode/directory;;;
-semdata:SEM_cement_batch2;sem:SEMImageSeries;Nested series of SEM images of cement batch2;...;Sigurd Wenner;Sigurd Wenner <Sigurd.Wenner@sintef.no>; ;;;sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2;inode/directory;;;
-sample:SEM_cement_batch2/77600-23-001;chameo:Sample;Series for SEM images for sample 77600-23-001.; ;;;;;;;;;;
+@id,@type,title,description,creator,contactPoint,inSeries,datamodel,datamodelStorage,distribution.downloadURL,distribution.mediaType,distribution.parser,fromSample,isDescriptionFor
+semdata:SEM_cement_batch2/77600-23-001/77600-23-001_5kV_400x_m001,sem:SEMImage,SEM image of cement,"Back-scattered SEM image of cement sample 77600 from Heidelberg, polished with 1 µm diamond compound.",Sigurd Wenner,Sigurd Wenner <Sigurd.Wenner@sintef.no>,semdata:SEM_cement_batch2/77600-23-001,http://onto-ns.com/meta/matchmaker/0.2/SEMImage,https://github.com/HEU-MatCHMaker/DataDocumentation/blob/master/SEM/datamodels/SEMImage.yaml,https://github.com/EMMC-ASBL/tripper/raw/refs/heads/master/tests/input/77600-23-001_5kV_400x_m001.tif,image/tiff,parser:sem_hitachi,sample:SEM_cement_batch2/77600-23-001,mat:concrete1
+semdata:SEM_cement_batch2/77600-23-001,sem:SEMImageSeries,Series of SEM image of cement sample 77600,"Back-scattered SEM image of cement sample 77600, polished with 1 µm diamond compound.",Sigurd Wenner,Sigurd Wenner <Sigurd.Wenner@sintef.no>,semdata:SEM_cement_batch2, ,,sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2/77600-23-001,inode/directory,,,
+semdata:SEM_cement_batch2,sem:SEMImageSeries,Nested series of SEM images of cement batch2,...,Sigurd Wenner,Sigurd Wenner <Sigurd.Wenner@sintef.no>, ,,,sftp://nas.aimen.es/P_MATCHMAKER_SHARE_SINTEF/SEM_cement_batch2,inode/directory,,,
+sample:SEM_cement_batch2/77600-23-001,chameo:Sample,Series for SEM images for sample 77600-23-001., ,,,,,,,,,,
diff --git a/tripper/dataset/datadoc.py b/tripper/dataset/datadoc.py
index 89a98eb6..bb666f4e 100644
--- a/tripper/dataset/datadoc.py
+++ b/tripper/dataset/datadoc.py
@@ -12,6 +12,7 @@
 from tripper.dataset import (
     TableDoc,
     get_jsonld_context,
+    load,
     load_dict,
     save_datadoc,
     save_dict,
@@ -88,8 +89,14 @@ def subcommand_find(ts, args):
 
 
 def subcommand_load(ts, args):
-    """Subcommand for loading data from a documented storage."""
-    print(ts, args)
+    """Subcommand for loading a documented dataset from a storage."""
+    data = load(ts, args.iri)
+
+    if args.output:
+        with open(args.output, "wb") as f:
+            f.write(data)
+    else:
+        print(data)
 
 
 def main(argv=None):
@@ -199,6 +206,25 @@ def main(argv=None):
         ),
     )
 
+    # Subcommand: load
+    parser_load = subparsers.add_parser(
+        "load", help="Load documented dataset from a storage."
+    )
+    parser_load.set_defaults(func=subcommand_load)
+    parser_load.add_argument(
+        "iri",
+        help="IRI of dataset to load.",
+    )
+    parser_load.add_argument(
+        "--output",
+        "-o",
+        metavar="FILENAME",
+        help=(
+            "Write the dataset to the given file. The default is to write "
+            "to standard output."
+        ),
+    )
+
     # General: options
     parser.add_argument(
         "--backend",
diff --git a/tripper/dataset/dataset.py b/tripper/dataset/dataset.py
index 7fd8b1c4..9f680ffc 100644
--- a/tripper/dataset/dataset.py
+++ b/tripper/dataset/dataset.py
@@ -889,8 +889,10 @@ def search_iris(ts: Triplestore, type=None, **kwargs) -> "List[str]":
     SeeAlso:
     [resource type]: https://emmc-asbl.github.io/tripper/latest/dataset/introduction/#resource-types
     """
-    crit = []
+    # Special handling of @id
+    id = kwargs.pop("@id") if "@id" in kwargs else kwargs.pop("_id", None)
 
+    crit = []
     if type:
         if ":" in type:
             expanded = ts.expand_iri(type)
@@ -933,4 +935,4 @@ def search_iris(ts: Triplestore, type=None, **kwargs) -> "List[str]":
     {criterias}
     }}
     """
-    return [r[0] for r in ts.query(query)]  # type: ignore
+    return [r[0] for r in ts.query(query) if not id or r[0] == id]  # type: ignore

From 54523e21a74865c4fd1c9b1a283e7085b24b13ef Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper-friis@users.noreply.github.com>
Date: Mon, 6 Jan 2025 14:14:36 +0100
Subject: [PATCH 59/59] Apply suggestions from code review

Co-authored-by: Tor S. Haugland <torshaugland@gmail.com>
---
 docs/dataset/customisation.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/dataset/customisation.md b/docs/dataset/customisation.md
index 52f28660..19279615 100644
--- a/docs/dataset/customisation.md
+++ b/docs/dataset/customisation.md
@@ -94,7 +94,7 @@ Both for the single-resource and multi-resource dicts, you can add a `"@context"
 
 For example
 
-```json
+```python
 {
     "@context": [
         # URL to a JSON file, typically a domain-specific context