ProjectsThatUseProtegeFtoK

Joint project between AMAL JYOTHI College of Engineering and Dr. M.G.R. University to support farm automation and agro-processing. Created a black pepper ontology for DataIndia.ORG.    (C49)

Applied Materials makes the tools that make the chips that make the Protege software run. We have 3000 field engineers working in bunny suits on our ~$1M tools worldwide. The FKM Project goals are (a) gather actual issue-cases from field engineers into KM system, (b) Diagnostic Drilldown Search to find existing cases, (c) experimenting with Bayesian drilldown - what test to do next based on cost, time, probability of success, (d) using Protege to build our Troubleshooting Ontology.    (5SX)

The aim of this project is to extract the regularities in the folksonomies created by user tagging on sites like del.icio.us. Social tagging is a new phenomenon which has recently been surrounded by a lot of noise. Many claim that they are superior to ontologies and that Semantic Web applications based on formal ontologies have been super ceded. My aim is to show that folksonomies and ontologies are not that different.    (5N3)

I am currently building a method for translating between folksonomy and ontology. This will be implemented in Protege. The link above points to my blog in which I discuss my ideas, and potential contributions to the Protege implementation are very welcome. Protege projects will be made available on that site.    (5N4)

An ontology and knowledgebase describing gene functions enabeling biologists to annotate (multiple) genes on Affymetrix Microarrays per simple drag and drop. Annotation-classes and genes (instances) can be linked for fast and intuitive context-exploration and extensive querying using relations and is_a subsumptions. Generated gene annotations can be explored as interactive semantic networks with advanced visualisation tools.    (5N7)

GOLD is an ontology for descriptive linguistics. It gives a formalized account of the most basic categories and relations used in the scientific description of human language. First and foremost, GOLD is intended to capture the knowledge of a well-trained linguist. It is an attempt to codify the general knowledge of the field. GOLD is aimed at facilitating automated reasoning over linguistic data and at establishing the basic concepts through which intelligent search can be carried out. Furthermore, GOLD is meant to be compatible with the general goals of the Semantic Web.    (5SZ)

The Generalized Upper Model (GUM) is a general task and domain independent `linguistically motivated ontology' intended for organizing information for expression in natural language. It is a descendent of the Penman Upper Model, originally developed by Bill Mann, Christian Matthiessen and others at the USC/ISI in Los Angeles. We are currently providing a full re-axiomatization of the Generalized Upper Model in OWL-DL using Protégé as the main development environment. The current ontology contains around 220 classes and 80 properties. Domain knowledge organized in terms of the GUM is known to be expressible in natural language and so forms a useful interface language for relating between applications and natural language technology. The GUM is a development of the Bremen Ontology Research Group.    (5N9)

Developing a next generation crop information platform which is very domain model and ontology driven. Protege is being incorporated as part of the strategy for ontology management on the project. We are also trying to couple Protege with other ontology systems, like the GMOD CV module. We are also working to directly integrate OWL/RDF with our Java-based platform, portions of which are using the Eclipse Rich Client Platform.    (5NB)

Dr. Richard Bruskiewich, Senior Scientist, Bioinformatics, International Rice Research Institute, (Principal Investigator: GCP domain modeling)    (5NC)

The multiplicity of Network Management models (SNMP, CMIP, DMI, CORBA, WBEM...) has posed in the last decade the set up of mechanisms to allow the interoperability among all involved management domains. One of the basic pillars of such interoperability is the mapping between the information models that each domain specifies. Usually, these mappings have been carried out with syntactical translations that do not bear in mind the semantic aspects of the defined information. These translations could reach the semantic level by using ontologies. These ontologies, widely used in Artificial Intelligence, exactly focus on the meaning of those concepts composing an information model. The goal of this project is the improvement of current network management interoperability techniques through the study and application of formal ontologies. They would eventually allow the specification of management information in an optimal way, obtaining the integration of all concepts that currently belongs to different management domains in the same model. One of the additional advantages of this approach is the ability of using the capacity of the ontologies to specify behavior for including it as part of the managed resources definitions, so that intelligent network managers can interpret these rules to perform management tasks.    (5NF)

In this way, the management information handling can be simplified, avoiding managers' current problems, which have to deal with independent information models for each domain, and without the possibility of setting up direct relationships between them.    (5NG)

The idea is to develop an ontology for the whole of the Ghana Tourism Industry.    (5NI)

This is a project to build a pilot knowledge base to serve a Service Management environment for Gist IT Service Delivery, the service support arm of Gist. That environment is in a state of evolution and migration to maximize utilization of best practice elements of ITIL (IT Infrastructure Library) and similar standards for customer and service management. Those standards are complimentary to international recommendations for process quality and service security.    (7SC)

GNU Classpath, Essential Libraries for Java, is a GNU project to create Free core class libraries for use with virtual machines and compilers for the java programming language. Protégé extensively uses Swing and multiple plugins, being an excellent (and also very serious) application to test. Protégé starts with Classpath 0.91 or CVS release, finds and loads plug-ins and it is possible to create ontologies with it. However more serious work reveals various instabilities and some features does not work as they probably should. As the GNU Classpath project is not yet complete, Protege on Classpath still is not yet ready for the end user, but it is interesing for the developers. See Protege entry in GNU Classpath Wiki    (7RO)

Multidisciplinary model-based water management projects have to follow a complex process and may encounter many problems, related to miscommunication, malpractice, misuse of the model, insufficient problem knowledge and overselling of model capabilities. This leads to model projects, which are not transparent and difficult to audit. The knowledge based system (KBS) discussed here provides guidelines on what to do, derived from an ontological knowledge base (KB) with state-of-the-art knowledge on 'best modelling practice' for teams, which members have different disciplinary backgrounds and play different roles in a project. Furthermore, the KBS monitors what team members actually do and helps in generating project reports for various audiences and purposes. Multimedia training material helps novice users to find their way in the KBS. The KBS is organized in a client-server architecture, enabling cooperation in distributed teams. The developers of this KBS learned that arriving at consensus on a process KB for model-based water management has an intrinsic value in itself. Professional users tested the KBS in two series of ten test cases, touching different types of problems and coping with a variety of environmental conditions across Europe. They like the KBS and their numerous comments have significantly improved the KBS. But they also expect that it will be hard to persuade the professional modelling community to use it.    (5NK)

The HarmonISA project uses Protege to model ontologies of land-use catalogues that are then used to provide semantic integration of land-use data.    (5NM)

HELEN is a framework for the whole life-cycle of clinical practice guidelines (CPGs). It provides both methods and tools for each step of the life-cycle. One of them is authoring, another one adaptation. For both steps we use Protege to easily create a user interface. Furthermore, we use a Protege ontology to represent CPGs and to export it to our own XML-based format.    (5SV)

Hermes is an human machine interface that allows users inexperienced in the image processing field to formulate their problem in their own terms. I use two ontologies for this project : one for the user with visual concepts to describe his images, the effects of the acquisition system, and his objectives of image transformation, the other ontology is made from an image processing viewpoint and permits the Hermes system to translate the user formulation in an image processing formulation for his application.    (5NP)

It is a research project as I work on this for my PhD. It is far to be efficient but the main goal of this work is to make explicit image processing knowledge used during application development. My home page is only in french at the moment. Translation into english will come soon.    (5NQ)

A Java-based platform for modelling and managing complex configuration data for various applications and systems.    (5NS)

The DiCo is French lexical database of semantic derivations (synonymy, antonymy, conversivity, standard names of actants/instruments/..., etc.) and collocations. In this project, we use semantic labels to tag each lexical unit described in the database. A semantic label can be seen as being the core (genus) of the definition of the lexical unit it is associated to, and is used as a classifying "semantic identifier" for that unit.    (5NU)

We make use of Protege as a tool for building, structuring, and accessing our hierarchy of semantic labels. Our methodology is data-driven and this hierarchy is developed together with the lexical database itself.    (5NV)

We use Protégé/OWL plugin for creating an ontology to represent knowledge relevant to data integration experiments to elucidate the relationship between the histone code, transcription activity, and DNA sequence. We see it as an experiment for the application of ontologies and semantic web technology for integration of biological data, and for learning how to best create useful OWL ontologies for computational (molecular) biology. For instance, we experiment with the use of upper ontologies from CO-ODE.    (840)

Histones are proteins that bind DNA to package the long DNA molecules. The proteins have a tail that can be chemically modified, there are distinct combinations of modifications. Consequently, histones along the DNA molecule form a code. The relationship of this code with gene expression and DNA sequence is poorly understood.    (841)

This work is funded by the Virtual Laboratory e-Science project in the Netherlands.    (842)

A Web-based system that models the the configuration, and applications to secure residences    (B1E)

HyBrow (Hypothesis Browser) system is a proof-of-concept, prototype tool for designing hypotheses and evaluating them for consistency with existing knowledge. HyBrow consists of a mathematical framework with the ability to represent diverse biological information sources, an ontology for describing biological processes at different levels of detail, a database to query information in the ontology, and programs to design, evaluate and revise hypotheses. HyBrow allows the integration of different types of biological information, such as gene expression data, gene and protein sequence homologies, as well as data on protein interactions and modifications for the purpose of evaluating alternative hypotheses about biological processes.    (5NY)

This vocabulary mapping project is one project within the Informatics for Integrating Biology and the Bedside (i2b2) initiative. It involves maintaining strict vocabulary control over a base hierarchy of concepts, using Protégé along with developing a new tool that can integrate with Protégé and allow mapping of other source terms to terms in the base hierarchy.    (5U9)

Development of a technical reference model for identity management for use with The Open Group Architecture Framework (TOGAF).    (5O0)

The Resource Aggregation Model for Learning Education and Training is a new activity within the IEEE Learning Technology Standards Committee (LTSC). This activity is defining a nomenclature and a conceptual model for digital aggregates of resources for learning, education, and training applications.    (5O2)

The project has the objective of increasing petroleum production from subsea systems by making accessible high quality real time information for decision support in operational centres onshore. An optimal set of real time data from reservoirs, wells and subsea production facilities will be identified, partially improved and integrated to provide an open and standardised information platform.    (5O4)

Integrated Knowledge Environment for development of PreAct knowledge bases.    (5O6)

INBIOMED is a Thematic Network of Cooperative Research about Biomedical Informatics funded by FIS (Health Investigation Found) of Institute Carlos III (Spain). In the technological context is the name of a storage, integration and clinical, genetics, epidemiology and images data analysis platform.    (5O8)

First an overview of insurance-related standards within the European countries participating to the eEG7 will be made. This overview can be completed with remaining European countries later on.    (5OB)

The focus will be initially on data standards, such as libraries and data models, and who is using them. Later on the overview should be extended with more technical standards such as internet protocols, XML etc.    (5OC)

INTEROP is a Network of Excellence supported by the European Commission for a three-year-period. INTEROP aims to create the conditions of an innovative and competitive research in the domain of Interoperability for Enterprise Applications and Software.    (8BU)

Uses Protégé-OWL with a GUI created by the CO-ODE group to develop a terminology for Anesthesia. It is a project originated by the Anesthetic Patient Safety Foundation (APSF) and the terms are submitted by IOTA for inclusion in SNOMED CT.    (5OE)

Creating a unified conceptual model used to integrate concepts and information about security, data privacy, and risks, as required by different methodologies and laws. This pilot project wants to explore the usage of Protege-OWL as a knowledge acquisition system, and a repository for company information. Financial sector, Italy.    (5SS)

Contact: mc at mcoletti dot net    (5ST)

This project is focused on development and support of a knowledge-based framework for integration and control to support research into individualized radiation therapy. This project builds on the EON project using protocol-based guidelines for process sequencing, data gathering, and decision support. Various existing systems to be integrated include medical image acquisition and analysis, treatment planning, and treatment delivery.    (5OG)

Contact: Daniel L. McShan (dlmcshan@umich.edu)    (5OH)

Affiliation: University of Michigan / Department of Radiation Oncology    (5OI)