Job ID: 3893
Job date: 2015-07-22
End Date:
Company : OHSU Library Ontology Development Group Country : Role : Faculty
Job date: 2015-07-22
End Date:
Company : OHSU Library Ontology Development Group Country : Role : Faculty
Job Description:
The Bioinformaticist serves as a member of the OHSU Library Ontology Development Group. This position works in the context of the Global Alliance for Genomics and Health (GA4GH), a global effort to develop schemas for health data sharing. The goal is to develop a semantic representation of cancer data from a variety of sources and use cases, build ontologies to help support data interrogation, and integrate ontologies and data in a graph database for evaluation. The Bioinformaticist will work with ontologists, bioinformaticians, and software engineers at OHSU, the National Cancer Institute, and other GA4GH consortium sites to design and implement methods for semantically navigating and manipulating cancer data.
The primary duties of the Bioinformatics Semantic Engineer will be to (1) Develop use cases to represent a diversity of cancer data types and user perspectives; (2) Analyze user queries for insight into building semantic data models; (3) Development of semantic models for cancer; (4) Graph-based data integration according to semantic models in order to evaluate the models; and (5) Requirements and landscape analysis of existing semantic modeling, including collaboration with the NCI Thesaurus team. This position will require the ability of explore possible solutions and make decisions that will lead to the identification and implementation of effective semantic models of cancer data, novel approaches for data analysis, and efficient testing to support data transformation.
Required:
Ph.D, or, Master’s degree with major courses in relevant field and 3 yrs experience, or Bachelor's degree with major courses in field of research plus 6 additional years related experience
3 years of relevant experience in cancer bioinformatics
Ability to perform research and make independent decisions about approaches and tools to reach specific goals
Experience with Software Project Management tools and version control systems (Jira, Confluence, SVN, Git)
Hands-on experience with one or more scripting languages (e.g. Perl, Python, Ruby, Bash)
Proven ability to analyze cancer data from a variety of modalities
Familiarity with relevant Bioinformatics protocols (e.g. quality control, differential expression analysis, eQTL, GWAS, etc.) and tools
Experience with retrieving and/or submitting data to biological data repositories (GenBank, Ensembl, etc.)
Strong verbal, written, and interpersonal communication skills (especially via teleconferencing venues)
Preferred:
Experience developing ontologies and data models
Experience managing semantically annotated data, such as in a triplestore, graph, or NoSQL database;
Experience with Neo4J and the Cypher Query Language
Knowledge of SPARQL, RDF, OWL and familiarity with relevant tools and APIs (e.g. Jena, Protégé).
Variant prioritization methods
Strong programming skills with a solid understanding of object oriented languages and principles
Hands-on experience with SQL (Postgres and MySQL preferred)
Experience developing and evaluating data curation workflows
Job Information
Position Type: Academic Staff
Reference (Job ID number): IRC48615
Start Date: ASAP
Duration: Full Time
Status: open
Contact Information
OHSU
Library
Melissa Haendel
haendel@ohsu.edu
http://www.ohsu.edu/xd/education/library/about/jobs.cfm
How To Apply: Apply online and search keyword IRC48615. Be sure to upload a resume and a cover letter. URL to apply:
http://www.ohsu.edu/xd/about/services/human-resources/
Additional Info:
[Click Here to Access the Original Job Post]
The Bioinformaticist serves as a member of the OHSU Library Ontology Development Group. This position works in the context of the Global Alliance for Genomics and Health (GA4GH), a global effort to develop schemas for health data sharing. The goal is to develop a semantic representation of cancer data from a variety of sources and use cases, build ontologies to help support data interrogation, and integrate ontologies and data in a graph database for evaluation. The Bioinformaticist will work with ontologists, bioinformaticians, and software engineers at OHSU, the National Cancer Institute, and other GA4GH consortium sites to design and implement methods for semantically navigating and manipulating cancer data.
The primary duties of the Bioinformatics Semantic Engineer will be to (1) Develop use cases to represent a diversity of cancer data types and user perspectives; (2) Analyze user queries for insight into building semantic data models; (3) Development of semantic models for cancer; (4) Graph-based data integration according to semantic models in order to evaluate the models; and (5) Requirements and landscape analysis of existing semantic modeling, including collaboration with the NCI Thesaurus team. This position will require the ability of explore possible solutions and make decisions that will lead to the identification and implementation of effective semantic models of cancer data, novel approaches for data analysis, and efficient testing to support data transformation.
Required:
Ph.D, or, Master’s degree with major courses in relevant field and 3 yrs experience, or Bachelor's degree with major courses in field of research plus 6 additional years related experience
3 years of relevant experience in cancer bioinformatics
Ability to perform research and make independent decisions about approaches and tools to reach specific goals
Experience with Software Project Management tools and version control systems (Jira, Confluence, SVN, Git)
Hands-on experience with one or more scripting languages (e.g. Perl, Python, Ruby, Bash)
Proven ability to analyze cancer data from a variety of modalities
Familiarity with relevant Bioinformatics protocols (e.g. quality control, differential expression analysis, eQTL, GWAS, etc.) and tools
Experience with retrieving and/or submitting data to biological data repositories (GenBank, Ensembl, etc.)
Strong verbal, written, and interpersonal communication skills (especially via teleconferencing venues)
Preferred:
Experience developing ontologies and data models
Experience managing semantically annotated data, such as in a triplestore, graph, or NoSQL database;
Experience with Neo4J and the Cypher Query Language
Knowledge of SPARQL, RDF, OWL and familiarity with relevant tools and APIs (e.g. Jena, Protégé).
Variant prioritization methods
Strong programming skills with a solid understanding of object oriented languages and principles
Hands-on experience with SQL (Postgres and MySQL preferred)
Experience developing and evaluating data curation workflows
Job Information
Position Type: Academic Staff
Reference (Job ID number): IRC48615
Start Date: ASAP
Duration: Full Time
Status: open
Contact Information
OHSU
Library
Melissa Haendel
haendel@ohsu.edu
http://www.ohsu.edu/xd/education/library/about/jobs.cfm
How To Apply: Apply online and search keyword IRC48615. Be sure to upload a resume and a cover letter. URL to apply:
http://www.ohsu.edu/xd/about/services/human-resources/
Skills :
Areas :
Additional Info:
[Click Here to Access the Original Job Post]