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QIAGEN OmicSoft Suite

Release date: 2022-12-01

QIAGEN OmicSoft Lands API expands access to curated ‘omics data

 

The new QIAGEN OmicSoft Lands API enables powerful searches across QIAGEN OmicSoft Lands data. Query data on any metadata field across Land databases, without needing to ingest data into your own SQL database.

 

Figure 1. QIAGEN OmicSoft Lands API schematic. Queries are submitted using SQL syntax via Python or R packages, which are processed by the QIAGEN OmicSoft Lands API query engine to find matching data within the QIAGEN curated ‘omics Land databases. Matching data are returned to the Python/R environment for analysis and visualization. Retrieved data can be downloaded as flat files or directly loaded into Python/R data frames.

Data

The QIAGEN OmicSoft Lands API provides direct access to OmicSoft’s collections of deeply-curated datasets, taking advantage of extensive controlled vocabularies and our human-centered curation approach to unlock powerful cross-project queries.

Learn more: Why is a curated ‘omics data portal important?

 

Data structure

OmicSoft’s structured tables of metadata and data can be queried on one or more fields and joined to return exactly the data needed to answer your biomarker-related questions.

QIAGEN OmicSoft OncoLand and DiseaseLand datasets have structured and curated metadata at project, sample and comparison level and are linked to ‘omics measurements for each sample, such as RNA-seq gene expression (gene, transcript, exon, junction, fusion and mutation), microarray expression (probe and gene), miRNA-seq, DNA-seq mutation calls, copy numbers and more.

Figure 2.  Schema of QIAGEN OmicSoft OncoLand and DiseaseLand datasets. Curated metadata (left) are represented within multiple tables with keys to join at the project and sample level, as well as comparisons between sample groups. Each curated data type (middle) is represented by a separate table, which can be filtered on associated metadata, data values or associated annotation (right).

Single-cell datasets within QIAGEN OmicSoft Single Cell Land databases include structured and curated metadata at project, sample, cluster, cell and comparison level, linking to gene expression (raw and normalized counts) for each cell, along with cell coordinates from pre-computed dimension reduction analyses.

 

Figure 3. Schema of single-cell RNA-seq datasets in QIAGEN OmicSoft Single Cell Land databases. In addition to curated information at the project, sample and comparison level (left), single-cell datasets include metadata and data describing cells and cell clusters (right).

 

Access to curated data

The initial release provides access to subscribed datasets within QIAGEN OmicSoft DiseaseLand, OncoLand and Single Cell Land databases, including the following:

 

  • 650,000+ manually curated samples
  • 1400+ diseases and 700+ tissues represented across 9000+ ‘omics projects
  • Rich harmonized metadata described across 6000+ metadata fields, allowing powerful queries to capture relevant samples across studies
  • 124,000+ comparisons from custom statistical models to reveal differentially expressed gene signatures across studies

 

API client system requirements

We offer simple-to-install clients supporting Python (Python version 3.7 or higher) and R (R version 3.6.0 or higher). These clients are used to submit SQL queries to retrieve data slices from the hosted database.

Ask your Sales Representative to add the OmicSoft Lands API to your license.