# ncbi

Fetches ncbi (opens new window) data from their API (opens new window).

# Enriched fields

Name	Type	Description
print_identifier	String	International Standard Serial Number for publications.
online_identifier	String	Electronic ISSN for publications.
publication_title	String	The full name of the journal.
doi	String	The digital object identifier.
title	String	The article title.

# Prerequisites

The NCBI Enrichment middleware uses the unit_id found in NCBI access events to request Pubmed metadata

You must use NCBI after filter, parser, deduplicator middleware.

# Headers

ncbi-cache : Set to false to disable result caching. Enabled by default.
ncbi-ttl : Lifetime of cached documents, in seconds. Defaults to 7 days (3600 * 24 * 7)
ncbi-throttle : Minimum time to wait between each query, in milliseconds. Defaults to 500ms. Make no more than 3 requests per second unless you are registered with the NCBI API.
ncbi-packet-size : Maximum number of memorized NCBI access events before sending requests. Defaults to 200.
ncbi-buffer-size : Maximum number of memorized access events before sending requests. Defaults to 1000.
ncbi-max-tries : Maximum number of attempts if an enrichment fails. Defaults to 5.
ncbi-email : The email for reference for API calls. Defaults to ezteam@couperin.org (from config.json of ezPAARSE). The email and tool can be registered with NCBI to increase the number of requests per second for the application.
ncbi-tool : The tool for reference for API calls. Defaults to ezPAARSE (https://readmetrics.org; mailto:ezteam@couperin.org). The email and tool can be registered with NCBI to increase the number of requests per second for the application.
ncbi-apikey : Apikey for rights holders to speed up processing (10 requests per second)

# How to use

# ezPAARSE admin interface

You can add ncbi by default to all your enrichments, To do this, go to the middleware section of administration.

# ezPAARSE process interface

You can use ncbi for an enrichment process. You just add the middleware.

# ezp

You can use ncbi for an enrichment process with ezp (opens new window) like this:

# enrich with one file
ezp process <path of your file> \
  --host <host of your ezPAARSE instance> \
  --settings <settings-id> \
  --header "ezPAARSE-Middlewares: ncbi" \
  --out ./result.csv

# enrich with multiples files
ezp bulk <path of your directory> \
  --host <host of your ezPAARSE instance> \
  --settings <settings-id> \
  --header "ezPAARSE-Middlewares: ncbi"

# curl

You can use ncbi for an enrichment process with curl like this:

curl -X POST -v http://localhost:59599 \
  -H "ezPAARSE-Middlewares: ncbi" \
  -H "Log-Format-Ezproxy: <line format>" \
  -F "file=@<log file path>"

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