Tobias Kuhn

The FAIR Guiding Principles for scientific data management and stewardship

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

Attempto Controlled English for Knowledge Representation

Attempto Controlled English (ACE) is a controlled natural language, i.e. a precisely defined subset of English that can automatically and unambiguously be translated into first-order logic. ACE may seem to be completely natural, but is actually a formal language, concretely it is a first-order logic language with an English syntax. Thus ACE is human and machine understandable. ACE was originally intended to specify software, but has since been used as a general knowledge representation language in several application domains, most recently for the semantic web. ACE is supported by a number of tools, predominantly by the Attempto Parsing Engine (APE) that translates ACE texts into Discourse Representation Structures (DRS), a variant of first-order logic. Other tools include the Attempto Reasoner RACE, the AceRules system, the ACE View plug-in for the Protege ontology editor, AceWiki, and the OWL verbaliser.

A survey and classification of controlled natural languages

What is here called controlled natural language (CNL) has traditionally been given many different names. Especially during the last four decades, a wide variety of such languages have been designed. They are applied to improve communication among humans, to improve translation, or to provide natural and intuitive representations for formal notations. Despite the apparent differences, it seems sensible to put all these languages under the same umbrella. To bring order to the variety of languages, a general classification scheme is presented here. A comprehensive survey of existing English-based CNLs is given, listing and describing 100 languages from 1930 until today. Classification of these languages reveals that they form a single scattered cloud filling the conceptual space between natural languages such as English on the one end and formal languages such as propositional logic on the other. The goal of this article is to provide a common terminology and a common model for CNL, to contribute to the understanding of their general nature, to provide a starting point for researchers interested in the area, and to help developers to make design decisions.

On controlled natural languages: properties and prospects

This collaborative report highlights the properties and prospects of Controlled Natural Languages (CNLs). The report poses a range of questions concerning the goals of the CNL, the design, the linguistic aspects, the relationships and evaluation of CNLs, and the application tools. In posing the questions, the report attempts to structure the field of CNLs and to encourage further systematic discussion by researchers and developers.

Inheritance Patterns in Citation Networks Reveal Scientific Memes

Memes are the cultural equivalent of genes that spread across human culture by means of imitation. What makes a meme and what distinguishes it from other forms of information, however, is still poorly understood. Our analysis of memes in the scientific literature reveals that they are governed by a surprisingly simple relationship between frequency of occurrence and the degree to which they propagate along the citation graph. We propose a simple formalization of this pattern and validate it with data from close to 50 million publication records from the Web of Science, PubMed Central, and the American Physical Society. Evaluations relying on human annotators, citation network randomizations, and comparisons with several alternative approaches confirm that our formula is accurate and effective, without a dependence on linguistic or ontological knowledge and without the application of arbitrary thresholds or filters.

Writing clinical practice guidelines in controlled natural language

Clinicians could benefit from decision support systems incorporating the knowledge contained in clinical practice guidelines. However, the unstructured form of these guidelines makes them unsuitable for formal representation. To address this challenge we translated a complete set of pediatric guideline recommendations into Attempto Controlled English (ACE). One experienced pediatrician, one physician and a knowledge engineer assessed that a suitably extended version of ACE can accurately and naturally represent the clinical concepts and the proposed actions of the guidelines. Currently, we are developing a systematic and replicable approach to authoring guideline recommendations in ACE.

AceRules: executing rules in controlled natural language

Expressing rules in controlled natural language can bring us closer to the vision of the Semantic Web since rules can be written in the notation of the application domain and are understandable by anybody. AceRules is a prototype of a rule system with a multisemantics architecture. It demonstrates the formal representation of rules using the controlled natural language ACE. We show that a rule language can be executable and easily understandable at the same time. AceRules is available via a web service and two web interfaces.

A Principled Approach to Grammars for Controlled Natural Languages and Predictive Editors

Controlled natural languages (CNL) with a direct mapping to formal logic have been proposed to improve the usability of knowledge representation systems, query interfaces, and formal specifications. Predictive editors are a popular approach to solve the problem that CNLs are easy to read but hard to write. Such predictive editors need to be able to “look ahead” in order to show all possible continuations of a given unfinished sentence. Such lookahead features, however, are difficult to implement in a satisfying way with existing grammar frameworks, especially if the CNL supports complex nonlocal structures such as anaphoric references. Here, methods and algorithms are presented for a new grammar notation called Codeco, which is specifically designed for controlled natural languages and predictive editors. A parsing approach for Codeco based on an extended chart parsing algorithm is presented. A large subset of Attempto Controlled English has been represented in Codeco. Evaluation of this grammar and the parser implementation shows that the approach is practical, adequate and efficient.

A Multilingual Semantic Wiki Based on Attempto Controlled English and Grammatical Framework

We describe a semantic wiki system with an underlying controlled natural language grammar implemented in Grammatical Framework (GF). The grammar restricts the wiki content to a well-defined subset of Attempto Controlled English (ACE), and facilitates a precise bidirectional automatic translation between ACE and language fragments of a number of other natural languages, making the wiki content accessible multilingually. Additionally, our approach allows for automatic translation into the Web Ontology Language (OWL), which enables automatic reasoning over the wiki content. The developed wiki environment thus allows users to build, query and view OWL knowledge bases via a user-friendly multilingual natural language interface. As a further feature, the underlying multilingual grammar is integrated into the wiki and can be collaboratively edited to extend the vocabulary of the wiki or even customize its sentence structures. This work demonstrates the combination of the existing technologies of Attempto Controlled English and Grammatical Framework, and is implemented as an extension of the existing semantic wiki engine AceWiki.

Broadening the Scope of Nanopublications

In this paper, we present an approach for extending the existing concept of nanopublications — tiny entities of scientific results in RDF representation — to broaden their application range. The proposed extension uses English sentences to represent informal and underspecified scientific claims. These sentences follow a syntactic and semantic scheme that we call AIDA (Atomic, Independent, Declarative, Absolute), which provides a uniform and succinct representation of scientific assertions. Such AIDA nanopublications are compatible with the existing nanopublication concept and enjoy most of its advantages such as information sharing, interlinking of scientific findings, and detailed attribution, while being more flexible and applicable to a much wider range of scientific results. We show that users are able to create AIDA sentences for given scientific results quickly and at high quality, and that it is feasible to automatically extract and interlink AIDA nanopublications from existing unstructured data sources. To demonstrate our approach, a web-based interface is introduced, which also exemplifies the use of nanopublications for non-scientific content, including meta-nanopublications that describe other nanopublications.