getNCBImetadata

Retrieves NCBI metadata from nucleotide or biosample accession ids.

Table of contents

• Requirements
• Installation
• Quick start
• Output
• License

Requirements

• Linux or MacOS or Windows with Windows Subsystem for Linux (WSL) installed
• Bash shell, which is the default shell on MacOS and many Linux distributions
• Python 2.7 or Python 3
• Edirect
• A computer with internet access via the HTTPS protocol - required for retrieving data from NCBI<br>

Installation

git clone https://github.com/AlexOrlek/getNCBImetadata.git
cd getNCBImetadata

You should find the getmetadata.py executable script within the repository directory. If you add the path of this directory to your $PATH variable, then the executable can be run by calling getmetadata.py [arguments...] from any directory location. Note also that the edirect directory must also be available in your $PATH variable.

Quick start

The -t flag specifies whether nucleotide or biosample accessions are provided in accessions.txt.<br> The -e flag should be your own email address; this is provided to NCBI so that they can monitor usage.<br> accessions.txt is a text file where the first column contains NCBI (nucleotide or biosample) accession ids.<br>

Nucleotide metadata can be retrieved by running the following code:

getmetadata.py -a accessions.txt -t nucleotide -o outdir -e first.last@company.com

Either Refseq or Genbank nucleotide accessions can be provided. Nucleotide accessions can be provided in either "accession" or "accession.version" format.<br>

BioSample metadata can be retrieved by running the following code:

getmetadata.py -a accessions.txt -t biosample -o outdir -e first.last@company.com --biosampleattributes attributes.txt

The --biosampleattributes flag is optional. It is used to specify a path to a file containing harmonized attribute names in the first column. A full list of BioSample attribute harmonized names is provided here. The specified attributes will be retrieved, in addition to default retrieved fields (see Output for details).<br>

Output

Nucleotide metadata

When nucleotide accessions are provided, the following fields are extracted:

• AccessionVersion
• Dates of first submission and last update: Create Date, Update Date
• Molecular characteristics: Molecule Type (e.g. dna), Length, Completeness, Source Genome Type (e.g. plasmid)
• Taxonomy data: Source Taxon, Source Taxonomic ID
• Genome assembly data: Assembly Method, Genome Coverage, Sequencing Technology
• Genome annotation data: Annotation Pipeline, Annotation Method
• DBLink data: Bioproject Accession, Biosample Accession, Sequence Read Archive Accession, Assembly Accession
• PubMedID<br>

Biosample metadata

When biosample accessions are provided, the following fields are extracted:

• Identifiers: Accession, Accession ID, Sample name
• Submission data: Model, Package
• Dates: last_update, publication_date, submission_date
• Title
• Comment
• Taxonomic data: taxonomy_id, taxonomy_name, OrganismName
• Affiliation data: Owner/Name, email, Contact/Name/First, Contact/Name/Last
• Attribute data will be retrieved if a file containing harmonized attribute names is provided to the --biosampleattributes flag.

License

MIT License