ADF Data Package Ontology v1.5.3 RF

The Allotrope Data Format (ADF) [[!ADF]] consists of several APIs and taxonomies. This document constitutes the specification for the ADF Data Package Ontology (ADF-DPO) which defines the concepts for files, folders and their metadata. The ADF-DPO provides the vocabulary for the operations available by the ADF Data Package API [[!ADF-DP]].

Disclaimer

THESE MATERIALS ARE PROVIDED "AS IS" AND ALLOTROPE EXPRESSLY DISCLAIMS ALL WARRANTIES, EXPRESS, IMPLIED OR STATUTORY, INCLUDING, WITHOUT LIMITATION, THE WARRANTIES OF NON-INFRINGEMENT, TITLE, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.

Introduction

The Allotrope Data Format (ADF) defines an interface for experimental data generated in analytical laboratory processes. It is intended for data exchange, long-term preservation and fast real-time data access. The ADF Data Package API [[!ADF-DP]] defines an interface for storing files and folder structures and thus provides one of most essential operations of the ADF. The ADF Data Package Ontology (ADF-DPO) provides concepts and terms which are used by ADF Data Package API operations. The concepts of the ADF-DPO are also used to define consistency and integrity constraints on data files and meta-data during storage and modification.

The ontology will be available for downloaded from http://purl.allotrope.org/ontologies/datapackage .

The document is structured as follows: Next, the requirements for the ADF Data Package Ontology are listed before the key concepts of the ontology and the relation to other ontologies are described.

Document Conventions

Namespaces

Within the ADF specifications, the following namespace prefix bindings are used:

Prefix	Namespace
owl:	http://www.w3.org/2002/07/owl#
rdf:	http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs:	http://www.w3.org/2000/01/rdf-schema#
xsd:	http://www.w3.org/2001/XMLSchema#
skos:	http://www.w3.org/2004/02/skos/core#
dct:	http://purl.org/dc/terms/
ldp:	http://www.w3.org/ns/ldp#
hdf:	http://purl.allotrope.org/ontologies/hdf5/1.8#
adf-dp:	http://purl.allotrope.org/ontologies/datapackage#

Indication of Requirement Levels

Within this document the definitions of MUST, SHOULD and MAY are used as defined in [[!rfc2119]].

Number Formatting

Within this document, decimal numbers will use a dot "." as the decimal mark.

ADF High-Level Structure

The following figure illustrates the high-level structure of the Allotrope Data Format (ADF):

The high-level structure of the Allotrope Data Format (ADF) API stack.

This document focuses on the ADF Data Package Ontology, which is used by the ADF Data Package API [[ADF-DP]] highlighted in the figure above.

Requirements

The scope to the ADF Data Package Ontology is the description of the metadata of files and folders within an ADF Data Package. This includes:

provenance data description: who? what? when? where? and how?
security data description: access rights, file attributes (e.g. read-only/executable/directory/archive/hidden)
audit trail

ADF Data Package Ontology High-level Structure

The ADF Data Package Ontology imports external ontologies:

SKOS [[!SKOS]] for annotation properties such as preferred and alternative labels, definitions etc.
A subset of DC Terms [[!DC-TERMS]] is used for meta data descriptions such as title, description or modification and creation date.
Linked Data Platform (LDP) Vocabulary (described by [[LDP]]) in order to ease later publishing file content as linked data.

ADF Data Package Ontology high-level structure with imported ontologies.

ADF Data Package Ontology Concept Details

An overview of the ADF Data Package Ontology is given in the next figure (namespaces are given in parentheses, external ontologies are in grey).

ADF Data Package Ontology high-level structure.

The key concepts of the ADF Data Package Ontology are adf-dp:File and adf-dp:Folder which are both subclasses of adf-dp:Node. They are described in the following subsections. Detailed descriptions of the entire ontology can be found in [[!AF-OWL-DOC]].

Node

A node is a resource within the ADF Data Package.

For a node identifier, the name (title), creator and creation time MUST be specified. Modifier and modification time MAY be optionally specified.

File

A file is a node of information that is meant to store information electronically. The storage is durable in the way that the information is still available after the creating process has closed.

For a file, the same information as for a node is specified. Additionally, the file size, file format, the corresponding HDF5 dataset, the containing folder and - for text files - a line separator and character encoding MUST be specified.

Folder

A folder is a special kind of node within the file system that is meant to create a hierarchical structure of resources by connecting to parent and child nodes.

For a folder, the same information as for a node is specified. Additionally, the corresponding HDF5 group and the parent folder MUST be specified.

Change History

Version	Release Date	Remarks
0.4.0	2015-06-29	Initial Working Draft Version
1.0.0 RC	2015-09-17	Alignment with other ADF specifications Updated figure on ADF-DCO classes Added figure for ADF-DCO components Shortened list of requirements
1.0.0	2015-09-29	Updated versions, dates and document status Fixed broken reference
1.1.0 RC	2016-03-11	Updated versions, dates and document status Added section on number formatting to document conventions Updated Fig. 1
1.1.0 RF	2016-03-31	Updated versions, dates and document status
1.1.5	2016-05-13	Updated versions and dates
1.2.0 Preview	2016-09-23	Updated versions and dates
1.2.0 RC	2016-12-07	Updated versions and dates
1.3.0 Preview	2017-03-31	Updated versions and dates
1.3.0 RF	2017-06-30	Updated versions and dates Updated images
1.4.3 RC	2018-10-11	Updated versions and dates
1.4.5 RF	2018-12-17	Updated versions and dates
1.5.0 RC	2019-12-12	Updated versions and dates
1.5.0 RF	2020-03-24	Updated HDF5 reference link Added overwritten images
1.5.3 RF	2020-11-30	Updated broken reference links Updated PURL and DOCS server links to relative links Reformat the document header