Elsevier’s New Biology Solution Helping researchers understand the biology of disease. Chris Cheadle PhD c.cheadle@elsevier.com

DataFind

What dataset finding looks like today Question: “I would like to rapidly review available gene expression data involving asthma studies for my gene of interest (e.g. CPA3)

Today finding information means scanning hundreds of dataset descriptions - one by one Actual number of total entries for asthma gene expression in GEO Today you will have to read the entire series of entries to find the dataset you might be interested in. You don’t want to miss anything important but it’s very likely that you will only be interested in a relatively small subset for further study. Filtering capabilities could be greatly enhanced using Elsevier text-mining capabilities.

Step 3 Extract data 1. Dataset Information Parsed 2. Retrieve All Datasets 4. Visualize Dataset Information 3. Annotate Datasets

Visualize Dataset Information ELS DataFind Asthma related gene expression datasets in GEO (by year)

Surface relevant information Summary of all asthma-related gene expression datasets in GEO, organized by tissue type, organism, and number of studies. Choose Selected Datasets

Choose Selected Datasets ELS DataFind Choose Selected Datasets Advanced Filtering

Choose Selected Datasets ELS DataFind (powered by Tableau™) Choose Selected Datasets Advanced Filtering w/ Highlighting

Choose Selected Datasets ELS DataFind (powered by Tableau™) Choose Selected Datasets Advanced Filtering/Subset Selection

View Description of Selected Datasets ELS DataFind (powered by Tableau™) View Description of Selected Datasets Advanced Filtering/Dataset Annotation

Search Unstructured Text ELS DataFind (powered by Tableau™) Keyword Search: “Smoking” Search Unstructured Text

Data Find Entellect Preprocesssed Public Datasets Find Asthma Retrieve All Datasets Visualization & Selection Data Analysis Raw Datasets Design experiment based on existing data Asthma related gene expression datasets in GEO (by year) Expert users may want to apply their own tools

Data Organization Automatically organize selected data for rapid analysis Return organized data to answer specific questions

ELS Data Import and Meta-analysis CPA3 carboxypeptidase A3 This gene encodes a member of the carboxypeptidase A family of zinc metalloproteases. The encoded preproprotein is proteolytically processed to generate a mature protease that is released by mast cells and may be involved in the degradation of endogenous proteins and the inactivation of venom-associated peptides. Expression of this gene may be elevated in human asthma patients.

What researchers really want to do is ask… “What’s my gene doing in other peoples data….?” “Data Find” Benefits to Researchers: Rapidly find out what is available in my area of interest Rapidly acquire data in format for immediate analysis Rapid acquisition of specific gene/protein results Empowers both professional bioinformaticians and general biologists

Thank you and please feel free to take our survey: DataFind Survey   . Copyright© 2017 Elsevier B.V. All rights January 2017