DSpace Integration with external databases

PubMed, Scopus, Web of Science, etc.

Disclaime

DSpace-CRIS is not directly or indirectly related to any commercial bibliographic database, the available integration is provided by the DSpace-CRIS developers as-is at the best of their knowledge without any guarantee of proper behaviour with such third part services and it is not an endorsement of such services


DSpace-CRIS implement three levels of integration with external databases

Realtime import of bibliographic records searching the external database by identifiers or title, authors

Periodic scanning of the external database to retrieve institutional publications to import

Retrieve of bibliometrics value for items in DSpace(-CRIS)

Realtime import of bibliographic records

Other than the providers already available in a standard DSpace installation such as ArXiv, PubMed, Cinii, CrossRef and generic OAI-PMH providers, DSpace-CRIS add to the Submission Lookup Step the ability to query PubMed Europe, Scopus, SciVal and/or Web of Science.


PubMed Europe

The class org.dspace.submit.lookup.PubmedEuropeFileDataLoader is the implementation of the submission lookup interface that enable the integration with the Web of Knowledge WokSearch API

To enable the integration it is necessary to uncomment the bean definitions in the [dspace-installDir]/config/spring/api/bte.xml file 


Scopus

The class org.dspace.submit.lookup.ScopusOnlineDataLoader is the implementation of the submission lookup interface that enable the integration with the Scopus API.

To enable the integration it is necessary to set the following property in the dspace.cfg (via build.properties)

submission.lookup.scopus.apikey = ${submission.lookup.scopus.apikey}

and uncomment the bean definition in the [dspace-installDir]/config/spring/api/bte.xml file

and the mapping is defined in the bean


The scopus online data provider exposes the ORCID, Scopus ID and Author Scopus URL for each authors, when not available for one or more authors the placeholder value #NODATA# is used. This allows the use of the metadata filler functionality to create from the publication richer author profiles. It also open to future development of custom BTE processor that can lookup to existent researcher profile using these IDs other than the name


SciVal

The class org.dspace.submit.lookup.SciValOnlineDataLoader is the implementation of the submission lookup interface that enable the integration with the SciVal AP

To enable the integration it is necessary to set the following property in the dspace.cfg (via build.properties

submission.lookup.scivalcontent.apikey = ${submission.lookup.scivalcontent.apikey}

and uncomment the bean definition in the [dspace-installDir]/config/spring/api/bte.xml file

and the mapping is defined in the bean


Web of Knowledge

The class org.dspace.submit.lookup.WOSOnlineDataLoader is the implementation of the submission lookup interface that enable the integration with the Web of Knowledge WokSearch API.


To enable the integration it is necessary to set the following property in the dspace.cfg (via build.properties)


submission.lookup.webofknowledge.user = ${submission.lookup.webofknowledge.user}

submission.lookup.webofknowledge.password = ${submission.lookup.webofknowledge.password}


PubMed Europe

The DSpace script to invoke is

./dspace dsrun org.dspace.app.cris.batch.PMCEuropeFeed -p submitter -c collectionID [-q query]  [-s start_date(yyyy-mm-dd)] [-e end_date(yyyy-mm-dd)] [-t] [-m <metadata-for-pmid>] [-n <metadata-for-pmcid>]

-p the id or the email address of the user that will be used to create / update items

-c the target collection for new item

-q the search query for pubmed. If not specified it is retrieved from the configuration fil

-s the start date to consider for new / updated record in pubmed. By default the script will search for changes since the previous successful execution of the script or today when executed for the first tim

-e the end date to consider (useful in conjuction with start_date to "recover" past record

-t the script is executed in DRY-RUN mode, the retrieved records are just displaye

-m specify the metadata used to store the pmid identifier, default dc.identifier.pmi

-n specify the metadata used to store the pmcid identifier, default dc.identifier.pmci


The script uses the configuration file [dspace-installDir]/config/modules/pmceuropefeed.cfg to get default values for some of the previous properties when not specified from the command line and additional configuration properties like the service endpoint URL


Read more: https://wiki.lyrasis.org/pages/viewpage.action?pageId=78163330