Beginner's Guide to RDF
Date: (Created) 17 February 2012; (Last modified) 19 Feb 2014
Document Status: Not part of any standard (Type 3 document)
Permanent URL: http://code.google.com/p/tdwg-rdf/wiki/Beginners
TDWG Task Group: TDWG RDF/OWL Task Group
Contributors: Steve Baskauf (TDWG RDF/OWL Task Group)
Abstract: This document provides concise information about topics related to RDF and OWL in the context of the biodiversity informatics community. It is intended as an introduction for persons who are not already familiar with RDF and OWL and as a reference for persons who are familiar but would like organized access to additional reference material.
Licensed under Creative Commons Attribution 3.0 License
Table of Contents:
0. Introduction (this page)
Beginner's guide to RDF: 0. Introduction
The purpose of this guide is to provide concise information about topics related to RDF and OWL which are significant to the work of the TDWG RDF/OWL Task Group (RDF/OWL TG) in particular and to the biodiversity informatics community in general. It is intended as an introduction for persons who are not already familiar with RDF and OWL and as a reference for persons who are familiar but would like organized access to additional reference material. Although it is intended that the information provided be correct, because it is intended as an introduction the amount of technical jargon and formal language has been kept to a minimum. For those who are interested in normative descriptions of the concepts and technologies discussed here, footnotes are provided to hyperlinks to more detailed information.
It should also be noted that in almost every instance, the URIs that are used in the examples are "real" URIs (no fake "example.org" URIs) from the wild which in most cases will actually dereference (at least in the case of HTTP URIs and LSIDs). This is not to imply that there is something special about those URIs or that the examples that they provide are a model of any sort, but rather it is to give the reader an opportunity to actually try out the tools that have been provided for validating, describing, browsing, etc.
The guide is laid out into sections, each of which deals with a major issue relevant to the work of the RDF/OWL TG. This allows users who wish to access the guide as a reference to jump quickly to the point of interest. However, the later sections presuppose knowledge of concepts discussed in earlier sections, so a beginner may have difficulty starting at a later section.
Within each section, subsections are laid out hierarchically and linked in a Table of Contents at the top of the section page. At the end of each section is a numbered reference list which is also linked to the Table of Contents as well as the actual references in the text.
A beginner who wants to gain a basic understanding of RDF and OWL should start with section 1 and work through the guide sequentially. However, it is not intended that this guide be a tutorial capable of enabling a beginner to write RDF or OWL. Consulting additional references will undoubtedly be required.
0.3 Significant documents, tools, and RDF implementations
The mention of any document or tool in this guide does not imply the endorsement of TDWG or the RDF/OWL TG. (The exception to this is ratified TDWG standards which are official recommendations of TDWG.) The referenced items below are simply ones which have been found to be helpful. The lists are not exhaustive; resources may be added when discovered or removed if they cease to be available.
An important general reference is Architecture of the World Wide Web, a W3C Recommendation.
The document Linked Data: Evolving the Web into a Global Data Space provides a general overview of Linked Data issues and implementation strategies.
See also a list of design issues intended to avoid repetition of discussions once resolved.
Information Standards Quarterly had a special issue (Vol. 24, No. 2/3, doi:10.3789/isqv24n2-3.2012 devoted to Linked Data in Libraries, Archives, and Museums.
0.3.1. Related to Uniform Resource Identifier (URI) and GUID/Persistent Identifier
Best Practice Recipes for Publishing RDF Vocabularies (content negotiation and URI dereferencing)
Jones et al. 2011. Identifying and relating biological concepts in the Catalogue of Life. Journal of Biomedical Semantics 2011,2:7. doi:10.1186/2041-1480-2-7
To locate DOIs for titles (books, monographs, or whole journal runs) in the Biodiversity Heritage Library (BHL), locate the title through searching, then access the URL
[title_number] is the BHL-assigned identifying number for the title. Currently, BHL does not assign DOIs to individual articles unless they happen to correspond to a monograph.
DOIs can be exported en masse through BHLs data export at http://biodivlib.wikispaces.com/Data+Exports and are exposed at the BHL API and OpenURL resolver http://biodivlib.wikispaces.com/Developer+Tools+and+API .
Thanks to Rod Page and Chris Freeland for this information.
0.3.2. Related to the Resource Description Framework (RDF) model
W3C Interest Group note: Mapping and linking life science data using RDF (Thanks to Hilmar Lapp for providing the link.)
Early draft of expressing Darwin Core taxonomies in SKOS (Thomas Bandholtz)
Open Annotation Core Data Model (for creating associations between distant pieces of information)
0.3.3. Related to the Dublin Core Metadata Initiative (DCMI) Abstract Model
0.3.4. Related to Web Ontology Language (OWL)
Some rule-based extensions to OWL/SPARQL/RDF
0.3.5. Software tools
See also http://www.w3.org/RDF/ for a listing of tools relevant to RDF
mx - a Ruby-based platform that consists of a Ruby on Rails application and various supporting gems/libraries developed as a collaborative web-based content management system for biodiversity informatics.
0.3.6. Web interfaces
Rod Page's OpenURL Resolver which can be used to proxy some identifiers as HTTP URIs which return RDF Paper: "bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics" doi:10.1186/1471-2105-10-S14-S5
0.3.7. Biodiversity-related and General vocabularies and ontologies
Australian Plant Name Index (APNI) vocabulary (in RDF)
Library of Congress Authorities and Vocabularies: ISO639 languages, MARC countries and geographic areas (Use view page source: ISO639, MARC geographic areas, etc. in RDF)
Natural Collections Descriptions (NCD) draft TDWG Standard (PDF non-normative document viewable in browser) (PDF normative document viewable in browser) (Collection in RDF) (Institution in RDF) (InstitutionType in RDF) (ContactDetails in RDF)
OBO foundry (http://www.obofoundry.org/ ) ontologies:
Basic Formal Ontology (BFO) http://www.ifomis.org/bfo . Includes definition of "process" and "material entity".
Environment Ontology (EnvO) http://www.environmentontology.org/ . Includes definition of "biome" and "environmental feature".
Information Artifact Ontology (IAO) http://code.google.com/p/information-artifact-ontology/ . Includes definition of "information content entity" and "data item".
Population and Community Ontology (PCO) http://code.google.com/p/popcomm-ontology/ (http://code.google.com/p/popcomm-ontology/source/browse/trunk/pco.owl view OWL as RDF]). Includes definition of "species", "population", "species", and "community".
Taxonomic Concept Transfer Schema (TCS) (TDWG Standard) (Users Guide PDF viewable in browser) (XML schema details PDF viewable in browser) (TaxonConcept in RDF) (TaxonName in RDF) (Common in RDF) Journal of Biomedical Semantics 2:7 article on application of LSIDs and TCS at Catalogue of Life
0.3.8. Biodiversity-related RDF in the wild
Questions? Comments? Contact Steve Baskauf