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Last modified: January 23, 2002
XOL - XML-Based Ontology Exchange Language

XOL is a language for ontology exchange. It is "designed to provide a format for exchanging ontology definitions among a set of interested parties. The ontology definitions that XOL is designed to encode include both schema information (meta-data), such as class definitions from object databases -- as well as non-schema information (ground facts) , such as object definitions from object databases. XOL is similar to other past ontology-exchange languages; its development was inspired by Ontolingua and OML. XOL differs from Ontolingua in having an XML-based syntax rather than a Lisp-based syntax; the semantics of OKBC-Lite are extremely similar to the semantics of Ontolingua. XOL differs from OML in that the semantics of OML are based on Conceptual Graphs, which have a number of differences from OKBC-Lite."

"The syntax of XOL is based on XML, which is a language for authoring documents for the WWW. XML syntax was chosen because it is reasonably simple to parse, its syntax is well defined, it is human readable, it appears that XML will be very widely used, and because it appears that many software tools for parsing and manipulating XML will soon be appearing. The semantics of XOL are based on OKBC-Lite, which is a simplified form of the knowledge model for the OKBC (Open Knowledge Base Connectivity.) OKBC is an API (application program interface) for accessing frame knowledge representation systems. Its knowledge model supports features most commonly found in knowledge representation systems, object databases, and relational databases. OKBC-Lite extracts most of the essential features of OKBC, while not including some of the more complex aspects of OKBC. XOL is a language for exchange of ontologies. By exchange language, we mean that XOL is intended to be used as an intermediate language for transferring ontologies among different database systems, ontology-development tools, or application programs. For example, a group developing a scientific database might use the Oracle DBMS to actually implement the DB. However, that group could translate the DBMS schema from SQL into XOL, and then publish the resulting file on the WWW for reference by users of the database, or by other groups who are developing similar databases. They might convert their schema into XOL using an existing SQL-to-XOL translator. Or, if that group used an object-level graphical tool to design their DBMS schema, such as a UML-based tool, they might employ a pre-existing UML-to-XOL translator to translate the schema into XOL." [based upon a Version 0.3 description from Peter D. Karp, Vinay K. Chaudhri and Jerome Thomere, July 1999]

From the Summary of the first report by the Molecular Biology Ontology Working Group: "Over the last two decades, the knowledge representation and object-oriented database communities have developed a number of languages that may be used for the expression of semantic database models. These languages share many elements in common, and are exemplified by the frame knowledge representation systems used in the knowledge representation community. Frame systems have been used in many different bioinformatics projects, and the authors believe that frame systems provide the necessary representational constructs to model ontologies for molecular biology. Furthermore, frame systems have a significant amount of history and use, so that they provide a stable representational paradigm. The authors also believe that the explosion of the web and the languages associated with it simply cannot be ignored. Acceptance of an exchange language that is expressed in a Lisp syntax will be limited within the bioinformatics community, even though the underlying representational system may be identical to that expressed in a web-based language. For this reason the authors believe that an XML-based syntax must be used for a bioinformatics ontology exchange language to increase the likelihood that the language will see widespread acceptance. In summary, the results of this evaluation suggest two directions for future work: development of an XML expression for the Ontolingua model, or adapting OML/CKML to include a frame-based semantic model... The authors support the use of a frame-based exchange language using an XML syntax. Several researchers on the evaluation team are currently developing a specification of XML expression of Ontolingua using OKBC. A separate set of researchers on the team are pursuing a frame-based version of OML. The exchange language evaluation team will meet again to consider the question of whether either, or both, of these efforts provide an acceptable exchange language that meets the groups requirements."


  • Molecular Biology Ontology Working Group

  • XOL Specification - "an OKBC-friendly, XML-based ontology exchange language." July, 1999, version 0.3. In .DOC/Word format. [local archive copy]

  • XOL Spec 0.3, HTML Format

  • "An Evaluation of Ontology Exchange Languages for Bioinformatics." First report of the Molecular Biology Ontology Working Group. By: Robin McEntire (SB), Peter Karp (Pangea Systems), Neil Abernethy (InGenuity), Frank Olken (LBNL), Robert E. Kent (WSU), Matt DeJongh (NetGenics), Peter Tarczy-Hornoch (U of Washington, Seattle), David Benton (SB), Dhiraj Pathak (GW), Gregg Helt (UC Berkeley), Suzanna Lewis (UC Berkeley), Anthony Kosky (GeneLogic), Eric Neumann (NetGenics), Dan Hodnett (NetGenics), Luca Toldo (Merck KGaA), Thodoros Topaloglou (GeneLogic). Abstract: "Ontologies are specifications of the concepts in a given field and the relationships among those concepts. The development of ontologies for molecular-biology information and the sharing of those ontologies within the bioinformatics community are central problems in bioinformatics. If the bioinformatics community is to share ontologies effectively, ontologies must be exchanged in a form that uses standardized syntax and semantics. This paper reports on an effort among the authors to evaluate a number of alternative ontology-exchange languages, and to recommend one or more languages for use within the larger bioinformatics community. The study selected a set of candidate languages, and defined a set of capabilities that the ideal ontology-exchange language should satisfy. The study scored the languages according to the degree to which they provided each capability. In addition, the authors performed several ontology-exchange experiments with the two languages that received the highest scores: OML and Ontolingua. The result of those experiments, and the main conclusions of this study, was that the frame-based semantic model of Ontolingua is preferable to the conceptual graph model of OML, but that the XML-based syntax of OML is preferable to the Lisp-based syntax of Ontolingua." In .DOC/Word format. [local archive copy]

  • Ontology Exchange Report, HTML Format

  • Stanford Medical Informatics (SMI) Home Page

  • [November 25, 2000] "Relating Ontology Languages and Web Standards." By Dieter Fensel. In J. Ebert et al. [eds.], Modelle und Modellierungssprachen in Informatik und Wirtschaftsinformatik, Modellierung 2000, St. Goar, April 5-7, 2000, Foelbach Verlag, Koblenz, 2000. 18 pages, with 34 references. "Currently computers are changing from single isolated devices to entry points in a world wide network of information exchange and business transactions called the World Wide Web (WWW). Therefore support in data, information, and knowledge exchange becomes the key issue in current computer technology. Ontologies provide a shared and common understanding of a domain that can be communicated between people and application systems. Therefore, they may play a major role in supporting information exchange processes in various areas. However, in order to develope their full power, the representation languages for ontologies must be compartible with existing data exchange standards in the World Wide Web. In this paper we investigate protoypical examples of ontology languages and web languages. Finally we show how these web standards can be used as a representation languages for ontologies... Ontologies are formal theories about a certain domain of discourse and therefore require a formal logical language to express them. The paper will discuss languages for describing ontologies in Section 2. In Section 3 we will investigate how recent web standards such as XML and RDF can be used as languages for expressing Ontologies, or at least some of their aspects. Finally, in Section 4 we will discuss XOL, a proposal for an XML-based standard for expressing ontologies. Section 3: XML, RDF, and Ontology Languages In the following we will examine how XML and RDF can be used to express ontologies... More details and further aspects of ontology to DTD translations can be found in [references]. In a nutshell, DTDs are rather weak in regard to what can be expressed with them. Work on XML-schemes may well contribute to bridging the gap between DTDs and ontologies. Schemes will be introducing: mechanisms for constraining document structure and content, mechanisms to enable inheritance for element, attribute, and data type definitions, mechanisms for application-specific constraints and descriptions, mechanisms to enable the integration of structural schemes with primitive data types, primitive data typing, including byte, date, integer, sequence, etc., and they shall allow creation of user-defined data types. Up to now we have discussed the mapping from ontologies to DTDs. [WeId 1999] discuss a mapping from DTDs to an ontological representation. [They] want to provide the reasoning service of description logic to query and manipulate XML documents. DTDs are therefore translated automatically into a representation of an ontology in description logic. This ontology simply consists of each element in the DTD. The taxonomy can be derived by the classifier of the description logic CLASSIC based on the use of entities and the type attributes... XOL shows how many aspects of an ontology can be represented in XML. However, important aspects which are lacking are rules and constraints (i.e., class definitions). They are often a significant part of the knowledge provided by an ontology, and XOL does not provide support for their representation. Besides XOL, RDF provide a proposal for specifying ontologies. However, many design decisions in RDF are rather particular. Properties are defined globally, violating all modeling experiences from object-oriented and frame-based approaches that define attributes locally for classes. RDF provides powerful reification, i.e., expressions can become terms in meta-level expressions. This makes reasoning service for RDF rather tricky. Most description logics do not provide such a service. Finally, RDF also does not provide a means for defining constraints and rules which allow us to specify information intensionally. Currently, there are initiatives to define a proper Ontology Interchange Language (OIL) that overcomes these shortcomings..." See also: M. Klein, D. Fensel, F. van Harmelen, and I. Horrocks, "The relation between ontologies and schema-languages: Translating OIL-specifications in XML-Schema." In Proceedings of the Workshop on Applications of Ontologies and Problem-solving Methods, 14th European Conference on Artificial Intelligence ECAI'00, Berlin, Germany August 20-25, 2000. [cache]

  • See also: "Ontology and Conceptual Knowledge Markup Languages."

  • See also: Ontolingua Ontology Editor (Stanford KSL Network Services)

  • See also: 'Ongoing KBS/Ontology Projects and Groups'

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