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Ontology Researcher

Mo. 08.08.2022
Sankt Augustin
Location: Sankt Augustin Ontology Researcher The Fraunhofer-Gesellschaft currently operates 76 institutes and research institutions throughout Germany and is the world's leading applied research organization. Around 30,000 employees work with an annual research budget of 2.9 billion euros. Fraunhofer is one of Europe's largest and most well-known non-profit research organizations. Fraunhofer's mission is to bridge academia and industry via translational research. Fraunhofer has been awarded as top employer in the categories “research“ and “public sector“ in 2019. The Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) is part of the Fraunhofer Society, focuses on the development of innovative approaches in computational sciences and brings them into industrial practice. The institute has currently around 200 employees.Fraunhofer SCAI is looking to employ an Ontology Researcher to join the Applied Semantics group. The Applied Semantics group within the Department of Bioinformatics is dedicated to the development and application of semantic technologies in the field of biomedicine, with a strong focus on neurogenerative and psychiatric diseases.The work of the Applied Semantics group covers a value chain ranging from building and validating semantic technologies in text-mining applications, for the construction of indication-specific knowledge graphs, and the interoperability and harmonization of data.The overall approach includes the development of algorithms that enable interoperability of data and knowledge representations. The team and the entire Department of Bioinformatics are internationally well connected and are working closely with leading European and US institutions from academia and industry. Development, curation, validation and integration of biomedical ontologies Linking ontologies to terminologies and enabling of text mining Development of semantic frameworks for handling ontologies and tools for semantic annotation of data using ontologies Community outreach, publishing the scientific work, joint development, and curation of ontologies with domain experts and ontology users You have successfully completed a scientific university degree (Master / PhD) in bioinformatics, computer science or a related field and have experience in semantic technologies, ontology engineering and data management. Excellent verbal and written communication skills are essential in o entity resolution to collaboratively develop ontologies together with the scientific community during workshops and discussions. In-depth experience with using, building, and maintaining or refining domain knowledge representations (ontologies, taxonomies) using semantic models, languages, tools and frameworks (e.g., RDF, SCHAL, SKOS, OWL, Protégé), with an application focus. Proficiency with medical standards (FHIR, HL7) and data models (OMOP) Knowledge about biomedical ontologies, vocabularies, and taxonomies, such as MeSH, SNOMED, ICD9/10, MedDRA, CDISC etc. along with experience in validating and querying semantic models Knowledge of semantic web standards such as RDF, SKOS, OWL, OBO coupled with a solid understanding of Natural Language Processing Ample experience in a scripting language (e.g., python) for querying of REST interfaces and conversion of various data formats Familiarity with use of database systems and their querying (e.g., SQL, SPARQL, Cypher), with specific experience with graph databases and formats (RDF and triplestores, labelled property graphs such as Neo4J) Basic knowledge about the (knowledge-) graphs in machine learning and how to implement ML models (pytorch, tensorflow etc.) Basic understanding of descriptive logic and ability to independently install, run, and maintain necessary software to build semantically annotated data repositories Interesting and multifaceted projects right at the interface between academic and industrial research Excellent hardware and software infrastructure A highly enthusiastic international team Possibilities for personal development and qualification Possibility to become part of an international network of excellent researchers Flexible working time and part time contracts Nice atmosphere within a unique environment containing a castle Various offerings of sports and healthcare activities We value and promote the diversity of our employees' skills and therefore welcome all applications - regardless of age, gender, nationality, ethnic and social origin, religion, ideology, disability, sexual orientation and identity. Severely disabled persons are given preference in the event of equal suitability and qualification. The weekly working time is 39 hours. The position can also be filled on a part-time basis and is initially limited to 2 years, with the possibility of extension.Appointment, remuneration and social security benefits based on the public-sector collective wage agreement (TVöD). Additionally, Fraunhofer may grant performance-based variable remuneration components. With its focus on developing key technologies that are vital for the future and enabling the commercial utilization of this work by business and industry, Fraunhofer plays a central role in the innovation process. As a pioneer and catalyst for groundbreaking developments and scientific excellence, Fraunhofer helps shape society now and in the future.
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