Illuminating the Druggable Genome Program: Consortium Policies
Finalized on July 11, 2018
The Illuminating the Druggable Genome (IDG) Consortium is a National Institutes of Health (NIH) Common Fund program that aims to illuminate select understudied proteins in three protein families: non-olfactory G protein-coupled receptors (GPCRs), ion channels, and protein kinases. These families were selected as they contain adequate numbers of understudied members and are well-established druggable families with high potential to impact human health once disease associations are made. This illumination is accomplished by the Consortium via multiple state-of-the-art experimental platforms and by gathering knowledge across the entire human proteome via cutting-edge informatics tools. Data and resources produced by the IDG Program are then made available to the scientific community at large through DruggableGenome.net and the IDG portal Pharos. The following IDG policies were developed to optimize the impact of the program, maximize access to program-generated resources, and minimize barriers to collaboration. These policies are available on https://druggablegenome.net/IDGPolicies and via FAIRsharing under the IDG collection (https://fairsharing.org/collection/IDGProject).
IDG Consortium members:
Current members of the IDG Consortium, as of June 19, 2018, include the recipients of grants from the following RFAs:
- DRGC: Data and Resource Generation Centers for Illuminating the Druggable Genome (U24) RFA-RM-16-026
- DRGC-GPCRs to the University of North Carolina Chapel Hill: U24 DK116195
- DRGC-Ion Channels to the University of California, San Francisco: U24 DK116214
- DRGC-Protein kinases to the University of North Carolina Chapel Hill: U24 DK116204
- KMC: Knowledge Management Center for Illuminating the Druggable Genome (U24) RFA-RM-16-024
- KMC component to the University of New Mexico: U24 CA224370
- KMC component to the Icahn School of Medicine at Mount Sinai: U24 CA224260
- RDOC: Resource Dissemination and Outreach Center for Illuminating the Druggable Genome (U24) RFA-RM-16-025
- RDOC at the University of Miami School of Medicine and University of New Mexico: U24 TR002278
The PIs and co-PIs from these grants serve on the IDG Steering Committee (abbreviated IDG SC) together with the NIH IDG Working Group (abbreviated NIH IDG WG), which is listed here (https://commonfund.nih.gov/idg/members).
What follows is a list of guidelines and principles that will be followed by the IDG Consortium addressing:
Guidelines and Principles for the Selection of the Use of 10% Restricted Funds by the DRGCs of the IDG Program
Policy for Communication of IDG Resources
Policy for IDG Data Sharing and Publication by IDG Members
Policy for Resource Sharing by IDG Members
Policy for Quality Control Metrics for Resources
Policy for Metadata Requirements for IDG Members
Policy for IDG Consortium Interaction with Other Entities (Consortia/Institutes /Associations/Biotech/Pharma)
Policies for IP/ Licensing for Data and Resources Generated by IDG Members
Requests for changes to IDG Consortium policies must be made to the NIH IDG WG. If approved by the NIH IDG WG, these changes will go to the IDG SC for final approval and posting on DruggableGenome.net.
Guidelines and Principles for the Selection of Use of 10% Restricted Funds by the DRGCs of the IDG Program
10% of the funds received by the DRGCs for IDG related work are restricted for collaborative projects that advance the IDG mission beyond the core proposed capabilities.
Structure of proposals for review by the IDG SC (1 page for items 1 - 2; additional 1 page for items 3-6)
- A written description of the proposed project(s), including which understudied proteins are proposed for study (or rationale for why a better studied protein is needed for method development or proof-of-concept first).
- How the proposed project(s) enhances the overall IDG effort to serve the broad scientific community by generating tools and reagents around understudied proteins and, if applicable, the collaborating DRGC(s).
- Identification of the 10% restricted funds approved use. The proposal should:
- Support experimental or informatics approaches not included in original proposals for the study of an eligible protein family; OR
- Explore upstream or downstream signaling or interactions amongst the GPCRs, protein kinases, and ion channels; OR
- Form new external collaborations to bring in new disease expertise and/or technologies not present within the IDG Consortium.
- List/describe the development of new deliverables, milestones, and metrics associated with the project(s).
- If applicable, justification for any changes to the core decision trees.
- A brief estimate of direct and total costs for the project(s).
Principles for review by the IDG SC
- Proposals should be vetted by the Principal Investigators and Project Scientists for all involved awards before proposals are considered by the IDG SC.
The IDG SC should consider proposals in May/June of each year with the goal of recommending these proposals to the NIH IDG WG for formal approval as part of the non-competing renewal RPPRs in July.
- Off-cycle requests are possible, but awardees should be aware that awarded funds can only be used in the (current) fiscal year in which they were awarded. Funds cannot automatically be carried forward into the next year; this occurs via a formal process once the Federal Financial Report for prior fiscal years is completed.
- While projects may be proposed that extend beyond one year, a progress report is required and request for continuation will occur at the next evaluation cycle.
- In the first year of the program only, IDG SC recommendations approved by the NIH IDG WG may be granted for projects that span the 1st and 2nd years of the program.
- The primary venue for NIH IDG WG input into the drafting of proposals will be through the Project Scientists and NIH staff participation in the IDG SC. However, in cases of no consensus in the IDG SC or insufficient funds for all proposals, the NIH IDG WG will make the final decision.
Formal Approval by the NIH
- The SC recommended proposal must be transmitted to the NIH by an authorized business official. In addition to the scientific proposal, a detailed budget breakdown and justification for each budget expense should be included.
- This may occur as part of the RPPR, or if it occurs during the current grant year, via an e-mail to Dr. Aaron Pawlyk and the grants management specialist.
NIH will review proposals recommended by the IDG SC for use of 10% restricted funds. Those proposals that are approved will have their restricted funds released via the Notice of Award. If the NIH IDG Working Group, via the Steering Committee, deems such collaborations scientifically unwarranted, the 10% budget may be re-allocated to the primary project on a yearly basis. A justification for the rebudgeting of restricted funds must be submitted for approval.
- In cases where there was a delay in recommendation of a proposal by the IDG SC to NIH (e.g., delays due to start-up in the 1st year, time required to negotiate sub-contracts, etc.), applicants may submit a request to the NIH for retroactive prior approval for use of funds (i.e., approval is requested in April 2018 for use of funds for a December 2018 to December 2019 award). In such cases, an explanation of the logistical delay must be included in the request. Note that these requests are still limited to the current fiscal and project year.
Communication of results stemming from work performed by members of the Consortium with NIH IDG funding can be made by individual IDG members and their institutions. For outreach purposes, information associated with IDG work performed by the members of the Consortium will be made available to the RDOC. Information can be shared via email (email@example.com) and/or entered on the IDG Google drive (IDG2_SharedFolder_viaRDOC). This information includes, but is not limited to:
- Publications in scientific journals or BioRxiv.org (complete citation with DOI)
- Presentations at conferences (Speaker name, preferably link to conference site/agenda)
- New developments of assays/techniques
- Launching of applications/data analysis software
- Proposals for joint publications across the IDG Consortium
The RDOC is charged with informing the greater public of Consortium progress on Illuminating the Druggable Genome and serves as an unbiased ambassador for the IDG Consortium. The RDOC takes on the responsibility to be impartial to all information received from IDG Consortium members and to give equal representation to all IDG Consortium members’ information. The outreach work by the RDOC is not a substitute for outreach conducted by other IDG members, and outreach efforts should be made by all IDG awardees. Mechanisms of outreach that will be employed by the RDOC include (but are not limited to):
- News announcements on the IDG website (druggablegenome.net)
- Social media (twitter: @druggablegenome)
- Listservs for IDG information (via idg.rdoc)
- Coordination with the NIH Common Fund website
- Coordination of External/Public Bi-annual meetings allowing for presentations by IDG members
Additional outlets for outreach and publication can be established by the RDOC on behalf of the IDG Consortium, with the understanding that the RDOC will inform the rest of the IDG Consortium via the IDG SC. These outlets will be established by RDOC members and with the intention of representing the IDG Consortium in the most effective way possible.
Approval of RDOC information sharing with the public is granted by the knowledge/data/resource generators (KMC or DRGCs) via their participation with the IDG. As an example, this would include sharing the status of recent data that will be published soon, such as through a twitter announcement. If there is a request to withhold information (i.e., pre-publication data), then it is up to the generator of the information to clearly state this request to the RDOC via firstname.lastname@example.org. For dispute resolution, cases will be brought to the IDG SC for discussion to resolve the issue. Should the IDG SC be unable to resolve the conflict, the matter will be elevated following the Dispute Resolution policy outline in the terms and conditions of NIH Grant Awards.
The Outreach working group of the IDG will summarize these outreach elements and will inform all other IDG members of updates during the Outreach working group’s monthly meetings.
All IDG members funded by the IDG Program are bound by their U24 cooperative agreements and FOA requirements for sharing of IDG data. Each DRGC is responsible for their individual raw data file storage and is accountable for sharing their resulting quality-controlled data via public data repositories. Data quality control (QC) remains the responsibility of the IDG Center where the data are generated and must be compliant with the IDG Policy for Quality Control Metrics for Resources. Compliance with metadata requirements per the IDG Policy for Metadata Requirements for IDG members, as well as IDG metadata standards, agreed upon by the IDG SC, will be the responsibility of the DRGCs, with RDOC assistance. Sharing of metadata standards and QC metrics to the whole IDG Consortium will be done via appropriate mechanisms: i.e., the IDG wiki site or the IDG website, the IDG portal Pharos, or via a public resource such as FAIRsharing. In some rare cases data may be released prior to meeting full quality control metrics. In these cases, the data must be accompanied by a caveat emptor notice for users. The IDG SC will review these cases to ensure that what quality control metrics can be met are being addressed.
Pre-publication dissemination of data through the bioRxiv is strongly encouraged although not mandated. The general intent of this policy is to release data as quickly as possible, consistent with the core principles of the IDG Program. IDG members are encouraged to share their data in public and open source formats with the use of a specific permissible license. The IDG portal Pharos utilizes the Creative Commons 4.0 license. Data generated by IDG members should be shared via data repositories that are public and open source and will not hinder the further use of these data.
Guidelines for reporting IDG results are in accordance with NIH policy. The NIH grant number must be listed in all publications when acknowledging financial support.
A noted exception for data sharing: In the event of developing a crowdsourcing competition (such as a DREAM challenge) for soliciting public input to analyze data and make associated predictions, it may be necessary to keep some data ‘hidden’ for comparison to these developed predictions. These crowdsourcing challenges will be made in collaboration with the IDG SC and their approval will govern the ‘hidden’ data.
The RDOC will serve as a reference for solutions to data repositories and/or general data storage. The RDOC proposes to develop a data submission and publication pipeline that includes a Resource Management System (RMS) for ensuring compliance with data standardization and annotation, e.g. Synapse (https://www.synapse.org/).
The knowledge stemming from IDG generated data, such as tool compound characterization data, visualization of expression data, and phenotypic mouse data, will be incorporated into the KMC’s various platforms (i.e., TCRD database for Pharos, Harmonizome, or other data visualization). The IDG Data Sharing policy does not require that generated data are made directly accessible via KMC platforms; for example, datasets can be submitted to an approved public data repository. However, compliance of IDG data standards, requires that data are sufficiently annotated to be Findable, Accessible, Interoperable and Reusable (FAIR) so that they can be re-used and incorporated into the KMC.
The RDOC will serve as a facilitator to ensure that the IDG Consortium fully approves of IDG data and resource submission to various IDG SC-approved public repositories.(SC-approved public repositories)
No additional considerations are needed for internal IDG data sharing as the data should already be available to the public. The mechanism of sharing data will depend on data type. Primary access to IDG data will be via public repositories where the data has been submitted. Following this, the use of submitted IDG data will be governed by the policies of those public repositories. It is the aim of the IDG Consortium to share all data and limit any hinderances for the reuse of IDG generated data and resources. Data elements to be shared are defined by the data generator with the aim of capturing the most critical information required for proper dissemination of the data. As new types of data are generated, these elements can be further developed.
To help protect the ability for trainees to publish their work and accommodate delays that may be incurred during intellectual property (IP) negotiation, a 180-day embargo on specific datasets may be requested. This 180-day embargo would begin following completion of verification that quality control metrics have been met for embargoed datasets (see Policy for Quality Control Metrics for Resources). The PI from the IDG Center generating the data will notify the NIH IDG WG with proposed dates of delay of actual data and provide appropriate justification. When requesting data embargo, the following should be addressed:
- What is the embargo on, data release or data deposition?
- Will data be stored internally via Synapse during the embargo?
- Is an embargo on others (IDG internal or external) publishing after data release being considered?
If the NIH IDG WG approves the request, the IDG SC will communicate this in writing to the PI, who remains responsible for tracking compliance. Passive approval from the NIH is not permissible and failure to obtain an NIH response to requests does not signify automatic approval. Extensions to the release date will follow the same procedure. These requests should be made within the bounds of the 90/10 rule, stating that no more than 10% of data can be placed under embargo for a given publishable project.
Resources generated by IDG members may include, but are not limited to, cell lines, mouse lines, small molecules, peptides, computational algorithms, machine learning models (“AI”), instrumentation, etc. The guiding principles for sharing IDG generated resources are set by NIH Sharing Policies (https://grants.nih.gov/policy/sharing.htm) and the Resource Sharing Plan guidelines stated in the original IDG FOAs: “A primary goal of the IDG Program is to facilitate discoveries of the broad scientific community for the improvement of public health. Restrictive licensing and sharing practices for IDG-generated data, tools, and resources could substantially diminish their value and public benefit. Accordingly, awardees should manage data, resources, protocols, tools, and software in a way that achieves this primary goal. Sharing practices that would prevent or block access to or use of IDG Program data, tools, and resources for research purposes will be considered to be hindering the goals of the IDG Program.”
IDG resources should be shared with the aim of limiting restrictive permissions. IDG members are committed to this goal and will utilize it as a guidance for allowing access to resources.
The role of the RDOC is to work with DRGCs to identify appropriate access points or venues for their resources to be shared. This might include vendors or resource repositories. The RDOC will aid in communication, facilitation, and record keeping for these distribution options.
To comply with the IDG Policy for Metadata Requirements for IDG Members, these resources should be well annotated and include a reference to track uptake of IDG resources by the scientific community, such as RRIDs, ChEMBL numbers, DOIs etc.
As IDG members may share their resources via different mechanisms (see Policy for Resource Sharing by IDG Members), the IDG Consortium expects that these resources comply with the quality control metrics listed on https://druggablegenome.net/QC_Metrics. It is expected that these metrics will be amended as new types of resources and data are developed by the IDG Consortium. In rare cases where quality control metrics cannot be met for certain reagents or data, this will be indicated in appropriate repositories along with a caveat emptor notice for users. The IDG SC will review these cases to ensure that what quality control metrics can be met are being addressed.
IDG Consortium members are required to make available metadata that describes generated datasets, “wet” (material) resources, such as reagents, and digital resources developed as part of the IDG project. Metadata should conform to the metadata standards developed and approved by the IDG Consortium and any metadata repository or distributor requirements for datasets, material resources or digital resources that will be made publicly available . These metadata requirements are aimed at ensuring that IDG datasets and digital research objects that correspond to IDG-developed resources are FAIR in the scientific community and allow for appropriate attribution of datasets and resources while maximizing their reproducibility. To accommodate new datasets or resources developed by the IDG Consortium, the minimum IDG metadata standards may be updated or revised.
The IDG Consortium intends to remain compliant with FAIR metrics, which are currently in development at NIH and internationally, as well as the specific requirements of repositories and distributors. Upon IDG Consortium approval, IDG metadata standards will be publicly released via the IDG website or Portal and via FAIRsharing under the IDG metadata standards collection (https://fairsharing.org/collection/IDGProject).
Policy for IDG Consortium Interaction with Other Entities (Consortia/Institutes /Associations/Biotech/Pharma)
IDG members are encouraged to foster collaborations and interactions with individual laboratories/researchers, consortia, associations, pharma, and biotech, as well as other outside entities. The guidelines outlined here are to enhance these interactions for the benefit of sharing IDG outcomes.
When IDG members establish interactions with other groups (not individual investigators) concerning potential future interactions with the IDG consortium as a whole, the RDOC should be informed of this network establishment to allow tracking of these interactions for the IDG record as well as for promoting this interaction through IDG websites as appropriate. The RDOC’s role is to record these interactions as part of its IDG outreach activities and to facilitate the development of future outreach activities, where appropriate. The RDOC is not responsible for establishing collaborations between non-IDG groups and individual IDG members.
Agreements between IDG awardees and non-IDG entities:
- Agreements between the IDG Consortium as a whole and another entity must be approved by the IDG SC.
- Agreements between an awardee and a non-IDG entity do not need IDG SC approval as long as the data is from that awardee alone and the data will be deposited publicly according to IDG policy.
- Material Transfer Agreements may be required for the IDG Consortium as a whole for IDG-wide collaborations. If only one awardee collaborates, that awardee should use the MTA template from their university.
A written proposal for a formal alignment between the IDG Consortium and an outside group must be reviewed by the IDG SC. Review criteria will include:
- Statement of required assets from the IDG Consortium with respect to:
- Requests for financial support (Requests for spending the 10% set-aside follows Policy 1, with additional requests for Supplemental Funding to be made in accordance with the NIH Supplemental Funding policy).
- Sharing of resources/data (beyond what is shared with the public, according to the IDG data sharing policy).
- Potential benefit/outcome from interaction (i.e., publications, conference event).
- Timeline of interaction.
- Appropriate reporting of the interaction through IDG websites or media, including funding support for the external entity to support the proposed interaction. The IDG Consortium will acknowledge the funding source for the non-IDG group on the IDG website and/or Twitter as it pertains to the interaction.
A main contact at the IDG awardee institution (required to be a member of the IDG SC) will be responsible for keeping the RDOC informed of the progress of the interaction.
It is imperative to avoid restrictive accessibility to the broad scientific community when establishing licenses and sharing practices, especially with consideration to the Resource Sharing Plan stated in the original IDG FOAs: “A primary goal of the IDG Program is to facilitate discoveries of the broad scientific community for the improvement of public health. Restrictive licensing and sharing practices for IDG-generated data, tools, and resources could substantially diminish their value and public benefit. Accordingly, awardees should manage data, resources, protocols, tools, and software in a way that achieves this goal. Sharing practices that would prevent or block access to or use of IDG Program data, tools, and resources for research purposes will be considered to be hindering the goals of the IDG Program.” IDG members remain committed to this goal of the IDG Program and it will be utilized as guidance for allowing access of resources.
The overall guiding principles for intellectual property of data and resources generated by IDG members are to allow each IDG member to own what they create, in accordance with Bayh-Dole Regulations. The specific elements of IP generation, management and licensing are handled by the Technology Transfer Offices of the institution(s) where the invention occurred. This handling must take into account the Terms and Conditions of each grantee’s Notice of Award that includes adherence to the principles and policies agreed upon by the IDG SC as detailed in this document. It is the responsibility of each grantee and their Technology Transfer Office to assure that any licensing agreements are compliant with the IDG SC’s policies.
If a creation to be patented or licensed results from work at multiple IDG sites or involves partnership with non-IDG members, then IP management must be agreed upon by those parties outside of the IDG Consortium as a whole. The IDG Consortium does not own any IP/licensing of data and resources generated by IDG members.
DRGCs should proactively contact their respective Tech Transfer offices in the early stages of the collaboration. The decision to protect specific IP remains with the inventors and the Center(s) where such IP originates. Should the invention (e.g., chemical structures) need non-disclosure status prior to filing the patent application, the Consortium should be flexible in creating value from said invention, e.g., by working with the substance without knowing the chemical structure until appropriate steps are taken.
The role of the RDOC is to set up processes for facilitation of collaboration among IDG members by aiding communication and maintaining record keeping. This includes assistance in finding potential distribution centers for data and resources. However, the RDOC does not provide support for arranging profit generating transactions among IDG members or commercial partners.