Collaborating with the Center
The National Center for Biomedical Ontology is eager to collaborate with the scientific community and to assist investigators 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 supports a program of research grants for collaboration with the National Centers for Biomedical Computing (NCBCs), including collaboration with the NCBO. The review of collaborating proposals and subsequent funding decisions are the responsibilities of the NIH, and not the responsibility of our Center. The NIH program announcement is for projects from individual investigators or small groups to collaborate with the National Centers for Biomedical Computing. The intention of the collaborating projects is to engage researchers across the nation in building an excellent biomedical computing environment, using the computational tools and biological and behavioral application drivers of the funded NCBCs as foundation stones. Please see the full funding announcement for further guidelines regarding this special class of proposals.
Areas of Interest
The NCBC collaborating R01 program outlines a number of possible interaction types, descriptions of which and examples relating to the NCBO are below.
- Investigate the application of existing Driving Biological Project (DBP) efforts in a single biological realm.
Current DBPs focus on using ontologies to (1) analyze and profile high throughput gene-expression data, (2) understand the aging process, and (3) integrate and analyze disparate pharmacological data sets.
Recent DBPs have focused on cardiovascular modeling using ontologies, use of ontologies to analyze data with the goal of discovering new genomic relationships in the rat model organism, and using ontologies to search for new nanoparticles, and integrating new sources of nanoparticle data into the NCBO Resource Index. Past DBPs have focused on using ontologies to annotate and analyze genomic data in the fruitfly and zebrafish, with the goal of using homology information and model-organism data to suggest the genetic basis for human disease, and also on using ontologies to search, explore, and analyze clinical trial evidence.
We would welcome new collaborations in closely related areas: for example, projects that apply novel reasoning methods to analysis of genomic data using ontologies, or that use ontologies to characterize biological pathways in new ways.
- Investigate Center capabilities in new biomedical realms.
We are very interested in expanding the scope of applicability of ontologies and of the use of ontologies for annotation of experimental data. We are particularly eager to identify new applications of the Center’s methodologies in clinical and translational research, for example, in the design of clinical trials and clinical guidelines, in the administration of protocol-based care, and in the application of evidence-based medicine.
- Study new ways to perform data mining, analysis, and reasoning with the Center’s data.
We are interested in developing algorithms and data-processing methods that will help scientists use meta-data annotations of experimental data to understand the current state of biomedical knowledge, to generate new hypotheses, and to identify new avenues of investigation. We would welcome collaborations that lead to the submission of software components to the NCBO that could ultimately be incorporated into BioPortal and other technologies, bringing new analytic and visualization capabilities to the NCBO community.
- Create new ontologies and meta-data annotations that can be contributed to BioPortal and the NCBO Resources Index.
We are interested in helping groups of researchers to develop their own ontologies and in relating such ontologies to other existing information resources. We would welcome collaborations in which new ontologies or important annotated data sets are shared with the Center’s user community and linked to other resources in order to bring about new system capabilities that enhance information retrieval or improve data analysis.
- Develop new methods and technologies that use ontologies in fundamental ways to advance biomedicine.
There are many ways in which ontologies have been used to enhance scientific discovery, but there still are many approaches to explore. We are eager to collaborate in ontology-driven projects that develop new methods for natural-language processing, for automated mapping and indexing of the published literature, for summarizing scientific results, for hypothesis generation and automated reasoning, among other exciting avenues of research.
- Develop new ontology-management tools for integration with BioPortal and other NCBO technologies.
While the Center is developing a wide range of tools and services to manage and integrate ontologies and meta-data annotations, many biomedical investigators may require services that are more specialized than those that our Center currently offers. We welcome collaborations that will create additional tools and services that we can integrate into NCBO software offerings and thereby increase the reach of ontology-based technologies within the biomedical community.
- Create and investigate new analytical methods and algorithms for analyzing data in the context of ontologies.
There are many approaches for summarizing and analyzing both scientific data and the published literature. The Center welcomes collaborations for integrating these tools into BioPortal and other software services, or for creating new tools and services that help scientists to understand their scientific results in terms of standard ontologies and informtion resources.
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 listed in the NCBO Resource Index, and that new ontologies or ontologies that are extended for the collaborating project will be hosted by BioPortal. If the potential collaborating investigator plans to develop analysis methods, services, and tools that will work with ontologies or annotations archived by the NCBO, then these software products should be delivered to the Center to be included in the NCBO’s technology offerings.
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:
- A potential collaborator should read carefully the relevant program announcement (PAR) at the NIH Web site. Applicants are encouraged to contact any of the NIH program staff listed in the PAR with questions about the relevance of a potential application to a given NIH Institute or Center, or any other programmatic questions.
- The potential collaborating investigator then contacts the NCBO’s principal investigator or any member of the NCBO Steering Committee with an indication of interest in collaboration.
- The Center investigator whom the potential collaborator contacts will explore scientific merit, possible interactions within the Center, and resources required, with the collaborating investigator.
- The contacted Center investigator will alert the Center’s Steering Committee and Executive Committee to the possible collaboration and will provide a summary of the information that he or she has gathered.
- The potential collaborating investigator should then send to the Center’s Principal Investigator (Mark Musen), the NIH Program Officer (Peter Good), and the NIH Lead Science Officer (Peter Lyster) a 1–4 page description of the proposed collaboration that includes:
- “Specific Aims” for the research to be conducted.
- Statement of relevance (how the work would be complementary to that of the NCBO).
- Personnel at the Center who would be involved in the collaboration, and a summary of the amount of intellectual and consultation time that will be requested from the Center’s scientific staff.
- A brief description of the plan for sharing software, data, and research resources.
- The NCBO Executive Committee and appropriate NCBO personnel will review the Specific Aims document and determine the fit of the Specific Aims of the proposed project to the Center’s goals and determine whether the NCBO should participate at an institutional level in the proposed research.
- The Center's Outreach Coordinator will help the potential collaborating investigator to refine the work plan and proposed collaborative activities.
- The potential collaborating investigator will prepare a budget to support the proposed collaborative project. The budget must be submitted at least 10 days before the potential collaborating investigator must send the letter of intent to the NIH.
- Preparation of the proposal is the responsibility of the collaborating investigator. The Center’s Principal 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.
- The proposal should be submitted to the NIH as described in the program announcement.
The Center's resources currently are fully devoted to technology development and to research support for our driving biological projects. Therefore, the costs for new collaborations must be built into new grant 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:
- An ontology hosting environment within BioPortal. This environment includes Web-based browsing of ontologies, alignment with related ontologies, community-based peer reviews, and metadata related to ontologies.
- The NCBO Annotator Service to process textual metadata and to annotate it programmatically with ontology terms.
- An annotation hosting environment in the NCBO Resource Index. The NCBO Resource Index include a repository for annotations of experimental data, and work in conjunction with annotation services created and disseminated by the NCBO.
- Consultation on how to develop new ontologies, annotations of experimental data, and raw data as part of the collaborating investigator's project.
- Consultation on how to engineer software tools and services that use ontologies in biomedical research and that interoperate with the Center's existing 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. Collaborators must be willing to agree to the policies as specified in the collaborating R01 Program Announcements.
Our Center seeks a variety of collaborations both with academia and industry. To explore explore other potential avenues of collaboration, including becoming a visiting scholar, please contact one of the members of the Center, or the Center’s Principal Investigator, Mark Musen.