Representation and use of chemistry in the global electronic age.

We present an overview of the current state of public semantic chemistry and propose new approaches at a strategic and a detailed level. We show by example how a model for a Chemical Semantic Web can be constructed using machine-processed data and information from journal articles.This manuscript addresses questions of robotic access to data and its automatic re-use, including the role of Open Access archival of data. This is a pre-refereed preprint allowed by the publisher's (Royal Soc. Chemistry) Green policy. The author's preferred manuscript is an HTML hyperdocument with ca. 20 links to images, some of which are JPEgs and some of which are SVG (scalable vector graphics) including animations. There are also links to molecules in CML, for which the Jmol viewer is recommended. We susgeest that readers who wish to see the full glory of the manuscript, download the Zipped version and unpack on their machine. We also supply a PDF and DOC (Word) version which obviously cannot show the animations, but which may be the best palce to start, particularly for those more interested in the text

CML: Evolution and design.

A retrospective view of the design and evolution of Chemical Markup Language (CML) is presented by its original authors.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

About Ontology Application to the Description of Syllabus

Publication describes the experience in application of ontology technique to structuring of educational materials. Several topics of physics were formalized by means of Protégé software tool. Some principal problems in building of knowledge structure were found, so the discussion may interest not only ontology users, but also the developers of ontology tools

A knowledge model-based BIM framework for automatic code-compliant quantity take-off

The results of quantity take-off (QTO) based on building information modeling (BIM) technology rely heavily on the geometry and semantics of 3D objects that may vary among BIM model creation methods. Furthermore, conventional BIM models do not contain all the required information for automatic QTO and the results do not follow the descriptive rules in the standard method of measurement (SMM). This paper presents a new knowledge model-based framework that incorporates the semantic information and SMM rules in BIM for automatic code-compliant QTO. It begins with domain knowledge modeling, taking into consideration QTO-related information, semantic QTO entities and relationships, and SMM logic formulation. Subsequently, linguistic-based approaches are developed to automatically audit the BIM model integrity for QTO purposes, with QTO algorithms developed and used in a case study for demonstration. The results indicate that the proposed new framework automatically identifies the semantic errors in BIM models and obtains code-compliant quantities

Engineering polymer informatics: Towards the computer-aided design of polymers

The computer-aided design of polymers is one of the holy grails of modern chemical informatics and of significant interest for a number of communities in polymer science. The paper outlines a vision for the in silico design of polymers and presents an information model for polymers based on modern semantic web technologies, thus laying the foundations for achieving the vision

Leveraging human-computer interaction and crowdsourcing for scholarly knowledge graph creation

The number of scholarly publications continues to grow each year, as well as the number of journals and active researchers. Therefore, methods and tools to organize scholarly knowledge are becoming increasingly important. Without such tools, it becomes increasingly difficult to conduct research in an efficient and effective manner. One of the fundamental issues scholarly communication is facing relates to the format in which the knowledge is shared. Scholarly communication relies primarily on narrative document-based formats that are specifically designed for human consumption. Machines cannot easily access and interpret such knowledge, leaving machines unable to provide powerful tools to organize scholarly knowledge effectively. In this thesis, we propose to leverage knowledge graphs to represent, curate, and use scholarly knowledge. The systematic knowledge representation leads to machine-actionable knowledge, which enables machines to process scholarly knowledge with minimal human intervention. To generate and curate the knowledge graph, we propose a machine learning assisted crowdsourcing approach, in particular Natural Language Processing (NLP). Currently, NLP techniques are not able to satisfactorily extract high-quality scholarly knowledge in an autonomous manner. With our proposed approach, we intertwine human and machine intelligence, thus exploiting the strengths of both approaches. First, we discuss structured scholarly knowledge, where we present the Open Research Knowledge Graph (ORKG). Specifically, we focus on the design and development of the ORKG user interface (i.e., the frontend). One of the key challenges is to provide an interface that is powerful enough to create rich knowledge descriptions yet intuitive enough for researchers without a technical background to create such descriptions. The ORKG serves as the technical foundation for the rest of the work. Second, we focus on comparable scholarly knowledge, where we introduce the concept of ORKG comparisons. ORKG comparisons provide machine-actionable overviews of related literature in a tabular form. Also, we present a methodology to leverage existing literature reviews to populate ORKG comparisons via a human-in-the-loop approach. Additionally, we show how ORKG comparisons can be used to form ORKG SmartReviews. The SmartReviews provide dynamic literature reviews in the form of living documents. They are an attempt address the main weaknesses of the current literature review practice and outline how the future of review publishing can look like. Third, we focus designing suitable tasks to generate scholarly knowledge in a crowdsourced setting. We present an intelligent user interface that enables researchers to annotate key sentences in scholarly publications with a set of discourse classes. During this process, researchers are assisted by suggestions coming from NLP tools. In addition, we present an approach to validate NLP-generated statements using microtasks in a crowdsourced setting. With this approach, we lower the barrier to entering data in the ORKG and transform content consumers into content creators. With the work presented, we strive to transform scholarly communication to improve machine-actionability of scholarly knowledge. The approaches and tools are deployed in a production environment. As a result, the majority of the presented approaches and tools are currently in active use by various research communities and already have an impact on scholarly communication.Die Zahl der wissenschaftlichen Veröffentlichungen nimmt jedes Jahr weiter zu, ebenso wie die Zahl der Zeitschriften und der aktiven Forscher. Daher werden Methoden und Werkzeuge zur Organisation von wissenschaftlichem Wissen immer wichtiger. Ohne solche Werkzeuge wird es immer schwieriger, Forschung effizient und effektiv zu betreiben. Eines der grundlegenden Probleme, mit denen die wissenschaftliche Kommunikation konfrontiert ist, betrifft das Format, in dem das Wissen publiziert wird. Die wissenschaftliche Kommunikation beruht in erster Linie auf narrativen, dokumentenbasierten Formaten, die speziell für Experten konzipiert sind. Maschinen können auf dieses Wissen nicht ohne weiteres zugreifen und es interpretieren, so dass Maschinen nicht in der Lage sind, leistungsfähige Werkzeuge zur effektiven Organisation von wissenschaftlichem Wissen bereitzustellen. In dieser Arbeit schlagen wir vor, Wissensgraphen zu nutzen, um wissenschaftliches Wissen darzustellen, zu kuratieren und zu nutzen. Die systematische Wissensrepräsentation führt zu maschinenverarbeitbarem Wissen. Dieses ermöglicht es Maschinen wissenschaftliches Wissen mit minimalem menschlichen Eingriff zu verarbeiten. Um den Wissensgraphen zu generieren und zu kuratieren, schlagen wir einen Crowdsourcing-Ansatz vor, der durch maschinelles Lernen unterstützt wird, insbesondere durch natürliche Sprachverarbeitung (NLP). Derzeit sind NLP-Techniken nicht in der Lage, qualitativ hochwertiges wissenschaftliches Wissen auf autonome Weise zu extrahieren. Mit unserem vorgeschlagenen Ansatz verknüpfen wir menschliche und maschinelle Intelligenz und nutzen so die Stärken beider Ansätze. Zunächst erörtern wir strukturiertes wissenschaftliches Wissen, wobei wir den Open Research Knowledge Graph (ORKG) vorstellen.Insbesondere konzentrieren wir uns auf das Design und die Entwicklung der ORKG-Benutzeroberfläche (das Frontend). Eine der größten Herausforderungen besteht darin, eine Schnittstelle bereitzustellen, die leistungsfähig genug ist, um umfangreiche Wissensbeschreibungen zu erstellen und gleichzeitig intuitiv genug ist für Forscher ohne technischen Hintergrund, um solche Beschreibungen zu erstellen. Der ORKG dient als technische Grundlage für die Arbeit. Zweitens konzentrieren wir uns auf vergleichbares wissenschaftliches Wissen, wofür wir das Konzept der ORKG-Vergleiche einführen. ORKG-Vergleiche bieten maschinell verwertbare Übersichten über verwandtes wissenschaftliches Wissen in tabellarischer Form. Außerdem stellen wir eine Methode vor, mit der vorhandene Literaturübersichten genutzt werden können, um ORKG-Vergleiche mit Hilfe eines Human-in-the-Loop-Ansatzes zu erstellen. Darüber hinaus zeigen wir, wie ORKG-Vergleiche verwendet werden können, um ORKG SmartReviews zu erstellen. Die SmartReviews bieten dynamische Literaturübersichten in Form von lebenden Dokumenten. Sie stellen einen Versuch dar, die Hauptschwächen der gegenwärtigen Praxis des Literaturreviews zu beheben und zu skizzieren, wie die Zukunft der Veröffentlichung von Reviews aussehen kann. Drittens konzentrieren wir uns auf die Gestaltung geeigneter Aufgaben zur Generierung von wissenschaftlichem Wissen in einer Crowdsourced-Umgebung. Wir stellen eine intelligente Benutzeroberfläche vor, die es Forschern ermöglicht, Schlüsselsätze in wissenschaftlichen Publikationen mittles Diskursklassen zu annotieren. In diesem Prozess werden Forschende mit Vorschlägen von NLP-Tools unterstützt. Darüber hinaus stellen wir einen Ansatz zur Validierung von NLP-generierten Aussagen mit Hilfe von Mikroaufgaben in einer Crowdsourced-Umgebung vor. Mit diesem Ansatz senken wir die Hürde für die Eingabe von Daten in den ORKG und setzen Inhaltskonsumenten als Inhaltsersteller ein. Mit der Arbeit streben wir eine Transformation der wissenschaftlichen Kommunikation an, um die maschinelle Verwertbarkeit von wissenschaftlichem Wissen zu verbessern. Die Ansätze und Werkzeuge werden in einer Produktionsumgebung eingesetzt. Daher werden die meisten der vorgestellten Ansätze und Werkzeuge derzeit von verschiedenen Forschungsgemeinschaften aktiv genutzt und haben bereits einen Einfluss auf die wissenschaftliche Kommunikation.EC/ERC/819536/E

Linked Research on the Decentralised Web

This thesis is about research communication in the context of the Web. I analyse literature which reveals how researchers are making use of Web technologies for knowledge dissemination, as well as how individuals are disempowered by the centralisation of certain systems, such as academic publishing platforms and social media. I share my findings on the feasibility of a decentralised and interoperable information space where researchers can control their identifiers whilst fulfilling the core functions of scientific communication: registration, awareness, certification, and archiving. The contemporary research communication paradigm operates under a diverse set of sociotechnical constraints, which influence how units of research information and personal data are created and exchanged. Economic forces and non-interoperable system designs mean that researcher identifiers and research contributions are largely shaped and controlled by third-party entities; participation requires the use of proprietary systems. From a technical standpoint, this thesis takes a deep look at semantic structure of research artifacts, and how they can be stored, linked and shared in a way that is controlled by individual researchers, or delegated to trusted parties. Further, I find that the ecosystem was lacking a technical Web standard able to fulfill the awareness function of research communication. Thus, I contribute a new communication protocol, Linked Data Notifications (published as a W3C Recommendation) which enables decentralised notifications on the Web, and provide implementations pertinent to the academic publishing use case. So far we have seen decentralised notifications applied in research dissemination or collaboration scenarios, as well as for archival activities and scientific experiments. Another core contribution of this work is a Web standards-based implementation of a clientside tool, dokieli, for decentralised article publishing, annotations and social interactions. dokieli can be used to fulfill the scholarly functions of registration, awareness, certification, and archiving, all in a decentralised manner, returning control of research contributions and discourse to individual researchers. The overarching conclusion of the thesis is that Web technologies can be used to create a fully functioning ecosystem for research communication. Using the framework of Web architecture, and loosely coupling the four functions, an accessible and inclusive ecosystem can be realised whereby users are able to use and switch between interoperable applications without interfering with existing data. Technical solutions alone do not suffice of course, so this thesis also takes into account the need for a change in the traditional mode of thinking amongst scholars, and presents the Linked Research initiative as an ongoing effort toward researcher autonomy in a social system, and universal access to human- and machine-readable information. Outcomes of this outreach work so far include an increase in the number of individuals self-hosting their research artifacts, workshops publishing accessible proceedings on the Web, in-the-wild experiments with open and public peer-review, and semantic graphs of contributions to conference proceedings and journals (the Linked Open Research Cloud). Some of the future challenges include: addressing the social implications of decentralised Web publishing, as well as the design of ethically grounded interoperable mechanisms; cultivating privacy aware information spaces; personal or community-controlled on-demand archiving services; and further design of decentralised applications that are aware of the core functions of scientific communication

Automatic rule verification for digital building permits

Dissertação de mestrado em Modelação de Informação na Construção de Edifícios BIM A+O sector da construção está a enfrentar grandes mudanças nas exigências do cliente e do mercado, empurrando para a transformação digital e para uma indústria orientada para os dados. Os governos tomaram parte ativa nesta mudança, apoiando a digitalização de processos como o das licenças de construção, introduzindo a utilização de modelos de informação de construção (BIM). A investigação sobre a digitalização do licenciamento municipal de construções mostrou grandes avanços no que diz respeito à extração de regras de forma interpretável e à automatização de verificações; contudo, a conciliação entre as definições semânticas do modelo de construção e os conceitos definidos nos regulamentos está ainda em discussão. Além disso, a validação da acuidade das informações incluídas nos modelos de construção relativamente às definições do regulamento é importante para garantir a qualidade ao longo do processo de licença de construção. Esta dissertação visa propor um fluxo de trabalho híbrido para verificar a informação extraída explicitamente do modelo BIM e a informação implicitamente derivada das relações entre elementos, seguindo as disposições contidas nos regulamentos no contexto de Portugal. Com base em alguma revisão de literatura, foi proposto um novo processo, e foi desenvolvido um código Python utilizando a biblioteca IfcOpenshell para apoiar a automatização do processo de verificação, tradicionalmente realizada por técnicos nos gabinetes de licenciamento municipal. Os elementos desenvolvidos neste documento foram comprovados num estudo de caso, demonstrando que a validação híbrida pode ajudar a detetar erros de modelação e melhorar a acuidade da informação durante a apresentação inicial de modelos para um processo de licença de construção. Os resultados indicam que a inclusão de uma validação automática do modelo contra definições regulamentares pode ser introduzida para melhorar o grau de certeza da qualidade da informação contida no Modelo de Informação, além disso, a proposta de métodos que produzem resultados a partir de informação implícita pode alargar as capacidades do esquema IFC. Contudo, os esquemas desenvolvidos neste trabalho estão ainda em constante revisão e desenvolvimento e têm limitações de aplicabilidade em relação a certas classes do IFC.The construction sector is facing major changes in the client and market requirements, pushing towards the digital transformation and a data driven industry. Governments have taken an active part in this change by supporting the digitalization of processes such as the one for building permits by introducing the use of building information models (BIM). The research on the digitalization of the building permit has shown great advancements in regarding the rule extraction in interpretable ways and the automation of the verification; however, the conciliation between the building model semantic definitions and the concepts defined in the regulations is still in discussion. Moreover, the validation of the correctness of the information included in building models regarding the regulation definitions is important to guarantee the quality along the digital building permit process. This dissertation aims to propose a hybrid workflow to check the information extracted explicitly from the BIM model and the information implicitly derived from relationships between elements by following the provisions contained in the regulations in the context of Portugal. Based on some context and literature review, a process reengineering was proposed, and a Python code was developed using the IfcOpenShell library to support the automation of the verification process, traditionally carried out by technicians in the building permit offices. The elements developed in this document were proven in a case-study, demonstrating that the hybrid validation can help to detect modelling errors and improve the certainty of correctness of information during the initial submission of models for a building permit process. The results indicate that the inclusion of an automated validation of the model against regulation definitions can be introduced to improve the degree of certainty of the quality of the information contained in the Building Information Model, moreover the proposal of methods that produce results from implicit information can extend the capabilities of the IFC schema. However, the scripts developed in this work are still under constant review and development and have limitations of applicability in relation to certain IFC classes.Erasmus Mundus Joint Master Degree Programme – ERASMUS