博文
“如何玩转生物大数据”系列：基于ArrayExpress网站快速搜索功能
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ArrayExpress is a database of functional genomics data (http://www.ebi.ac.uk/arrayexpress/). It stores data from high-throughput functional genomics experiments, and provides these data for reuse to the research community. Objectives of this post is to show you how to effectively search and retrieve data from the ArrayExpress website.
1. What kinds of data types are stored in ArrayExpress?
These are the different experiment types that are currently reposited in ArrayExpress.
2. Programmatic access and retrieval by constructing URLs
The main object in ArrayExpress is the experiment.
An experiment usually groups several assays belonging to one study or publication.
Each experiment contains metadata describing the biological specimen and experimental procedures, as well as resulting data files.
Experiments can be searched for by keywords and specific fields (e.g. sample attributes or experiment types)
Keyword searches of all fields for experiments and files linked to experiments can be made using the following format of URLs:
1. https://www.ebi.ac.uk/arrayexpress/xml/v3/experiments?keywords=prostate+AND+breast
2. https://www.ebi.ac.uk/arrayexpress/xml/v3/experiments?keywords=prostate+breast (same as above)
3. https://www.ebi.ac.uk/arrayexpress/xml/v3/experiments?keywords=prostate+OR+breast
4. https://www.ebi.ac.uk/arrayexpress/xml/v3/experiments?keywords=prostate+NOT+breast
A few points to note when using keyword search:
Accession number and keyword searches are case insensitive
Use an asterisk * as a multiple character wild card e.g. keywords=colo* will search for colon, colorectal, color etc
Use a question mark ? as a single character wild card e.g. keywords=te?t will search for text and test
Phrases of more than one word must be entered in quotes e.g. keywords=“growth condition”
More than one keyword can by searched for using the ‘+’ sign e.g. keywords=lung+cancer
3. Case Studies
what experiment data types are frequently used to study stem cells?
what experiment study designs are frequently used to study stem cells?
what cell types are frequently used to study stem cells?
what cell lines are frequently used to study stem cells?
what organism parts are frequently used to study stem cells?
what antibodies are frequently used to study stem cells?
what disease states are frequently studies in stem cells related projects?
3.2 find experiments samples of which have survival-time records in metadata
https://www.ebi.ac.uk/arrayexpress/xml/v3/experiments?species=%22homo%20sapiens%22&sac=survival
what diseases are studied by these experiments?
4. Conclusions and References
Programmatic access: query and download data using web services or JSON,http://www.ebi.ac.uk/arrayexpress/help/programmatic_access.html
Welcome to ArrayExpress Help, http://www.ebi.ac.uk/arrayexpress/help/index.html
ArrayExpress: Discover functional genomics data quickly and easily, https://www.ebi.ac.uk/training/online/course/arrayexpress-discover-functional-genomics-data-qui
ArrayExpress: Quick tour, https://www.ebi.ac.uk/training/online/course/arrayexpress-quick-tour-1
https://blog.sciencenet.cn/blog-3291578-1066688.html
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