R01 and R21 Collaborations with the National Center for Biomedical Ontology - A Guide to Process and Content

Executive Committee

Mark Musen, Principal Investigator ( )
Suzanna Lewis, Co-principal Investigator ( )
Michael Montegut, Chief Operating Officer ( )

Peter Good, NIH Program Officer ( )
Carol Bean, NIH Lead Science Officer ( )

Last Updated: 08/08/06

The National Center for Biomedical Ontology is eager to collaborate with the scientific community and to assist researchers in advancing their research. We believe that many areas of scientific investigation can be enabled by our Center’s technologies and methods, and we welcome a broad range of collaborating proposals that require the use of biomedical ontology as a core component of their research plan.

The NIH has released a program announcement (PAR) to encourage R01 and R21 grant applications to support collaborations with the National Centers for Biomedical Computing (NCBCs) such as the NCBO (http://grants1.nih.gov/grants/guide/pa-files/PAR-08-184.html). It is important to remember that the review of collaborating R01 and R21 proposals and subsequent funding decisions are responsibilities of the NIH, and not the responsibility of our Center. The intention of this PAR is to develop new collaborations between the NCBCs and relevant biomedical researchers to help build a national biocomputing infrastructure. The NIH has also stated that: “These collaborations should not be a continuation or renewal of a previous collaborative relationship as these collaborations are intended to broaden both the biological and computational expertise of the NIH NCBCs.”

NIH Program Announcements

Types of Collaborations

The NCBC collaborative R01 and R21 program outlines a number of possible interaction types, and we describe those types of interaction with our own Center below. Contributions of ontologies and terminologies should be delivered to the Open Biomedical Ontologies (OBO) library.

  1. Investigate the application of existing driving biological project (DBP) efforts in a single biological realm.

    The current DBPs are focusing on using ontologies to annotate and analyze data in the fruitfly and zebrafish model organisms, with the goal of using homology information to discover the genetic basis for human disease from data acquired in the model organisms, as well as that of using ontologies to analyze clinical trial evidence regarding HIV infection in humans. We would welcome new collaborations in closely related areas: for example, work on other model organisms, particularly if these projects would promote identifying the basis of human disease through homology, and where existing technologies developed by the Center can be applied with little modification, or application of clinical-trial ontology to analyzing trials from other clinical domains.

  2. Investigate Center capabilities in new biomedical realms.

    We are very interested in expanding the scope of applicability of ontologies and annotation of experimental data to make new discoveries in biomedicine and to cure disease. We are particularly interested in identifying applications of the Center’s methodologies in clinical research – especially clinical trial design, execution, and registration, clinical guidelines, protocol-based care, and evidence-based medicine.

  3. Study ways to perform data mining and analysis of and reasoning with the Center’s data.

    We are interested in developing algorithms and processing methods that will help scientists use annotations on experimental data to understand the current state of biomedical knowledge, generate new hypotheses, and identify new avenues of investigation.  We would welcome collaborations that lead to the submission of code libraries to cBiO that could ultimately be incorporated into BioPortal, bringing new analytic and visualization capabilities to the cBiO community.
  4. Create new ontologies and annotations that can be contributed to the OBO and OBD resources.

    We are interested in helping groups of researchers in developing their own ontologies and in relating such ontologies to other existing ontologies and information resources, as part of a repository for wide dissemination. We would welcome collaborations in which new ontologies or important annotated data sets are shared with the Center’s user community.

  5. Develop new methods and technologies that use OBO ontologies in fundamental ways to advance biomedicine.

    There are many ways in which ontologies have been used to enhance scientific discovery, but we believe that there are still many unexplored approaches to pursue, such as natural-language processing, automated mapping and indexing of published literature to ontologies, summarizing scientific results with ontologies, hypothesis generation and reasoning, and detecting errors and conflicting results, among other exciting possible avenues of research.

  6. Develop new ontology-management tools for integration with BioPortal.

    While the Center will be developing tools to manage and integrate ontologies and annotations using those ontologies, many investigators in the community confronting specific biomedical problems may require specialized tools for their domain that our Center may not be developing. We welcome collaborations that would create additional tools that could be integrated into BioPortal and increase the reach of ontology-based technologies in the biomedical community.

  7. Create and investigate new analytical methods and algorithms for analyzing data in the context of ontologies.

    Many approaches for summarizing and analyzing scientific data and published literature are being developed, and the Center welcomes collaborations the would entail integrating these tools into BioPortal, or creating new tools that help scientists understand their scientific results in the context of ontologies used to annotate experimental data.

For all collaborations with the Center in which annotated experimental data are collected, it is expected that the proposal will specify that the annotated data will be delivered to the Open Biomedical Data (OBD) resource, and that new ontologies or ontologies that are extended for the collaborating project will be delivered to the Open Biomedical Ontologies (OBO) resource. If the potential collaborating investigator plans to develop analysis methods and tools that will work with OBO ontologies and/or OBD annotations, then these tools will be delivered to the Center to be included in its software library and potentially to be included in the BioPortal platform.

Process and Schedule

We have created a standardized process to facilitate and encourage those investigators who would like to pursue collaborative proposals with the Center. The overall objective is to give all potential investigators a fair and equal opportunity to prepare a competitive collaborating R01 proposal. The process will enable our Center to track and manage requests for collaboration, and to gather other necessary information. This process is summarized here:

  1. Potential collaborators should study the following two documents from the Center’s Web site (Working With the Center):
    1. Guide to Process and Content document (this web page), which summarizes the process and discusses the general types of collaborations that are possible, and how they fit into the Center’s plan; and
    2. Center Overview. This document describes our research and development activities, active research areas, and current driving biological projects. It is suitable as a starting point for the summary (up to five pages in length) required with the collaborating investigator’s R01 or R21 application to the NIH that describes the NCBC with which the investigator will collaborate. The purpose of this section is to make the grant application completely self-contained, so that a reviewer will not need to consult any material other than the application itself in order to judge its merit, and in particular so that the reviewer will not need to consult the Web site of the partnering NCBC. This section is in addition to the 25 pages allotted for the Research Plan.
  2. A potential collaborating investigator contacts a Center participating investigator (listed at http://bioontology.org/overview-team.html) with an indication of interest in collaboration.
    1. This Center investigator will explore potential interactions, resources required, scientific merit, and impact with the potential collaborating investigator.
    2. The Center investigator will alert a member of the Center’s executive committee (PI, Co-PI, executive director, or associate director) and provide a summary of the information that he or she has gathered.
  3. The potential collaborators also should read carefully the collaborating R01 and R21 PAR from the NIH Web site (http://grants1.nih.gov/grants/guide/pa-files/PAR-08-184.html) Applicants are encouraged to contact NIH program staff listed in the PAR with any questions about the relevance of a potential application to an NIH Institute or Center or any other programmatic questions.
  4. The potential collaborating investigator should then send to the executive director ( ), the NIH Program Officer (Peter Good, ), and the Lead Science Officer (Carol Bean, ) a 1-4 page draft describing the proposed collaboration that includes:
    1. Proposed “Specific Aims” for the research to be conducted.
    2. Statement of relevance (how the work would be complementary to that of the Center).
    3. Personnel or cores at the Center that you would anticipate working with, and a summary of the amount of intellectual and consultation time requested with the Center’s scientific staff.
    4. A summary of other resources (software/hardware, instrumentation, supplies, or other expenses) required from the Center, the collaborating institution, and the expected additional resources for the proposed collaboration that will be requested by the potential collaborating institution.
    5. A brief description of the plan for sharing data and research resources.
  5. The executive committee and appropriate Center investigator will review the Specific Aims document and do the following: 
    1. The executive committee in collaboration with the relevant Center investigator will determine the fit of the Specific Aims of the proposed project to the Center’s goals.
    2. The committee will relay the Specific Aims to the appropriate Center investigators and NIH staff possessing the appropriate expertise for comment and coordination.
  6. The potential collaborating investigator should send a letter of intent to NIH, with a copy to the Center’s executive director. Letters of intent are due in either mid-December or mid-April. (please see http://grants1.nih.gov/grants/guide/pa-files/PAR-08-184.html for key dates)
  7. The potential collaborating investigator will prepare a budget to support the proposed project and collaboration with the Center in undertaking the project. The budget must be submitted to the Center’s executive committee at least 10 days before sending the letter of intent to NIH.
  8. Preparation of the proposal is the responsibility of the collaborating investigator. The Center’s principle investigator will write a letter affirming support for the collaborating investigator’s proposal, if appropriate, after reviewing the research plan and approving the budget for the proposed collaboration.
  9. Th proposal should be submitted to NIH (approximately one month after letter of intent).

Resources

The Center’s resources are currently devoted to technology development and to research support for the three initial driving biological projects. Therefore, costs for new collaborations should be built into new applications through well justified subcontracts to Center investigators. The NIH does not provide the Center with direct funds that are set aside for collaboration. The Center can provide the following collaborative resources as part of its core mission:

  1. An ontology hosting environment within the Open Biomedical Ontologies (OBO) framework. This environment includes Web-based browsing of ontologies, alignment with related ontologies, peer reviews, and other metadata related to ontologies.
  2. Data hosting environment in Open Biomedical Data (OBD). This environment includes a storage repository for annotations of experimental data, and works in conjunction with annotation tools created and disseminated by cBiO.
  3. Consultation on how to develop new ontologies, annotations on experimental data, and raw data as part of the collaborating investigator’s project.
  4. Consultation on how to engineer software tools that use ontologies in biomedical research and that interoperate with the Center’s current ontologies and tools.

Code and Data Sharing

The Center adheres to the code and data sharing policies specified in the initial National Centers for Biomedical Computing RFA (http://grants1.nih.gov/grants/guide/rfa-files/RFA-RM-04-022.html). Collaborators must be willing to agree to the policies as specified in the collaborating R01 PAR (http://grants1.nih.gov/grants/guide/pa-files/PAR-08-184.html).

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