- Course overview
- Search within this course
- Overview of key IMPC concepts and tools
- Introduction to the Solr API: accessing IMPC data programmatically
- What is Apache Solr?
- Important definitions: query, field, core, document, parameter
- Quiz 2: get yourself familiar with Solr terminology
- What is the difference between an IMPC parameter and a Solr parameter?
- Using simple Solr syntax in your browser
- Output of the simplest request in your browser
- A Python module to access IMPC data: installation and available functions
- Quiz 3: explain Solr request
- Filtering data in Solr: narrowing down your results
- How to query a specific field: filter by value
- Exercise 4: filtering by a single field
- How to filter numbers: range search
- Exercise 5: changing the p-value threshold
- How to combine multiple filters: Boolean operators
- Exercise 6: applying multiple filters
- How to exclude data: NOT operator
- Why parentheses are important: combine multiple Boolean operators
- Quiz 5: Boolean operators
- How to handle with null values: exclude empty fields
- Exercise 7: explore null values
- Downloading data: getting large results efficiently
- How to download large dataset effectively: pagination
- How to download the data: batch_solr_request function
- What formats are available for downloading: wt parameter
- Exercise 8: download the data
- What is the difference: JSON vs CSV
- What you need to keep in mind: query responsibly
- Quiz 6: request only necessary data
- Advanced Solr query techniques: faceting and iterating over entities
- Understanding IMPC data: resources and assistance
- Your feedback
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Exercise 1: getting familiar with the core
We will be working with the genotype-phenotype core. To familiarise yourself with the data, request everything from this core using the solr_request function and the q parameter.
Go to Exercise 1 in the Google Colab.
Once you’ve finished Exercise 1 in the Google Colab, return here to continue the tutorial but keep the Colab open as it contains the other exercises you will complete during this tutorial.
Show the correct answer
num_found, df = solr_request(
core='genotype-phenotype',
params={
'q': '*:*'
}
)
Here we specify the core name and use an asterisk (*) to get all the data from the genotype-phenotype core.