Related Experiment Video
Updated: Jan 30, 2026
07:41
Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases
Published on: May 17, 2019
9.6K
Invited Commentary: Improving the Accessibility of Human Microbiome Project Data Through Integration With
Jocelyn C Griffith1, Xochitl C Morgan1
1Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
American Journal of Epidemiology
|January 17, 2019
Summary
The Human Microbiome Project (HMP) offers valuable data on healthy microbiomes. A new R package simplifies access to this complex HMP data, aiding public health research.
Area of Science:
- Microbiology
- Bioinformatics
- Public Health
Background:
- Microbiota alterations are linked to numerous diseases.
- The Human Microbiome Project (HMP) established a reference dataset of the healthy human microbiome.
- Analyzing HMP data presents significant bioinformatic challenges.
Purpose of the Study:
- To simplify access to and analysis of the Human Microbiome Project data.
- To provide researchers with an integrated data object combining 16S taxonomic abundance, metadata, and phylogenetic trees.
- To facilitate the use of HMP data for public health research.
Main Methods:
- Development of the HMP16SData R/Bioconductor package.
- Integration of 16S rRNA gene sequencing data, patient metadata, and phylogenetic trees.
- Creation of an interface for accessing controlled-access HMP metadata via dbGaP.
Main Results:
- The HMP16SData package consolidates HMP data into a single, accessible object.
- The package simplifies the retrieval and merging of public and restricted HMP metadata.
- The tool is designed for researchers with varying levels of R and statistical expertise.
Conclusions:
- The HMP16SData package significantly enhances accessibility to HMP data.
- Improved data accessibility supports public health research by providing a reference for disease-associated studies.
- This resource benefits a broad range of researchers across disciplines.
More Related Videos
Related Concept Videos
02:18Fischer Projections
16.5K
Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...
16.5K
02:06Newman Projections
20.9K
Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...
20.9K
01:29Coordinates and Map Projections
612
Coordinates and map projections are essential tools in accurately representing the Earth's surface for various applications, ranging from navigation to spatial analysis. The latitude and longitude coordinate system is a universally recognized framework for defining locations. Latitude specifies the distance of a point north or south of the equator, measured in degrees from 0° at the equator to 90° at the poles. Longitude indicates a location's position east or west of the prime meridian,...
612
01:24Data Reporting and Recording
5.4K
Reporting and recording are crucial in data documentation. The timely, thorough, and accurate documentation of facts is essential when recording patient data. Failure to record findings during an assessment or interpretation of a problem will result in loss of information and make the patient document unreliable. The reader is left with general impressions if the information is not specific. A recording is documenting data of the individual's health information in a traceable, secure, and...
5.4K
01:26Integration by Parts: Indefinite Integrals
166
Integration by parts is a fundamental technique in calculus for evaluating integrals involving the product of two functions. It is particularly useful when direct integration is not feasible. The method is based on the product rule for differentiation, which states that the derivative of a product equals the derivative of the first function times the second, plus the first function times the derivative of the second. By integrating this identity and rearranging terms, the integration by parts...
166
01:23Integration by Parts: Definite Integrals
75
Definite integrals involving the product of two functions over a fixed interval can be evaluated using integration by parts. This method rewrites the integral as the difference of a product evaluated at the endpoints and a remaining definite integral that is often simpler to compute.A representative example is the definite integral of the inverse tangent function. Since there is no direct integration formula for arctan x, the integrand is rewritten as a product of arctan x and the...
75