HMPDACC: a Human Microbiome Project Multi-omic data resource

Abstract

The Human Microbiome Project (HMP) explored microbial communities of the human body in both healthy and disease states. Two phases of the HMP (HMP and iHMP) together generated >48TB of data (public and controlled access) from multiple, varied omics studies of both the microbiome and associated hosts. The Human Microbiome Project Data Coordination Center (HMPDACC) was established to provide a portal to access data and resources produced by the HMP. The HMPDACC provides a unified data repository, multi-faceted search functionality, analysis pipelines and standardized protocols to facilitate community use of HMP data. Recent efforts have been put toward making HMP data more findable, accessible, interoperable and reusable. HMPDACC resources are freely available at www.hmpdacc.org.

Figure 1.

HMPDCC OSDF entity relationship data model. This figure represents the organization of data types listed in Table 1 along with higher level entities. Each white box represents an object, or a node as they are referred to in OSDF, with lines representing the relationships, or linkages, between nodes. Linkages can be traversed as in the following example: [samples] are collected_during a [visit] by a [subject] who participates_in a [study] that is part_of a [project]. Nodes with a red background represent project-specific subject, visit or sample metadata, which became very important during the iHMP when each study involved vastly different phenotypes requiring collection of different types of clinical metadata. Nodes with a green background represent sequence-based omics data types. Nodes with a purple background represent other omics data types. Nodes with a blue background represent summary data aggregated over multiple samples/subjects within a project or study, for example study level BIOM files. Each node depicted here in turn has a corresponding metadata schema that defines required properties, for example subject_id, checksum, or date file path. Schemas are freely available at https://github.com/ihmpdcc/osdf-schemas

Figure 2.

The Free Text Search tool is available under the Data tab of the HMPDACC website. This tool allows for exact or wildcard text searches of metadata fields associated with data elements. The interactive data table is dynamically updated as search terms are entered, allowing users to click and view selected elements.

Figure 3.

Identifying a dataset of interest, step by step, using the HMP Data Portal Faceted Search and Advanced Query Tools. (A) The simple faceted search allows for point-and-click query building with dynamic, interactive graphical summaries of query results; (B) advanced search features allow for more customized queries; (C) files added to the data cart can be downloaded individually or via a manifest file.