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 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