Applications of Natural Language Processing in Biodiversity Science

Centuries of biological knowledge are contained in the massive body of scientific literature, written for human-readability but too big for any one person to consume. Large-scale mining of information from the literature is necessary if biology is to transform into a data-driven science. A computer can handle the volume but cannot make sense of the language. This paper reviews and discusses the use of natural language processing (NLP) and machine-learning algorithms to extract information from systematic literature. NLP algorithms have been used for decades, but require special development for application in the biological realm due to the special nature of the language. Many tools exist for biological information extraction (cellular processes, taxonomic names, and morphological characters), but none have been applied life wide and most still require testing and development. Progress has been made in developing algorithms for automated annotation of taxonomic text, identification of taxonomic names in text, and extraction of morphological character information from taxonomic descriptions. This manuscript will briefly discuss the key steps in applying information extraction tools to enhance biodiversity science

Using ontology and semantic web services to support modeling in systems biology

This thesis addresses the problem of collaboration among experimental biologists and modelers in the study of systems biology by using ontology and Semantic Web Services techniques. Modeling in systems biology is concerned with using experimental information and mathematical methods to build quantitative models across different biological scales. This requires interoperation among various knowledge sources and services. Ontology and Semantic Web Services potentially provide an infrastructure to meet this requirement. In our study, we propose an ontology-centered framework within the Semantic Web infrastructure that aims at standardizing various areas of knowledge involved in the biological modeling processes. In this framework, first we specify an ontology-based meta-model for building biological models. This meta-model supports using shared biological ontologies to annotate biological entities in the models, allows semantic queries and automatic discoveries, enables easy model reuse and composition, and serves as a basis to embed external knowledge. We also develop means of transforming biological data sources and data analysis methods into Web Services. These Web Services can then be composed together to perform parameterization in biological modeling. The knowledge of decision-making and workflow of parameterization processes are then recorded by the semantic descriptions of these Web Services, and embedded in model instances built on our proposed meta-model. We use three cases of biological modeling to evaluate our framework. By examining our ontology-centered framework in practice, we conclude that by using ontology to represent biological models and using Semantic Web Services to standardize knowledge components in modeling processes, greater capabilities of knowledge sharing, reuse and collaboration can be achieved. We also conclude that ontology-based biological models with formal semantics are essential to standardize knowledge in compliance with the Semantic Web vision

Validation and Evaluation

In this technical report, we present prototypical implementations of innovative tools and methods for personalized and contextualized (multimedia) search, collaborative ontology evolution, ontology evaluation and cost models, and dynamic access and trends in distributed (semantic) knowledge, developed according to the working plan outlined in Technical Report TR-B-12-04. The prototypes complete the next milestone on the path to an integral Corporate Semantic Web architecture based on the three pillars Corporate Ontology Engineering, Corporate Semantic Collaboration, and Corporate Semantic Search, as envisioned in TR-B-08-09

The Lexicon Graph Model : a generic model for multimodal lexicon development

Trippel T. The Lexicon Graph Model : a generic model for multimodal lexicon development. Bielefeld (Germany): Bielefeld University; 2006.Das Lexicon Graph Model stellt ein Modell für Lexika dar, die korpusbasiert sein können und multimodale Informationen enthalten. Hierbei wird die Perspektive der Lexikontheorie eingenommen, wobei die zugrundeliegenden Datenstrukturen sowohl vom Lexikon als auch von Annotationen betrachtet werden. Letztere fallen dadurch in das Blickfeld, weil sie als Grundlage für die Erstellung von Lexika gesehen werden. Der Begriff des Lexikons bezieht sich hier sowohl auf den Bereich des Wörterbuchs als auch der in elektronischen Applikationen integrierten Lexikondatenbanken. Die existierenden Formalismen und Ansätze der Lexikonentwicklung zeigen verschiedene Probleme im Zusammenhang mit Lexika auf, etwa die Zusammenfassung von existierenden Lexika zu einem, die Disambiguierung von Mehrdeutigkeiten im Lexikon auf verschiedenen lexikalischen Ebenen, die Repräsentation von anderen Modalitäten im Lexikon, die Selektion des lexikalischen Schlüsselbegriffs für Lexikonartikel, etc. Der vorliegende Ansatz geht davon aus, dass sich Lexika zwar in ihrem Inhalt, nicht aber in einer grundlegenden Struktur unterscheiden, so dass verschiedenartige Lexika im Rahmen eines Unifikationsprozesses dublettenfrei miteinander verbunden werden können. Hieraus resultieren deklarative Lexika. Für Lexika können diese Graphen mit dem Lexikongraph-Modell wie hier dargestellt modelliert werden. Dabei sind Lexikongraphen analog den von Bird und Libermann beschriebenen Annotationsgraphen gesehen und können daher auch ähnlich verarbeitet werden. Die Untersuchung des Lexikonformalismus beruht auf vier Schritten. Zunächst werden existierende Lexika analysiert und beschrieben. Danach wird mit dem Lexikongraph-Modell eine generische Darstellung von Lexika vorgestellt, die auch implementiert und getestet wird. Basierend auf diesem Formalismus wird die Beziehung zu Annotationsgraphen hergestellt, wobei auch beschrieben wird, welche Maßstäbe an angemessene Annotationen für die Verwendung zur Lexikonentwicklung angelegt werden müssen.The Lexicon Graph Model provides a model and framework for lexicons that can be corpus based and contain multimodal information. The focus is more from the lexicon theory perspective, looking at the underlying data structures that are part of existing lexicons and corpora. The term lexicon in linguistics and artificial intelligence is used in different ways, including traditional print dictionaries in book form, CD-ROM editions, Web based versions of the same, but also computerized resources of similar structures to be used by applications. These applications cover systems for human-machine communication as well as spell checkers. The term lexicon in this work is used as the most generic term covering all lexical applications. Existing formalisms in lexicon development show different problems with lexicons, for example combining different kinds of lexical resources, disambiguation on different lexical levels, the representation of different modalities in a lexicon. The Lexicon Graph Model presupposes that lexicons can have different structures but have fundamentally a similar structure, making it possible to combine lexicons in a unification process, resulting in a declarative lexicon. The underlying model is a graph, the Lexicon Graph, which is modeled similar to Annotation Graphs as described by Bird and Libermann. The investigation of the lexicon formalism contains four steps, that is the analysis of existing lexicons, the introduction of the Lexicon Graph Model as a generic representation for lexicons, the implementation of the formalism in different contexts and an evaluation of the formalism. It is shown that Annotation Graphs and Lexicon Graphs are indeed related not only in their formalism and it is shown, what standards have to be applied to annotations to be usable for lexicon development

Semantics for virtual humans

Population of Virtual Worlds with Virtual Humans is increasing rapidly by people who want to create a virtual life parallel to the real one (i.e. Second Life). The evolution of technology is smoothly providing the necessary elements to increase realism within these virtual worlds by creating believable Virtual Humans. However, creating the amount of resources needed to succeed this believability is a difficult task, mainly because of the complexity of the creation process of Virtual Humans. Even though there are many existing available resources, their reusability is difficult because there is not enough information provided to evaluate if a model contains the desired characteristics to be reused. Additionally, the knowledge involved in the creation of Virtual Humans is not well known, nor well disseminated. There are several different creation techniques, different software components, and several processes to carry out before having a Virtual Human capable of populating a virtual environment. The creation of Virtual Humans involves: a geometrical representation with an internal control structure, the motion synthesis with different animation techniques, higher level controllers and descriptors to simulate human-like behavior such individuality, cognition, interaction capabilities, etc. All these processes require the expertise from different fields of knowledge such as mathematics, artificial intelligence, computer graphics, design, etc. Furthermore, there is neither common framework nor common understanding of how elements involved in the creation, development, and interaction of Virtual Humans features are done. Therefore, there is a need for describing (1) existing resources, (2) Virtual Human's composition and features, (3) a creation pipeline and (4) the different levels/fields of knowledge comprehended. This thesis presents an explicit representation of the Virtual Humans and their features to provide a conceptual framework that will interest to all people involved in the creation and development of these characters. This dissertation focuses in a semantic description of Virtual Humans. The creation of a semantic description involves gathering related knowledge, agreement among experts in the definition of concepts, validation of the ontology design, etc. In this dissertation all these procedures are presented, and an Ontology for Virtual Humans is described in detail together with the validations that conducted to the resulted ontology. The goal of creating such ontology is to promote reusability of existing resources; to create a shared knowledge of the creation and composition of Virtual Humans; and to support new research of the fields involved in the development of believable Virtual Humans and virtual environments. Finally, this thesis presents several developments that aim to demonstrate the ontology usability and reusability. These developments serve particularly to support the research on specialized knowledge of Virtual Humans, the population of virtual environments, and improve the believability of these characters

LifeWatch deliverable 5.1.3: Technical construction plan –Reference Model

The LifeWatch Reference Model (LifeWatch-RM) provides a common conceptual framework for understanding the significant relations and key characteristics of the Information and Communications Technologies (ICT) elements of LifeWatch that should appear consistently across different implementations. Its intention is to represent a common view of the ICT dimension between all those involved in and contributing to the LifeWatch Research Infrastructure and to provide guidelines for the construction and management process. The LifeWatch-RM defines a number of components and architectural concepts as a basis for the future LifeWatch Architecture. It is neither a blueprint nor does it define a technological mapping, but identifies some key aspects and components that should be present in the final implementation of the LifeWatch System

Graph Data-Models and Semantic Web Technologies in Scholarly Digital Editing

This volume is based on the selected papers presented at the Workshop on Scholarly Digital Editions, Graph Data-Models and Semantic Web Technologies, held at the Uni- versity of Lausanne in June 2019. The Workshop was organized by Elena Spadini (University of Lausanne) and Francesca Tomasi (University of Bologna), and spon- sored by the Swiss National Science Foundation through a Scientific Exchange grant, and by the Centre de recherche sur les lettres romandes of the University of Lausanne. The Workshop comprised two full days of vibrant discussions among the invited speakers, the authors of the selected papers, and other participants.1 The acceptance rate following the open call for papers was around 60%. All authors – both selected and invited speakers – were asked to provide a short paper two months before the Workshop. The authors were then paired up, and each pair exchanged papers. Paired authors prepared questions for one another, which were to be addressed during the talks at the Workshop; in this way, conversations started well before the Workshop itself. After the Workshop, the papers underwent a second round of peer-review before inclusion in this volume. This time, the relevance of the papers was not under discus- sion, but reviewers were asked to appraise specific aspects of each contribution, such as its originality or level of innovation, its methodological accuracy and knowledge of the literature, as well as more formal parameters such as completeness, clarity, and coherence. The bibliography of all of the papers is collected in the public Zotero group library GraphSDE20192, which has been used to generate the reference list for each contribution in this volume. The invited speakers came from a wide range of backgrounds (academic, commer- cial, and research institutions) and represented the different actors involved in the remediation of our cultural heritage in the form of graphs and/or in a semantic web en- vironment. Georg Vogeler (University of Graz) and Ronald Haentjens Dekker (Royal Dutch Academy of Sciences, Humanities Cluster) brought the Digital Humanities research perspective; the work of Hans Cools and Roberta Laura Padlina (University of Basel, National Infrastructure for Editions), as well as of Tobias Schweizer and Sepi- deh Alassi (University of Basel, Digital Humanities Lab), focused on infrastructural challenges and the development of conceptual and software frameworks to support re- searchers’ needs; Michele Pasin’s contribution (Digital Science, Springer Nature) was informed by his experiences in both academic research, and in commercial technology companies that provide services for the scientific community. The Workshop featured not only the papers of the selected authors and of the invited speakers, but also moments of discussion between interested participants. In addition to the common Q&A time, during the second day one entire session was allocated to working groups delving into topics that had emerged during the Workshop. Four working groups were created, with four to seven participants each, and each group presented a short report at the end of the session. Four themes were discussed: enhancing TEI from documents to data; ontologies for the Humanities; tools and infrastructures; and textual criticism. All of these themes are represented in this volume. The Workshop would not have been of such high quality without the support of the members of its scientific committee: Gioele Barabucci, Fabio Ciotti, Claire Clivaz, Marion Rivoal, Greta Franzini, Simon Gabay, Daniel Maggetti, Frederike Neuber, Elena Pierazzo, Davide Picca, Michael Piotrowski, Matteo Romanello, Maïeul Rouquette, Elena Spadini, Francesca Tomasi, Aris Xanthos – and, of course, the support of all the colleagues and administrative staff in Lausanne, who helped the Workshop to become a reality. The final versions of these papers underwent a single-blind peer review process. We want to thank the reviewers: Helena Bermudez Sabel, Arianna Ciula, Marilena Daquino, Richard Hadden, Daniel Jeller, Tiziana Mancinelli, Davide Picca, Michael Piotrowski, Patrick Sahle, Raffaele Viglianti, Joris van Zundert, and others who preferred not to be named personally. Your input enhanced the quality of the volume significantly! It is sad news that Hans Cools passed away during the production of the volume. We are proud to document a recent state of his work and will miss him and his ability to implement the vision of a digital scholarly edition based on graph data-models and semantic web technologies. The production of the volume would not have been possible without the thorough copy-editing and proof reading by Lucy Emmerson and the support of the IDE team, in particular Bernhard Assmann, the TeX-master himself. This volume is sponsored by the University of Bologna and by the University of Lausanne. Bologna, Lausanne, Graz, July 2021 Francesca Tomasi, Elena Spadini, Georg Vogele