Presented at the 2011 ICBO Workshop on working with multiple biomedical ontologies. We present a framework for designing and interrelating ontology modules which are indvidually represented in different underlying logical formalisms.
Using multiple ontologies to characterise the bioactivity of small moleculesJanna Hastings
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Presented at the 2011 ICBO workshop on working with multiple biomedical ontologies. We describe work on text mining for relationship extraction between chemical and biological entities via a language model for bioactivity.
Using multiple ontologies to characterise the bioactivity of small moleculesJanna Hastings
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Presented at the 2011 ICBO workshop on working with multiple biomedical ontologies. We describe work on text mining for relationship extraction between chemical and biological entities via a language model for bioactivity.
Using ChEBI to explore the underlying biology in metabolomics studiesJanna Hastings
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ChEBI is a chemical database and ontology that is widely used to annotate biological data. Here, we show a tool that is currently in development that allows exploration of the biological annotations for metabolites that are found to be enriched in metabolomics investigations. This tool will be made available online soon.
Presented at the AI center of the Stanford Research Institute: chemical ontologies provide a chemical view into biological systems. Various challenges with modelling "active properties" (roles, functions, dispositions) are discussed.
Presented at the ICBO 2011 conference in Buffalo, we tackle the controversial 'is about' relationship in the information artifact ontology (IAO) in the context of chemical diagrams.
Using ChEBI to explore the underlying biology in metabolomics studiesJanna Hastings
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ChEBI is a chemical database and ontology that is widely used to annotate biological data. Here, we show a tool that is currently in development that allows exploration of the biological annotations for metabolites that are found to be enriched in metabolomics investigations. This tool will be made available online soon.
Presented at the AI center of the Stanford Research Institute: chemical ontologies provide a chemical view into biological systems. Various challenges with modelling "active properties" (roles, functions, dispositions) are discussed.
Presented at the ICBO 2011 conference in Buffalo, we tackle the controversial 'is about' relationship in the information artifact ontology (IAO) in the context of chemical diagrams.
ICBO 2018 Poster - Current Development in the Evidence and Conclusion Ontolog...dolleyj
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The Evidence & Conclusion Ontology (ECO) has been developed to provide standardized descriptions for types of evidence within the biological domain. Best
practices in biocuration require that when a biological assertion is made (e.g. linking a Gene Ontology (GO) term for a molecular function to a protein), the type of evidence
supporting it is captured. In recent development efforts, we have been working with other ontology groups to ensure that ECO classes exist for the types of curation they
support. These include the Ontology for Microbial Phenotypes and GO. In addition, we continue to support user-level class requests through our GitHub issue tracker. To
facilitate the addition and maintenance of new classes, we utilize ROBOT (a command line tool for working with Open Biomedical Ontologies) as part of our standard workflow.
ROBOT templates allow us to define classes in a spreadsheet and convert them to Web Ontology Language (OWL) axioms, which can then be merged into ECO. ROBOT is
also part of our automated release process. Additionally, we are engaged in ongoing work to map ECO classes to Ontology for Biomedical Investigation classes using logical
definitions. ECO is currently in use by dozens of groups engaged in biological curation and the number of ECO users continues to grow. The ontology, in OWL and Open
Biomedical Ontology (OBO) formats, and associated resources can be accessed through our GitHub site (https://github.com/evidenceontology/evidenceontology) as well as
the ECO web page (http://evidenceontology.org/).
Systems Biology Model Semantics and IntegrationAllyson Lister
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A short description of my research experiences using OWL to perform semantic data integration and, ultimately, the addition of annotation for systems biology models.
A statistical framework for multiparameter analysis at the single cell levelShashaanka Ashili
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Phenotypic characterization of individual cells provides crucial insights into intercellular heterogeneity and enables access to information that is unavailable from ensemble averaged, bulk cell analyses. Single-cell studies have attracted significant interest in recent years and spurred the development of a variety of commercially available and research-grade technologies. To quantify cell-to-cell variability of cell populations, we have developed an experimental platform for real-time measurements of oxygen consumption (OC) kinetics at the single-cell level. Unique challenges inherent to these single-cell measurements arise, and no existing data analysis
methodology is available to address them. Here we present a data processing and analysis method that addresses challenges encountered with this unique type of data in order to extract biologically relevant information. We applied the method to analyze OC profiles obtained with single cells of two different cell lines derived from metaplastic and dysplastic human Barrettās esophageal epithelium. In terms of method development, three main challenges were considered for this heterogeneous dynamic system: (i) high levels of noise, (ii) the lack of a priori knowledge of single-cell dynamics, and (iii) the role of intercellular variability within and across cell types.
Several strategies and solutions to address each of these three challenges are presented. The features such as slopes, intercepts, breakpoint or change-point were extracted for every OC profile and compared across individual cells and cell types. The results demonstrated that the extracted features facilitated exposition of subtle differences between individual cells and their responses to
cellācell interactions. With minor modifications, this method can be used to process and analyze
data from other acquisition and experimental modalities at the single-cell level, providing a valuable statistical framework for single-cell analysis.
Chattanooga Research Institute PresentationPhilip Bourne
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A presentation made to Chattanooga officials about the importance of computational biology to the future of health care and what it might mean to the Chattanooga Research Institute (CRI).
Three reasons to disuse continuous cell lines.pdfRWDLifeScience
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Continuous cell lines have the characteristics of convenient culture, wide variety, fast growth rate, low cost, and rapid research, which makes them have always been the first choice for cell-level studies .Although continuous cell lines are full of treasures, there are still some limitations in their application.
In order to better understand the essence of life and reveal the laws of life activities of cells, scientists have carried out a series of researches on cell proliferation, movement, metabolism, death and other activities.
This artical intruduce three reasons to disuse continuous cell lines.Let's click here to learn more.
Towards integration of systems biology and biomedical ontologiesRobert Hoehndorf
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Systems biology is an approach to biology that emphasizes the
structure and dynamic behavior of biological systems and the
interactions that occur within them. To succeed, systems biology
crucially depends on the accessibility and integration of data across
domains and levels of granularity. Biomedical ontologies were
developed to facilitate such an integration for data and are often
used to annotate biosimulation models in systems biology.
Here, I present an approach towards combining both disciplines in a common framework that enables information to flow between both.
Pipeline for automated structure-based classification in the ChEBI ontologyJanna Hastings
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Presented at the ACS in Dallas: ChEBI is a database and ontology of chemical entities of biological interest, organised into a structure-based and role-based classification hierarchy. Each entry is extensively annotated with a name, definition and synonyms, other metadata such as cross-references, and chemical structure information where appropriate. In addition to the
classification hierarchy, the ontology also contains diverse chemical and ontological relationships. While ChEBI is primarily manually maintained, recent developments have focused on improvements in curation through partial automation of common tasks. We will describe a pipeline we have developed for structure-based classification of chemicals into the ChEBI structural classification. The pipeline connects class-level structural knowledge encoded in Web Ontology Language (OWL) axioms as an extension to the ontology, and structural information specified in standard MOLfiles. We make use of the Chemistry Development Kit, the OWL API and the OWLTools library. Harnessing the pipeline, we are able to suggest the best structural classes for the classification of novel structures within the ChEBI ontology.
Data integration is a perennial challenge facing large-scale data scientists. Bio-ontologies are useful in this endeavour as sources of synonyms and also for rules-based fuzzy integration pipelines.
Chemical classification for the Semantic WebJanna Hastings
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Classification conveys the type for data that is published in the Semantic Web. Classification using OWL ontoloiges dramatically enhances the potential of the chemical Semantic Web. ChEBI provides a classification that can be used across multiple data resources.
Representing addiction in Mental Functioning and Disease ontologiesJanna Hastings
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Enabling querying and browsing of biomedical and neuroscientific research on addiction using interoperable ontologies and cross-products. Presented at ICBO 2012.
Bio-ontologies in bioinformatics: Growing up challengesJanna Hastings
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Bio-ontologies are growing up, and their use is becoming widespread in many areas of computational science. The new maturity is bringing new challenges, however, in particular visualization of complex ontologies; moving from OBO to OWL; using multiple ontologies in conjunction; training appropriate for biologists and community building.
Mental functioning ontology for interdisciplinary research into mental diseas...Janna Hastings
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Presented at the Neuroscience Information Framework (NIF) webinar series on 24/04/2012. An overview of the Mental Functioning Ontology aims and objectives.
From chemicals to minds: Integrated ontologies in the search for scientific u...Janna Hastings
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Presented at the 2012 Interdisciplinary Ontology (InterOntology) Conference in Tokyo, February 24th 2012. This presentation gives a whirlwind tour of some "reports from the front lines" of practical bio-ontology development in ChEBI and in the Mental Functioning and Emotion Ontology projects.
Modularity requirements in bio-ontologies: a case study of ChEBIJanna Hastings
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A wish list for tools for modularity support in bio-ontology engineering based on the ChEBI ontology requirements. Presented at the workshop on modular ontologies, WoMO, 2011, in Ljubljana.
The SHAPES workshop, and Holes in living beings Janna Hastings
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The SHAPES workshop brought together interdisciplinary shape researchers. Our paper presents some challenges in applying shapes -- and holes -- in living beings.
The emotion ontology: enabling interdisciplinary research in the affective sc...Janna Hastings
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Presented at the 2011 ICBO, we motivate and introduce the Emotion Ontology currently under development in the Swiss Centre for Affective Sciences in collaboration with the University at Buffalo.
Presented at the 2011 ISMB Bio-ontologies SIG. A detour into the difficulties of representing the properties of processes in ontologies, and some steps towar
Ontological dependence, dispositions and institutional reality in chemistryJanna Hastings
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Presented at the 2010 Formal Ontology in Information Systems conference (FOIS 2010). Discusses different classifications of the activity of chemical entities (in the context of the ChEBI ontology).
Presented at the 2nd ChEBI User Group Workshop. Discusses some of the difficulties encountered in the project which aims to classify chemicals in the ChEBI ontology automatically based on their structures.
State of ICS and IoT Cyber Threat Landscape Report 2024 previewPrayukth K V
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The IoT and OT threat landscape report has been prepared by the Threat Research Team at Sectrio using data from Sectrio, cyber threat intelligence farming facilities spread across over 85 cities around the world. In addition, Sectrio also runs AI-based advanced threat and payload engagement facilities that serve as sinks to attract and engage sophisticated threat actors, and newer malware including new variants and latent threats that are at an earlier stage of development.
The latest edition of the OT/ICS and IoT security Threat Landscape Report 2024 also covers:
State of global ICS asset and network exposure
Sectoral targets and attacks as well as the cost of ransom
Global APT activity, AI usage, actor and tactic profiles, and implications
Rise in volumes of AI-powered cyberattacks
Major cyber events in 2024
Malware and malicious payload trends
Cyberattack types and targets
Vulnerability exploit attempts on CVEs
Attacks on counties ā USA
Expansion of bot farms ā how, where, and why
In-depth analysis of the cyber threat landscape across North America, South America, Europe, APAC, and the Middle East
Why are attacks on smart factories rising?
Cyber risk predictions
Axis of attacks ā Europe
Systemic attacks in the Middle East
Download the full report from here:
https://sectrio.com/resources/ot-threat-landscape-reports/sectrio-releases-ot-ics-and-iot-security-threat-landscape-report-2024/
Enhancing Performance with Globus and the Science DMZGlobus
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ESnet has led the way in helping national facilitiesāand many other institutions in the research communityāconfigure Science DMZs and troubleshoot network issues to maximize data transfer performance. In this talk we will present a summary of approaches and tips for getting the most out of your network infrastructure using Globus Connect Server.
The Metaverse and AI: how can decision-makers harness the Metaverse for their...Jen Stirrup
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The Metaverse is popularized in science fiction, and now it is becoming closer to being a part of our daily lives through the use of social media and shopping companies. How can businesses survive in a world where Artificial Intelligence is becoming the present as well as the future of technology, and how does the Metaverse fit into business strategy when futurist ideas are developing into reality at accelerated rates? How do we do this when our data isn't up to scratch? How can we move towards success with our data so we are set up for the Metaverse when it arrives?
How can you help your company evolve, adapt, and succeed using Artificial Intelligence and the Metaverse to stay ahead of the competition? What are the potential issues, complications, and benefits that these technologies could bring to us and our organizations? In this session, Jen Stirrup will explain how to start thinking about these technologies as an organisation.
Le nuove frontiere dell'AI nell'RPA con UiPath Autopilotā¢UiPathCommunity
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In questo evento online gratuito, organizzato dalla Community Italiana di UiPath, potrai esplorare le nuove funzionalitĆ di Autopilot, il tool che integra l'Intelligenza Artificiale nei processi di sviluppo e utilizzo delle Automazioni.
š Vedremo insieme alcuni esempi dell'utilizzo di Autopilot in diversi tool della Suite UiPath:
Autopilot per Studio Web
Autopilot per Studio
Autopilot per Apps
Clipboard AI
GenAI applicata alla Document Understanding
šØāš«šØāš» Speakers:
Stefano Negro, UiPath MVPx3, RPA Tech Lead @ BSP Consultant
Flavio Martinelli, UiPath MVP 2023, Technical Account Manager @UiPath
Andrei Tasca, RPA Solutions Team Lead @NTT Data
SAP Sapphire 2024 - ASUG301 building better apps with SAP Fiori.pdfPeter Spielvogel
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Building better applications for business users with SAP Fiori.
ā¢ What is SAP Fiori and why it matters to you
ā¢ How a better user experience drives measurable business benefits
ā¢ How to get started with SAP Fiori today
ā¢ How SAP Fiori elements accelerates application development
ā¢ How SAP Build Code includes SAP Fiori tools and other generative artificial intelligence capabilities
ā¢ How SAP Fiori paves the way for using AI in SAP apps
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
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Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
Climate Impact of Software Testing at Nordic Testing DaysKari Kakkonen
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My slides at Nordic Testing Days 6.6.2024
Climate impact / sustainability of software testing discussed on the talk. ICT and testing must carry their part of global responsibility to help with the climat warming. We can minimize the carbon footprint but we can also have a carbon handprint, a positive impact on the climate. Quality characteristics can be added with sustainability, and then measured continuously. Test environments can be used less, and in smaller scale and on demand. Test techniques can be used in optimizing or minimizing number of tests. Test automation can be used to speed up testing.
DevOps and Testing slides at DASA ConnectKari Kakkonen
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My and Rik Marselis slides at 30.5.2024 DASA Connect conference. We discuss about what is testing, then what is agile testing and finally what is Testing in DevOps. Finally we had lovely workshop with the participants trying to find out different ways to think about quality and testing in different parts of the DevOps infinity loop.
PHP Frameworks: I want to break free (IPC Berlin 2024)Ralf Eggert
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In this presentation, we examine the challenges and limitations of relying too heavily on PHP frameworks in web development. We discuss the history of PHP and its frameworks to understand how this dependence has evolved. The focus will be on providing concrete tips and strategies to reduce reliance on these frameworks, based on real-world examples and practical considerations. The goal is to equip developers with the skills and knowledge to create more flexible and future-proof web applications. We'll explore the importance of maintaining autonomy in a rapidly changing tech landscape and how to make informed decisions in PHP development.
This talk is aimed at encouraging a more independent approach to using PHP frameworks, moving towards a more flexible and future-proof approach to PHP development.
Why You Should Replace Windows 11 with Nitrux Linux 3.5.0 for enhanced perfor...SOFTTECHHUB
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The choice of an operating system plays a pivotal role in shaping our computing experience. For decades, Microsoft's Windows has dominated the market, offering a familiar and widely adopted platform for personal and professional use. However, as technological advancements continue to push the boundaries of innovation, alternative operating systems have emerged, challenging the status quo and offering users a fresh perspective on computing.
One such alternative that has garnered significant attention and acclaim is Nitrux Linux 3.5.0, a sleek, powerful, and user-friendly Linux distribution that promises to redefine the way we interact with our devices. With its focus on performance, security, and customization, Nitrux Linux presents a compelling case for those seeking to break free from the constraints of proprietary software and embrace the freedom and flexibility of open-source computing.
Observability Concepts EVERY Developer Should Know -- DeveloperWeek Europe.pdfPaige Cruz
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Monitoring and observability arenāt traditionally found in software curriculums and many of us cobble this knowledge together from whatever vendor or ecosystem we were first introduced to and whatever is a part of your current companyās observability stack.
While the dev and ops silo continues to crumbleā¦.many organizations still relegate monitoring & observability as the purview of ops, infra and SRE teams. This is a mistake - achieving a highly observable system requires collaboration up and down the stack.
I, a former op, would like to extend an invitation to all application developers to join the observability party will share these foundational concepts to build on:
zkStudyClub - Reef: Fast Succinct Non-Interactive Zero-Knowledge Regex ProofsAlex Pruden
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This paper presents Reef, a system for generating publicly verifiable succinct non-interactive zero-knowledge proofs that a committed document matches or does not match a regular expression. We describe applications such as proving the strength of passwords, the provenance of email despite redactions, the validity of oblivious DNS queries, and the existence of mutations in DNA. Reef supports the Perl Compatible Regular Expression syntax, including wildcards, alternation, ranges, capture groups, Kleene star, negations, and lookarounds. Reef introduces a new type of automata, Skipping Alternating Finite Automata (SAFA), that skips irrelevant parts of a document when producing proofs without undermining soundness, and instantiates SAFA with a lookup argument. Our experimental evaluation confirms that Reef can generate proofs for documents with 32M characters; the proofs are small and cheap to verify (under a second).
Paper: https://eprint.iacr.org/2023/1886
Transcript: Selling digital books in 2024: Insights from industry leaders - T...BookNet Canada
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The publishing industry has been selling digital audiobooks and ebooks for over a decade and has found its groove. Whatās changed? What has stayed the same? Where do we go from here? Join a group of leading sales peers from across the industry for a conversation about the lessons learned since the popularization of digital books, best practices, digital book supply chain management, and more.
Link to video recording: https://bnctechforum.ca/sessions/selling-digital-books-in-2024-insights-from-industry-leaders/
Presented by BookNet Canada on May 28, 2024, with support from the Department of Canadian Heritage.
Transcript: Selling digital books in 2024: Insights from industry leaders - T...
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Hyperontology for the biomedical ontologist
1. ICBO, Buffalo, July 2011 Hyperontology for the Biomedical OntologistA Sketch and Some Examples Oliver Kutz1 Till Mossakowski1, 2 Janna Hastings3,4 Alexander Garcia Castro 5 Aleksandra Sojic6 1 Research Center on Spatial Cognition, University of Bremen, Germany 2 DFKI GmbH Bremen and University of Bremen, Germany 3 Chemoinformatics and Metabolism, European Bioinformatics Institute, UK 4 Swiss Centre for Affective Sciences, University of Geneva, Switzerland 5 University of Arkansas for Medical Sciences, USA 6 European School of Molecular Medicine, Milan; and University of Milan, Italy
3. Tuesday, July 26, 2011 3 Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
4. Heterogeneous Content Tuesday, July 26, 2011 4 age etiology family history diet cell type Patient information Disease information genotype pathways Granularity social status symptoms Time Qualitative /Quantative Physiological information metabolic profile blood pressure Pathological / Canonical Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
5. Modularity as desiderata Small modules: human understandable, re-usable, one level at a time, etc. Proving-in-the-small Large programs constructed from modules: Composition, Linkage, etc. Proving-in-the-large ļ Idea of a Module Interconnection Language Tuesday, July 26, 2011 5 Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
6. Modularity at design-time Subject-specific modules Logic-specific modules (extensions) āMinimalā expressivity for a given topic Imports and complex interrelationships Tuesday, July 26, 2011 6 Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
7. Hyperontologyis a framework for interrelating heterogeneous ontologymodules Tuesday, July 26, 2011 7 Logical translation Modular connections Integrated tools and reasoners Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
8. Systematically linking ontology modules defined in different formalisms requires: A logic graph Fixed logic translations Tuesday, July 26, 2011 8 Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
9. Common Algebraic Specification Language Standardised many-sorted first-order specification language Various extensions and sublanguages, including higher-order dialects, modal logic, OWL-DL; Supports structured specifications including: imports, hiding, renaming, union, extensions. Tuesday, July 26, 2011 9 Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
10. Semantics of structured specifications Tuesday, July 26, 2011 10 Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
11. HETCASL Extension of CASL for seamless combination of different logics Provides syntactic āsugarā Tuesday, July 26, 2011 11 Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
12. HETS ā The Heterogeneous Tool Set Structured representations Reuse/independent development of modules Library of logics/formalisms supported, incl. OWL-DL Various provers connected: incl. OWLDL, first-order, higher-order, model checker Tuesday, July 26, 2011 12 Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
14. Applications A sketch of some scenarios from bio-ontologies Tuesday, July 26, 2011 14 Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
15. HOL as constraint Both the Sequence Ontology (SO) and the RNAO provide axiomatizations in first-order and higher-order logic to further constrain the semantics of the relationships that they use in OWL (not explicitly linked to the OWL version) Tuesday, July 26, 2011 15 Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
16. Tuesday, July 26, 2011 16 Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011) SIMULATION ANATOMY
18. Fullerenes Tuesday, July 26, 2011 18 Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011) Cubic, 3-connected, planar graphs in which all faces are either pentagons or hexagons (5 or 6 atoms). Cubic 3-connected Planar (Kuratowski) Can be defined with Monadic Second Order Logic (MSOL)
20. Tuesday, July 26, 2011 20 Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
21. Conclusions Biomedical ontologies are highly complex and need diverse formalisms for proper treatment The Hyperontology framework provides the āplumbingā to seamlessly integrate such formalisms Tuesday, July 26, 2011 21 Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
22. Acknowledgements Funding DFG-funded collaborative research centre SFB/TR 8 `Spatial Cognition' The German Federal Ministry of Education and Research (Project 01 IW 07002 FormalSafe). Tuesday, July 26, 2011 22
Editor's Notes
Although there is movement towards a standardisation on OWL as the central currency of ontology representation and exchange, diversity remains, since different profiles of OWL are good for different representation and reasoning tasks (and there is the usual tradeoff between complexity and scalability). OWLDifferent profiles of OWLDifferent logical languagesDifferent subjects require different levels of expressivity to adequately treat the subject matter The emphasis here is on different tools and syntaxes; differences in the underlying logic are treated in the next slide.
The example of disease, different qualitative and quantitative data, and so on. Temporal data, etc. Granularity, epistemic differences. In particular, ontologies for complex diseases such as cancer have to deal with spatio-temporal het-erogeneity, combinations of qualitative and quantitative data, and missing links betweenphysiological and pathological data
The benefits of modular design are well known in other engineering disciplines, including software engineering. To make modularity work for ontologies, however, requires the possibility of combining modules of different underlying formalisms.
Features of hyper ontology framework: onto-logical translation graph
Features of hyper ontology framework: different logical formalisms
Features of hyper ontology framework: modularity
Features of hyperontology framework: Implementation of HETS and HETCASL.
DOLCE as an upper level ontology, and a treatment of mereologyUpper level ontologies in general can aim for a sophisticated axiomatization. Also, both the Sequence Ontology and the RNAO provide axiomatizations in first-order and higher-order logic to further constrain the semantics of the relationships that they use in OWL. But these axiomatizations are not explicitly linked to the OWL version.
DICOM (Digital Imaging and Communications in Medicine) is a standard for handling, storing, printing, and transmitting information in medical imaging. It includes a file format definition and a network communications protocol. Biomedical example one: COMPUTATIONAL SIMULATION OF MECHANICAL PROPERTIES OF BONES When assessing the mechanical properties of bones, researchers use computational sim-ulations to evaluate stress and strain maps under several boundary and load conditions.Such evaluations involve clinical data, e.g. pathological conditions of the patients, andmechanical properties of the materials to be used. For describing a medical image it is often necessary to use several ontologies. Forinstance, Fig. 2(b) (left) illustrates the model for knee joints; hard tissue, e.g. Femurand Tibia bones, and soft tissue, e.g. Tibia and Femur cartilage, need to be identi-ed. The osteoarthritis of the patient requires shaving the cartilage injury as presentedin Fig. 2(b) (right). Such self-descriptiveness makes it possible for users to express complexqueries such as: `Retrieve knee joints images with cartilage injury.āFacilitating the execution of such a query requires the orchestration of several ontolo-gies, namely: Radiology, Anatomy, Pathology, CAD.
Also the RNAO suffers from the problem of needing to represent cyclical structures in protein motifs
ChEBIāGO, OBIThe existing OWL:import mechanism requires the full content ofboth ontologies be loaded into an application (such as Protege) in order to work with thecross-ontology denitions. The hyperontology framework allows us to bypass this problemwith its built-in support for modularisation, even across ontology languages.The hyperontology framework allows domain specicationssuch as the LO to eortlessly re-use parts of core ontologies such as ChEBI and even re-name or redene certain of their entities where needed. Also, more complex relationshipsbetween the ontologies' terms can be formalised in a heterogeneous ontology in the styleof Bridge Rules as they are known from distributed DL or E-Connections (see [12]).These classesare usually brought together via either OWL imports of the full ontologies (leading to asize explosion and the accompanying decrease in performance for reasoning) or simplyby \\slicing" the ontologies and putting together the classes on a need-to-have basis ac-cording to the MIREOT methodology [2]. This mechanism is facilitated by tools such asOntoFox [22], which allows users to input terms, fetch selected properties, annotations,and certain classes of related terms from source ontologies and save the results using theRDF/XML serialization of OWL. These hand-selected modules of external ontologies arethen brought manually into the target ontology through imports, and the procedure hasto be repeated every time the source ontology changes.
Systems biology ontology (SBO): Combining mathematical expressions with ontologies. The types of questions that we might want to have answered relate to the ontological implications of the mathematical expressions rather than just to their answers, although some interesting work in extending concrete domains in this direction is surely taking place. SBO contains manydierent types of entities: material entities such as proteins and small molecules; processparticipation roles such as inhibitor and stimulant; mathematical laws such as rate lawsfor biochemical reactions; and types of mathematical model experiments such as discreteand continuous, and many more besides. The hyperontology framework would allow areformulation of the SBO as composed of modular units sourced from separate domainontologies, a highly desirable goal. Furthermore, of particular interest in the SBO is thatit captures complex mathematical relationships that can exist between biological entitiesin dynamic conditions. In SBO, these relationships are currently expressed in MathML.It is an open challenge to expose some of the relational information encoded in the SBOmathematical equations to ontological reasoning.