oai4schemas

This repo contains a XML schema that can embed JSON+LD (bio)schema metadata, crosswalks and examples. They are designed to work with https://radar.products.fiz-karlsruhe.de/en/radarfeatures/radar-oai-provider.

Creating the format

Neither OAI-PMH nor the FIZ OAI-PMH provider are (currently) designed to import and serve JSON+LD schema.org metadata. As workaround, we use a super-simple XML schema (metadataPrefix in OAI language) with the sole purpose to hold JSON content.

The format is created via the REST interface of the FIZ OAI-PMH backend by calling

createFormats.sh [URLofBackend]

If no URL is provided, http://localhost:8081/oai-backend is assumed.

Creating the crosswalk

The FIZ OAI-PMH provider allows to specify crosswalks between metadata formats as XSLT that also has to be created with the backend:

createCrosswalks.sh [URLofBackend]

Currently, there is only a super simple crosswalk creating (broken) oai_dc metadata. See #1 for more information.

Create sets holding subset of records

Using the sets you can tag uploaded records, and query by sets

./createSets.sh [URLofBackend]

Adding data

An individual example is part of this repository, and there are examples how to import data from the Chemotion repository and the MassBank spectral database.

Adding example record(s)

The example data is a Chemotion Molecule with DOI 10.14272/MIIFHRBUBUHJMC-UHFFFAOYSA-N.1 downloaded from the Chemotion REST API at https://www.chemotion-repository.net/api/v1/public/molecule.json?id=6338 and converted/crosswalked to Bioschemas JSON+LD using https://gist.github.com/sneumann/072adeb302ca010e2eb5de24e3bdb413

./addItems.sh [URLofBackend]

Importing MassBank data dumps

The script massbank-jsonld2oai.sh can import a MassBank data dump to OAI.

Chemotion repository

Code snippet to import Chemotion metadata to OAI: https://gist.github.com/sneumann/6c814c5357bb35a948cd8e3c8b57fca1 (Caveat! This crosswalk is known to be slightly incorrect!)

nmrXiv

An example DataSet is available in data/nmrxiv-D506.json. The script nmrxiv2oai.sh can import that nmrXiv data to OAI, which is available from https://msbi.ipb-halle.de/oai/OAIHandler?verb=GetRecord&metadataPrefix=json_container&identifier=D506

Radar4Chem

A manually created example DataSet is available in data/10.22000-702.json. The script radar2oai.sh can import that RADAR data to OAI, which is available from https://msbi.ipb-halle.de/oai/OAIHandler?verb=GetRecord&metadataPrefix=json_container&identifier=https://dx.doi.org/10.22000/702

Retrieving the data and using it

Retrieval works just like all other OAI-PMH services.

Extracting the JSON content

We have an IPB NFDI4Chem OAI test instance with some example data: https://msbi.ipb-halle.de/oai/OAIHandler?verb=GetRecord&metadataPrefix=json_container&identifier=10.14272/MIIFHRBUBUHJMC-UHFFFAOYSA-N.1

The following is a snippet to retrieve the example with curl, and extract the actual JSON with xmllintusing an xpath expression. Note that the local-name()="json" trick is required to ignore the XML namespace of the <json> element. Similarly, sed is used to strip off the CDATA in the XML (any suggestion of a more elegant solution welcome! Doesn't have to use xmllint, but needs to fit the commandline). The optional jq is a nice way to pretty-print JSON, see https://blog.lazy-evaluation.net/posts/linux/jq-xq-yq.html and https://stedolan.github.io/jq/

OAIURL=https://msbi.ipb-halle.de/oai/OAIHandler
curl -s "$OAIURL?verb=GetRecord&metadataPrefix=json_container&identifier=10.14272/MIIFHRBUBUHJMC-UHFFFAOYSA-N.1" |\
  xmllint --xpath '//*[local-name()="json"]/text()' - |\
  sed -e 's/<!\[CDATA\[//g; s/\]\]>//g' |\
  jq

In case our IPB NFDI4Chem OAI test instance disappears, the example response of the above curl is available in this repo for reference (https://github.com/NFDI4Chem/oai4schemas/blob/main/10.14272-MIIFHRBUBUHJMC-UHFFFAOYSA-N.1.xml)

Validating the oai_dc conversion

Since the <oai_dc:dc> version of the metadata is embedded in the <OAI-PMH> response, for the validation and use it needs to be extracted and piped into the validation or some other consumer:

xmllint --xpath '//*[namespace-uri()="http://www.openarchives.org/OAI/2.0/oai_dc/" and local-name()="dc"]' \
  examples/oai_dc-MIIFHRBUBUHJMC-UHFFFAOYSA-N.1.xml  |\
  xmllint --schema oai_dc.xsd -

More OAI call examples:

• Get (a small part of) the above example record in oai_dc metadata format: https://msbi.ipb-halle.de/oai/OAIHandler?verb=GetRecord&metadataPrefix=oai_dc&identifier=10.14272/MIIFHRBUBUHJMC-UHFFFAOYSA-N.1
• List all schemas records: https://msbi.ipb-halle.de/oai/OAIHandler?verb=ListIdentifiers&metadataPrefix=json_container
• List the set of all MassBank molecules: https://msbi.ipb-halle.de/oai/OAIHandler?verb=ListIdentifiers&metadataPrefix=json_container&set=MassBank:MolecularEntity

Acknowledgments

Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI4Chem – Projektnummer 441958208.