This position works with investigators in the Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS) to assist with ongoing development of an application ontology for the management, annotation, and assessment of information extracted from scientific literature, specifically related to natural product (NP) entities (including plants or other natural organisms, their extracts or chemical isolates) that have been evaluated for pain modulation. The literature set will consist of detailed information on NP entities that have been reported to be useful for pain management and/or that have undergone experimental biological evaluation (in vivo, in vitro and/or clinical evidence).
Duties include working with domain specialists in pharmacognosy and pain management to harmonize terminologies with existing ontologies and new classes; developing a prototype ontology; help deploy solutions based on the developed ontology, including support data input and filtering, as well as enhanced interoperability across domains, particularly the biomedical realm; maintaining detailed documentation of the work and productions; writing, editing, and submitting manuscripts/abstracts related to the project; assisting with projects that may require input on knowledge management/ontology engineering; planning, assigning and reviewing work of staff to ensure that group objectives are met. Hire, train, develop and manage staff to ensure that a qualified staff exists to meet group objectives; perform other related duties and participate in special projects as assigned.
Applicants must have a M.S. in bioinformatics, library/information science, linguistic science, natural sciences, or other related field required. PhD in bioinformatics, library/information science, linguistic science, natural sciences, or other related field OR equivalent training/experience preferred. Experience with Basic Formal Ontology (BFO) based ontologies. Demonstrable experience building ontologies in collaboration with domain specialist. Knowledge of writing and editing scientific research articles, review papers, as well as technical and programmatic reports. Knowledge of ontological principles, engineering and alignment. Competence in an ontology editor (such as Protege or similar). Ability to demonstrate the ability to balance independent and collaborative work as needed. Demonstrate the ability to pay attention to detail and careful documentation.
Additional preferred skills and experience include: Experience with software development. The ability to demonstrate understanding of database structure and data management. Demonstrate proficiency in working with RDF/OWL, XML, or any ontology serialization format. Versed in information extraction and ontology alignment. 2 years of experience with a programming language, preferably in relation with ontologies. Knowledge of SPARQL and ability to work with triple stores.