DLite-Python 0.4.0

Lightweight data-centric framework for working with scientific data

DLite

A lightweight data-centric framework for semantic interoperability

DLite is a C implementation of the SINTEF Open Framework and Tools (SOFT), which is a set of concepts and tools for using data models (aka Metadata) to efficiently describe and work with scientific data.

The core of DLite is a framework for formalised representation of data described by data models (called Metadata or Entity in DLite). On top of this, DLite has a plugin system for various representations of the data in different formats and storages, as well as bindings to popular languages like Python, mappings to ontological concepts for enhanced semantics and a set of tools.

Documentation

The official documentation for DLite can be found on https://sintef.github.io/dlite/.

Installation

DLite is available on PyPI and can be installed with pip

pip install dlite-python[full]

The bracket [full] is optional, but ensures that you install all optional dependencies together with DLite. Without [full] you get a minimal DLite installation that only depends on NumPy. This would disable most storage plugins, except for the built-in "json", "bson" and "rdf" (when compiled against Redland librdf). For alternative installation methods, see the installation instructions.

Usage

All data in DLite is represented by a instance, which is described by a simple data model (aka Metadata). An Instance is identified by a unique UUID and have a set of named dimensions and properties. The dimensions are used to describe the shape of multi-dimensional properties.

DLite Metadata are identified by an URI and have an (optional) human readable description. Each dimension is given a name and description (optional) and each property is given a name, type, shape (optional), unit (optional) and description (optional). The shape of a property refers to the named dimensions. Foe example, a Metadata for a person serialised in YAML may look like:

uri: http://onto-ns.com/meta/0.1/Person
description: A person.
dimensions:
  nskills: Number of skills.
properties:
  name:
    type: string
    description: Full name.
  age:
    type: float32
    unit: year
    description: Age of person.
  skills:
    type: string
    shape: [nskills]
    description: List of skills.

Assume that you have file Person.yaml with this content. In Python, you can load this Metadata with

import dlite
Person = dlite.Instance.from_location("yaml", "Person.yaml", options="mode=r")

where the first argument is the "driver", i.e. the name of storage plugin to use for loading the Metadata. The options argument is optional. By providing "mode=r" you specify that the storage is opened in read-only mode.

You can verify that Person is a Metadata

>>> isinstance(Person, dlite.Metadata)
True

We can create an instance of Person with

homes = Person(
    dimensions={"nskills": 4},
    properties={
      "name": "Sherlock Homes",
      "skills": ["observing", "chemistry", "violin", "boxing"],
    }
)

The dimensions argument must be supplied when a Metadata is instantiated. It ensures that the shape of all properties are initialised consistently. The properties argument is optional. By specifying it, we initialise the properties to the provided values (otherwise, they will be initialised to zero).

In this case we didn't initialised the age

>>> homes.age
0.0
>>> homes.age = 34  # Assign the age

We can view (a JSON representation of) the instance with

>>> print(homes)
{
  "uuid": "314ac1ad-4a7e-477b-a56c-939121355112",
  "meta": "http://onto-ns.com/meta/0.1/Person",
  "dimensions": {
    "nskills": 4
  },
  "properties": {
    "Sherlock Holmes" {
      "age": 34.0,
      "skills": [
        "observing",
        "chemistry",
        "violin",
        "boxing"
      ]
    }
  }
}

The instance can also be stored using the save() method

homes.save("yaml", "homes.yaml", "mode=w")

which will produce the a YAML file with the following content

8cbd4c09-734d-4532-b35a-1e0dd5c3e8b5:
  meta: http://onto-ns.com/meta/0.1/Person
  dimensions:
    nskills: 4
  properties:
    Sherlock Holmes:
      age: 34.0
      skills:
      - observing
      - chemistry
      - violin
      - boxind

This was just a brief example. There is much more to DLite as will be revealed in the documentation.

License

DLite is licensed under the MIT license. However, it include a few third party source files with other permissive licenses. All of these should allow dynamic and static linking against open and propritary codes. A full list of included licenses can be found in LICENSES.txt.

Acknowledgment

In addition from internal funding from SINTEF and NTNU this work has been supported by several projects, including:

• AMPERE (2015-2020) funded by Forskningsrådet and Norwegian industry partners.
• FICAL (2015-2020) funded by Forskningsrådet and Norwegian industry partners.
• Rational alloy design (ALLDESIGN) (2018-2022) NTNU internally funded project.
• SFI Manufacturing (2015-2023) funded by Forskningsrådet and Norwegian industry partners.
• SFI PhysMet (2020-2028) funded by Forskningsrådet and Norwegian industry partners.
• OntoTrans (2020-2024) that receives funding from the European Union’s Horizon 2020 Research and Innovation Programme, under Grant Agreement n. 862136.
• OpenModel (2021-2025) that receives funding from the European Union’s Horizon 2020 Research and Innovation Programme, under Grant Agreement n. 953167.
• DOME 4.0 (2021-2025) that receives funding from the European Union’s Horizon 2020 Research and Innovation Programme, under Grant Agreement n. 953163.
• VIPCOAT (2021-2025) that receives funding from the European Union’s Horizon 2020 Research and Innovation Programme, under Grant Agreement n. 952903.
• MEDIATE (2022-2025) that receives funding from the RCN, Norway; FNR, Luxenburg; SMWK Germany via the M-era.net programme, project9557,
• MatCHMaker (2022-2026) that receives funding from the European Union’s Horizon 2020 Research and Innovation Programme, under Grant Agreement n. 101091687.

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DLite is developed with the hope that it will be a delight to work with.