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 
https://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
Peter_Good@nih.gov

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
wolfep@nigms.nih.gov

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
Ken_Nakamura@nih.gov

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 
Jean_Cahill@nih.gov

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 Peter_Good@nih.gov

SUBMITTING AN APPLICATION

The PHS 398 research grant application instructions and forms (rev. 5/2001) at 
https://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 GrantsInfo@nih.gov.

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: 
https://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 
(https://grants.nih.gov/grants/guide/notice-files/NOT-OD-02-001.html); 
a complete copy of the updated Guidelines are available at 
https://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 
https://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 
https://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:  
https://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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