update

README.md

@@ -7,17 +7,41 @@
 
 *Note, that the project is still under development!*
 
-The "HDF5 Research Data Management Toolbox" (h5RDMtoolbox) is a python package supporting everybody who is working with
-HDF5 to achieve a sustainable data lifecycle which follows
+The "HDF5 Research Data Management Toolbox" (h5RDMtoolbox) is a python package supporting everybody who is working 
+with HDF5 to achieve a sustainable data lifecycle which follows
 the [FAIR (Findable, Accessible, Interoperable, Reusable)](https://www.nature.com/articles/sdata201618)
-principles. It specifically supports the five main steps of
+principles. It specifically supports the five main steps of *planning*, *collecting*, *analyzing*, *sharing* and
+*reusing* data. Please visit the [documentation](https://h5rdmtoolbox.readthedocs.io/en/latest/) for detailed 
+information of try the [quickstart using colab](#quickstart).
 
-1. **Planning** (defining an internal layout for HDF5, a metadata convention or/and an ontology for attribute usage)
-2. **Collecting** data (creating HDF5 files with a convention in place supervising metadata usage)
-3. **Analyzing** and processing data (E.g. through interface with [xarray](https://docs.xarray.dev/en/stable/), ...)
-4. **Sharing data** (upload and download to repositories. Currently implemented: [Zenodo](https://zenodo.org/))
-5. **Reusing data** (Map metadata to dedicated databases like [mongoDB](https://www.mongodb.com/) or use local HDF5
-   files themselves as a database to search for attributes).
+
+
+[//]: # (1. **Planning** (defining an internal layout for HDF5, a metadata convention or/and an ontology for attribute usage))
+
+[//]: # (2. **Collecting** data (creating HDF5 files with a convention in place supervising metadata usage))
+
+[//]: # (3. **Analyzing** and processing data (E.g. through interface with [xarray](https://docs.xarray.dev/en/stable/), ...))
+
+[//]: # (4. **Sharing data** (upload and download to repositories. Currently implemented: [Zenodo](https://zenodo.org/)))
+
+[//]: # (5. **Reusing data** (Map metadata to dedicated databases like [mongoDB](https://www.mongodb.com/) or use local HDF5)
+
+[//]: # (   files themselves as a database to search for attributes).)
+
+
+## Highlights
+
+- Combining HDF5 and [xarray](https://docs.xarray.dev/en/stable/) to allow easy access to metadata and data during
+  analysis and processing (see [here](https://h5rdmtoolbox.readthedocs.io/en/latest/gettingstarted/quickoverview.html#datasets-xarray-interface).
+- Assigning [metadata with "globally unique and persistent identifiers"]() as required by [F1 of the FAIR 
+  principles](https://www.go-fair.org/fair-principles/f1-meta-data-assigned-globally-unique-persistent-identifiers/). 
+  This "remove[s] ambiguity in the meaning of your published data...".
+- Define standard attributes through 
+  [conventions](https://h5rdmtoolbox.readthedocs.io/en/latest/userguide/convention/index.html) and enforce users 
+  to use them
+- Upload HDF5 files directly to [repositories](https://h5rdmtoolbox.readthedocs.io/en/latest/userguide/repository/index.html)
+  like [Zenodo](https://zenodo.org/) or [use them with noSQL databases](https://h5rdmtoolbox.readthedocs.io/en/latest/userguide/database/index.html) like
+  [mongoDB](https://www.mongodb.com/).
 
 ## Who is the package for?
 For everybody, who is...
@@ -35,13 +59,6 @@ For everybody, who ...
 - ... has established conventions and managements approaches in his or her community
 
 
-## Highlights
-
-- Assigning [metadata with "globally unique and persistent identifiers"]() as required by [F1 of the FAIR 
-  principles](https://www.go-fair.org/fair-principles/f1-meta-data-assigned-globally-unique-persistent-identifiers/). 
-  This "remove[s] ambiguity in the meaning of your published data...".
-- To be completed...
-
 ## Package Architecture/structure
 
 The toolbox implements five modules, which are shown below. The numbers reference to their main usage in the stages in
@@ -79,7 +96,6 @@ on the image, which shows the research data lifecycle in the center and the resp
 
 A paper is published in the journal [inggrid](https://preprints.inggrid.org/repository/view/23/).
 
-<a href="https://h5rdmtoolbox.readthedocs.io/en/latest/"><img src="docs/_static/new_icon_with_text.svg" alt="RDM lifecycle" style="widht:600px;"></a>
 
 ## Installation
 

codemeta.json

@@ -4,7 +4,7 @@
     "license": "https://spdx.org/licenses/MIT",
     "codeRepository": "git+https://github.com/matthiasprobst/h5RDMtoolbox.git",
     "name": "h5RDMtoolbox",
-    "version": "1.1.0",
+    "version": "1.2.0",
     "description": "Supporting a FAIR Research Data lifecycle using Python and HDF5.",
     "applicationCategory": "Engineering",
     "programmingLanguage": [

docs/index.rst

@@ -16,10 +16,17 @@ with HDF5 to achieve a sustainable data lifecycle which follows the
 
 Highlights
 ----------
-- Assigning [metadata with "globally unique and persistent identifiers"]() as required by [F1 of the FAIR 
-  principles](https://www.go-fair.org/fair-principles/f1-meta-data-assigned-globally-unique-persistent-identifiers/). 
+- Combining HDF5 and [xarray](https://docs.xarray.dev/en/stable/) to allow easy access to metadata and data during
+  analysis and processing (see [here](https://h5rdmtoolbox.readthedocs.io/en/latest/gettingstarted/quickoverview.html#datasets-xarray-interface).
+- Assigning [metadata with "globally unique and persistent identifiers"]() as required by [F1 of the FAIR
+  principles](https://www.go-fair.org/fair-principles/f1-meta-data-assigned-globally-unique-persistent-identifiers/).
   This "remove[s] ambiguity in the meaning of your published data...".
-- To be completed...
+- Define standard attributes through
+  [conventions](https://h5rdmtoolbox.readthedocs.io/en/latest/userguide/convention/index.html) and enforce users
+  to use them
+- Upload HDF5 files directly to [repositories](https://h5rdmtoolbox.readthedocs.io/en/latest/userguide/repository/index.html)
+  like [Zenodo](https://zenodo.org/) or [use them with noSQL databases](https://h5rdmtoolbox.readthedocs.io/en/latest/userguide/database/index.html) like
+  [mongoDB](https://www.mongodb.com/).
 
 
 .. grid:: 3

docs/userguide/wrapper/FAIRAttributes.ipynb

@@ -9,7 +9,7 @@
     "\n",
     "According to [F1 of the *FAIR Principles*](https://www.go-fair.org/fair-principles/f1-meta-data-assigned-globally-unique-persistent-identifiers/) attributes shall be assigned to globally unique and persistent identifiers.\n",
     "\n",
-    "Here's what www.g-fair.org says about it:\n",
+    "Here's what www.go-fair.org says about it:\n",
     "\n",
     "*Globally unique and persistent identifiers remove ambiguity in the meaning of your published data by assigning a unique identifier to every element of metadata and every concept/measurement in your dataset. In this context, identifiers consist of an internet link (e.g., a URL that resolves to a web page that defines the concept such as a particular human protein). Many data repositories will automatically generate globally unique and persistent identifiers to deposited datasets. Identifiers can help other people understand exactly what you mean, and they allow computers to interpret your data in a meaningful way (i.e., computers that are searching for your data or trying to automatically integrate them). Identifiers are essential to the human-machine interoperation that is key to the vision of Open Science. In addition, identifiers will help others to properly cite your work when reusing your data.*\n",
     "\n",
@@ -31,9 +31,9 @@
     "Then, we can \"explain\" the data in the following way:\n",
     "- The *group \"contact\"* <u>is</u> **Person**\n",
     "- The *group \"contact\"* <u>has ORCiD</u> **\\<value\\>**\n",
-    "- The *dataset \"u\"* <u>hasUnit/u> **\"m/s\"**\n",
+    "- The *dataset \"u\"* <u>hasUnit</u> **\"m/s\"**\n",
     "- *\"m/s\"* <u>is</u> **\"https://qudt.org/vocab/unit/M-PER-SEC\"**\n",
-    "- The *dataset \"u\"* <u>has kind of quantity/u> **Velocity** (defined by qudt)\n",
+    "- The *dataset \"u\"* <u>has kind of quantity</u> **Velocity** (defined by qudt)\n",
     "- etc.\n",
     "\n",
     "Let's build such a file:"
@@ -54,7 +54,7 @@
    "id": "23f59915-a00a-4f30-b7d0-37f1b58aa6b5",
    "metadata": {},
    "source": [
-    "## Attribute-IRI-Association\n",
+    "## Associate IRI to attributes\n",
     "\n",
     "An IRI can be assigned during or after attribute creation. Various possibilities are shown below.\n",
     "\n",