Hi everyone.
I'm currently using RNAcentral for my research project, but I don't know how to get information from the databases included in RNAcentral by using relational databases. I know that RNAcentral has an API to access to data programmatically using python code. Also, I have explored sqlite3 python module, but I don`t know how to use it in order to call the RNAcentral API, so I could get a sketch of the tables that conform the databases, so I can identify where is the information that I need.
Thank you in advance.
In order to get the schema of your SQLite3 database you can install Sqlite Browser for example:
http://sqlitebrowser.org
Then open your file with that software and you will be able to browse your tables and figure out what they store, before you get hands into the API. Best regards.
look at this github repo
https://github.com/RNAcentral/rnacentral-webcode
you can generate a web interface to access the rnacentral data
Hi, Laura!
RNAcentral has quite well documented api and code example how to use it from Python.
Pandas, a Python library, is a good choice to perform data analysis using Python.
Latest versions of Pandas could handle urls directly, so, to get data from the RNACentral hub, execute, for example, these lines of code:
import pandas as pd
theurl = 'http://rnacentral.org/api/v1/rna/?format=json&max_length=10'
# theurl is formed in accordance to the API http://rnacentral.org/api
data = pd.read_json(theurl)
print(data.results[0]) # show a bit of data
Another way to get data from the API is to use: 1) requests library, 2) naitive urllib.requests Python library
and form a proper GET-request to the RNACentral server. In this case you will need to parse server's response; Fortunately, you can choose response format by passing . E.g. format = json tells the server that you need to get data in JSON format; In Python json format is easily parsed by means of json library.
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