This document outlines a roadmap for making BioPortal, an ontology repository, more multilingual. It proposes representing the natural language of ontologies, distinguishing between monolingual and multilingual ontologies, and representing relations between translated ontologies. It also discusses reconciling multilingual mappings and representing multilingual content overall. Making BioPortal multilingual could enable new discoveries by connecting data in different languages and addressing cultural differences reflected in language. Some challenges include dealing with partial multilingual ontologies and multiple mappings between terms. The proposals aim to better support multilingual ontologies, translations, and mappings within BioPortal.
This document discusses ontology and vocabulary management technologies in France. It describes challenges for ontology repositories, including metadata, evaluation, multilingual support, ontology alignment, scalability and interoperability. Two collaborative projects are highlighted that reuse NCBO ontology repository technology: SIFR BioPortal for French biomedical ontologies and AgroPortal for agronomy. Shared technology visions are proposed, with ontology repositories working together through a unified open source platform to support multiple domains. Open questions remain around long-term support, the European Open Science Cloud, and France's role in this area.
Ontology selection in repositories like AgroPortal and BioPortal can be done through browsing ontologies by category or metadata search. Users can define metadata for their own ontologies to aid discovery. The ontology recommender system can also suggest related ontologies. Evaluation of ontologies is challenging due to the large number and variety of ontologies in different formats and complexity levels for various user needs. Careful selection is important to avoid issues with missing relevant information or connections between data.
The document discusses developing an extension of the DCAT2 metadata vocabulary called MOD2 to describe semantic artifacts. MOD2 would extend DCAT2's classes of Resource and Dataset to have a new SemanticArtifact class. This would specialize the Distribution class to capture metadata about different formats and versions of semantic artifacts. The goal is to have a standardized way of describing semantic resources like ontologies and thesauri in order to make them more FAIR. Key issues discussed include how to model SemanticArtifact and Distribution classes and which existing metadata properties from DCAT2 and other vocabularies should be included in the MOD2 profile.
This document outlines a roadmap for making BioPortal, an ontology repository, more multilingual. It proposes representing the natural language of ontologies, distinguishing between monolingual and multilingual ontologies, and representing relations between translated ontologies. It also discusses reconciling multilingual mappings and representing multilingual content overall. Making BioPortal multilingual could enable new discoveries by connecting data in different languages and addressing cultural differences reflected in language. Some challenges include dealing with partial multilingual ontologies and multiple mappings between terms. The proposals aim to better support multilingual ontologies, translations, and mappings within BioPortal.
This document discusses ontology and vocabulary management technologies in France. It describes challenges for ontology repositories, including metadata, evaluation, multilingual support, ontology alignment, scalability and interoperability. Two collaborative projects are highlighted that reuse NCBO ontology repository technology: SIFR BioPortal for French biomedical ontologies and AgroPortal for agronomy. Shared technology visions are proposed, with ontology repositories working together through a unified open source platform to support multiple domains. Open questions remain around long-term support, the European Open Science Cloud, and France's role in this area.
Ontology selection in repositories like AgroPortal and BioPortal can be done through browsing ontologies by category or metadata search. Users can define metadata for their own ontologies to aid discovery. The ontology recommender system can also suggest related ontologies. Evaluation of ontologies is challenging due to the large number and variety of ontologies in different formats and complexity levels for various user needs. Careful selection is important to avoid issues with missing relevant information or connections between data.
The document discusses developing an extension of the DCAT2 metadata vocabulary called MOD2 to describe semantic artifacts. MOD2 would extend DCAT2's classes of Resource and Dataset to have a new SemanticArtifact class. This would specialize the Distribution class to capture metadata about different formats and versions of semantic artifacts. The goal is to have a standardized way of describing semantic resources like ontologies and thesauri in order to make them more FAIR. Key issues discussed include how to model SemanticArtifact and Distribution classes and which existing metadata properties from DCAT2 and other vocabularies should be included in the MOD2 profile.
FAIR data requires FAIR ontologies and standards. There has been an explosion in the number of ontologies but they are difficult to identify and manage due to a lack of consistent metadata. Existing ontology metadata practices were reviewed, finding that developers use various metadata vocabularies inconsistently and important ontology-specific metadata is underused. Ontology repositories help make ontologies more FAIR by providing interfaces for publishing, accessing, and reusing ontologies and their metadata. The presentation focuses on the NCBO BioPortal as an example ontology repository and how its technologies have been adopted by other repositories. Improving ontology metadata will help comprehension of the ontology landscape; a new AgroPortal metadata model was created to better describe ontologies and their
FAIR data requires FAIR ontologies, how do we do?EUDAT
This document discusses making ontologies FAIR (Findable, Accessible, Interoperable, Reusable) through the use of ontology repositories. It provides examples of existing repositories like NCBO BioPortal and how they help standardize ontologies and make them more discoverable and reusable. The document also describes related projects that are reusing NCBO's technology like AgroPortal for agricultural ontologies and SIFR for French biomedical ontologies and terminologies. Key challenges discussed are scaling repositories to many domains and large numbers of ontologies while maintaining features and curation.
This document describes Clement Jonquet's presentation at SIMBig'17 in Lima, Peru on September 6th 2017. It discusses two collaborative projects involving ontology repositories and ontology-based services. It highlights challenges for ontology repositories, including better use of ontology metadata, multilingual support, alignment of ontologies, and scaling to multiple domains as the number and variety of ontologies increases. The document also provides details on the NCBO BioPortal and AgroPortal projects, which aim to make biomedical and agricultural ontologies more accessible and reusable.
A Comparative Study Ontology Building Tools for Semantic Web Applications IJwest
This document provides a comparative study of four popular ontology building tools: Protégé 3.4, IsaViz, Apollo, and SWOOP. It discusses the features and functionalities of each tool, including their capabilities for ontology editing, browsing, documentation, import/export of formats, and visualization. The document aims to identify existing ontology tools that are freely available and can be used to develop ontologies for various application domains such as transport, tourism, health, and natural language. It evaluates the tools based on criteria like interoperability, openness, ease of updating/maintaining ontologies, and market penetration.
Workshop on Learning Technology Standards for Agriculture and Rural Development (AgroLT 2008)
September 19, 2008, Athens, Greece
In conjunction with
4th International Conference on Information and Communication Technologies in Bio and Earth Sciences (HAICTA 2008)
The document discusses ontology alignment, which is the process of finding correspondences between concepts in different ontologies to allow them to be used together. It notes that there is no single unified ontology, so alignment helps integrate overlapping conceptualizations. The key constructs for expressing alignments are relations like equivalence and subclass between concepts. Techniques discussed for finding mappings include string-based, linguistic/language-based, taxonomy comparison, and using example instances. The challenges of alignment evaluation and interpretation of results are also covered.
This document provides an overview of the evolution of 3GPP UMTS/HSPA mobile broadband technology. It discusses the progress and commercial deployment of earlier 3GPP releases such as Release 99, Release 5, and Release 6. It then focuses on Release 7, describing enhancements like MIMO for HSDPA, IMS/core network updates, and improved RAN capabilities. Looking ahead, it outlines the 3GPP work on developing a new radio interface and system architecture through initiatives like SAE, HSPA+, and LTE to support rapidly growing IP data traffic over the next decade with peak rates above 100 Mbps.
Ontology Building and its Application using HozoKouji Kozaki
The document provides information about an upcoming tutorial on ontology building and its applications using the Hozo ontology development tool. The tutorial will take place on November 9th, 2014 in Chiang Mai, Thailand and will cover how to build ontologies using Hozo, some characteristic functions of Hozo, and examples of ontology-based application developments. The tutorial agenda outlines the topics to be covered in each time block, including hands-on experience building ontologies with Hozo.
For efficient and innovative use of big data, it is important to integrate multiple data bases across domains. For example, various public data bases are developed in life science, and how to find a novel scientific result using them is an essential technique. In social and business areas, open data strategies in many countries promote diversity of public data, how to combine big data and open data is a big challenge. That is, diversity of dataset is a problem to be solved for big data.
Ontology gives a systematized knowledge to integrate multiple datasets across domains with semantics of them. Linked Data also provides techniques to interlink datasets based on semantic web technologies. We consider that combinations of ontology and Linked Data based on ontological engineering can contribute to solution of diversity problem in big data.
In this talk, I discuss how ontological engineering could be applied to big data with some trial examples.
Yang Yu is proposing research on improving machine learning based ontology mapping by automatically obtaining training samples from the web. The proposed system would parse two input ontologies to generate queries to search engines and collect documents to use as samples for each ontology class. These samples would then be used to train text classifiers, which would produce probabilistic mappings between classes in the two ontologies. The results would be evaluated by comparing to mappings from human experts. Current work involves exploring alternative text classification tools and ways to utilize the probabilistic mapping values generated by the classifiers.
Supporting User's Exploration of Digital Libraries, Suedl 2012 workshop proce...pathsproject
Workshop proceedings from the International workshop on Supporting Users Exploration of Digital Libraries, SUEDL 2012 which was held at TPDL 2012 (the international conference on Theory and Practice in Digital Libraries), Paphos, Cyprus, September 2012.
The aim of the workshop was to stimulate collaboration from experts and stakeholders in Digital Libraries, Cultural Heritage, Natural Language Processing and Information Retrieval in order to explore methods and strategies to support exploration of Digital Libraries, beyond the white box paradigm of search and click.
The proceedings includes:
"Browsing Europeana - Opportunities and Challenges', David Haskiya
"Query re-writing using shallow language processing effects', Anna Mastora and Sarantos Kapidakis
"Visualising Television Heritage" Johan Ooman et al,
"Providing suitable information access for new users of Digital Libraries", Rike Brecht et al
"Exploring Pelagios: a Visual Browser for Geo-tagged datasets" Rainer Simon et al
Eurogene is an e-learning system in the domain of genetics that provides free multimedia learning resources in nine languages for statistical, medical and molecular genetics and delivers them to students and professionals. The Eurogene content includes presentations, reviewed research articles, images, videos and learning packages submitted by world-leading geneticists.
An essential part of the Eurogene system is a multilingual search engine that allows to search for content in one language while retrieving the results in other languages. This is complemented by the use of a machine translation system fine-tuned for genetic terminology. The search engine uses a query language similar to PubMed.
Eurogene also aims at providing intelligent ways of navigation through the e-Learning system. As new learning resources are being continuously submitted to the system, it is not possible to maintain links between them manually. Eurogene automatically links resources that are semantically similar using natural language processing.
The document summarizes a seminar on ontology mapping presented by Samhati Soor. The seminar covered the need for ontology mapping due to the proliferation of ontologies, and the purpose of mapping ontologies to achieve interoperability and sharing knowledge. It defined ontologies and ontology mapping and discussed categories of mapping including between global and local ontologies, between local ontologies, and for merging ontologies. Tools for ontology mapping discussed included GLUE and SAM. Evaluation criteria and challenges of ontology mapping were also summarized along with conclusions and references.
ONTOLOGY VISUALIZATION PROTÉGÉ TOOLS – A REVIEW ijait
The document discusses ontology visualization tools in Protégé. It reviews four main visualization methods used in Protégé tools: indented list, node-link and tree, zoomable, and focus+context. It then examines specific Protégé tools that use each method, including their key features and limitations. The tools assessed are Protégé Class Browser (indented list), Protégé OntoViz and OntoSphere (node-link and tree), Jambalaya (zoomable), and Protégé TGVizTab (focus+context). The document concludes by summarizing and comparing the visualization characteristics of these Protégé tools.
Conférence donéée au LGI2P (Conférence Communication Science et Société) à Nimes le 17 mars 2015. Contenu en partie produit par le travail de Juan Antonio Lossio Ventura.
EdReNe brings together members from webbased repositories of learning resources with content owners and other stakeholders within education.
We share, develop and document strategies, experiences and solutions on the organisation, structuring and functionality of repositories. The overall goal is to improve the provision of and access to learning resources.
The document discusses the need to develop services to facilitate the long-term interpretation of archived data through the use of semantic artifacts like ontologies. It notes that semantic artifacts must themselves be archived long-term using repositories that deal with format heterogeneity and versioning over time. The talk then describes an open-source ontology repository called OntoPortal and its use in projects like AgroPortal for agronomy and SIFR BioPortal for French biomedical data. OntoPortal alliances are working to synchronize development and improve ontology repositories and uptake of semantic technologies.
EdReNe is a European network that aims to connect providers and users of educational resources through repositories. It brings together members from repositories, content owners, and other stakeholders. EdReNe identifies key issues for repositories through workshops, develops recommendations, and shares best practices. Its goals are to improve access, use, and sharing of educational resources across Europe.
EdReNe is a European network focused on improving access to learning resources through educational repositories. The network brings together repository providers and stakeholders to share strategies and best practices. EdReNe aims to address challenges around connecting users and content providers, establish quality frameworks, and make recommendations to optimize access and use of learning resources across repositories. The network holds workshops and seminars to facilitate collaboration and outputs guides and documentation on its website.
B2NOTE is a semantic annotation service that allows adding additional information to data elements without changing the original data. It indexes over 5 million concepts from biomedical ontologies to facilitate semantic annotations. The presenter discusses expanding this approach to other domains by indexing more semantic resources. There are challenges around discoverability, interoperability, and metadata standards for semantic resources across domains. An EUDAT working group is developing a proof-of-concept semantic lookup service to register, aggregate, and provide analytics on multi-disciplinary semantic resources to help address these issues. Continued community support is needed to further develop semantic services and standards with broader disciplinary coverage.
PhD presentation for the public defense of the dissertation entitled 'Bridging the gap between Open and User Innovation? Exploring the value of Living Labs as a means to structure user contribution and manage distributed innovation.' This was a joint PhD between Ghent University and the VUB.
Promotors:Prof. dr. Lieven De Marez, Universiteit Gent, Faculteit Politieke & Sociale Wetenschappen, vakgroep Communicatiewetenschappen and Prof. dr. Pieter Ballon, Vrije Universiteit Brussel, Faculteit Economische en Sociale Wetenschappen, vakgroep Communicatiewetenschappen
President of the jury:
Prof. dr. Gino Verleye, Universiteit Gent
Jury:
Prof. dr. Pieter Verdegem, Universiteit Gent
Prof. dr. Marcel Bogers, Associate Professorat Mads Clausen Institute, Faculty of Engineering, University of Southern Denmark
Prof. dr. Esteve Almirall, Profesor Asociado at ESADE Business & Law School
Prof. dr. Seppo Leminen, Principal lecturer at Laurea University of Applied Sciences & Adjunct Professor at Aalto University School of Economics
CDAO presentation.
The idea of the comparative analysis ontoloty has been presented worldwide, including: NESCent (USA), IGBMC (France), UFRJ (Brazil). Providing a semantic framework for evolutionary analysis in a high-throughtput way after the next and third generation sequencing is the way to approach evolutionary-based studies into genome-wide analysis. The darwinian core of reasoning also allows CDAO to be used with other entities.
FAIR data requires FAIR ontologies and standards. There has been an explosion in the number of ontologies but they are difficult to identify and manage due to a lack of consistent metadata. Existing ontology metadata practices were reviewed, finding that developers use various metadata vocabularies inconsistently and important ontology-specific metadata is underused. Ontology repositories help make ontologies more FAIR by providing interfaces for publishing, accessing, and reusing ontologies and their metadata. The presentation focuses on the NCBO BioPortal as an example ontology repository and how its technologies have been adopted by other repositories. Improving ontology metadata will help comprehension of the ontology landscape; a new AgroPortal metadata model was created to better describe ontologies and their
FAIR data requires FAIR ontologies, how do we do?EUDAT
This document discusses making ontologies FAIR (Findable, Accessible, Interoperable, Reusable) through the use of ontology repositories. It provides examples of existing repositories like NCBO BioPortal and how they help standardize ontologies and make them more discoverable and reusable. The document also describes related projects that are reusing NCBO's technology like AgroPortal for agricultural ontologies and SIFR for French biomedical ontologies and terminologies. Key challenges discussed are scaling repositories to many domains and large numbers of ontologies while maintaining features and curation.
This document describes Clement Jonquet's presentation at SIMBig'17 in Lima, Peru on September 6th 2017. It discusses two collaborative projects involving ontology repositories and ontology-based services. It highlights challenges for ontology repositories, including better use of ontology metadata, multilingual support, alignment of ontologies, and scaling to multiple domains as the number and variety of ontologies increases. The document also provides details on the NCBO BioPortal and AgroPortal projects, which aim to make biomedical and agricultural ontologies more accessible and reusable.
A Comparative Study Ontology Building Tools for Semantic Web Applications IJwest
This document provides a comparative study of four popular ontology building tools: Protégé 3.4, IsaViz, Apollo, and SWOOP. It discusses the features and functionalities of each tool, including their capabilities for ontology editing, browsing, documentation, import/export of formats, and visualization. The document aims to identify existing ontology tools that are freely available and can be used to develop ontologies for various application domains such as transport, tourism, health, and natural language. It evaluates the tools based on criteria like interoperability, openness, ease of updating/maintaining ontologies, and market penetration.
Workshop on Learning Technology Standards for Agriculture and Rural Development (AgroLT 2008)
September 19, 2008, Athens, Greece
In conjunction with
4th International Conference on Information and Communication Technologies in Bio and Earth Sciences (HAICTA 2008)
The document discusses ontology alignment, which is the process of finding correspondences between concepts in different ontologies to allow them to be used together. It notes that there is no single unified ontology, so alignment helps integrate overlapping conceptualizations. The key constructs for expressing alignments are relations like equivalence and subclass between concepts. Techniques discussed for finding mappings include string-based, linguistic/language-based, taxonomy comparison, and using example instances. The challenges of alignment evaluation and interpretation of results are also covered.
This document provides an overview of the evolution of 3GPP UMTS/HSPA mobile broadband technology. It discusses the progress and commercial deployment of earlier 3GPP releases such as Release 99, Release 5, and Release 6. It then focuses on Release 7, describing enhancements like MIMO for HSDPA, IMS/core network updates, and improved RAN capabilities. Looking ahead, it outlines the 3GPP work on developing a new radio interface and system architecture through initiatives like SAE, HSPA+, and LTE to support rapidly growing IP data traffic over the next decade with peak rates above 100 Mbps.
Ontology Building and its Application using HozoKouji Kozaki
The document provides information about an upcoming tutorial on ontology building and its applications using the Hozo ontology development tool. The tutorial will take place on November 9th, 2014 in Chiang Mai, Thailand and will cover how to build ontologies using Hozo, some characteristic functions of Hozo, and examples of ontology-based application developments. The tutorial agenda outlines the topics to be covered in each time block, including hands-on experience building ontologies with Hozo.
For efficient and innovative use of big data, it is important to integrate multiple data bases across domains. For example, various public data bases are developed in life science, and how to find a novel scientific result using them is an essential technique. In social and business areas, open data strategies in many countries promote diversity of public data, how to combine big data and open data is a big challenge. That is, diversity of dataset is a problem to be solved for big data.
Ontology gives a systematized knowledge to integrate multiple datasets across domains with semantics of them. Linked Data also provides techniques to interlink datasets based on semantic web technologies. We consider that combinations of ontology and Linked Data based on ontological engineering can contribute to solution of diversity problem in big data.
In this talk, I discuss how ontological engineering could be applied to big data with some trial examples.
Yang Yu is proposing research on improving machine learning based ontology mapping by automatically obtaining training samples from the web. The proposed system would parse two input ontologies to generate queries to search engines and collect documents to use as samples for each ontology class. These samples would then be used to train text classifiers, which would produce probabilistic mappings between classes in the two ontologies. The results would be evaluated by comparing to mappings from human experts. Current work involves exploring alternative text classification tools and ways to utilize the probabilistic mapping values generated by the classifiers.
Supporting User's Exploration of Digital Libraries, Suedl 2012 workshop proce...pathsproject
Workshop proceedings from the International workshop on Supporting Users Exploration of Digital Libraries, SUEDL 2012 which was held at TPDL 2012 (the international conference on Theory and Practice in Digital Libraries), Paphos, Cyprus, September 2012.
The aim of the workshop was to stimulate collaboration from experts and stakeholders in Digital Libraries, Cultural Heritage, Natural Language Processing and Information Retrieval in order to explore methods and strategies to support exploration of Digital Libraries, beyond the white box paradigm of search and click.
The proceedings includes:
"Browsing Europeana - Opportunities and Challenges', David Haskiya
"Query re-writing using shallow language processing effects', Anna Mastora and Sarantos Kapidakis
"Visualising Television Heritage" Johan Ooman et al,
"Providing suitable information access for new users of Digital Libraries", Rike Brecht et al
"Exploring Pelagios: a Visual Browser for Geo-tagged datasets" Rainer Simon et al
Eurogene is an e-learning system in the domain of genetics that provides free multimedia learning resources in nine languages for statistical, medical and molecular genetics and delivers them to students and professionals. The Eurogene content includes presentations, reviewed research articles, images, videos and learning packages submitted by world-leading geneticists.
An essential part of the Eurogene system is a multilingual search engine that allows to search for content in one language while retrieving the results in other languages. This is complemented by the use of a machine translation system fine-tuned for genetic terminology. The search engine uses a query language similar to PubMed.
Eurogene also aims at providing intelligent ways of navigation through the e-Learning system. As new learning resources are being continuously submitted to the system, it is not possible to maintain links between them manually. Eurogene automatically links resources that are semantically similar using natural language processing.
The document summarizes a seminar on ontology mapping presented by Samhati Soor. The seminar covered the need for ontology mapping due to the proliferation of ontologies, and the purpose of mapping ontologies to achieve interoperability and sharing knowledge. It defined ontologies and ontology mapping and discussed categories of mapping including between global and local ontologies, between local ontologies, and for merging ontologies. Tools for ontology mapping discussed included GLUE and SAM. Evaluation criteria and challenges of ontology mapping were also summarized along with conclusions and references.
ONTOLOGY VISUALIZATION PROTÉGÉ TOOLS – A REVIEW ijait
The document discusses ontology visualization tools in Protégé. It reviews four main visualization methods used in Protégé tools: indented list, node-link and tree, zoomable, and focus+context. It then examines specific Protégé tools that use each method, including their key features and limitations. The tools assessed are Protégé Class Browser (indented list), Protégé OntoViz and OntoSphere (node-link and tree), Jambalaya (zoomable), and Protégé TGVizTab (focus+context). The document concludes by summarizing and comparing the visualization characteristics of these Protégé tools.
Conférence donéée au LGI2P (Conférence Communication Science et Société) à Nimes le 17 mars 2015. Contenu en partie produit par le travail de Juan Antonio Lossio Ventura.
EdReNe brings together members from webbased repositories of learning resources with content owners and other stakeholders within education.
We share, develop and document strategies, experiences and solutions on the organisation, structuring and functionality of repositories. The overall goal is to improve the provision of and access to learning resources.
The document discusses the need to develop services to facilitate the long-term interpretation of archived data through the use of semantic artifacts like ontologies. It notes that semantic artifacts must themselves be archived long-term using repositories that deal with format heterogeneity and versioning over time. The talk then describes an open-source ontology repository called OntoPortal and its use in projects like AgroPortal for agronomy and SIFR BioPortal for French biomedical data. OntoPortal alliances are working to synchronize development and improve ontology repositories and uptake of semantic technologies.
EdReNe is a European network that aims to connect providers and users of educational resources through repositories. It brings together members from repositories, content owners, and other stakeholders. EdReNe identifies key issues for repositories through workshops, develops recommendations, and shares best practices. Its goals are to improve access, use, and sharing of educational resources across Europe.
EdReNe is a European network focused on improving access to learning resources through educational repositories. The network brings together repository providers and stakeholders to share strategies and best practices. EdReNe aims to address challenges around connecting users and content providers, establish quality frameworks, and make recommendations to optimize access and use of learning resources across repositories. The network holds workshops and seminars to facilitate collaboration and outputs guides and documentation on its website.
B2NOTE is a semantic annotation service that allows adding additional information to data elements without changing the original data. It indexes over 5 million concepts from biomedical ontologies to facilitate semantic annotations. The presenter discusses expanding this approach to other domains by indexing more semantic resources. There are challenges around discoverability, interoperability, and metadata standards for semantic resources across domains. An EUDAT working group is developing a proof-of-concept semantic lookup service to register, aggregate, and provide analytics on multi-disciplinary semantic resources to help address these issues. Continued community support is needed to further develop semantic services and standards with broader disciplinary coverage.
PhD presentation for the public defense of the dissertation entitled 'Bridging the gap between Open and User Innovation? Exploring the value of Living Labs as a means to structure user contribution and manage distributed innovation.' This was a joint PhD between Ghent University and the VUB.
Promotors:Prof. dr. Lieven De Marez, Universiteit Gent, Faculteit Politieke & Sociale Wetenschappen, vakgroep Communicatiewetenschappen and Prof. dr. Pieter Ballon, Vrije Universiteit Brussel, Faculteit Economische en Sociale Wetenschappen, vakgroep Communicatiewetenschappen
President of the jury:
Prof. dr. Gino Verleye, Universiteit Gent
Jury:
Prof. dr. Pieter Verdegem, Universiteit Gent
Prof. dr. Marcel Bogers, Associate Professorat Mads Clausen Institute, Faculty of Engineering, University of Southern Denmark
Prof. dr. Esteve Almirall, Profesor Asociado at ESADE Business & Law School
Prof. dr. Seppo Leminen, Principal lecturer at Laurea University of Applied Sciences & Adjunct Professor at Aalto University School of Economics
CDAO presentation.
The idea of the comparative analysis ontoloty has been presented worldwide, including: NESCent (USA), IGBMC (France), UFRJ (Brazil). Providing a semantic framework for evolutionary analysis in a high-throughtput way after the next and third generation sequencing is the way to approach evolutionary-based studies into genome-wide analysis. The darwinian core of reasoning also allows CDAO to be used with other entities.
This document discusses three case studies that applied visualization techniques to develop interfaces for educational repositories: Organic.Lingua, Organic.Edunet, and VOA3R. Usability tests were conducted on the interfaces to identify problems. Three key issues were found: whether the interfaces provided utility to users, how learnable the interfaces and classification schemes were, and usability of the classification schemes. The conclusion is that while visualization techniques could help users of educational repositories, significant usability work is still needed to address these three key problems in order for users to widely adopt such interfaces.
The document summarizes a presentation on keyphrase extraction from scholarly documents. It discusses keyphrase extraction at different scales, from keywords to sentences and summaries. It also covers sources of evidence for keyphrases, common errors in keyphrase extraction, directions for improving the task by addressing these errors and leveraging external resources, and proposes using scholarly articles as a platform for shared tasks in keyphrase extraction and summarization.
Learning and Text Analysis for Ontology Engineeringbutest
This document calls for papers and participation in a workshop on learning and text analysis for ontology engineering to be held in conjunction with the ECAI 2002 conference in Lyon, France. The workshop aims to bring together researchers from linguistics, natural language processing, knowledge representation, and machine learning to discuss issues around building, maintaining, and reusing ontologies and terminological resources. Topics of interest include using texts and linguistic/terminological resources as knowledge sources for building ontologies, applying machine learning and NLP tools to ontology engineering, and learning ontologies from sources like the web. The deadline for paper submissions is March 15th and for motivation abstracts is May 24th. The workshop will include paper presentations, discussions, and
Innovative and Inquiry-based Teaching for Excellenceglhanley
Description of an international collaborative project between the California State University, Long Beach, MERLOT (www.merlot.org), and the Academic Staff College of Lucknow University, India to redesign higher education instruction in India. The project is partially funded by the William and Flora Hewlett Foundation. Inquiry-based learning and the innovative use of Open Educational Resources within the context of defining and assessing student learning outcomes is the focus of the collaborative effort.
The document discusses platforms and quality assurance in eLearning at the Technical University of Crete. It provides an overview of the university and the MUSIC lab, their research areas including multimedia management systems and eLearning platforms. It then summarizes several European projects conducted by MUSIC related to digital libraries, personalization and interoperability in eLearning. Finally, it presents the iQTool project which developed a quality assurance methodology and open source tool for evaluating training materials.
Breif overview of the FAIR Cookbook for the UK Conference of Bioinformatics and Computational Biology 2021: https://www.earlham.ac.uk/uk-conference-bioinformatics-and-computational-biology-21
The document summarizes the development of the Research Information Centre (RIC) virtual research environment project. It describes the RIC as addressing the entire research lifecycle and "pain points" of research. It then outlines the timeline of the RIC's development from initial sprints in 2007-2008 to test versions released in 2009 and enhancements made through 2011. The RIC development is positioned as a community effort, with an example given of its use in a collaboration between clinicians and researchers.
The document summarizes the development of the Research Information Centre (RIC) virtual research environment project by the British Library. It describes the RIC as addressing the entire research lifecycle and "pain points" of research through information management tools. It then outlines the timeline of the RIC's development from initial sprints in 2007-2008 to test versions and community feedback, with the first public source code release in December 2009 and ongoing enhancements since. The RIC development is positioned as a community effort, with an example project described for automated clinical trial metadata extraction and image analysis workflows.
The document discusses ontology repositories and the OntoPortal technology, describing several ontology repositories including AgroPortal, EcoPortal, and others that use OntoPortal, and highlighting how OntoPortal enables collaboration and sharing of semantic artifacts across domains through its open source repository platform. It also provides an overview of ontology repositories in general and examples of ontologies hosted in AgroPortal.
This document provides an overview of ontology repositories and the OntoPortal technology. It discusses several ontology repositories including BioPortal and how they help make ontologies FAIR. It then describes the OntoPortal Alliance which aims to promote semantic services by generalizing and reusing the ontology repository technology. Specific instances of OntoPortal are mentioned, including AgroPortal for agronomy. The document concludes by inviting participation in OntoPortal and feedback to continue improving the technology.
O'FAIRe is an ontology FAIRness evaluator tool and methodology that provides automatic FAIRness assessments of semantic resources using their metadata. It consists of a 61 question methodology specialized for semantic resources that maps to 15 FAIR principles. The tool is implemented as a web service that works with any OntoPortal repository using a unified MOD 1.4 metadata model to generate a JSON report with a resource's FAIR score and explanations. O'FAIRe aims to help make ontologies and other semantic resources more FAIR through standardized evaluation and identification of areas for improvement.
The document summarizes work done by an ontology metadata task group to make ontologies and other semantic resources more findable, accessible, interoperable, and reusable (FAIR). The group analyzed ontology metadata practices, vocabularies, and libraries/repositories. They developed a new unified metadata model and implemented it in the AgroPortal ontology repository. The repository harvests ontologies and vocabularies, extracts and aggregates their metadata, and makes it available and searchable to help users find and select relevant semantic resources.
Challenges, contributions and applications to
biomedicine & agronomy
Presentation at "Journée thématique sur les autorités de données
8 avril 2019, Toulouse"
AgroPortal is an ontology repository for agronomy, plant sciences, biodiversity and nutrition. It hosts 64 public ontologies, including 38 not present in other repositories. The objectives are to develop a reference repository, reuse the NCBO BioPortal technology, and enable use of agronomy ontologies. Key activities include publishing ontologies, searching/downloading, aligning ontologies, and recommending relevant ontologies for data. Future work includes hosting additional ontologies and developing ontology mapping capabilities.
Presentation du SIFR BioPortal a la DSSIS lors de la réunion sur les serveurs mult terminologiques, Juin 2017. Présentation tirée de la presentation aux JFIM 2016 de Juin 2016 (+ nouveautées).
- AgroPortal is an ontology repository for agronomy that aims to be a one-stop-shop for agricultural ontologies and services. It reuses the NCBO BioPortal technology while focusing specifically on agronomy.
- Over 50 ontologies are already included in AgroPortal from various agronomy projects that need a place to publish and share ontologies. More ontologies are being considered for inclusion.
- The goal is for AgroPortal to become a reference platform for the agronomy community to find and use ontologies, with functionality like SPARQL querying and web services APIs. Community involvement is encouraged to help customize and expand its capabilities.
Presentation Sommet iPad en education 2014 Polytech Montpellier
Scénarios pédagogiques numériques……via l’utilisation de l'iPad par et pour les étudiants de Polytech Montpellier
Clement Jonquet et la cellule iPad des enseignants
The document discusses dynamic service generation through agent interactions on the Grid. It introduces dynamic service generation and describes key concepts of service-oriented computing and the Grid, including Grid services and their lifecycle. It also covers multi-agent systems and the STROBE model, which defines agent representation and communication. Finally, it proposes a service-based integration of Grid and multi-agent system technologies.
More from INRAE (MISTEA) and University of Montpellier (LIRMM) (13)
These lecture slides, by Dr Sidra Arshad, offer a simplified look into the mechanisms involved in the regulation of respiration:
Learning objectives:
1. Describe the organisation of respiratory center
2. Describe the nervous control of inspiration and respiratory rhythm
3. Describe the functions of the dorsal and respiratory groups of neurons
4. Describe the influences of the Pneumotaxic and Apneustic centers
5. Explain the role of Hering-Breur inflation reflex in regulation of inspiration
6. Explain the role of central chemoreceptors in regulation of respiration
7. Explain the role of peripheral chemoreceptors in regulation of respiration
8. Explain the regulation of respiration during exercise
9. Integrate the respiratory regulatory mechanisms
10. Describe the Cheyne-Stokes breathing
Study Resources:
1. Chapter 42, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 36, Ganong’s Review of Medical Physiology, 26th edition
3. Chapter 13, Human Physiology by Lauralee Sherwood, 9th edition
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share - Lions, tigers, AI and health misinformation, oh my!.pptxTina Purnat
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Cell Therapy Expansion and Challenges in Autoimmune DiseaseHealth Advances
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- Video recording of this lecture in English language: https://youtu.be/Pt1nA32sdHQ
- Video recording of this lecture in Arabic language: https://youtu.be/uFdc9F0rlP0
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Demystifying Fallopian Tube Blockage- Grading the Differences and Implication...
A few contributions of the SIFR (Semantic Indexing of French biomedical Resources project) and how we reuse NCBO technology
1. Atelier Recherche d’Information Sémantique, RISE’15
30 juin 2015 – Rennes
Clement Jonquet – jonquet@lirmm.fr
A few contributions of
the SIFR
(Semantic Indexing of French
biomedical Resources project)
and how we reuse NCBO
technology
2. How is this relevant to RISE?
Modèles de Recherche d'Information Sémantique
Extraction d'Information
Annotation Sémantique
Indexation Sémantique
Alignement d'ontologies et correspondances pour la Recherche
d'Information
Langages de Représentation des connaissances pour la Recherche
d'Information
Utilisation des distances Sémantiques pour la Recherche
d'Information
Atelier RISE 2015
30 juin 2015, Rennes
4. Biologist have adopted
ontologies
To provide canonical representation of scientific
knowledge
To annotate experimental data to enable
interpretation, comparison, and discovery across
databases
To facilitate knowledge-based applications for
Decision support
Natural language-processing
Data integration
But ontologies are: spread out, in different formats, of
different size, with different structures
Atelier RISE 2015
30 juin 2015, Rennes
5. Working with terminologies &
ontologies – a portal please!
You’ve built an ontology, how do you let the world know?
You need an ontology, where do you go o get it?
How do you know whether an ontology is any good?
How do you find resources that are relevant to the
domain of the ontology (or to specific terms)?
How could you leverage your ontology to enable new
science?
How could you use ontologies without managing them ?
Atelier RISE 2015
30 juin 2015, Rennes
6. Atelier RISE 2015
30 juin 2015, Rennes
Comparison of the
approaches
[IWBBIO'14]
7. Annotation challenge
Explosion of biomedical data: diverse,
distributed, unstructured… not linked to
ontologies
Hard for biomedical researchers to find the
data they need
Data integration problem
Translational discoveries are prevented
Good examples
GO annotations
PubMed (biomedical literature) indexed with
Mesh headings
Annotate data with ontology concepts
Horizontal approach
ONTOLOGIES
RESOURCES
Atelier RISE 2015
30 juin 2015, Rennes
8. Good use of the semantics (1/2)
Simple keywords based search miss results
Atelier RISE 2015
30 juin 2015, Rennes
9. Good use of the semantics (2/2)
Atelier RISE 2015
30 juin 2015, Rennes
10. A few words about SIFR
project
Atelier RISE 2015
30 juin 2015, Rennes
12. People
Young researchers
Clement Jonquet
Mathieu Roche
Sandra Bringay
Advisors
Stefano A. Cerri
Maguelonne Teisseire
Pascal Poncelet
Staff
Vincent Emonet
Students
Juan Antonio Lossio Ventura
Guillaume Surroca
~3 MSc students / year
Close collaborators
Philippe Lemoisson (TETIS)
Pierre Larmande (IRD / IBC)
Mark Musen (BMIR)
Stefan Darmoni (CISMEF)
Sebastien Harispe (LGI2P)
Atelier RISE 2015
30 juin 2015, Rennes
13. Increasing number of biomedical
data + multilingualism
Limits of keyword-based indexing
Biomedical community has turned to ontologies to describe their
data and turn them into structured and formalized knowledge
Using ontologies is by means of creating semantic annotations
Crucial need for tools & services for French biomedical data
Biomedical data integration challenge
New potential sceintific discoveries hidden in data
Translational research
Atelier RISE 2015
30 juin 2015, Rennes
14. Use ontologies for indexing, mining
and searching (French) biomedical
data
Obj1: Design, development and deployment
of the French Annotator.
Obj2: Obtain new research results to exploit
and enhance ontology-based indexing
services.
semantic distances
ontology alignment
ontology enrichment and disambiguation
Obj3: Valorization of indexing services
Atelier RISE 2015
30 juin 2015, Rennes
16. Atelier RISE 2015
30 juin 2015, Rennes
Use biomedical ontologies-based
annotations end-user applications
17. Reuse of the NCBO
technology
Atelier RISE 2015
30 juin 2015, Rennes
18. Bioportal : A “one stop shop”
for Biomedical Ontologies
Web repository for biomedical ontologies
Make ontologies accessible and usable – abstraction on
format, locations, structure, etc.
Users can publish, download, browse, search, comment,
align ontologies and use them for annotations both online
and via a web services API.
Online support for ontology
Peer review
Notes (comments and discussion)
Versioning
Mapping
Search
Resources
Atelier RISE 2015
30 juin 2015, Rennes
20. http://data.bioontology.org
Ontology
Services
• Search
• Traverse
• Comment
• Download
Widgets
• Tree-view
• Auto-complete
• Graph-view
Annotation
Data Access
Mapping
Services
• Create
• Upload
• Download
Term recognition
Search “data”
annotated with a
given term
http://bioportal.bioontology.org Atelier RISE 2015
30 juin 2015, Rennes
21. Current axes of research
Atelier RISE 2015
30 juin 2015, Rennes
22. SIFR axes of research (1/8):
Design of the SIFR (French)
Annotator service
Deployment of a local instance of BioPortal at LIRMM
16 French terminologies imported from UMLS, EHTOP & BioPortal
UTF8 compliant Mgrep concept recognizer (Univ. of Michigan)
http://bioportal.lirmm.fr/annotator
New improvement to the annotation workflow
Automatic term extraction measures (C-value, LIDF-value, etc.)
Scoring of annotations & representation in RDF using the AO
[SWAT4LS 2014]
Atelier RISE 2015
30 juin 2015, Rennes
23. Improving the Annotator(s) –
example with scoring
Objective : To improve the Annotator(s) results by ranking
the annotations according to their relevance
While not changing the service implementation
Take into account their frequencies (as originally proposed in
2009 and removed)
Add a term extraction measure, called C-Value, used to
positively discriminate annotations generated from matches
with multi-word terms.
2 new scoring methods allowing to score and rank
annotations by their importance in the given input data
Interesting results validated against PubMed manual
annotations
[SWAT4LS 2014]
Atelier RISE 2015
30 juin 2015, Rennes
24. SIFR axes of research (2/8):
Dealing with multilingualism within
BioPortal
Status of multilingualism in BioPortal – quite negative
Set of propositions [MSW 2014]
Representation of natural language property for an ontology
Representation of the distinction between ontologies
Representation of relation between ontologies
Representation of multilingual translation mappings
Reconciliation of multilingual mappings (possible PhD collaboration with
ESI)
Currently being tested/implemented within our local instance
Atelier RISE 2015
30 juin 2015, Rennes
25. What is being multilingual?
Interface internationalization = displaying static elements of
the user interface (e.g., menu names, help, etc.) in
different languages
Content internationalization = displaying BioPortal content
(e.g., ontology labels, mappings, etc.) in different languages
Multilingual = internationalization (display) + to enabling a
complete use of the functionalities and services of BioPortal
for multilingual ontologies or monolingual ontologies
completely and properly addressed (languages, translations,
multilingual mappings, etc.)
rich semantic description
Being able to parse multilingual content in ontologies (from
xmllang to Lemon)
Atelier RISE 2015
30 juin 2015, Rennes
26. multilingual
ontology
Atelier RISE 2015
30 juin 2015, Rennes
en:disease
fr:maladie
...
en:cancer
fr:cancer
en:spindel cell sarcome
fr:sarcome à cellules fusiformes
en:melanoma
fr:mélanome
disease
... cancer
spindle cell sarcome melanoma
maladie
... cancer
sarcome à cellules
fusiformes
mélanome
language specific
ontology
(monolingual)
27. SIFR axes of research (3/8):
Automatic extraction of biomedical
terminology from text
Context of the PhD of Juan Antonio Lossio
[LBM 2013][TALN 2014][PolTAL 2014]
BioTex , software
http://tubo.lirmm.fr/biotex [ISWC 2014]
Work in French, English and Spanish
Motivations for automatic terminology
extraction
Experiment and validate approaches for
French data
Contribute to the ontology enrichment
process
Acquire some NLP expertise for the
annotation workflow
Atelier RISE 2015
30 juin 2015, Rennes
29. Statistical methods
C-value: Improves the extraction of longest terms
soft contact soft contact lens
Frantzi, K., Ananiadou, S., & Mima, H. (2000). Automatic recognition of multi-word terms:. the
c-value/nc-value method. International Journal on Digital Libraries, 3(2), 115-130.
Atelier RISE 2015
30 juin 2015, Rennes
32. Include BioTex into BioPortal
Use BioPortal dictionary for validation
New ontology enrichment service… give a corpus of data and
see what are the terms not yet covered
Atelier RISE 2015
30 juin 2015, Rennes
33. SIFR axes of research (4/8):
Semantic distance framework
Automatically compute existing (Rada, Wu&Palmer, Resnik)
semantic similarity measures over BioPortal ontologies
For a given concept get all semantically closed concepts
Get the semantic distance between 2 concepts
Collaboration with LGI2P to reuse Semantic Measure Library
(SML) within BioPortal
1st prototype: http://tubo.lirmm.fr/BioMedicalSemantic/web/app_dev.php
To include SML within BioPortal backend to bring semantic
distance services to the ontologies and data annotated
Atelier RISE 2015
30 juin 2015, Rennes
34. SIFR axes of research (5/8):
Informal patient data analysis
Dealing with public patient data on blogs, forums and
tweets (Sandra Bringay)
Detection of emotion [EGC 2014][eTELEMED 2014]
Patient vocabulary (crabe vs. cancer)
Project “Parlons de nous” (www.lirmm.fr/patient-mind)
MSH-M
A patient vocabulary currently being constructed [IC 2015]
Hosted and available in our local instance of BioPortal
Used for annotations, indexing, information retrieval
Atelier RISE 2015
30 juin 2015, Rennes
35. SIFR axes of research (6/8):
Viewpoint: a subjective knowledge
representation formalism
Collaboration with P. Lemoisson (CIRAD) & PhD of G. Surroca
Graph based knowledge representation formalism
Linked data from the semantic Web and user contributions
from the social Web.
Unified topological approach
First prototype for semantic search over HAL-LIRMM
publications [IC2014]
Capture the phenomenon of Serendipity
(i.e., incidental learning) [IC 2015]
Atelier RISE 2015
30 juin 2015, Rennes
36. SIFR axes of research (7/8):
Pharmacogenomics use case
PGx studies how individual gene variations cause variability in
drug responses
Validation of pharmacogenomics state-of-the-art knowledge on
the basis of practice-based evidences
Compare pharmacogenomics literature (in English) and electronic
health records (in French)
EHRs from Paris (HEGP) & St Etienne hospitals
Improvement of the AnnotatorS to come to handle clinical data:
negation, disambiguation, modularity, temporality
Project submitted to ANR generic call 2015 (April 27th)
Collaborative action lead by Adrien Coulet (LORIA)
Stanford is in the loop (Russ, Mark, Michel, Nigam)
Atelier RISE 2015
30 juin 2015, Rennes
37. SIFR axes of research (8/8):
application to agronomy & plant
Within the Institute of Computational Biology of
Montpellier
Design of a semantic annotation workflow for plant data -
collaboration with IBC project [CO-PDI 2014]
AgroLD: to build an RDF knowledge base to house plant data
resources: SouthGreen, Gramene, OryGeneDB… [RDA 2014]
AgroPortal: reference ontology repository for the agronomic
domain [IN-OVIVE 2015]
Experiment NCBO technologies for the plant community
4 driving agronomic use cases
Atelier RISE 2015
30 juin 2015, Rennes
38. Objectives of AgroPortal project
Develop and support a reference ontology repository for the
agronomic domain
One-stop-shop for plant/agronomic related ontologies
Primary focus on the agronomic & plant domain
Reusing the NCBO BioPortal technology
Avoid to re-implement what has been done
Facilitate interoperability
Reusing the scientific outcomes, experience & methods of the
biomedical domain
Enable straightforward use of agronomic related ontologies
Respect the requirements of the agronomic community
Fully semantic web compliant infrastructure
Atelier RISE 2015
30 juin 2015, Rennes
41. Next future
Continue to move different prototypes into production
Release of the French Annotator
Find more use cases
Collaboration with the plant/agro community
Continue reusing and contributing to NCBO technology
Atelier RISE 2015
30 juin 2015, Rennes
42. Online resources
Web page: www.lirmm.fr/sifr
https://www.researchgate.net/projects
Code repository: https://github.com/sifrproject
13 developpers
10 repositories
Publications: http://bit.ly/194ImnR
Direct link to HAL-LIRMM platform
with advance search features
Portals & services:
http://bioportal.lirmm.fr
http://agroportal.lirmm.fr
Atelier RISE 2015
30 juin 2015, Rennes