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Ontology Ecosystem
The SWAN project makes use of the "SWAN ontology" [1]. This ontology, which was originally organized in a single block, has been modularized to foster reusability and integration with other existing ontologies in a software ecosystem. Thus, when we refer to the SWAN ontology, we refer to the collection of ontologies used by our software ecosystem to create, manage and share SWAN knowledge bases. In general, an ontology, together with a set of instances of its classes, constitutes a knowledge base.
A SWAN knowledge base is a database collecting knowledge about scientific discourse in one particular domain (for example Alzheimer diesease). It is organized in RDF triples and its structure is specified by the SWAN ontology.
SWAN Ontology v. 1.2 (release candidate) - last updated on Jan 17th, 2009
The SWAN ontology version 1.2 is at the stage of "release candidate" and the final realease is planned for before the end of the year 2008. It will be characterized by a significant revision of the swan ontologies v. 1.1. It will also include a new module that will focus on provenance, authoring and versioning.
Basics
These are a set of ontologies that can be easily reused in other contexts. They don't have any dependecies from any other modules.
| Our implementation of FOAF in OWL-DL | v. 1.2 | spec | owl | final draft | Our OWL-DL version of a subset of the FOAF Vocabulary. The Friend of a Friend (FOAF) project is creating a Web of machine-readable pages describing people, the links between them and the things they create and do. It defines an open, decentralized technology for connecting social Web sites, and the people they describe. |
| Provenance, authoring and versioning | v. 1.0 | spec | owl | final draft | It provides all the relationships that we need for defining provenance, authoring and versioning. For application that are heavily based on integration of data from different sources, it is really important to be able to keep track of data provenance and authoring. |
| Collections | v. 1.2 | spec | owl | final draft | Defines a vocabulary for unordered (Set) and ordered collections (List) |
| Scientific Discourse Relationships | v. 1.0 | spec | owl | final draft | It provides a set of relationships that can be used to build discourse and in particular scientific discourse. |
| Reification | v. 1.0 | spec | owl | final draft | It provides a vocabulary for defining reified relationships. |
Agents
The Agents ontology has been created as an extension of the FOAF (Friend Of A Friend) vocabulary. It makes use of the basics ontologies for defining provenance and collections of agents.
| Agents | v. 1.2 | spec | owl | final draft | Defines software agents, person names and list of agents. |
Scientific Discourse Ontology
| Scientific DIscourse | v. 1.2 | spec | owl | final draft | Defines the life science entities and the related records. |
Qualifiers
The "Qualifiers" mechanism has been introduced for performing entities annotation through controlled vocabularies.
| Our implementation of SKOS in OWL-DL | v. 1.0 | spec | owl | draft | Our OWL-DL version of a subset of the SKOS (Simple Knowledge Organization System) vocabulary. |
| Qualifiers | v. 1.0 | spec | owl | final draft | It provides basic mechanisms (qualifiers) for defining organized terms for performing tagging using controlled vocabularies. It can make use of SKOS. |
SWAN Commons
SWAN Commons is a general purpose distribution of our ontology.
| SWAN Commons Ontology | v. 1.2 | spec | owl | draft | A distribution of the SWAN ontology which includes all the modules and the extensions that can be used by any application managing scientific discourse. |
| Included Modules: | |||||
| Citations | v. 1.2 | spec | owl | draft | Defines the citations records. |
| Life Science Entities | v. 1.2 | spec | owl | final draft | Defines the life science entities and the related records. |
| Research Statements Qualifiers | v. 1.2 | spec | owl | final draft | Research Statements qualifiers controlled vocabulary (SKOS based). |
| Gene Ontology Connector | v. 1.0 | spec | owl | final draft | Defines the Gene Ontology connector for the Life Science Emtities ontology. |
SWAN Alzheimer
SWAN Alzheimer is the distribution of our ontology in use in the SWAN Alzheimer application (Beta).
| SWAN Alzheimer Ontology | v. 1.2 | spec | owl | draft | A distribution of the SWAN ontology which includes the SWAN Commons distribution and the extensions used in the SWAN Alzheimer application. |
| Included Modules: | |||||
| Pathogenic Narrative Qualifiers | v. 1.2 | spec | owl | final draft | Pathogenic Narrative qualifiers controlled vocabulary (SKOS based). |
| Mechanisms Taxonomy Qualifiers | v. 1.2 | spec | owl | final draft | Taxonomy of mechanisms for qualifying Research Statements (SKOS based). |
| Nature Stem Cells Cheat Sheet | v. 0.5 | spec | owl | draft | Nature Stem Cells Cheat Sheet (SKOS based). |
Collaborations on ontologies development and ontologies integration
» SWAN and SIOC ontologies integration - For providing a Semantic Web platform for biomedical discourse which can be evolved over time into a more general facility for many types of scientific discourse, and which is linked to key biological categories specified by ontologies. The SIOC initiative (Semantically-Interlinked Online Communities) aims to enable the integration of online community information. SIOC provides a Semantic Web ontology for representing rich data from the Social Web in RDF. More information here: Semantic Web for Health Care and Life Sciences Interest Group @ W3C
» SWAN ontologies in SCF - For sharing out suite of ontology with SCF with the vision of enabling interoperability in between the two software environments. The Science Collaboration Framework (SCF) is reusable software that can be used to develop web-based, collaborative, scientific communities. The framework is designed to support interdisciplinary scientists in publishing, annotating, sharing and discussing content such as articles, perspectives, interviews and news items, as well as assert personal biographies and research interests - the basics of any online community.
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