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Major zenodo and serialization enhancements (#28)
* improve zenodo and serialization (#27) - fix issues with ZenodoRecord - add support of Literals in RDF attributes, e.g. h5.frdf["description"].object = rdflib.Literal("An english description", "en") - removed deprecated methods in `ZenodoSandboxDeposit` - add support of Literals in RDF attributes, e.g. `h5.frdf["description"].object = rdflib.Literal("An english description", "en")` - improve serializing HDF5 contextual and structural metadata to RDF-based formats - minor bugfixes * fix docs and datetime serialization * update readme and CITATION.cff
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‎CHANGELOG.md‎

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Log of changes in the versions
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## v2.4.0-rc.2
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- fix issues with ZenodoRecord
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- add support of Literals in RDF attributes, e.g. h5.frdf["description"].object = rdflib.Literal("An english
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description", "en")
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- removed deprecated methods in `ZenodoSandboxDeposit`
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- add support of Literals in RDF attributes, e.g.
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`h5.frdf["description"].object = rdflib.Literal("An english description", "en")`
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- improve serializing HDF5 contextual and structural metadata to RDF-based formats
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- minor bugfixes
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- default dtime format used within h5rdmtoolbox is now ISO 8601 ('%Y-%m-%dT%H:%M:%S%f')
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## v2.4.0-rc.1
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- allow numpy 2.x versions
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## v2.3.1
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- fixing error in parsing obj name. "/" is safed and will not be converted anymore
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- fixing error in parsing obj name. "/" is saved and will not be converted anymore
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## v2.3.0
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‎CITATION.cff‎

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given-names: "Lucas"
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orcid: "https://orcid.org/0000-0002-4116-0065"
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title: "h5rdmtoolbox - HDF5 Research Data Management Toolbox"
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version: 2.4.0-rc.1
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doi: 10.5281/zenodo.17088483
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version: 2.4.0-rc.2
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doi: 10.5281/zenodo.17334652
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date-released: 2025-10-12
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url: "https://github.com/matthiasprobst/h5rdmtoolbox"

‎README.md‎

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## Installation
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Use python 3.8 or higher (automatic testing is performed until 3.12). If you are a regular user, you can install the
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Use python 3.9 or higher (automatic testing is performed until 3.13). If you are a regular user, you can install the
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package via pip:
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pip install h5RDMtoolbox
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or if you prefer `uv`:
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uv install h5RDMtoolbox
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### Install from source:
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## Citing the package
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If you intend to use the package in your work, you may cite the software itself as published on paper in the
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[Zenodo](https://zenodo.org/records/14473697) repository. A related paper is published in the
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[Zenodo (latest version)](https://zenodo.org/records/13309253) repository. A related paper is published in the
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journal [inggrid](https://www.inggrid.org/article/id/4028/). Thank you!
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Here's the bibtext to it:
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Alternatively or additionally, you can consult the `CITATION.cff` file.
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Here is the BibTeX entry:
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```
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@article{probst2024h5rdmtoolbox,

‎codemeta.json‎

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"license": "https://spdx.org/licenses/MIT",
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"codeRepository": "git+https://github.com/matthiasprobst/h5RDMtoolbox.git",
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"name": "h5RDMtoolbox",
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"version": "2.4.0-rc.1",
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"version": "2.4.0-rc.2",
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"description": "Supporting a FAIR Research Data lifecycle using Python and HDF5.",
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"applicationCategory": "Engineering",
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"programmingLanguage": [

‎docs/colab/quickstart.ipynb‎

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"scrolled": true
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},
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"outputs": [],
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"source": "# !pip install h5rdmtoolbox==2.4.0rc1"
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"source": "# !pip install h5rdmtoolbox==2.4.0rc2"
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},
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{
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"cell_type": "code",

‎docs/gettingstarted/quickoverview.ipynb‎

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‎docs/practical_examples/knowledge_graph.ipynb‎

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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": null,
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"id": "a9b58411-88af-4972-b5c8-b01391df58fc",
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"metadata": {
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"scrolled": true
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": null,
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"id": "feb70a18-b9e7-40db-b369-4e6c927301e5",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": null,
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"id": "690c0219-d7f5-4b0d-a897-59cf8f354149",
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"metadata": {},
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": null,
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"id": "d4d871e0-5bff-42f7-a27d-f1f0337dd964",
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"metadata": {
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"scrolled": true
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"@prefix dcterms: <http://purl.org/dc/terms/> .\n",
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"@prefix ex: <https://example.org#> .\n",
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"@prefix foaf: <http://xmlns.com/foaf/0.1/> .\n",
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"@prefix hdf: <http://purl.allotrope.org/ontologies/hdf5/1.8#> .\n",
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"@prefix prov: <http://www.w3.org/ns/prov#> .\n",
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"@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .\n",
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"\n",
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"ex:tmp0.hdf a hdf:File ;\n",
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" hdf:rootGroup <https://example.org#tmp0.hdf/> .\n",
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"\n",
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"<https://example.org#tmp0.hdf/> a hdf:Group ;\n",
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" hdf:member <https://example.org#tmp0.hdf/contact>,\n",
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" <https://example.org#tmp0.hdf/nd-array>,\n",
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" <https://example.org#tmp0.hdf/test> ;\n",
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" hdf:name \"/\"^^xsd:string .\n",
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"\n",
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"<https://example.org#tmp0.hdf/contact> a hdf:Group ;\n",
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" hdf:attribute <https://example.org#tmp0.hdf/contact@fname>,\n",
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" <https://example.org#tmp0.hdf/contact@hint>,\n",
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" <https://example.org#tmp0.hdf/contact@lname> ;\n",
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" hdf:name \"/contact\"^^xsd:string ;\n",
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" dcterms:relation <https://orcid.org/0000-0001-8729-0482> .\n",
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"\n",
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"<https://example.org#tmp0.hdf/contact@fname> a hdf:StringAttribute ;\n",
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" hdf:data \"Matthias\"^^xsd:string ;\n",
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" hdf:name \"fname\" .\n",
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"\n",
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"<https://example.org#tmp0.hdf/contact@hint> a hdf:StringAttribute ;\n",
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" hdf:data \"This group could be representing a person.\"^^xsd:string ;\n",
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" hdf:name \"hint\" .\n",
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"\n",
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"<https://example.org#tmp0.hdf/contact@lname> a hdf:StringAttribute ;\n",
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" hdf:data \"Probst\"^^xsd:string ;\n",
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" hdf:name \"lname\" .\n",
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"\n",
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"<https://example.org#tmp0.hdf/nd-array> a hdf:Dataset ;\n",
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" hdf:chunk <https://example.org#tmp0.hdf/nd-array__chunk_dimensions> ;\n",
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" hdf:dataspace <https://example.org#tmp0.hdf/nd-array__dataspace> ;\n",
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" hdf:datatype hdf:H5T_IEEE_F64LE,\n",
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" \"H5T_FLOAT\" ;\n",
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" hdf:layout hdf:H5D_CHUNKED ;\n",
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" hdf:maximumSize 6 ;\n",
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" hdf:name \"/nd-array\" ;\n",
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" hdf:rank 2 ;\n",
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" hdf:size 6 .\n",
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"\n",
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"<https://example.org#tmp0.hdf/nd-array__chunk_dimension_0> a hdf:DataspaceDimension ;\n",
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" hdf:dimensionIndex 0 ;\n",
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" hdf:size 1 .\n",
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"\n",
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"<https://example.org#tmp0.hdf/nd-array__chunk_dimension_1> a hdf:DataspaceDimension ;\n",
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" hdf:dimensionIndex 1 ;\n",
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" hdf:size 3 .\n",
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"\n",
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"<https://example.org#tmp0.hdf/nd-array__chunk_dimensions> a hdf:ChunkDimension ;\n",
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" hdf:dimension <https://example.org#tmp0.hdf/nd-array__chunk_dimension_0>,\n",
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" <https://example.org#tmp0.hdf/nd-array__chunk_dimension_1> .\n",
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"\n",
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"<https://example.org#tmp0.hdf/nd-array__dataspace> a hdf:SimpleDataspace ;\n",
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" hdf:dimension <https://example.org#tmp0.hdf/nd-array__dataspace_dimension_0>,\n",
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" <https://example.org#tmp0.hdf/nd-array__dataspace_dimension_1> .\n",
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"\n",
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"<https://example.org#tmp0.hdf/nd-array__dataspace_dimension_0> a hdf:DataspaceDimension ;\n",
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"\n",
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"<https://example.org#tmp0.hdf/nd-array__dataspace_dimension_1> a hdf:DataspaceDimension ;\n",
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"\n",
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"<https://example.org#tmp0.hdf/test> a hdf:Dataset ;\n",
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" hdf:dataspace <https://example.org#tmp0.hdf/test__dataspace> ;\n",
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" hdf:datatype hdf:H5T_IEEE_F64LE,\n",
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" \"H5T_FLOAT\" ;\n",
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" hdf:maximumSize -1 ;\n",
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" hdf:name \"/test\" ;\n",
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" hdf:value 4.3e+00 .\n",
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"\n",
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"<https://example.org#tmp0.hdf/test__dataspace> a hdf:ScalarDataspace .\n",
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"\n",
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"<https://orcid.org/0000-0001-8729-0482> a prov:Person ;\n",
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" foaf:firstName \"Matthias\"^^xsd:string ;\n",
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"hdf:H5T_IEEE_F64LE a hdf:Datatype .\n",
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]
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"outputs": [],
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"id": "ce1a26f6-ad59-4014-b5b2-dcee38f11a26",
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"Warning: When cdn_resources is 'local' jupyter notebook has issues displaying graphics on chrome/safari. Use cdn_resources='in_line' or cdn_resources='remote' if you have issues viewing graphics in a notebook.\n"
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"outputs": [],
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"pyvis_graph = subgraph.build_pyvis_graph(notebook=True, style=VIS_STYLE)\n",
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"{\n",
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" \"@context\": {\n",
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" \"dcterms\": \"http://purl.org/dc/terms/\",\n",
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" \"foaf\": \"http://xmlns.com/foaf/0.1/\",\n",
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"Warning: When cdn_resources is 'local' jupyter notebook has issues displaying graphics on chrome/safari. Use cdn_resources='in_line' or cdn_resources='remote' if you have issues viewing graphics in a notebook.\n"
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]
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"outputs": [],
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"version": "3.9.23"
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