NATIONAL SCIENCE FOUNDATION

RESEARCH COORDINATION NETWORKS
NOVEMBER 2001

CONTEXT STATEMENT

The National Science Foundation received 21 proposals in response to the Research Coordination Networks in Biological Sciences (RCN) announcement, NSF 00_56. Proposals were distributed to one or more disciplinary panels based on their main scientific focus. Three or more panelists read and evaluated each proposal using both the standard NSF review criteria and the potential of the activities proposed to "... encourage and foster communications and collaborations  among scientists" (NSF 00_56).

The proposals were considered further by a committee of Program Officers from across the Directorate of Biological Sciences. Based on panel comments and further evaluation by the Program Officers, 7 proposals were recommended for funding.

Principal Investigators should keep in mind that the final recommendation is an evaluation of the relative merits of the proposed activities as described in the application.

If you have questions regarding the review of your proposal, please contact one of the program officers identified in the RCN program announcement directly or at biorcn@nsf.gov.

Context Statement
Biological Databases and Informatics
Fall FY02

The Biological Databases and Informatics Program is a component of the Research Resources Cluster of the Division of Biological Infrastructure, a division of the NSF Biological Sciences Directorate. The program focuses on the development of database systems in support of biological research, the design of innovative models, data structures and management systems for biological data, as well as the planning, prototyping and deployment of community servers for storing, integrating and accessing biological data.

The Biological Databases and Informatics Panel met on October 29_30, 2001 at NSF in Arlington, VA. Eleven panelists evaluated thirty_one proposals. After review of the research proposed and all reviews, the Biological Databases and Informatics panel assigned each of the proposals in one of three categories. The number and percentage of proposals placed in each category were:

High Priority	8	26%
Medium Priority	17	55%
Low Priority	6 	19%

Program officers establish relative merit on the basis of the context of the proposal. They depend on advice from the panel and outside reviewers, who have reviewed proposal in concordance with the NSF criteria of intellectual merit and broader impacts, as described in the NSF Grant Proposal Guide (NSF 01_2). The program officer made recommendations for funding within the constraints of the program budget, utilizing reviews and analysis within the program. In the previous fiscal year, the award rate was approximately 40%. More detail on the awards of the program can be found at: http://www.nsf.gov/bio/award.htm, or for all previous BDI awards, http://www.nsf.gov/, using the fielded search function and program reference code 1165.

If you have questions regarding the review of your proposal, please contact the program officer.

PROPOSAL NUMBER.: 0130291
INSTITUTION: University of Missouri_Columbia
NSF PROGRAM: BIOLOGICAL DATABASES & INFORMA
PRINCIPAL INVESTIGATOR: Polacco, Mary L.
PROPOSAL TITLE: Plant Ontology Consortium
PANEL SUMMARY:

The panel had a strong consensus that a plant ontology consortium was an excellent idea. A similar consensus exists that the investigators could assemble a controlled vocabulary. There was some doubt that the investigators would go beyond a controlled vocabulary to a full ontology. 
	
The project's connection with GO is good and necessary; the panel was surprised that more of the GO philosophy did not survive into the proposal. There is a need to identify the major systems descriptions that will be revised or created de novo to cause a plant ontology to form. A 
clear action plan involving the GO would enhance the proposal.

The panel was quite concerned about the plans to make the "consortium" part real. Those involved with the proposal, e.g. TAIR, are not those creating the gene names. Finally there was concern about the confusion in roll of PI and co_Pl. The panel is of the opinion that people able to be PIs should be permitted to be PI. 

PANEL RECOMMENDATION: Low priority for funding
Recommendation Key: High priority for funding = H, Medium priority for funding, Low priority for funding = L

PROPOSAL NO.: 0130291
INSTITUTION: U of Missouri Columbia
NSF PROGRAM: BIOLOGICAL DATABASES & INFORMA
PRINCIPAL INVESTIGATOR: Polacco, Mary L.
TITLE: Plant Ontology Consortium
RATING: Fair

REVIEW:
What is the intellectual merit of the proposed activity?

Proposing an ontology for regularizing the way information is stored about plant is an excellent idea. A project to create an ontology for plants should exist to prevent database chaos. This proposal, however, has some areas of concern. An ontology has at its core a graphical structure that contains a controlled vocabulary. The controlled vocabulary must contain a set of terms covering the area of interest including variants such as synonyms and the proposed investigators and collaborators are well qualified to assemble the vocabulary. The graphical structure must organize the controlled vocabulary so as to reflect the semantic, structural, and biological relationships among the terms. There is no evidence in the proposal or biographical sketches that the current team of investigators has done this before or understands how to do it.

The example given within the proposal on page 3 or the project description show a tree structured example. When a structure is involved in multiple entities within the plant the trees cross. The tassel in corn, for example, is both an anatomical and a reproductive feature and so appears in at least two significant systems. Likewise the larger controlled vocabulary shown at the MaizeDB site seems to have a pure tree structure. Building and maintaining the directed acyclic graph of parent_child relationships in the terminology requires substantial training in the computational sciences. At present the project seems focused only on developing the vocabulary, not on placing it in the ontological form.

In the gene ontology the ontology is broken up into broad categories of molecular function, biological processes, and cellular components. A plant ontology should have such broad categories as well. These categories might be anatomy, developmental features, and
abnormal phenotypes. This broad brush division into domains of interest within plants does not seem to have taken place yet in the proposed plant ontology consortium. This procedure, or an	
explanation of why this is not needed, seems a natural first step.

A plant ontology is an excellent idea and the proposed team has one half of the needed skills in hand. They must document in themselves or add via a new co_PI the skill in formal grammars and ontology maintenance to build a viable plant ontology project. In essence the concern is that the proposal extends the investigators efforts into a field related to their own where they do not have clearly documented expertise. The letter of support from Dr. Ashburner is a step in the right direction, but far clearer collaborative links ought to be built into the project. At present the investigators look like ontology consumers, not ontology producers. Provision 6 of the Overall objectives seems to fill the computational gap by importing outside experts, but this is not likely to provide sufficient in_project skill.

What are the broader impacts of the proposed activity?

As with any ontology proposal, the greatest broad impact would be the availability of a controlled, defined vocabulary for the field and a documentations of the relationships of the terms in the context of the field. Such an informational object acts to prevent whimsical and arbitrary storage and annotation of biological information. The goal is worthwhile and the proposed ontology does not yet exist. With the addition of someone with practical experience in ontologies this would be a worthwhile proposal.

The training and outreach portions of the grant are adequate and follow fairly standard lines. Publication of results via the web in collaboration with the GO project is the correct way to go.

Summary Statement

The target of the proposed research is excellent; I have reservations that the proposed investigators have all the required skills.

PROPOSAL NO.: 0130291
INSTITUTION: U of Missouri Columbia
NSF PROGRAM: BIOLOGICAL DATABASES & INFORMA
PRINCIPAL INVESTIGATOR: Polacco, Mary L.
TITLE: Plant Ontology Consortium
RATING: Excellent

REVIEW:
What is the intellectual merit of the proposed activity?

The authors state: "Integral to this proposal is the use and extension of the Gene Ontology (GO) Consortium paradigm." This is an important guiding principle and reflects the fact that the principal investigator is a member of current core group of collaborators on gene ontology and controlled vocabulary development, which will make it possible to annotate homology in gene and protein sequences across organisms. The GO system uses directed acyclic graphs, DAG structure, which allows associations to be made upward and downward, which is more flexible than a simple tree hierarchy. It shoukld be noted that The Arabidopsis Information resource (TAIR) is already a member of GO Consortium. This work will contribute to GO development by including other ontologies for anatomy and phenotype. The developed ontology should have broad usefulness to other plant_based research groups. The results will provide for versioning and all outcomes will be in the public domain, free of any restraint.

The proposal has a clearly outlined management plan, which is necessary for such a collaboration and includes coordination with GO activities.

What are the broader impacts of the proposed activity?

The proposal includes travel to Philippines, which reflects a commitment to bringing the results of this work to underdeveloped countries. The proposal also includes stipends for a number of internships to be distributed by collaborators.

Summary Statement

This proposal is for a project to bring together researchers in plant bioinformatics to develop a standard ontology for plant informatics. The group of collaborators includes researcher on maize, rice, Arabidopsis, and grain. The work addresses the need to accurately and consistently document features in plant genomic databases: gene structures, products, functions, phenotypes, traits, developmental stages, and anatomical parts.

PROPOSAL NO.: 0130291
INSTITUTION: U of Missouri Columbia
NSF PROGRAM: BIOLOGICAL DATABASES & INFORMA
PRINCIPAL INVESTIGATOR: Polacco, Mary L.
TITLE: Plant Ontology Consortium
RATING: Fair

REVIEW:
What is the intellectual merit of the proposed activity?

The primary objective of this proposal is to facilitate communication between plant genomics researchers. The initial core sets of participants include the Maize Mapping Project, The International Rice Research Institute, The Arabidopsis Information resource and Gramene: A Comparative Mapping Resource for grains, Cornell University.

Principal Investigator Leadership Role: RCN proposals typically have one Pl. The current proposal include a Co_PI that is central to the establishment of the proposed Plant Ontology Consortium. In the initial section of the proposal, The PI explains the reason for the exception in this proposal, which is prior commitments of the Co_PI. This lead to some confusion related to the management and reporting in the proposal.

Group Members: The involvement of Mary Polacco and Paul Vincent in the Gene Ontology project is a definite plus for this project. It is not clear however that the PIs have garnered the support of a broad coalition of organizations that would be needed for the eventual acceptance of a controlled vocabulary. The mechanisms for future addition of terminology by other groups is insufficient to completely overcome this initial weakness. (one option would be to provide seed money to form the coalition with critical mass.

Coordination / Management Mechanism: 
The PIs propose to spit management of the project with the PI taking primary responsibility for administrative leadership while the Co_PI takes responsibility for scientific leadership. The steering committee composition is not yet set. The PIs report that some members of the research, groups may not wish to participate in the steering committee. This is a problem for building consensus. The Steering Committee would provide support for setting objectives and selecting internships.

Merit:
The use of CVS to manage the ontology is commendable but the complexity of the development
effort dwarfs the functionality provided by CVS. ISO and ANSI standards for thesauri development would be more appropriate. The failure to mention these standards in an ontology paper is a major oversight in proposal writing. The Pls' experience with ontology development testifies to their knowledge of ontology development, but they have not explained the relationship of the project to the standards.

What are the broader impacts of the proposed activity?

The impact could be substantial is sufficient backing were found from the community.

Summary Statement

The proposal needs further development of formal associations with other organizations that would benefit from this project.

PROPOSAL NO.: 0130291
INSTITUTION: U of Missouri Columbia
NSF PROGRAM: BIOLOGICAL DATABASES & INFORMA
PRINCIPAL INVESTIGATOR: Polacco, Mary L.
TITLE: Plant Ontology Consortium
RATING: Good

REVIEW:
What is the intellectual merit of the proposed activity?

The goal is to form a Plant Ontology Consortium to facilitate data exchange and interoperability among plant genome databases. The proponents plan to cooperate with and extend the work done by the Gene Ontology group. Support letters from key members of the GO Consortium are included.

This is a good idea and fit well with the RCN program. The topic deserves attention, the PI has long been a productive member of the plant genome community. I would have liked to read a more detailed description of a plan. The overall objectives are filled with vague statements such Networking, collaboration with plant scientists, mentoring of students, etc. Since GO is already working they should have been able to convey a better plan on how to achieve developing a plant ontology. Similarly the community sharing plans could be more detailed better developed.

What are the broader impacts of the proposed activity?

A POC has a potentially big impact on plant biology.

Summary Statement

A POC is a worthwhile undertaking and deserves NSF funding. A better developed plan would have increased my enthusiasm.