FAIR data presupposes their successful communication between machines and humans while preserving meaning reference, requiring all parties involved to share the same background knowledge. Inspired by English as a natural language, we investigate linguistic structure that ensures reliable of information draw parallels with structures, understanding both models systems interest. We conceptualize semantic interoperability comprising terminological propositional interoperability. The former...


 The current COVID-19 pandemic emphasizes the use of so-called preprints - a type publication that is not subject to peer review. Due its global relevance, there an immense number COVID-19-related every day. To help researchers find relevant information, we have developed semantic search engine preVIEW, it integrates from currently seven different preprint servers. For indexing, implemented various text mining components tag, for example, diseases or SARS-CoV-2 specific proteins. While...

We introduce Semantic Ontology-Controlled application for web Content Management Systems (SOCCOMAS), a development framework FAIR ('findable', 'accessible', 'interoperable', 'reusable') Web (S-WCMSs). Each S-WCMS run by SOCCOMAS has its contents managed through corresponding knowledge base that stores all data and metadata in the form of semantic graphs Jena tuple store. Automated procedures track provenance, user contributions detailed change history. is accessible via both graphical...

We demonstrate the early prototype of a new module for Morph∙D∙Base that allows generation highly formalized semantic morphological descriptions (http://escience.biowikifarm.net/wiki/EScience-Compliant_Standards_for_Morphology). The resulting follow individuals-based Instance Anatomy data scheme (as opposed to class-based Semantic Phenotypes scheme). description specimen's anatomy by generating granular representation parts specimen be described, using ontology-terms from known ontologies....

Currently, morphological data and metadata are still mostly published as unstructured free texts, which lack semantic transparency, cannot be parsed by computers, do not comply with the FAIR (Findable, Accessible, Interoperable, Reusable; Wilkinson et al. (2016) principles, thus hampering their reuse non-experts integration across many fields in life sciences. With an ever-increasing amount of available ontologies development adequate technology, however, a solution to this problem becomes...

Ontologies are usually utilized for representing knowledge. Here, we extend this use and demonstrate that ontologies also can be used describing controlling semantic Web-Content-Management-Systems (WCMS). We call the resulting application SOCCOMAS: a self-describing content-independent ontology-controlled (http://escience.biowikifarm.net/wiki/SOCCOMAS). SOCCOMAS manages contents of its WCMS through corresponding knowledge base is stored in tuple store. It makes accessible via flexible...

Providing data in a semantically structured format has become the gold standard science. However, significant amount of is still provided as unstructured text - either because it legacy or adequate tools for storing and disseminating are missing. We have developed description module Morph∙D∙Base, semantic knowledge base taxonomic morphologic data, that enables users to generate highly standardized formalized descriptions anatomical entities using free ontology-based descriptions. The main...

The National Research Data Infrastructure (NFDI) strives to develop FAIR research data and services for major scientific disciplines, using terminologies as a key factor semantic annotations interoperability of data. Several NFDI consortia provide domain-specific through Terminology or registries, offering access, search capabilities, visualization, downloads. Prioritizing user-friendly terminology seamlessly integrate concepts into applications, often operating in the background enable...

SOCCOMAS is a ready-to-use Semantic Ontology-Controlled Content Management System (http://escience.biowikifarm.net/wiki/SOCCOMAS). Each web content management system (WCMS) run by controlled set of ontologies and an accompanying Java-based middleware with the data housed in Jena tuple store. The describe behavior WCMS, including all its input forms, controls, schemes workflow processes (Fig. 1). Data organized into different types entries, which represent collections referring to particular...

The landscape of currently existing repositories specimen data consists isolated islands, with each applying its own underlying model. Using standardized protocols such as DarwinCore or ABCD, and metadata are exchanged published on web portals GBIF. However, models differ across repositories. This can lead to problems when comparing integrating content from different systems. for example, in one system there is a field the label 'determination', another 'taxonomic identification'. Both might...