and Human Services (HHS)
EXPIRED
DEVELOPING ROBUST COMPONENTS FOR MODEL ORGANISM DATABASES RELEASE DATE: February 14, 2002 RFA: RFA-HG-02-002 PARTICIPATING INSTITUTES AND CENTERS (ICs): National Human Genome Research Institute (NHGRI) (http://www.nhgri.nih.gov/) National Institute of General Medical Sciences (NIGMS) (http://www.nigms.nih.gov/) LETTER OF INTENT RECEIPT DATE: April 17, 2002 APPLICATION RECEIPT DATE: May 17, 2002 THIS RFA CONTAINS THE FOLLOWING INFORMATION o Purpose of this RFA o Research Objectives o Mechanism of Support o Funds Available o Eligible Institutions o Individuals Eligible to become Principal Investigators o Special Requirements o Where to send Inquiries o Letter of Intent o Submitting an Application o Peer Review Process o Review Criteria o Receipt and Review Schedule o Award Criteria o Required Federal Citations: PURPOSE The National Human Genome Research Institute (NHGRI) and the National Institute of General Medical Sciences (NIGMS) propose to improve model organism databases by supporting the development of robust software components, called modules. Each module will perform a particular database function, in a way that is well documented, robust, potentially usable by more than one database, and compatible with standard data formats. These database modules will enhance existing model organism databases and will be useful for developing new ones. These shared modules will promote coordination and interoperability between databases. Eventually the modules could be used to create generic model organism databases that will be used by researchers to integrate genomic and genetic information for additional organisms. RESEARCH OBJECTIVES Background Much of our understanding of biological processes has resulted from the study of model organisms. Research with model organisms has generated large amounts of data. Model organism databases exist for a few well-studied organisms. These databases integrate information from multiple sources. Expert curators scan the scientific literature for data on gene mutations, gene function, interactions, homologies with other organisms, and references. Large datasets submitted directly by computer are also included, such as genome sequence and gene expression patterns. This experimental information is integrated with computer predictions of gene structure and function. Researchers depend on these databases in order to interpret their own observations and to design new experiments. These databases are an efficient way for large amounts of organized information to be available to researchers. The genomes of many microbes, fungi, plants, and animals have been sequenced recently and many more genomes will be sequenced in the future. In addition, new types of genetic and genomic information are becoming available, such as expression arrays, metabolic pathways, and systematic phenotyping. Integrating this information opens up new opportunities for research in understanding biological and disease processes. Thus there is an accelerating need for creating databases for additional organisms and for integrating new types of data into existing databases. Existing databases generally cannot simply be copied to create databases for other organisms. On the other hand, new databases for model organisms are expensive to develop de novo. Researchers who wish to develop new model organism databases should not have to reinvent methods for functions they need that already work well in existing databases. Doing so would mean an unnecessary duplication of resources. Furthermore, when investigators independently develop methods to deal with a particular type of data, there is no assurance that the data scheme developed for one database has exactly the same scientific meaning as one developed for a separate database. These different data definitions would make queries across multiple databases difficult. This RFA is intended to improve existing model organism databases and provide tools for creating new model organism databases by supporting the development of robust software components, called modules. The goal is for each module to perform a database function in a generic manner that can be adopted by other databases. Each module should improve an existing database function, or add a new function. To accomplish these goals, the modules should make use of data formats that are independent of the software module. The use of these modules by existing databases and newly developing ones will promote standardization and interoperability between the databases. The term "model organism database" here refers to a database for any organism. Some species are classic model organisms for studying many basic biological processes, while others are studied because of their role in particular diseases or processes. Learning about the function of a gene in one species is very useful for understanding it in other species. Using common modules will promote the transfer of information from well-studied organisms to their less intensively studied relatives, as well as aid in the discovery of patterns across large groups of organisms. NHGRI already funds a set of model organism databases that work closely together. Groups other than these may have the expertise and creativity to develop useful modules. This RFA will allow other investigators as well as the currently funded groups to develop modules that are integrated with the current model organism databases for mouse, fly, yeast, and worm. Developing a robust and generic module that can be used by other model organism databases takes more effort than developing it for just one database. This RFA provides funding for this extra effort with the expectation that the incorporation of modules into other databases will be more efficient than the repeated funding of the development of these functions in different databases. Some modules may improve on the functionality of a single established model organism databases. Alternatively, this software may be designed in a more generic manner and be useful for all databases. A longer-term goal, for a future initiative, is for these modules to be assembled together to form a generic model organism database toolkit. The availability of this generic toolkit will simplify the task of creating new model organism databases that will become resources for organism-specific data such as genomic sequence, gene expression data, mutant phenotypes, and literature citations. Research Scope and Objectives The goal of this RFA is to support the development of robust software modules that will perform discrete functions of a model organism database. Applicants may propose to develop one or more modules. o Module development must be closely coordinated with the current model organism databases funded by NHGRI, to promote creation of useful and non-redundant modules. A letter of collaboration will be required from the Principal Investigator of at least one of these, Mouse Genome Database (http://www.informatics.jax.org/), FlyBase (http://flybase.bio.indiana.edu/), Saccharomyces Genome Database (http://genome-www.stanford.edu/Saccharomyces/), or WormBase (http://www.wormbase.org, outlining how the module fits with other module development and how it will be useful for the collaborating database. If Principal Investigators of these databases apply to this RFA, they must explain how each module will enhance the functions of one or more other databases. o The function of each module must be carefully defined and justified. The justification must take into account the modules that are already under development by the fly, mouse, yeast, and worm databases. Highest priority will be given to modules that address central needs of a model organism database that are not yet being worked on. Proposed modules may be for improving existing functions of an established model organism database or for developing new functions. o Each module must be exportable and useful to model organism databases beyond that of interest to the group proposing it. o Each module must be robust and generic. Plans for the software development must be described, including needs analysis, quality assurance, implementation, evaluation, and refinement. Issues of scalability, extensibility, and interoperability must be addressed. The development of the module must use clearly defined software engineering principles. o The coordination of each module with other database components must be described, including how different versions will be kept compatible. o The schema underlying each module must be clearly defined. The utility of the proposed schema must be clearly justified for the function that each module will perform. o Any middleware layer used for a module must be clearly defined. The capacity of this middleware to handle the large amounts of data typical of genomic databases must be demonstrated if appropriate. o All data files produced by a module must be in an explicitly defined, parsable format such as XML conforming to a Document Type Definition (DTD). An emphasis must be placed on the ability of the data format to promote interoperability of the databases that use this format. o Plans for documentation of software must be described. o Plans for informing the research community about the module and training individuals in the use of the module must be described. o Plans for the user support of each module during and after the award must be described. o Each module must be easily available to any interested database developer. The applicant should identify a repository for each module to allow access by all interested parties. If the applicant proposes to use an open-source model of software development, the mechanisms for developing and maintaining the software must be described. MECHANISM OF SUPPORT This RFA will use the National Institutes of Health (NIH) R01 research project grant award mechanism. Responsibility for the planning, direction, and execution of the proposed project will be solely that of the applicant. This RFA is a one-time solicitation. Future unsolicited competing continuation applications will compete with all investigator-initiated applications and will be reviewed according to the customary peer review procedures. The earliest anticipated award date is September 20, 2002. This RFA uses just-in-time concepts. It also uses the modular format (see http://grants.nih.gov/grants/funding/modular/modular.htm). Specifically, if you are submitting an application with direct costs in each year of $300,000 or less, use the modular format. FUNDS AVAILABLE The NHGRI and NIGMS together intend to commit a total of $2 million for each of two years. It is anticipated that four to eight new grants will be funded. An applicant may request a project period of up to two years and direct costs of up to $300,000 per year. If a subcontract is involved, the direct cost cap will be $325,000 per year to accommodate the F&A costs associated with the subcontract. Because the nature and scope of the research proposed may vary, it is anticipated that the size of the awards will also vary. Awards are contingent upon the availability of funds. ELIGIBLE INSTITUTIONS You may submit application if your institution has any of the following characteristics: o For-profit or non-profit organizations o Public or private institutions, such as universities, colleges, hospitals, and laboratories o Units of State and local governments o Eligible agencies of the Federal government o Domestic or foreign organizations INDIVIDUALS ELIGIBLE TO BECOME PRINCIPAL INVESTIGATORS Any individual with the skills, knowledge, and resources necessary to carry out the proposed research is invited to work with their institution to develop an application for support. Individuals from underrepresented racial and ethnic groups as well as individuals with disabilities are always encouraged to apply for NIH programs. SPECIAL REQUIREMENTS The Principal Investigators of all awards from this RFA should plan on meeting together once a year in the Bethesda area to review progress with NIH staff and to discuss implementation of these modules. Funds for travel to this meeting should be budgeted in the application. WHERE TO SEND INQUIRIES We encourage inquiries concerning this RFA and welcome the opportunity to answer questions from potential applicants. Inquiries may fall into three areas: scientific/research, peer review, and financial or grants management issues: o Direct your questions about scientific/research issues to: Dr. Peter Good National Human Genome Research Institute Building 31, Room B2B07 Bethesda, MD 20892-2033 Telephone: (301) 435-5796 FAX: (301) 480-2770 [email protected] Dr. Paul Wolfe Division of Genetics and Developmental Biology National Institute of General Medical Sciences Building 45, Room 2AS25 Bethesda, MD 20892-6200 Telephone: (301) 594-0943 FAX: (301) 480-2228 [email protected] o Direct your questions about peer review issues to: Dr. Ken Nakamura Scientific Review Branch National Human Genome Research Institute National Institutes of Health Building 31, Room B2B37 Bethesda, MD 20892-2032 Telephone: (301) 402-0838 FAX: (301) 435-1580 [email protected] o Direct your questions about financial or grants management matters to: Ms. Jean Cahill Grants Administration Branch National Human Genome Research Institute Building 31, Room B2B34 Bethesda, MD 20892-2031 Telephone: (301) 402-0733 FAX: (301) 402-1951 [email protected] LETTER OF INTENT Prospective applicants are asked to submit a letter of intent that includes the following information: o Descriptive title of the proposed research o Name, address, and telephone number of the Principal Investigator o Names of other key personnel o Participating institutions o Number and title of this RFA Although a letter of intent is not required, is not binding, and does not enter into the review of a subsequent application, the information that it contains allows NHGRI staff to estimate the potential review workload and plan the review. Potential applicants are encouraged to contact Dr. Good early in this planning process. The letter of intent should be sent by April 17, 2002 to: Dr. Peter Good Program Director, Genome Informatics National Human Genome Research Institute National Institutes of Health Building 31, Room B2B07 Bethesda, MD 20892-2033 E-mail [email protected] SUBMITTING AN APPLICATION The PHS 398 research grant application instructions and forms (rev. 5/2001) at http://grants.nih.gov/grants/funding/phs398/phs398.html are to be used in applying for these grants. This version of the PHS 398 is available in an interactive, searchable PDF format. The NIH will return applications that are not submitted on the 5/2001 version. For further assistance contact GrantsInfo, at (301) 710-0267 or [email protected]. The RFA label available in the PHS 398 application form must be affixed to the bottom of the face page of the application. Type the RFA number on the label. Failure to use this label could result in delayed processing of the application such that it may not reach the review committee in time for review. In addition, the RFA title and number must be typed on line 2 of the face page of the application form and the YES box must be marked. The sample RFA label is available at: http://grants.nih.gov/grants/funding/phs398/label-bk.pdf. Please note this is in pdf format. Submit a signed original of the application, including the Checklist, and three signed photocopies in one package to: CENTER FOR SCIENTIFIC REVIEW NATIONAL INSTITUTES OF HEALTH 6701 ROCKLEDGE DRIVE, ROOM 1040 BETHESDA, MD 20892-7710 BETHESDA, MD 20817 (for express/courier service) At the time of submission, two additional copies of the application must be sent to: Dr. Ken Nakamura Scientific Review Administrator Scientific Review Branch National Human Genome Research Institute Building 31, Room B2B37 Bethesda, MD 20892-2032 Applications must be received by May 17, 2002. If an application is received after that date, it will be returned to the applicant without review. The Center for Scientific Review (CSR) will not accept any application in response to this RFA that is essentially the same as one currently pending initial review, unless the applicant withdraws the pending application. The CSR will not accept any application that is essentially the same as one already reviewed. This does not preclude the submission of substantial revisions of applications already reviewed, but such applications must include an Introduction addressing the previous critique. PEER REVIEW PROCESS Upon receipt, applications will be reviewed for completeness by the CSR and responsiveness by the NHGRI. Incomplete or non-responsive applications will be returned to the applicant without further consideration. Applications that are complete and responsive to the RFA will be evaluated for scientific and technical merit by an appropriate peer review group convened by the (IC) in accordance with the review criteria stated below. As part of the initial merit review, all applications will: o Receive a written critique o Undergo a process in which only those applications deemed to have the highest scientific merit, generally the top half of the applications under review, will be discussed and assigned a priority score o Receive a second level review by the National Advisory Council for Human Genome Research and the National Advisory General Medical Sciences Council. REVIEW CRITERIA The goals of NIH-supported research are to advance our understanding of biological systems, improve the control of disease, and enhance health. In the written comments, reviewers will be asked to discuss the following aspects of your application in order to judge the likelihood that the proposed research will have a substantial impact on the pursuit of these goals: o Significance o Approach o Innovation o Investigator o Environment The scientific review group will address and consider each of these criteria in assigning your application's overallscore, weighting them as appropriate for each application. Your application does not need to be strong in all categories to be judged likely to have major scientific impact and thus deserve a high priority score. For example, you may propose to carry out important work that by its nature is not innovative but is essential to move a field forward. (1) SIGNIFICANCE: Does your study address an important problem? If the aims of your application are achieved, how do they advance scientific knowledge? What will be the effect of these studies on the concepts or methods that drive this field? (2) APPROACH: Are the conceptual framework, design, methods, and analyses adequately developed, well integrated, and appropriate to the aims of the project? Do you acknowledge potential problem areas and consider alternative tactics? (3) INNOVATION: Does your project employ novel concepts, approaches or methods? Are the aims original and innovative? Does your project challenge existing paradigms or develop new methodologies or technologies? (4) INVESTIGATOR: Are you appropriately trained and well suited to carry out this work? Is the work proposed appropriate to your experience level as the principal investigator and to that of other researchers (if any)? (5) ENVIRONMENT: Does the scientific environment in which your work will be done contribute to the probability of success? Do the proposed experiments take advantage of unique features of the scientific environment or employ useful collaborative arrangements? Is there evidence of institutional support? ADDITIONAL REVIEW CRITERIA In addition to the above criteria, your application will also be reviewed with respect to the following: o PROTECTIONS: The adequacy of the proposed protection for humans, animals, or the environment, to the extent they may be adversely affected by the project proposed in the application. o INCLUSION: The adequacy of plans to include subjects from both genders, all racial and ethnic groups (and subgroups), and children as appropriate for the scientific goals of the research. Plans for the recruitment and retention of subjects will also be evaluated. (See Inclusion Criteria included in the section on Federal Citations, below) o DATA SHARING: The adequacy of the proposed plan to share data and software. o BUDGET: The reasonableness of the proposed budget and the requested period of support in relation to the proposed research. OTHER REVIEW CRITERIA: o NEEDS ASSESSMENT: How is the function of the proposed module consistent with the needs of the user communities? o COLLABORATIVE INTERACTIONS: Has the application identified a model organism database to collaborate with on the development of the proposed module? Have the proper collaborative arrangements been made to ensure the use of the software in a model organism database? o SOFTWARE DEVELOPMENT: Do the principal investigator and other professional staff have the appropriate database and software design and development experience to carry out this work? Does the application evaluate and use existing software where appropriate? Are the software engineering principles and development process clearly described and adequate for the module? Does the module promote the interoperability of databases that use it? o RESOURCE MAINTENANCE: How adequate are the plans to maintain the module? Are there plans to improve the software upon the recommendations of users? Are appropriate procedures developed for quality control of the software? o SERVICE: How adequate are the plans to make available the software, software code, and documentation? How adequate are the plans to provide consultation and technical assistance in their use? o OUTREACH: If appropriate, how adequate are the proposed plans for informing the scientific community about the module? o TRAINING: If appropriate, how adequate are the proposed plans for providing educational programs to explain to members of the research community the use of the module? RECEIPT AND REVIEW SCHEDULE Letter of Intent Receipt Date: April 17, 2002 Application Receipt Date: May 17, 2002 Peer Review Date: July, 2002 Council Review: September, 2002 Earliest Anticipated Start Date: September 20, 2002 AWARD CRITERIA Award criteria that will be used to make award decisions include: o scientific merit, as determined by peer review; o availability of funds; o programmatic priorities. REQUIRED FEDERAL CITATIONS INCLUSION OF WOMEN AND MINORITIES IN RESEARCH INVOLVING HUMAN SUBJECTS It is the policy of the NIH that women and members of minority groups and their sub-populations must be included in all NIH-supported biomedical and behavioral research projects involving human subjects, unless a clear and compelling rationale and justification are provided indicating that inclusion is inappropriate with respect to the health of the subjects or the purpose of the research. This policy results from the NIH Revitalization Act of 1993 (Section 492B of Public Law 103-43). All investigators proposing clinical research should read the AMENDMENT "NIH Guidelines for Inclusion of Women and Minorities as Subjects in Clinical Research - Amended, October, 2001," published in the NIH Guide for Grants and Contracts on October 9, 2001 (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-02-001.html); a complete copy of the updated Guidelines are available at http://grants.nih.gov/grants/funding/women_min/guidelines_amended_10_2001.htm. The amended policy incorporates: the use of an NIH definition of clinical research; updated racial and ethnic categories in compliance with the new OMB standards; clarification of language governing NIH-defined Phase III clinical trials consistent with the new PHS Form 398; and updated roles and responsibilities of NIH staff and the extramural community. The policy continues to require for all NIH-defined Phase III clinical trials that: a) all applications or proposals and/or protocols must provide a description of plans to conduct analyses, as appropriate, to address differences by sex/gender and/or racial/ethnic groups, including subgroups if applicable; and b) investigators must report annual accrual and progress in conducting analyses, as appropriate, by sex/gender and/or racial/ethnic group differences. INCLUSION OF CHILDREN AS PARTICIPANTS IN RESEARCH INVOLVING HUMAN SUBJECTS The NIH maintains a policy that children (i.e., individuals under the age of 21) must be included in all human subjects research, conducted or supported by the NIH, unless there are scientific and ethical reasons not to include them. This policy applies to all initial (Type 1) applications submitted for receipt dates after October 1, 1998. All investigators proposing research involving human subjects should read the "NIH Policy and Guidelines" on the inclusion of children as participants in research involving human subjects that is available at http://grants.nih.gov/grants/funding/children/children.htm. REQUIRED EDUCATION ON THE PROTECTION OF HUMAN SUBJECT PARTICIPANTS NIH policy requires education on the protection of human subject participants for all investigators submitting NIH proposals for research involving human subjects. You will find this policy announcement in the NIH Guide for Grants and Contracts Announcement, dated June 5, 2000, at http://grants.nih.gov/grants/guide/notice-files/NOT-OD-00-039.html. URLS IN NIH GRANT APPLICATIONS OR APPENDICES All applications for NIH funding must be as self-contained as possible. Reviewers may need to look at Web pages to properly evaluate software applications. Internet addresses (URLs) should be provided as needed. PUBLIC ACCESS TO RESEARCH DATA THROUGH THE FREEDOM OF INFORMATION ACT The Office of Management and Budget (OMB) Circular A-110 has been revised to provide public access to research data through the Freedom of Information Act (FOIA) under some circumstances. Data that are (1) first produced in a project that is supported in whole or in part with Federal funds and (2) cited publicly and officially by a Federal agency in support of an action that has the force and effect of law (i.e., a regulation) may be accessed through FOIA. It is important for applicants to understand the basic scope of this amendment. NIH has provided guidance at: http://grants.nih.gov/grants/policy/a110/a110_guidance_dec1999.htm. Applicants may wish to place data collected under this RFA in a public archive, which can provide protections for the data and manage the distribution for an indefinite period of time. If so, the application should include a description of the archiving plan in the study design and include information about this in the budget justification section of the application. In addition, applicants should think about how to structure informed consent statements and other human subjects procedures given the potential for wider use of data collected under this award. HEALTHY PEOPLE 2010 The Public Health Service (PHS) is committed to achieving the health promotion and disease prevention objectives of "Healthy People 2010," a PHS-led national activity for setting priority areas. This Request for Applications (RFA), DEVELOPING ROBUST COMPONENTS FOR MODEL ORGANISM DATABASES, is related to one or more of the priority areas including cancer, diabetes, immunization and infectious diseases, oral health, and maternal, infant, and child health. Potential applicants may obtain a copy of "Healthy People 2010" at http://www.health.gov/healthypeople/. AUTHORITY AND REGULATIONS This program is described in the Catalog of Federal Domestic Assistance No. 93.172. Awards are made under authorization of Sections 301 and 405 of the Public Health Service Act as amended (42 USC 241 and 284) and administered under NIH grants policies and Federal Regulations 42 CFR 52 and 45 CFR Parts 74 and 92. This program is not subject to the intergovernmental review requirements of Executive Order 12372 or Health Systems Agency review. The PHS strongly encourages all grant recipients to provide a smoke-free workplace and promote the non-use of all tobacco products. In addition, Public Law 103-227, the Pro-Children Act of 1994, prohibits smoking in certain facilities (or in some cases, any portion of a facility) in which regular or routine education, library, day care, health care, or early childhood development services are provided to children. This is consistent with the PHS mission to protect and advance the physical and mental health of the American people.
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