CiteULike: leechuck's library [111 articles]

Philosophische Untersuchungen zu Raum, Zeit und Kontinuum

Franz Brentano — 2008-08-06T10:37:44-00:00

(1976)

Combining Evidence, Specificity, and Proximity towards the Normalization of Gene Ontology Terms in Text.

S Gaudan — 2008-06-03T09:54:50-00:00

EURASIP journal on bioinformatics & systems biology (2008)

Structured information provided by manual annotation of proteins with Gene Ontology concepts represents a high-quality reliable data source for the research community. However, a limited scope of proteins is annotated due to the amount of human resources required to fully annotate each individual gene product from the literature. We introduce a novel method for automatic identification of GO terms in natural language text. The method takes into consideration several features: (1) the evidence for a GO term given by the words occurring in text, (2) the proximity between the words, and (3) the specificity of the GO terms based on their information content. The method has been evaluated on the BioCreAtIvE corpus and has been compared to current state of the art methods. The precision reached 0.34 at a recall of 0.34 for the identified terms at rank 1. In our analysis, we observe that the identification of GO terms in the "cellular component" subbranch of GO is more accurate than for terms from the other two subbranches. This observation is explained by the average number of words forming the terminology over the different subbranches.

The Ontological Level

Nicola Guarino — 2007-08-25T19:10:53-00:00

(1994)

In 1979, Ron Brachman discussed... In this paper I argue against this neutrality, claiming that a rigorous ontological foundation for knowledge representation can improve the quality of the knowledge engineering process, making it easier to build at least understandable (if not reusable) knowledge bases. We contrast the notion of formal ontology, intended as a theory of the a priori forms and natures of objects, to that of (formal) epistemology, intended as a theory of meaning connections...

The Construction of Social Reality

John Searle — 2005-06-14T01:24:39-00:00

(01 January 1997)

Information Flow : The Logic of Distributed Systems

Jon Barwise — 2005-11-02T00:24:04-00:00

(1997)

On semantic interoperability and the flow of information

M Schorlemmer — 2006-09-01T09:13:32-00:00

(2003)

We discuss current approaches that, for the sake of automation, provide formal treatments to the problem of semantic interoperability and integration, and we reflect upon the suitability of the Barwise-Seligman theory of information flow as a candidate for a theoretical framework that favours the analysis and implementation of semantic interoperability scenarios.

BOWiki -- a collaborative annotation and ontology curation framework

Michael Backhaus — 2008-02-07T13:39:56-00:00

Non-lexical approaches to identifying associative relations in the gene ontology.

O Bodenreider — 2007-11-20T15:43:52-00:00

Pac Symp Biocomput (2005), pp. 91-102.

The Gene Ontology (GO) is a controlled vocabulary widely used for the annotation of gene products. GO is organized in three hierarchies for molecular functions, cellular components, and biological processes but no relations are provided among terms across hierarchies. The objective of this study is to investigate three non-lexical approaches to identifying such associative relations in GO and compare them among themselves and to lexical approaches. The three approaches are: computing similarity in a vector space model, statistical analysis of co-occurrence of GO terms in annotation databases, and association rule mining. Five annotation databases (FlyBase, the Human subset of GOA, MGI, SGD, and WormBase) are used in this study. A total of 7,665 associations were identified by at least one of the three non-lexical approaches. Of these, 12% were identified by more than one approach. While there are almost 6,000 lexical relations among GO terms, only 203 associations were identified by both non-lexical and lexical approaches. The associations identified in this study could serve as the starting point for adding associative relations across hierarchies to GO, but would require manual curation. The application to quality assurance of annotation databases is also discussed.

Towards a top-domain ontology for linking biomedical ontologies.

H Stenzhorn — 2008-01-04T13:00:48-00:00

Medinfo, Vol. 12, No. Pt 2. (2007), pp. 1225-1229.

In this paper we present the ongoing development and extension work on BioTop--a top-domain ontology for linking biomedical domain ontologies. We start by making the case for the application of a common ontology to interface independent biomedical domain ontologies by introducing a set of more general classes. Then we briefly depict the relation of BioTop to the GENIA ontology as starting point of its initial developement. Afterwards we propose our distinction of ontologies into top, top-domain and domain ones and describe our approach to the integration of the top ontology BFO into BioTop. Then we present our plans to join the OBO and OBO Foundry repository of ontologies and list its admission principles in relation to our ontology. Some actual BioTop interface classes are shown subsequently. We conclude by detailing on some planned BioTop usages in the area of BioNLP and cancer research and show some further intended improvements.

Granularity, scale and collectivity: When size does and does not matter

Alan Rector — 2008-01-04T10:56:35-00:00

Journal of Biomedical Informatics, Vol. 39, No. 3. (June 2006), pp. 333-349.

Bridging levels of "granularity" and "scale" are frequently cited as key problems for biomedical informatics. However, detailed accounts of what is meant by these terms are sparse in the literature. We argue for distinguishing two notions: "size range," which deals with physical size, and "collectivity," which deals with aggregations of individuals into collections, which have emergent properties and effects. We further distinguish these notions from "specialisation," "degree of detail," "density," and "connectivity." We argue that the notion of "collectivity"--molecules in water, cells in tissues, people in crowds, stars in galaxies--has been neglected but is a key to representing biological notions, that it is a pervasive notion across size ranges--micro, macro, cosmological, etc.--and that it provides an account of a number of troublesome issues including the most important cases of when the biomedical notion of parthood is, or is not, best represented by a transitive relation. Although examples are taken from biomedicine, we believe these notions to have wider application.

Towards Ontologically Based Semantics for UML Constructs

Joerg Evermann — 2007-12-11T15:42:08-00:00

(2001), pp. 354-367.

An Ontologically Well-Founded Profile for UML Conceptual Models

Giancarlo Guizzardi — 2007-12-04T08:46:57-00:00

Advanced Information Systems Engineering (2004), pp. 112-126.

UML class diagrams can be used as a language for expressing a conceptual model of a domain. In a series of papers [1,2,3] we have been using the General Ontological Language (GOL) and its underlying upper level ontology, proposed in [4,5], to evaluate the ontological correctness of a conceptual UML class model and to develop guidelines for how the constructs of the UML should be used in conceptual modeling. In this paper, we focus on the UML metaconcepts of classes and objects from an ontological point of view. We use a philosophically and psychologically well-founded theory of classifiers to propose a UML profile for Ontology Representation and Conceptual Modeling. Moreover, we propose a design pattern based on this profile to target a recurrent problem in role modeling discussed in the literature. Finally, we demonstrate the relevance of the tools proposed by applying them to solve recurrent problems in the practice of conceptual modeling.

A Meta-ontological Architecture for Foundational Ontologies

Heinrich Herre — 2007-12-03T12:33:34-00:00

On the Move to Meaningful Internet Systems 2005: CoopIS, DOA, and ODBASE (2005), pp. 1398-1415.

In this paper we present and discuss a meta-ontological architecture for ontologies which centers on abstract core ontologies (ACOs). An ACO is the most abstract part of a foundational ontology. It is useful for an ontologically founded description of ontologies themselves, therefore ACOs are lifted to the meta-level. We propose a three-layered meta-ontological architecture which distinguishes an object level comprising foundational, generic or domain-specific ontologies, a meta-level with abstract core ontologies, and a meta-meta-level employing abstract top ontologies for the formalization of the underlying levels. Moreover, two axiomatic fragments for ACOs are provided, one of which is applied to formal concept lattices [1]. This demonstrates the use of ACOs for the ontological foundation of representation formalisms and illustrates advantages in comparison to the usual direct formal reduction to set theory. Finally, related work with respect to the architecture is briefly discussed.

Formal Ontology and Information Systems

Nicola Guarino — 2007-12-03T12:13:36-00:00

(1998), pp. 3-15.

Domain-Specific Concepts and Ontological Reduction within a Data Dictionary Framework

Barbara Heller — 2007-12-03T09:40:09-00:00

Data Integration in the Life Sciences (2004), pp. 47-62.

This paper describes a new method for the ontologically based standardization of concepts in the medical domain. As an application of this method we developed a data dictionary which firstly focused on trial-specific context-dependent concepts and relations. The data dictionary has been provided to different medical research networks via the internet by means of the software tool Onto-Builder. It is based on an architecture which includes terminologies, domain-specific ontologies and the top-level categories of GOLGeneral Ontological Language is a formal framework for building ontologies. GOL is being developed by the Onto-Med Research Group at the University of Leipzig [http://www.onto-med.de].. According to our approach top-level concepts are used to build definitions of domain-specific concepts on a firm ground through the process of ontological reduction, which is currently under development and the main ideas of which are outlined in this paper.

In the Defense of a Trope-Based Ontology for Conceptual Modeling: An Example with the Foundations of Attributes, Weak Entities and Datatypes

G Guizzardi — 2007-11-23T14:36:30-00:00

(2006)

In the Defense of Ontological Foundations for Conceptual Modeling

N Guarino — 2007-11-23T14:31:05-00:00

Scandinavian Journal of Information Systems, Vol. 18, No. 1. (2006)

Towards Ontological Foundations for UML Conceptual Models

Giancarlo Guizzardi — 2007-11-23T14:27:06-00:00

(2002), pp. 1100-1117.

On the General Ontological Foundations of Conceptual Modeling

Giancarlo Guizzardi — 2007-11-23T14:24:27-00:00

(2002), pp. 65-78.

Ontological Foundations for Structural Conceptual Models

Giancarlo Guizzardi — 2007-11-23T14:22:00-00:00

Vol. 015 (2005)

Theoretical foundations for conceptual modelling in information systems development

Yair Wand — 2006-07-17T16:16:59-00:00

Decision Support Systems, Vol. 15, No. 4. (December 1995), pp. 285-304.

Conceptual modelling in information systems development is the creation of an enterprise model for the purpose of designing the information system. It is an important aspect of systems analysis. The value of a conceptual modelling language (CML) lies in its ability to capture the relevant knowledge about a domain. To determine which constructs should be included in a CML it would be beneficial to use some theoretical guidelines. However, this is usually not done. The purpose of this paper is to promote the idea that theories related to human knowledge can be used as foundations for conceptual modelling in systems development. We suggest the use of ontology, concept theory, and speech act theory. These approaches were chosen because: (1) they deal with important and different aspects relevant to conceptual modelling and (2) they have already been used in the context of systems analysis. For each approach we discuss: the rationale for its use, its principles, its application to conceptual modelling, and its limitations. We also demonstrate the concepts of the three approaches by analysing an example. The analysis also serves to show how each approach deals with different aspects of modelling.

Overview of BioCreAtIvE: critical assessment of information extraction for biology.

L Hirschman — 2006-04-21T22:25:04-00:00

BMC Bioinformatics, Vol. 6 Suppl 1 (2005)

BACKGROUND: The goal of the first BioCreAtIvE challenge (Critical Assessment of Information Extraction in Biology) was to provide a set of common evaluation tasks to assess the state of the art for text mining applied to biological problems. The results were presented in a workshop held in Granada, Spain March 28-31, 2004. The articles collected in this BMC Bioinformatics supplement entitled "A critical assessment of text mining methods in molecular biology" describe the BioCreAtIvE tasks, systems, results and their independent evaluation. RESULTS: BioCreAtIvE focused on two tasks. The first dealt with extraction of gene or protein names from text, and their mapping into standardized gene identifiers for three model organism databases (fly, mouse, yeast). The second task addressed issues of functional annotation, requiring systems to identify specific text passages that supported Gene Ontology annotations for specific proteins, given full text articles. CONCLUSION: The first BioCreAtIvE assessment achieved a high level of international participation (27 groups from 10 countries). The assessment provided state-of-the-art performance results for a basic task (gene name finding and normalization), where the best systems achieved a balanced 80% precision / recall or better, which potentially makes them suitable for real applications in biology. The results for the advanced task (functional annotation from free text) were significantly lower, demonstrating the current limitations of text-mining approaches where knowledge extrapolation and interpretation are required. In addition, an important contribution of BioCreAtIvE has been the creation and release of training and test data sets for both tasks. There are 22 articles in this special issue, including six that provide analyses of results or data quality for the data sets, including a novel inter-annotator consistency assessment for the test set used in task 2.

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

Barry Smith — 2007-11-08T02:21:16-00:00

Nat Biotech, Vol. 25, No. 11. (November 2007), pp. 1251-1255.

OntoWiki - A Tool for Social, Semantic Collaboration

Sören Auer — 2007-03-10T20:40:14-00:00

The 5th International Semantic Web Conference (ISWC 2006), Vol. 4273 (2006), pp. 736-749.

We present OntoWiki, a tool providing support for agile, distributed knowledge engineering scenarios. OntoWiki facilitates the visual presentation of a knowledge base as an information map, with different views on instance data. It enables intuitive authoring of semantic content, with an inline editing mode for editing RDF content, similar to WYSIWYG for text documents. It fosters social collaboration aspects by keeping track of changes, allowing to comment and discuss every single part of a knowledge base, enabling to rate and measure the popularity of content and honoring the activity of users. Ontowiki enhances the browsing and retrieval by offering semantic enhanced search strategies. All these techniques are applied with the ultimate goal of decreasing the entrance barrier for projects and domain experts to collaborate using semantic technologies. In the spirit of the Web 2.0 OntoWiki implements an ”architecture of participation” that allows users to add value to the application as they use it. It is available as open-source software and a demonstration platform can be accessed at http://3ba.se

Abstract vs. social roles –- Towards a general theoretical account of roles

Frank Loebe — 2007-10-29T18:20:56-00:00

Applied Ontology, Vol. 2, No. 2. (2007), pp. 127-158.

Semantic foundations of medical information systems based on top-level ontologies

H Herre — 2007-10-29T10:25:08-00:00

Knowledge-Based Systems, Vol. 19, No. 2. (June 2006), pp. 107-115.

The modeling of knowledge and its implementation in software systems is not sufficiently supported by proper guidelines and well-established principles. An interdisciplinary approach seems to be necessary because the development of guidelines for sound knowledge modeling--in particular in medicine--requires expertise from areas such as linguistics, informatics, medicine, cognitive science and philosophy. In the present paper, we discuss relevant aspects of such an approach and outline some results of the work of the research group Onto-Med. In particular, we expound a methodology, which supports the semantic foundation of medical information systems by using top-level ontologies.

Defining N-ary Relations on the Semantic Web

Natasha Noy — 2007-10-26T12:23:18-00:00

(12 April 2006)

A logic for default reasoning

R Reiter — 2007-05-22T19:18:22-00:00

Artificial Intelligence, Vol. 13, No. 2. (1980), pp. 81-132.

A novel method for automatic functional annotation of proteins

W Fleischmann — 2007-10-25T13:03:58-00:00

Bioinformatics, Vol. 15, No. 3. (1 March 1999), pp. 228-233.

10.1093/bioinformatics/15.3.228

DLP and FaCT

Peter Patel-Schneider — 2005-10-07T08:57:52-00:00

(1999), pp. 19-23.

FaCT++ Description Logic Reasoner: System Description

Dmitry Tsarkov — 2007-10-23T07:03:16-00:00

Automated Reasoning (2006), pp. 292-297.

This is a system description of the Description Logic reasoner FaCT++. The reasoner implements a tableaux decision procedure for the well known description logic, with additional support for datatypes, including strings and integers. The system employs a wide range of performance enhancing optimisations, including both standard techniques (such as absorption and model merging) and newly developed ones (such as ordering heuristics and taxonomic classification). FaCT++ can, via the standard DIG interface, be used to provide reasoning services for ontology engineering tools supporting the OWL DL ontology language.

Representing default knowledge in biomedical ontologies: Application to the integration of anatomy and phenotype ontologies

Robert Hoehndorf — 2007-10-09T12:09:59-00:00

BMC Bioinformatics, Vol. 8, No. 1. (2007)

BACKGROUND:Current efforts within the biomedical ontology community focus on achieving interoperability between various biomedical ontologies that cover a range of diverse domains. Achieving this interoperability will contribute to the creation of a rich knowledge base that can be used for querying, as well as generating and testing novel hypotheses. The OBO Foundry principles, as applied to a number of biomedical ontologies, are designed to facilitate this interoperability. However, semantic extensions are required to meet the OBO Foundry interoperability goals. Inconsistencies may arise when ontologies of properties - mostly phenotype ontologies - are combined with ontologies taking a canonical view of a domain - such as many anatomical ontologies. Currently, there is no support for a correct and consistent integration of such ontologies.RESULTS:We have developed a methodology for accurately representing canonical domain ontologies within the OBO Foundry. This is achieved by adding an extension to the semantics for relationships in the biomedical ontologies that allows for treating canonical information as default. Conclusions drawn from default knowledge may be revoked when additional information becomes available. We show how this extension can be used to achieve interoperability between ontologies, and further allows for the inclusion of more knowledge within them. We apply the formalism to ontologies of mouse anatomy and mammalian phenotypes in order to demonstrate the approach.CONCLUSION:Biomedical ontologies require a new class of relations that can be used in conjunction with default knowledge, thereby extending those currently in use. The inclusion of default knowledge is necessary in order to ensure interoperability between ontologies.

Clinical Methods: The History, Physical and Laboratory Examinations

Kenneth Walker — 2005-01-20T00:29:54-00:00

(1990)

Wright on Functions

Christopher Boorse — 2007-08-13T12:35:00-00:00

The Philosophical Review, Vol. 85, No. 1. (1976), pp. 70-86.

Functions: Consensus without Unity

Peter Godfrey-Smith — 2007-08-13T12:30:56-00:00

Pacific Philosophical Quarterly, Vol. 74 (1993), pp. 196-208.

Language, Thought and Other Biological Categories: New Foundations for Realism

Ruth Millikan — 2007-08-13T11:46:41-00:00

(1984)

Functions

Larry Wright — 2007-08-13T09:06:09-00:00

The Philosophical Review, Vol. 82, No. 2. (1973), pp. 139-168.

WonderWeb Deliverable D17. The WonderWeb Library of Foundational Ontologies and the DOLCE ontology

Claudio Masolo — 2007-01-12T15:26:28-00:00

entities ............................................................................................................. 13 2.3 Basic functions and relations ..................................................... 13 Parthood and Temporary Parthood ...................................................................................... 14 Dependence and Spatial Dependence ................................................................................... 14 Constitution...

HyBrow: a prototype system for computer-aided hypothesis evaluation.

SA Racunas — 2005-07-04T13:59:39-00:00

Bioinformatics, Vol. 20 Suppl 1 (4 August 2004)

MOTIVATION: Experimental design, hypothesis-testing and model-building in the current data-rich environment require the biologists' to collect, evaluate and integrate large amounts of information of many disparate kinds. Developing a unified framework for the representation and conceptual integration of biological data and processes is a major challenge in bioinformatics because of the variety of available data and the different levels of detail at which biological processes can be considered. RESULTS: We have developed the HyBrow (Hypothesis Browser) system as a prototype bioinformatics tool for designing hypotheses and evaluating them for consistency with existing knowledge. HyBrow consists of a modeling framework with the ability to accommodate diverse biological information sources, an event-based ontology for representing biological processes at different levels of detail, a database to query information in the ontology and programs to perform hypothesis design and evaluation. We demonstrate the HyBrow prototype using the galactose gene network in Saccharomyces cerevisiae as our test system, and evaluate alternative hypotheses for consistency with stored information. AVAILABILITY: www.hybrow.org

Abstract vs. Social Roles: A Refined Top-Level Ontological Analysis

Frank Loebe — 2007-08-12T10:54:19-00:00

(2005)

BFO in a Nutshell: A Bi-categorial Axiomatization of BFO and Comparison with DOLCE

Pierre Grenon — 2007-08-12T10:49:56-00:00

(June 2003)

The OBO to OWL mapping, GO to OWL 1.1!

Christine Golbreich — 2007-08-12T10:39:03-00:00

(2007)

GALEN: a third generation terminology tool to support a multipurpose national coding system for surgical procedures

B Trombert-Paviot — 2005-08-25T08:39:29-00:00

International Journal of Medical Informatics, Vol. 58-59 (1 September 2000), pp. 71-85.

Generalised architecture for languages, encyclopaedias and nomenclatures in medicine (GALEN) has developed a new generation of terminology tools based on a language independent model describing the semantics and allowing computer processing and multiple reuses as well as natural language understanding systems applications to facilitate the sharing and maintaining of consistent medical knowledge. During the European Union 4 Th. framework program project GALEN-IN-USE and later on within two contracts with the national health authorities we applied the modelling and the tools to the development of a new multipurpose coding system for surgical procedures named CCAM in a minority language country, France. On one hand, we contributed to a language independent knowledge repository and multilingual semantic dictionaries for multicultural Europe. On the other hand, we support the traditional process for creating a new coding system in medicine which is very much labour consuming by artificial intelligence tools using a medically oriented recursive ontology and natural language processing. We used an integrated software named CLAW (for classification workbench) to process French professional medical language rubrics produced by the national colleges of surgeons domain experts into intermediate dissections and to the Grail reference ontology model representation. From this language independent concept model representation, on one hand, we generate with the LNAT natural language generator controlled French natural language to support the finalisation of the linguistic labels (first generation) in relation with the meanings of the conceptual system structure. On the other hand, the Claw classification manager proves to be very powerful to retrieve the initial domain experts rubrics list with different categories of concepts (second generation) within a semantic structured representation (third generation) bridge to the electronic patient record detailed terminology.

dlvhex: A System for Integrating Multiple Semantics in an Answer-Set Programming Framework

Thomas Eiter — 2007-08-10T12:56:05-00:00

(2006), pp. 206-210.

Nonmonotonic Reasoning

Grigoris Antoniou — 2006-04-09T01:52:49-00:00

(04 April 1997)

Nonmonotonic reasoning provides formal methods that enable intelligent systems to operate adequately when faced with incomplete or changing information. In particular, it provides rigorous mechanisms for taking back conclusions that, in the presence of new information, turn out to be wrong and for deriving new, alternative conclusions instead. Nonmonotonic reasoning methods provide rigor similar to that of classical reasoning; they form a base for validation and verification and therefore increase confidence in intelligent systems that work with incomplete and changing information.<br /> <br /> Following a brief introduction to the concepts of predicate logic that are needed in the subsequent chapters, this book presents an in depth treatment of default logic. Other subjects covered include the major approaches of autoepistemic logic and circumscription, belief revision and its relationship to nonmonotonic inference, and briefly, the stable and well-founded semantics of logic programs.

A reference ontology for biomedical informatics: the foundational model of anatomy

Cornelius Rosse — 2007-08-10T12:53:31-00:00

J. of Biomedical Informatics, Vol. 36, No. 6. (December 2003), pp. 478-500.

The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information.

CL Smith — 2007-04-20T13:30:11-00:00

Genome Biol, Vol. 6, No. 1. (2005)

The Mammalian Phenotype (MP) Ontology enables robust annotation of mammalian phenotypes in the context of mutations, quantitative trait loci and strains that are used as models of human biology and disease. The MP Ontology supports different levels and richness of phenotypic knowledge and flexible annotations to individual genotypes. It continues to develop dynamically via collaborative input from research groups, mutagenesis consortia, and biological domain experts. The MP Ontology is currently used by the Mouse Genome Database and Rat Genome Database to represent phenotypic data.

Faceted Information Representation

U Priss — 2006-12-11T14:12:23-00:00

(2000)

This paper presents an abstract formalization of the notion of "facets".

Autopoiesis and Cognition : The Realization of the Living (Boston Studies in the Philosophy of Science)

HR Maturana — 2006-01-08T06:19:03-00:00

(31 August 1991)

What makes a living system a living system? What kind of biological phenomenon is the phenomenon of cognition? These two questions have been frequently considered, but, in this volume, the authors consider them as concrete biological questions. Their analysis is bold and provocative, for the authors have constructed a systematic theoretical biology which attempts to define living systems not as objects of observation and description, nor even as interacting systems, but as self-contained unities whose only reference is to themselves. The consequence of their investigations and of their living systems as self-making, self-referring autonomous unities, is that they discovered that the two questions have a common answer: living systems are cognitive systems, and living as a process is a process of cognition. The result of their investigations is a completely new perspective of biological (human) phenomena. During the investigations, it was found that a complete linguistic description pertaining to the ‘organization of the living’ was lacking and, in fact, was hampering the reporting of results. Hence, the authors have coined the word ‘autopoiesis’ to replace the expression ‘circular organization’. Autopoiesis conveys, by itself, the central feature of the organization of the living, which is autonomy.

OWL Web Ontology Language Overview

2007-08-10T12:48:24-00:00

(10 February 2004)