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Introduction to the database lookup ​

Database lookup serves to efficiently access and analyze data across various databases, integrating seamlessly into your workflow.

When to use database lookup ​

A database lookup is a valuable tool when you need to contextualize nodes (e.g., proteins) of interest. It summarises multiple databases and gives insight into, e.g., alternative names, expression specificity, and disease-suggested/reported relations.

How to get started ​

Before starting, ensure you have a list. If you have not yet created one, please consult our guide on creating My List.

To begin your database search, follow these two steps:

  1. Select your list of interest from Choose a List.
  2. Click Database Search to initiate the database lookup.

Hereafter you can now easily access relevant information pertinent to your My List in either of the tabs representing litterature and biomarker related databases:Protein, Protein properties, Drug and disease, ClinicalTrials.gov, or PheWeb.

Databases available ​

Here is a list of the current available databases:

  • Protein Provides information about different names/synonyms of the proteins/genes.
  • Protein properties Focuses interaction, tissue specificity and subcellular locations.
  • Drug and disease Provides insight to suggested diseases and uses as well as link to drugs own to manipulate the protein or gene expression
  • ClinicalTrials.gov Access to summerisations of records from clinical trials, including link to more information.
  • PheWeb Insight to phenotype-genotype associations, offering link to data crucial for genetic research and understanding disease etiologies.

For detailed information on each database, including how to effectively utilize them in your research, please refer to their respective documentation.

Search in your data ​

For each database, you can easily search for identifiers or values of interest, enabling you to quickly pinpoint the information you need. Here's how:

💡 Good to know

Ensure to that you're searching within the correct database to successfully find the information you need.

  • Simple search: Use the the search tool to easily find what you are looking for. The search tool enables you to quickly locate specific items within your data using keywords like identifiers (e.g., P01730), gene names (e.g., CD4), DrugBank (e.g., DB00098), and more.

  • Advanced search: For more refined searches, each category offers specialized search tools, allowing for multi-factor searches. Find data by specific keywords, such as an identifier (CXCR4).

Sorting data ​

Omics Studio enables users to sort tables by the highest/lowest values or in alphabetical order (A-Z or Z-A). This helps to quickly identify key findings or patterns in the data.

Select items ​

Within any of the databases, items can be selected effortlessly by clicking on one or more entries.

💡 Good to know

Please note that, in the current version, the selection functionality is present but does not yet serve a functional purpose.

Download your data ​

Your data can be downloaded in CSV or Excel format, reflecting your preference and the specific tab you are viewing (Pathways, Molecular Function, or Cellular Compartment). Note that the download will include only the data visible at the moment, ensuring relevance and specificity to your search criteria.