Request for Information (RFI): An Internet Resource for Placental Research - Placental Atlas Tool

Notice Number: NOT-HD-15-005

Key Dates
Release Date:  February 25, 2015
Response Date:  May 1, 2015 

Related Announcements
None

Issued by
Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD

Purpose

The purpose of the initiative is to create a basic placental atlas that would act as important resource for the placental research community. It should be underscored that the initiative is not to simply create a redundant resource of information, but instead to identify gaps in knowledge and explore and integrate the current foundation of knowledge upon which future pipelines of analysis would be built.  This initial initiative is the first step in an envisioned trajectory for reaching the ultimate goal of creating a comprehensive placental atlas that encompasses all the molecular regulatory pathways that drives both normal and abnormal placental development and function. The knowledge gained by completion of the atlas is anticipated to be invaluable for formulating effective molecular based interventions to improve pregnancy outcomes.  

Background

There is a critical need in hastening our understanding of the human placenta. Although the placenta is a short-lived organ, its importance is often underappreciated in being a crucial organ for the propagation of our species and future health of our progeny.  In the era of digital big data, enhanced internet tools for data centralization, cataloguing, integration and dissemination has resulted in a boon for many areas of science. In contrast to many other research fields, there is a lack of any substantial internet based resources for hastening placental research. An initiative is currently planned to address that need.

This RFI is to solicit input from investigators in placental research on the planned initiative to create a WEB-based resource freely accessible to all interested researchers. Some of the main expectations would include the following: The function of the resource would be to collate, annotate and integrate placental data obtained from peer reviewed journals and reputable databases into a coherent assembly for model building and hypothesis generation. It would mainly focus on human data, but would be supplemented with animal data where beneficial and/or where human data is lacking. The resource would be diverse and assemble molecular data in the context of physiology and morphology.  It would also be dynamic in terms of being current with regularly scheduled periodic updates.  The resource would also act as an informational source by providing links to pertinent research funding opportunities, research societies and biobanks. A special emphasis of the resource would be to meld numerous and diverse datasets into an integrated resource to encourage a “systems biology” approach for the study of both normal and abnormal placental development and function throughout gestation.  It is expected that the resource would be a particularly useful tool to identify research gaps, potential therapeutic targets for drug development, and potential biomarkers. In addition, this resource is expected to help support in accomplishing some of the goals of the NICHD’s Human Placental Project (http://www.nichd.nih.gov/research/hpp/Pages/default.aspx).

Information Requested

Comments to the following areas are requested for planning and budgetary purposes, but any and all comments pertaining to this planned initiative are encouraged.  It is anticipated that molecular data (i.e., DNA, RNA and protein) would be searched from a number of scientific journals, annotated and catalogued into a coherent assembly to populate the WEB-based platform.  Therefore, comments can include but are not limited to the following areas:

  • The reputable, peer-reviewed, scientific journals that should be searched.  (Please limit your response to the top 10-25 journals in order of priority.)
  • The length of time the search should go back in time to be the most informative and cost effective (last 5 years, last 10 years, last 20 years).
  • Other species, in addition to humans, for which it would be beneficial to collect information (e.g., non-human primate, mouse, rat, etc. Please limit your response to the top 3 species in order of their priority.)

  It is anticipated that the resource will utilize the available features of reputable public-access, WEB-based, molecular databases, referred here as reference databases. We seek comments on:

It is anticipated the molecular data gleaned from the scientific journals and reference databases will be interfaced and harmonized into a coherent WEB-based platform that would include a searchable tool to answer a number of basic queries to identify the following:

  • Whether it is known if the molecule is expressed in the human placenta; and if not in the human placenta, in another species.
  • If not known to be expressed in the human placenta, other human organ(s) in which it is known to be expressed, or organ(s) in other species in which it is known to be expressed.
  • Spatial and temporal expression of the molecule throughout placental development.
  • Information on the molecule, to include the molecular pathway of the molecule; drugs and small molecules that affect the pathway; interaction of the molecular pathway with other pathways; gene information; placental pathologies associated with the molecule; of other pathologies that may be associated.
  • Pertinent literature reference links to each of the listed queries.
  • Any other queries that might be desirable, and prioritization of those queries.

The resource is also expected to incorporate a placental molecular interactome map. This map is expected to contain an interactive representation that can be viewed at different development stages separately for the human, non-human primate, mouse and rat.  The interactome map feature is also anticipated to have the ability to superimpose the placental interactomes of all these species, and incorporate a generic interactome in which placental specific data is missing but is available from other non-placental sources.  We seek comments on:

  • Any ideas and suggestions that can be incorporated into the interactome map in terms of its interactive features to make it more useful.

It is anticipated that the resource will act as a general information resource by providing links to pertinent research funding opportunities, research societies and biobanks. We seek comments on:

  • The specific links or other types of links that would be useful.

The resource is anticipated to incorporate a physical 3-D visual representation of gene expression in the placenta (viewed separately for the human and other species-e.g., non-human primate, mouse and rat) during various stages of placental development with the ability to zoom to highlighted areas of interest at different levels starting from gene expression at the gross morphological level, to the cellular expression level, and finally at the level of intra-cellular expression.  We seek comments on:

  • The ideas and suggestions that can be incorporated into the physical 3-D map in terms of its interactive features.

We also seek comments on these other logistical considerations:

  • Existing placental research focused curated datasets (national or international) that should be utilized; whether these data sets are publically available; and point of contact information.
  • Specific tools, algorithms, etc. that should be considered as part of the resource.
  • Semantic standards (terminology, metadata, ontology, taxonomy, data dictionary, etc.) that focus on placental research that should be incorporated into the resource. 
  • For both the interactome and 3-D map, the usefulness of providing centralized visualization tools to use these maps, or the usefulness of downloading visualizations tools to be used locally at your institute.           
  • Any other features would be desirable to be included in the resource, and their prioritization.

How to Submit a Response

All responses must be submitted via email to ilekisj@mail.nih.gov.   Responses will be accepted until May 1, 2015.  Please include the notice number NOT-HD-15-005 in the subject line and include your complete contact information with your response. 

Responses to this RFI are voluntary. The submitted information will be reviewed by the NIH staff and may be made available to the public. Submitted information will not be considered confidential. 

No awards will be made based on responses to this Request for Information and it is not a solicitation for applications or an obligation on the part of the United States (U.S.) Government to provide support for any ideas identified in response to it. Those who respond are advised that NIH is under no obligation to acknowledge receipt of your comments, or provide comments on your submission.

No proprietary, classified, confidential and/or sensitive information should be included in your response.  No basis for claims against the U.S. Government shall arise as a result of a response to this request for information or from the Government’s use of such information. The NIH and the government reserve the right to use any non-proprietary technical information in any future solicitation(s).

Inquiries

Please direct all inquiries to:

John V. Ilekis, PhD
Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)
Telephone:  301-435-6895
Email: ilekisj@mail.nih.gov