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12.data Retrieval

The document discusses several methods for retrieving biological data from databases. It describes how nearly all databases allow downloading data as flat text files for local processing. It also explains that Entrez is a search engine that integrates many biological databases and literature and allows querying and retrieving data through its website. Finally, it mentions that bulk data retrieval is best done through FTP for large data transfers and that data often needs processing using programming languages like Perl and Python.

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ahsan
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77 views8 pages

12.data Retrieval

The document discusses several methods for retrieving biological data from databases. It describes how nearly all databases allow downloading data as flat text files for local processing. It also explains that Entrez is a search engine that integrates many biological databases and literature and allows querying and retrieving data through its website. Finally, it mentions that bulk data retrieval is best done through FTP for large data transfers and that data often needs processing using programming languages like Perl and Python.

Uploaded by

ahsan
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
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Data Retrieval

Data Retrieval
• Nearly all biological
databases are
available for download
as simple text (flat) files
• A local version of the
database allows one
greater freedom in
processing the data
Data Retrieval
Entrez
• is an integrated search
engine which allows
users to search and
retrieve different data
from the NCBI
• It can be accessed from
the site
www.ncbi.nlm.nih.gov/
Entrez/
Data Retrieval
Entrez
• integrates PubMed and
39 other scientific
literatures, nucleotide
and protein databases
• protein domain data,
population studies,
expression data,
pathways, genome
details and taxonomic
information
Data Retrieval
Data Retrieval
Data Retrieval
Bulk Data Retrieval
• The best option is to use
ftp (File transfer protocol)
• The File Transfer
Protocol (FTP) is a
standard network
protocol used to transfer
files
• Via command line or
application programs like
FTP clients
Data Retrieval
Bulk Data Retrieval
• Data needs to be
transformed or
processed using
programming languages
• PERL and Python are
good for processing
Biological data
Data Retrieval
Conclusions
• Data is transferred over
the internet
• Data needs to be
transformed or
processed

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