DSpace PubMed Integration
duraspace - pubmed

DSpace PubMed Integration

DSpace PubMed Integration Introduction

First read the base documentation on external importing This documentation explains the implementation of the importer framework using PubMed (http://www.ncbi.nlm.nih.gov/pubmed) as an example.

Enabling PubMed Lookup (XMLUI Only)

The PubMed specific integration of the external sources import requires the following to be active.

The PubMed lookup is done during the "XMLUIStartSubmissionLookupStep" and this can be enabled by adjusting one step

in the [dspace.dir]/config/item-submission.xml

Uncommenting this step will permit the user to do the PubMed based lookups during their submission.


<!-- Find publications based on ID/DOI/Title/Author to pre-fill the submission. XMLUI ONLY.
     For JSPUI version, see JSPUIStartSubmissionLookupStep under <step-definitions> above.

After uncommenting hat step, simply restart your servlet container, and this lookup step will be available within your deposit process.

Publication Lookup URL

To be able to do the lookup for our configured import-service, we need to be able to know what URL to use to check for publications.  This URL the publication-lookup.url setting defined within the [dspace.dir]/config/modules/publication-lookup.cfg.  You may choose to modify this setting or override it within your local.cfg.

This setting can be modified in one of two ways:

You can choose to specific a single, specific URL. This will tell the lookup service to only use one location to lookup publication information.  Valid URLs are any that are defined as a baseAddress for beans within the [src]/dspace-api/src/main/resources/spring/spring-dspace-addon-import-services.xml Spring config file.

For example, this setting will ONLY use PubMed for lookups: publication-lookup.url=http://eutils.ncbi.nlm.nih.gov/entrez/eutils/

By default, publication-lookup.url is set to an asterisk ('*').  This default value will attempt to lookup the publication using ALL configured importServices in the [src]/dspace-api/src/main/resources/spring/spring-dspace-addon-import-services.xml Spring config file

PubMed Metadata Mapping

The PubMed metadata mappings are defined in the [dspace.dir]/config/spring/api/pubmed-integration.xml Spring configuration file.  These metadata mappings can be tweaked as desired. The format of this file is described in the "Metadata mapping" section above

PubMed specific classes Config

These classes are simply implementations based of the base classes defined in importer/external. They add characteristic behavior for services/mapping for the PubMed specific data.

Metadata mapping classes

"PubmedFieldMapping". An implementation of AbstractMetadataFieldMapping, linking to the bean that serves as the entry point of other metadata mapping

"PubmedDateMetadatumContributor"/"PubmedLanguageMetadatumContributor". Pubmed specific implementations of the "MetadataContributor" interface

Service classes

"GeneratePubmedQueryService". Generates the pubmed query which is used to retrieve the records. This is based on a given item.

"PubmedImportMetadataSourceServiceImpl". Child class of "AbstractImportMetadataSourceService", retrieving the records from pubmed.

DSpace PubMed Integration
Mehmet Demirel 2 Şubat, 2020
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