DRAFT_Tagging_Project_SOW_12-9-16.doc

DRAFT STATEMENT OF WORK (SOW)

SUPPORT FOR THE UNIQUE IDENTIFICATION OF DCM-FUNDED

RESEARCH SOURCES

1. BACKGROUND

Rigor and reproducibility has 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) reported that 54% of the resources published in journal articles of 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 requirement for the applicants is the necessity 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 are contributing to the experimental variability.

Another important aspect of improving reproducibility of experimental results is the support that NIH provides to the useful 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 them for use by other biomedical researchers. In such resources, organisms and biologicals are produced in standard conditions and are delivered to the scientists with guaranteed assurance of the quality and reproducibility of the phenotype and properties as well as significant accompanied information regarding 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 they are cited, it is very difficult to conduct a global search to extract that information. The major reason is the absence of the standards and sufficient identifying information. Scientists should also be blamed for the problem since, despite the existence of the nomenclature authorities, they often are not unambiguously identifying the exact source of the biomaterials used for the experiments in their publications. Therefore, there is a need for the development and maintenance of the citation system for research resources which will serve the biomedical community to correctly report the animal research resources, accurately replicate and extend the findings and will allow resource distributors and funding agencies to monitor the use of the model organisms and biomaterials. One of the effective solutions to the problem is the use of research resource identifiers on which all stakeholders, such as scientists, government representatives, publishers, and commercial producers, can agree.

2. CONTRACT REQUIREMENTS

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 and assistance to the biomedical investigators in the assignment and use to fulfill obligation of the NIH-funded investigators to adhere to Rigor and Reproducibility standards. The results of the use of implemented system shall be reported to the model organism repositories as well as NIH staff.

2.1 Collaboration

The Contractor shall furnish all of the 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. However, only the Contracting Officer has the authority to make changes to the terms and conditions of the contract.

2.2 Contractor Tasks

Task 2.2.1 – Maintenance of Existing Indexes Contractor shall maintain the “integrated animal” index and all of the subparts of 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;

· JAX;

· Zebrafish International Resource Center;

· Bloomington Drosophila Stock Center at Indiana University;

· Mutant Mouse Resource and Research Center;

· Mutant Mouse Resource and Research Center (MMRRC) at UC Davis;

· Caenorhabditis Genetics Center;

· The Mouse Mutant Resource (MMR);

· Cre Driver Strain Resources;

· Drosophila Genomics Resource Center;

· Mutant Mouse Regional Resource Center at University of North Carolina;

· Mutant Mouse Resource and Research Center 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 (SMSR) at The Jackson Laboratory; and

· Xiphophorus Genetic Stock Center.

Task 2.2.2 – Curation of New Resources

In coordination with the DCM program, the Contractor shall add new sources of data as they become available and wish to join the project. This shall include at least two sources per year for the duration of the contract. The criteria to determine suitable sources will be based on the scientific importance of that source to the biomedical community, stakeholder needs, and availability of funding.

Task 2.2.3 – 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 the 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 to be posted on specified websites. Press releases could be written at the end of the calendar year to update on unusual high level of citation of the specific resource;

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 standards;

e. Reach out to 12 journals per year while giving priority to journals covering broad biomedical fields and intend to communicate 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 participation in the unique identifiers initiative.

Task 2.2.4 – Reporting to NIH and Model Organism Repositories

Contractor shall report to both NIH and the Model Organism Repositories, via at least one web conference, the results of the previous year’s efforts, including the outcome of dissemination activities, curation issues, and the data that has been gathered about model organism citation and use in the literature.