Guidelines for writing definitions in ontologies

Ontologies are being used increasingly to promote the reusability of scientific information by allowing heterogeneous data to be integrated under a common, normalized representation. Definitions play a central role in the use of ontologies both by humans and by computers. Textual definitions allow ontologists and data curators to understand the intended meaning of ontology terms and to use these terms in a consistent fashion across contexts. Logical definitions allow machines to check the integrity of ontologies and reason over data annotated with ontology terms to make inferences that promote knowledge discovery. Therefore, it is important not only to include in ontologies multiple types of definitions in both formal and in natural languages, but also to ensure that these definitions meet good quality standards so they are useful. While tools such as Protégé can assist in creating well-formed logical definitions, producing good definitions in a natural language is still to a large extent a matter of human ingenuity supported at best by just a small number of general principles. For lack of more precise guidelines, definition authors are often left to their own personal devices. This paper aims to fill this gap by providing the ontology community with a set of principles and conventions to assist in definition writing, editing, and validation, by drawing on existing definition writing principles and guidelines in lexicography, terminology, and logic

Definitions in ontologies

Definitions vary according to context of use and target audience. They must be made relevant for each context to fulfill their cognitive and linguistic goals. This involves adapting their logical structure, type of content, and form to each context of use. We examine from these perspectives the case of definitions in ontologies

The functions of definitions in ontologies

To understand what ontologies do through their definitions, we propose a theoretical explanation of the functions of definitions in ontologies backed by empirical neuropsychological studies. Our goal is to show how these functions should motivate (i) the systematic inclusion of definitions in ontologies and (ii) the adaptation of definition content and form to the specific context of use of ontologies

Création de clusters sémantiques dans des familles morphologiques à partir du TLFi

National audienceBuilding lexical resources is a time-consuming and expensive task, mainly when it comes to morphological lexicons. Such resources describe in depth and explicitly the morphological organization of the lexicon, completed with semantic information to be used in NLP applications. The work we present here goes on such direction, and especially, on refining an existing resource with automatically acquired semantic information. Our goal is to semantically characterize morpho-phonological families (words sharing a same base form and semantic continuity). To this end, we have used data from the TLFi which has been morpho-syntactically annotated. The first results of such a task will be analyzed and discussed.La constitution de ressources linguistiques est une tâche longue et coûteuse. C'est notamment le cas pour les ressources morphologiques. Ces ressources décrivent de façon approfondie et explicite l'organisation morphologique du lexique complétée d'informations sémantiques exploitables dans le domaine du TAL. Le travail que nous présentons dans cet article s'inscrit dans cette perspective et, plus particulièrement, dans l'optique d'affiner une ressource existante en s'appuyant sur des informations sémantiques obtenues automatiquement. Notre objectif est de caractériser sémantiquement des familles morpho-phonologiques (des mots partageant une même racine et une continuité de sens). Pour ce faire, nous avons utilisé des informations extraites du TLFi annoté morpho-syntaxiquement. Les premiers résultats de ce travail seront analysés et discutés

SmaRT visualisation of legal rules for compliance

This paper presents a visualization technique to assist legal experts in formalising their interpretation of legal texts in terms of regulatory requirements. (Semi-)automation of compliance processes requires a machine-readable version of legal requirements in a format that enables effective compliance assessment. The use of a semi-structured controlled natural language as an intermediate step of the translation from a human-readable text to a machine-readable and understandable format ensures that the process of interpretation of those requirements is as simple as possible. However, it does not ensure that the formal representation resulting from the interpretation faithfully represents the intended semantics provided by the legal expert. Visualization techniques such as property graphs in Neo4j could fill this gap, allowing legal experts to understand and control the formal representation of the result of their act of interpretation

Genetic and Epigenetic Characteristics of Inflammatory Bowel Disease–Associated Colorectal Cancer

doi: 10.1053/j.gastro.2021.04.042Background & Aims Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder associated with an elevated risk of colorectal cancer (CRC). IBD-associated CRC (IBD-CRC) may represent a distinct pathway of tumorigenesis compared to sporadic CRC (sCRC). Our aim was to comprehensively characterize IBD-associated tumorigenesis integrating multiple high-throughput approaches, and to compare the results with in-house data sets from sCRCs. Methods Whole-genome sequencing, single nucleotide polymorphism arrays, RNA sequencing, genome-wide methylation analysis, and immunohistochemistry were performed using fresh-frozen and formalin-fixed tissue samples of tumor and corresponding normal tissues from 31 patients with IBD-CRC. Results Transcriptome-based tumor subtyping revealed the complete absence of canonical epithelial tumor subtype associated with WNT signaling in IBD-CRCs, dominated instead by mesenchymal stroma-rich subtype. Negative WNT regulators AXIN2 and RNF43 were strongly down-regulated in IBD-CRCs and chromosomal gains at HNF4A, a negative regulator of WNT-induced epithelial–mesenchymal transition (EMT), were less frequent compared to sCRCs. Enrichment of hypomethylation at HNF4α binding sites was detected solely in sCRC genomes. PIGR and OSMR involved in mucosal immunity were dysregulated via epigenetic modifications in IBD-CRCs. Genome-wide analysis showed significant enrichment of noncoding mutations to 5′untranslated region of TP53 in IBD-CRCs. As reported previously, somatic mutations in APC and KRAS were less frequent in IBD-CRCs compared to sCRCs. Conclusions Distinct mechanisms of WNT pathway dysregulation skew IBD-CRCs toward mesenchymal tumor subtype, which may affect prognosis and treatment options. Increased OSMR signaling may favor the establishment of mesenchymal tumors in patients with IBD.BACKGROUND & AIMS: Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder associated with an elevated risk of colorectal cancer (CRC). IBD-associated CRC (IBD-CRC) may represent a distinct pathway of tumorigenesis compared to sporadic CRC (sCRC). Our aim was to comprehensively characterize IBD-associated tumorigenesis integrating multiple high-throughput approaches, and to compare the results with in-house data sets from sCRCs. METHODS: Whole-genome sequencing, single nucleotide polymorphism arrays, RNA sequencing, genome-wide methylation analysis, and immunohistochemistry were performed using fresh-frozen and formalin-fixed tissue samples of tumor and corresponding normal tissues from 31 patients with IBD-CRC. RESULTS: Transcriptome-based tumor subtyping revealed the complete absence of canonical epithelial tumor subtype associated with WNT signaling in IBD-CRCs, dominated instead by mesenchymal stroma-rich subtype. Negative WNT regulators AXIN2 and RNF43 were strongly down-regulated in IBD-CRCs and chromosomal gains at HNF4A, a negative regulator of WNTinduced epithelial-mesenchymal transition (EMT), were less frequent compared to sCRCs. Enrichment of hypomethylation at HNF4 alpha binding sites was detected solely in sCRC genomes. PIGR and OSMR involved in mucosal immunity were dysregulated via epigenetic modifications in IBD-CRCs. Genome-wide analysis showed significant enrichment of noncoding mutations to 50 untranslated region of TP53 in IBD-CRCs. As reported previously, somatic mutations in APC and KRAS were less frequent in IBD-CRCs compared to sCRCs. CONCLUSIONS: Distinct mechanisms of WNT pathway dysregulation skew IBD-CRCs toward mesenchymal tumor subtype, which may affect prognosis and treatment options. Increased OSMR signaling may favor the establishment of mesenchymal tumors in patients with IBD.Peer reviewe

Improving the Quality and Utility of Electronic Health Record Data through Ontologies

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs

A Proposal for a Framework to Evaluate Feature Relevance for Terminographic Definitions

In this paper, a terminological framework, both theoretical and methodological, backed by empirical data, is proposed in order to highlight the particular questions to which attention should be paid when conceiving an evaluation scheme for definition extraction (DE) in terminology. The premise is that not just any information is relevant to defining a given concept in a given expert domain. Therefore, evaluation guidelines applicable to DE should integrate some understanding of what is relevant for terminographic definitions and in which cases. This, in turn, requires some understanding of the mechanisms of feature selection. An explanatory hypothesis of feature relevance is then put forward and one of its aspects examined, to see to what extent the example considered may serve as a relevance referential. To conclude, a few methodological proposals for automating the application of relevance tests are discussed. The overall objective is to explore ways of empirically testing broader theoretical hypotheses and principles that should orient the conception of general guidelines to evaluate DE for terminographic purposes

Repérage automatique de génériques dans les définitions terminographiques

Cet article présente une procédure de repérage et de balisage de l'élément générique de la définition terminographique exploitant les caractéristiques formelles du sous langage définitoire. La procédure, qui comporte quatre étapes, constitue l'une des sous tâches d'un analyseur (semi-)automatique de la structure conceptuelle des définitions terminographiques, destiné à faciliter l'annotation d'un corpus en vue de l'étude de régularités dans cette structure. La tâche décrite consiste à mettre au point un système d'annotation automatique basé sur le repérage d'indices morphosyntaxiques, sans recourir à d'autres ressources linguistiques informatisées