Tagging_Project_SOW_FINAL.doc

STATEMENT OF WORK (SOW)

SUPPORT FOR UNIQUE IDENTIFICATION TAGGING OF DCM-FUNDED

RESEARCH SOURCES

1. BACKGROUND

Rigor and reproducibility have become an important subject of biomedical research policies due to the realization that the inability to uniquely identify research resources, such as antibodies and model organisms, makes it difficult or impossible to reproduce experiments even if findings are supported by the original scientific observations. Recent studies (PeerJ, DOI 10.7717, 2013) have reported that 54% of the resources public shed in journal articles from several major biomedical fields are not uniquely identifiable in publications, regardless of domain, journal impact factor or reporting requirements. The National Institutes of Health (NIH) is committed to promoting rigorous and transparent research in all areas of science supported by a variety of grant programs. Recently, updates to application instructions and review language intended to enhance reproducibility through rigor and transparency have been implemented for research grants and mentored career development awards. One of the key requirements for applicants is the need to address key biological and/or chemical resources which include, but are not limited to, cell lines, animals, specialty chemicals, antibodies and other biologics. These biological resources are an integral part of the research and contribute to the experimental variability.

Another important aspect of improving reproducibility of experimental results is the support that NIH provides to research resources. The Division of Comparative Medicine (DCM), one of the Office of Research Infrastructure Program’s (ORIP’s) major components, supports research to develop new animal models (e.g. rodents, invertebrates, nonhuman primates), cultured cells, biological materials, reagents and informatics systems, as well as shared resources with the goal to distribute, characterize, maintain, and archive these diverse resources for use by other biomedical researchers. In such resources, organisms and biologicals are produced under defined conditions and are delivered to the scientists with a guaranteed assurance of the quality and reproducibility of the phenotype and properties as well as access to information regarding the description and original source of the biomaterials.

Unfortunately, the current publication practices do not make it easy to identify when these or other resources are used. Even if resources are cited, it is very difficult to conduct a global search of the literature to extract that information. The major reason is the absence of standards and sufficient identifying information for such resources. Researchers also contribute to this problem since, despite the existence of nomenclature authorities, they often ambiguously identify in their publications the exact source of the biomaterials used for the experiments. These constraints create a need for the development and maintenance of a citation system for research resources, which will enable authors to authenticate biological resources by generating, using, and finding stable unique identifiers. Such a system will serve the biomedical community to correctly report, accurately replicate and extend findings from animal research resources and will allow resource distributors and funding agencies to monitor the use of these model organisms and biomaterials. One of the effective solutions to the problem is the creation and use of research resource identifiers on which all stakeholders, such as scientists, government representatives, publishers, and commercial producers, can agree.

2. SCOPE OF WORK

The objective of this requirement is to support a method/system of creating and maintaining biological resource identifiers that will allow NIH personnel, as well as the research community, to monitor the use and conduct citation analysis of the supported DCM/ORIP research resources, such as animal models, cultured cells and other biological materials.

This contract shall provide maintenance and further develop the citation system for research resources supported by the DCM. The system shall allow the following:

a. Uniquely identify the particular resource;

b. Be machine processable;

c. Be outside any paywall; and

d. Be uniform across publishers.

The system shall maintain and update, as needed, existing indexes already assigned to the primary catalog data from DCM supported resources and shall curate new sources of the data when they become available. A very important function of the system is the dissemination of knowledge about the unique identifiers. The system will also provide assistance to biomedical investigators in the assignment and use of unique identifiers as a means of fulfilling the obligation of NIH-funded investigators to adhere to NIH policy on rigor and reproducibility. The results of the use of the implemented system shall be reported to participating model organism repositories as well as to NIH staff.

3. CONTRACTOR REQUIREMENTS

3.1 Collaboration

The Contractor shall furnish all necessary labor, materials, supplies, equipment and services to successfully carry out the SOW. It is expected that the Contractor will work collaboratively with federal staff as well as non-governmental third party personnel and stakeholders. This collaboration may include day-to-day activities, planning, development, and creating and sharing documentation. The Contractor will act, where possible, to minimize the effort required by the participating Resource Centers. Only the Contracting Officer has the authority to make changes to the terms and conditions of the contract.

3.2 Contractor Tasks

Task 3.2.1 – Maintenance of Existing Indexes Contractor shall maintain the “integrated animal” index and all of the subparts of its various databases. Maintenance is defined as follow:

a. Monthly verification of a subset of links (typical numbers are 5 per source);

b. Monthly outreach to all sources via an e-mail list shall include, but not limited to, the status of the system, version of the catalog of the resources currently in use or being updated, news about the service in general, and statistics on the reference to the resource in the published literature; and

c. Weekly verification that the data in the index is uncorrupted and that totals have not changed unexpectedly. In case of changes, the Contractor curator shall investigate the errors with programming staff and correct them. After the investigation and correction are completed, if necessary, the Contractor shall report to the resources.

Applicable databases include the following:

· Ambystoma Genetic Stock Center;

· A Resource Center for Tetrahymena thermophile;

· Development of Validated Drosophila in vivo RNAi Models of Human Diseases;

· Zebrafish International Resource Center;

· Bloomington Drosophila Stock Center at Indiana University;

· Mutant Mouse Resource and Research Center (MMRRC) at the Jackson Laboratory;

· MMRRC at UC Davis;

· Caenorhabditis Genetics Center;

· The Mouse Mutant Resource;

· Cre Driver Strain Resources;

· Drosophila Genomics Resource Center;

· MMRRC at University of North Carolina;

· MMRRC at the University of Missouri;

· National Swine Resource and Research Center;

· National Xenopus Resource Center;

· Rat Resource and Research Center;

· Sperm Stem Cell Libraries for Biological Research;

· The Special Mouse Strain Resource at The Jackson Laboratory; and

· Xiphophorus Genetic Stock Center.

Task 3.2.2 – Curation of New Resources

In coordination with the DCM program staff, the Contractor shall add data from new resources when such information becomes available. This shall include at least two new resources per year for the duration of the contract. The criteria to determine suitable new resources will be based on the scientific importance of that resource to the biomedical community, stakeholder needs, and availability of funding.

Task 3.2.3 – Dissemination of Unique Identification System

Under this task, the Contractor shall perform the following:

a. Disseminate – using the Contractor’s website, social media, presentations at biomedical meetings, publications, etc. – the idea that unique identifiers shall help authors/grantees meet rigor and transparency guidelines;

b. Write one or more press releases per year around the activities of the standards groups (as recommended by DCM program staff) to be posted on specified websites. Press releases could be written at the end of the calendar year to update an unusually high level of citation of specific resources;

c. Maintain applicable project webpages to reflect the state of the project;

d. Create and execute a plan to improve journal staff knowledge about and adoption of rigor and reproducibility guidelines;

e. Reach out to 12 journals per year, with priority being given to journals covering broad biomedical fields, as a means of communicating with a wider community; and

f. Present or exhibit at one scientific meeting per year, as appropriate. The meeting venue shall include larger scientific society meetings, such as the Society for Neuroscience, the American Society for Cell Biology or other similar venues. The exhibit shall encourage author/grantee participation in the unique identifiers initiative.

Task 3.2.4 – Reports to NIH and Model Organism Repositories

Annual reports consisting of summary statistics and a simple file format file of all raw data about the use of organisms in the biomedical literature shall be provided to the organism repositories and the Contracting Officer. The Contractor shall meet annually (or by webinar) with model organism repository owners to report on progress. In the event that organism repository owners are unable to make it, materials should be provided to them by email or the file transfer protocol (FTP) as data size dictates.

During year one of the award, the contractor shall create a dashboard feature within its infrastructure where the Model Organism Repositories and interested NIH program officers can view a current citations report. Weekly updates shall be provided as regular data is released. Organism repository owners shall be able to view and download the data or select push notifications in standard data formats such as Comma Separated Values (CSV) or xml. The Contractor shall make reasonable accommodations to present the data as requested by the repositories/NIH. The NIH Program Officials shall have a ‘master’ section where the current data of the entire project shall be accessible, downloadable, and graphically represented.

Task 3.2.5 – Final Progress Report All data gathered and code written as part of this contract shall be made available electronically to the NIH Contracting Officer within one month prior to the end of the contract. Curated data shall be covered under a CC-0 license to ensure maximum reuse by organism repositories or other users.

3.3 Deliverables