Jobs

ICBO Biomedical Ontology Jobs Service

Participants in the ICBO meeting interested in employment opportunities in the biomedical ontology field, and employers seeking to recruit in this field, are invited to write to Leonard Jacuzzo <jacuzzo@buffalo.edu>, who is in charge of the ICBO conference Jobs Service.

Available Positions:

Position A

Research Associate, Graduate Student and PDF positions

Applications are invited for Research Associate, Graduate Student and PDF positions in the Knowledge Navigation Infrastructure Team (KNIT) lead by the Innovatia Research Chair at the University of New Brunswick, Saint John http://www.unb.ca/news/view.cgi?id=1680

Researchers will collaboratively develop reusable infrastructures to support custom vertical search across multiple application domains in biomedical, health care, energy and telecom. Researchers will develop solutions for enterprise search using semantic web technologies, service oriented architecture, ontologies and text mining. Successful candidates will have demonstrated software development expertise and familiarity with knowledge engineering lifecycles. Candidates with demonstrated experience with two or more of the following technologies are encouraged to apply:

1) Web based Content Acquisition Strategies 2) Knowledge Representation with OWL / RDF 3) Text Mining / Natural Language Processing 4) Ontology based reasoning over instance / triple stores 5) Terminology Management and Curation 6) Literature and (Meta) Data Integration 7) Provenance Tracking / Tracability 8) Algorithm Design / Graph Matching 9) Human Computer Interaction 10) Semantically Enabled Software Architecture 11) Semantic Desktops and Publishing

Enquiries and applications and can be made by sending a full CV and cover letter to: bakerc@unbsj.ca

Position B

Project Coordinator: Plant Ontology Project

Position Title: Research Associate / Research Associate (Post Doc)

Department of Botany and Plant Pathology Oregon State University, 2082 Cordley Hall, Corvallis, Oregon 97331-2902 T 541-737-3451 | F 541-737-3573 | www.science.oregonstate.edu/bpp

Position description: The Plant Ontology Consortium is seeking applicants for a full-time position of scientific curator who will coordinate the Consortium’s efforts. The Plant Ontology Consortium is a collaboration among researchers at Oregon State University, Cornell University and New York Botanical Garden. The Consortium also collaborates with the curators of many model organism databases including rice, Arabidopsis, maize, grasses, legumes, Solanaceae, bryophytes and plant phylogenomics. The project aims to develop shared vocabularies on plant anatomy and growth and developmental stages, to describe patterns of phenotype(s) and gene expression.

For more details please see the following publications: Avraham, et al. (2008). "The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations." Nucleic Acids Res. 36 (Database issue): D449-54. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18194960

Ilic, e al. (2007). "The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant." Plant Physiol. 143 (2): 587-599. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17142475

Pujar, et al. (2006). "Whole-plant growth stage ontology for angiosperms and its application in plant biology." Plant Physiol 142 (2): 414-28. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16905665

Jaiswal, et al. (2005). "Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages." Comp Funct Genomics 6 (7-8): 388-97. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18629207

Duties / Responsibilities: Develop and refine the ontologies with the PO curators in participating databases and core labs, annotate gene products and germplasms with the vocabularies in the ontologies, participate in the development and application of methods to streamline and enhance the quality of annotations, manage website content, set project milestones, organize and moderate monthly teleconferences, and work with the project members to deliver the database releases and project reports on strict timelines.

Required qualifications: Ph.D. in an aspect of plant biology (e.g. Development, Physiology, Biochemistry, Genetics, Plant Pathology, Systematics) and/or genomics, Plant Pathology, Phylogenomics, Systematics, Plant Biology and Plant Anatomy. Available immediately to start working on the project. Experience in High Performance Scientific Computing and Network maintenance. Demonstrated ability for independent, critical thinking and excellent communication, networking and teamwork skills. Previous work in any one or more areas of Plant Development, Plant Physiology, Plant Biochemistry, Plant Genetics and/or genomics, Plant Pathology, Museum specimen curation, Phylogenomics, Systematics, Plant Biology and Plant Anatomy. Excellent communication skills in English is a must. Experience in teaching and outreach. Familiarity with Plant Development and Anatomy. Able to travel and attend 3-4 meetings/year of the PO consortium.

In order to be considered for the Research Associate position, the candidate must have 3 or more years of postdoctoral/scientist research experience and supporting publications in peer reviewed international journals. The selection committee will judge the candidate based on the qualifications below; in addition, to showing the ability to lead on a scientific project as an independent researcher. Preferred qualifications: A demonstrable commitment to promoting and enhancing diversity. Past experience in project coordination, large scale gene expression and phenotype evaluation, familiarity with basic UNIX commands, spreadsheets, and commonly used biological research tools such as BLAST and Literature Databases searching is desired. A working knowledge of PERL and/or SQL will be considered an asset but not required.

How to Apply: To review the position description and apply, go to posting #0004322 at http://oregonstate.edu/jobs. When applying, you will be required to electronically submit your application, a cover letter citing your interest in the position and your experience, and a CV/resume including 3 references. Closing date 7/15/09.

Oregon State University is an Affirmative Action/Equal Opportunity Employer and has a policy of being responsive to dual-career needs.

Position C

Vaccine Informatics Postdoctoral Position in University of Michigan

A postdoctoral position is available in the area of vaccine bioinformatics. The broad goals of this collaborative project are to develop a community-based Vaccine Ontology (VO, http://www.violinet.org/vaccineontology/), and develop a VO-based natural language process (NLP) program, and use them to study vaccine-induced immune networks. The responsibilities of this postdoctoral position include: coordinating the project among all participants, actively participating in the VO ontology development, helping software team develop VO-based literature mining system, and investigate driving biological problems through specific use case studies.

The applicant will work in an interdisciplinary and collaborative environment in the University of Michigan Medical School. The laboratory is located in the Ann Arbor campus of University of Michigan. We are collaborating with well-known experts from the National Center for Integrated Biomedical Informatics (NCIBI), National Center for Biomedical Ontology (NCBO), Infectious Disease Ontology (IDO) Initiative, Ontology for Biomedical Investigation (OBI), Canadian Pandemic Influenza Preparedness Networks, etc.

We are looking for highly motivated individuals who thrive on intellectual challenges. Applicants must have a PhD degree and a strong background in microbiology, immunology, and/or biomedical ontology development. Familiarity with literature mining and biological network simulation is a plus. Applicants should have the ability to annotate and present data, and be able to write manuscripts based on the research. Candidates with a strong academic record and good primary publication record will be considered.

Please submit a C.V., a brief statement of research interests and background, and the names of three references (preferably by email) to the address below:

Dr. Yongqun Oliver He, DVM, PhD Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, and Center for Computational Medicine and Bioinformatics 018 ARF, 1150 W. Medical Center Dr. University of Michigan Medical School Ann Arbor, MI 48105-5614, USA Email: yongqunh@med.umich.edu

Position D

Knowledge Management (KM) related consulting and service activities

The European Centre for Disease Prevention and Control is pleased to inform you that there is a call for tender published for: “Knowledge Management Related Tasks” – OJ/2009/06/18 – PROC/2009/028”

Short Description:

The assignment presented in this call for tenders aims to Knowledge Management (KM) related consulting and service activities. Specific tasks will be in the domain of developing (ontology based) terminology services, developing enterprise search with semantic support, expert competence mapping and other, KM related tasks. Applied ‘standards’ are: SKOS, OWL, DCMI, SOAP.Development platform is .Net, database is MSSQL and integration with MOSS is in some cases required. The summary value of all the six lots is an estimated 600 000 EUR for the next two years. The applicants must prove their experience, competencies, references in the areas of described activities and give a price/day offer for different roles, as defined in the call.

The deadline for submission of tenders is 31 August 2009 at 4 pm local time

For more information, please click on the link or consult ECDC website at http://ecdc.europa.eu/en/Procurement/Competitions/PROC_2009_028/Default.aspx Should you require more information, please contact ECDC procurement office at procurement@ecdc.europa.eu

Position(s) E

Research Associate

We are looking for a Research Associate to join our research team at Georgia State University (Atlanta, Georgia) and to participate in the collaborative development of Neural ElectroMagnetic Ontologies (NEMO). This NIH-sponsored position would involve developing ontologies for representation and integration of patterns in event-related brain potentials (ERP) data.

The Associate would work with members of our International NEMO Consortium (experts in EEG and MEG studies of language and cognition) communities to develop, manage, and curate ontology and database structures for this project. Please see http://nemo.nic.uoregon.edu for more information, and contact Dr. Gwen Frishkoff if you have any questions (sasha@cs.uoregon.edu).

The ideal candidate would have a background in cognitive neuroscience, experience with database design and curation, and familiarity with OWL and Protégé. Salary will be commensurate with experience in the range of $30-$40K per year. Funding for the position begins in September 2008, but a later start date can be negotiated.

Please send a cover letter, c.v. and the names and contact information for three professional references via e-mail to Dr. Gwen Frishkoff (sasha@cs.uoregon.edu).

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Post-doctoral Associate

We are looking for a Post-doctoral Associate to join our group at Georgia State University in the development of NeuronBank.org. This NSF sponsored position would involve developing ontologies for neurons and neural circuits.

The post-doc would work with members of various neuroscience research communities to develop neuromic representations. Please see http://neuronbank.org for more information. The ideal candidate would have a neuroscience background and familiarity with OWL and Protégé. Preference will be given for candidates with a Ph.D. in neuroscience or related fields. Salary will be commensurate with experience in the range of $30-$40K per year. Funding for the position begins in September 2008, but a later start date can be negotiated.

Please send a cover letter, c.v. and the names and contact information for three professional references via e-mail to Paul Katz (pkatz@gsu.edu).

Georgia State University is an equal-opportunity employer.

Position F

Software engineer

We are looking for a software engineer to work on ChEBI, the resource of Chemical Entities of Biological Interest developed by the Chemoinformatics and Metabolism Team at the European Bioinformatics Institute (EBI). The EBI, an outstation of the European Molecular Biology Laboratory, is located on a beautiful campus in Hinxton south of Cambridge.

We are a friendly, multi-national team with collaborations all around the world. The ChEBI project is the Chemistry Portal of the EBI, using a chemical ontology we aim to standardise chemical and biochemical terminology across biological databases. It is used extensively as a reference resource for various bioinformatics databases worldwide.

We have recently received funding to restructure our chemical ontology into a formal ontology. The post-holder will work with us towards this goal and work closely with a chemical curator to enhance the ChEBI ontology.

Applicants should have a degree in Computer Science or related field. Good knowledge of Java and relational databases is essential. A good knowledge of ontologies, open source ontology tools and ontology formats such as OWL/OBO would be desirable. Previous experience in the fields of chemistry / chemoinformatics would be a bonus. Self-motivated candidates with good communication skills and ambition to work in an international environment are invited to apply. Advanced English language and excellent interpersonal skills are required.

Position G

Chemist or Cheminformatician

We are looking for a chemist or cheminformatician to work on ChEBI, the resource of Chemical Entities of Biological Interest developed by the Chemoinformatics and Metabolism Team at the European Bioinformatics Institute (EBI) in cooperation with Michael Ashburner's team at the University of Cambridge.

The successful applicant will be associated to the Ashburner group but spend significant time together with the ChEBI team at the EBI.

The EBI, an outstation of the European Molecular Biology Laboratory, is located on a beautiful campus in Hinxton south of Cambridge. We are a friendly, multi-national team with collaborations all around the world. The ChEBI project is the Chemistry Portal of the EBI - using a chemical ontology we aim to standardise chemical and biochemical terminology across biological databases. It is used extensively as a reference resource for various bioinformatics databases worldwide.

We have recently received funding to restructure our chemical ontology into a formal ontology. The post-holder will work with us towards this goal and work closely with a software engineer to enhance the ChEBI ontology.

Applicants should have a degree in chemistry, cheminformatics, bioinformatics or related field. Excellent knowledge of organic and biochemistry is essential. A good knowledge of ontologies and ontology formats such as OWL/OBO would be desirable. Previous programming experience would be a bonus. Self-motivated candidates with good communication skills and ambition to work in an international environment are invited to apply. Advanced English language and excellent interpersonal skills are required.

Position H

Post Doctoral positions

The Duke Ontology Group seeks highly motivated candidates for Post Doctoral positions within the Department of Biostatistics and Bioinformatics. The group’s primary focus is the application of computational biology and bioinformatics to the study of the immune system and infectious diseases. The Department seeks a candidate to work on the development of an Infectious Disease Ontology and to test the ontology's utility in the prediction of disease genes conferring susceptibility to Staphylococcus aureus infection. Candidates with a background in microbiology and/or infectious diseases are strongly preferred. No experience with computational methods or ontology is required. Interested candidates should send a CV and three letters of recommendation by email as pdf attachments to:

Dr. Lindsay Cowell, PhD 
LGCOWELL@DUKE.EDU 

Department of Biostatistics and Bioinformatics Duke University Medical Center 2424 Erwin Road, Suite 1102, 11086 Durham, NC 27705 DukeUniversity is an EOAA Employer

Position I

Research Associate (Senior Postdoc) / Research Associate (Postdoc)

Working Title: Plant Ontology Project Coordinator

The Plant Ontology Consortium (www.plantontology.org) is seeking applicants for a full-time position of scientific curator who will coordinate the Consortium’s efforts. The Plant Ontology Consortium is a collaboration among researchers at Oregon State University, Cornell University and New York Botanical Garden. The project is funded by the National Science Foundation. The Consortium also collaborates with the curators of many model organism databases including rice, Arabidopsis, maize, grasses, legumes, Solanaceae, Bryophytes, Rosaceae and plant phylogenomics. The project aims to develop shared vocabularies on plant anatomy and growth and developmental stages, to describe patterns of phenotype(s) and gene expression. For more details on the project please see the publications (PubMed IDs:18194960, 17142475, 16905665, 18629207)

How to Apply: To review the position description in detail and apply, go to posting

1. 0004322 at http://oregonstate.edu/jobs. When applying, you will be

required to electronically submit your application, a cover letter citing your interest in the position and your experience, and a CV/resume including 3 references. Closing date 7/31/09.

Required qualifications: Ph.D. in an aspect of plant biology (e.g. Development, Physiology, Biochemistry, Genetics, Plant Pathology, Systematics) and/or genomics, Phylogenomics, Systematics, Plant Biology and Plant Anatomy. Available immediately to start working on the project. Demonstrated ability for independent, critical thinking and excellent communication, networking and teamwork skills.

Position(s) J

Center for Brain and Behavior Informatics

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Position 1: Molecular Geneticist, Oral Diagnostic Sciences, University at Buffalo School of Dental Medicine

A full-time tenure-track Assistant Professor position is available for an early career scientist with PhD-level training in molecular genetics or in a related area. The successful candidate will be employed by the Department of Oral Diagnostic Sciences (ODS) in the University at Buffalo School of Dental Medicine and be a member of the new Center for Brain and Behavior Informatics (CBBI), which has been established in the University at Buffalo to foster multidisciplinary translational research at the frontiers of biomedical informatics and clinical, cognitive, social and behavioral neuroscience. The successful candidate will have responsibilities (1) in ODS to engage in research applying genetics to dental disease, with particular emphasis on both acute and chronic pain, and (2) in CBBI, to contribute to collaborative information-driven research bridging clinical and basic science in the domain of complex functional disorders. Areas of focus may include biomedical ontology research, characterization of disease phenotypes, statistical models of genotype-phenotype association. Salary will be commensurate with experience. The start date is expected to be Fall 2009 or as soon as possible thereafter. The University at Buffalo is an Equal Opportunity / Affirmative Action Employer. For further information please contact Barry Smith <phismith@buffalo.edu>.

Position 2: Cognitive Neuroscientist, Department of Neurology, University at Buffalo

A full-time tenure-track Assistant Professor position is available for an early career scientist with MD or PhD-level training in cognitive neuroscience. The successful candidate will be employed by the Department of Neurology in the University at Buffalo School of Medicine and Biomedical Sciences and be a member of the new Center for Brain and Behavior Informatics (CBBI), which has been established in the University at Buffalo to foster multidisciplinary translational research at the frontiers of biomedical informatics and clinical, cognitive, social and behavioral neuroscience. Responsibilities in the Department of Neurology may include teaching and clinical service (subject to negotiation). In CBBI the successful candidate will contribute to collaborative information-driven research projects bridging clinical and basic science in areas such as Multiple Sclerosis, Systemic Lupus Erythematosus, posttraumatic stress disorder, cognitive development, and the use of electrophysiological methods and advanced imaging techniques in the study of cognitive function. Salary will be commensurate with experience. The start date is expected to be Fall 2009 or as soon as possible thereafter. The University at Buffalo is an Equal Opportunity / Affirmative Action Employer. For further information please contact Barry Smith <phismith@buffalo.edu>.

Position 3: Neuroinformatician, Department of Neurology, University at Buffalo

A full-time tenure-track Assistant Professor position is available for an early career scientist with PhD-level training in informatics / computer science and an interest in the application of advanced computational expertise in clinical research. The successful candidate will be employed by the Department of Neurology in the University at Buffalo School of Medicine and Biomedical Sciences and be a member of the new Center for Brain and Behavior Informatics (CBBI), which has been established in the University at Buffalo to foster multidisciplinary translational research at the frontiers of biomedical informatics and clinical, cognitive, social and behavioral neuroscience. Responsibilities in the Department of Neurology may include some teaching. In CBBI the successful candidate will contribute to collaborative information-driven research bridging clinical and basic science in the domain of neurological disease. Areas of focus will include some or all of: biomedical ontology research, representation and analysis of neurological disease phenotypes, measures of brain functioning, and neuroimage analysis. Salary will be commensurate with experience. The start date is expected to be Fall 2009 or as soon as possible thereafter. The University at Buffalo is an Equal Opportunity / Affirmative Action Employer. For further information please contact Barry Smith <phismith@buffalo.edu>.

Position K

Ontologist/Vocabulary Developer Wanted

Position Description Assist with the development and execution of a business strategy focused on delivering service-oriented architecture (SOA) solutions with authoritative data to address the Next Generation Air Transportation System community's business processes and mission specific services needs. This is an exciting and important opportunity to shape the future of our Nation's air transportation system so as to make this system safer and more efficient, primarily through aviation-related data and information sharing in the context of what is known as Net-Centric Operations.

The employer is The Analysis Group, LLC (TAG, http://www.tag-llc.com/). TAG is headquartered in Falls Church, VA just outside of Washington, DC, and the work itself would be performed in Washington, DC at the Joint Planning and Development Office (JPDO, http://www.jpdo.gov/), which was established by an act of Congress and itself is composed of Federal Aviation Administration (FAA) and Air Force personnel. The TAG team assigned to this NextGen project is made up of ontologists, architects, and engineers, and our client is the U.S. Air Force under the guidance of the Net-Centric Operations Division of the JPDO.

Required Skills  Develop ontologies, semantic data models, glossaries, thesauri, and data dictionaries, to include identification and tagging of data sources  Provide ontology development support to DoD and non-DoD stakeholders, including training and instruction in ontology development and semantic data modeling processes and the use of ontology development tools  Solicit and facilitate the capture of business knowledge objects and business processes from stakeholder/mission Subject Matter Experts  Supports integration and handoff of ontology products to XML developers  Supports optimization of search engine tuning parameters based on content of domain vocabularies, ontologies and semantic data models  Conducts analysis of business objects, vocabularies, business processes and information exchanges requirements  Taxonomy and ontology development for enterprise information management systems  Entity extraction or automated tagging  Commercial search engine technology/search optimization techniques  Metadata creation and indexing  Develops supporting documentation and presentations for delivery to clients  Works well in a collaborative development environment

Desired Skills Experience in and/or knowledge of a substantial subset of the following technologies and engineering practices:  XML and OWL schema development  Automated tools to support schema integration and analysis (i.e. Protégée, TopBraid)  Content and taxonomy management systems  Taxonomy and ontology workbenches and analysis tools, and related current and emerging representation and query standards  Proficiency in systems integration analysis  Experience working with software system engineers and architects  Service oriented architecture (SOA)  Project management and project management tools  Working knowledge of Microsoft Word, Excel, PowerPoint, Access, and Project  Exceptional written and verbal communication skills  Master’s degree in a related field  5-7 years recent related experience  Active DoD collateral Secret clearance or eligible to obtain a DoD Secret Clearance

If interested, contact: Bruce McKenzie Vice President The Analysis Group, TAG (703) 945-3392 bmckenzie@tag-llc.com