Provide MassBank data to NFDI4Chem search services

[sneumann]

Similar to PubChem and Wikidata, we'd like to make our data accessible. @okoepler, @hujo91 and @bhavin2897 would like to do metadata harvesting and create a search service and are looking for a collection of data available.

For MassBank, we can provide 1) links to MassBank in Wikidata 2) The file of MassBank data that is ingested by PubChem importer and 3) The embedded and harvestable Bioschemas compliant JSON-LD and 4) Pointers into our docs on the record format.

This issue is to track things which eventually also should go into the documentation. Yours, Steffen

[sneumann]

The JSON-LD and Bioschemas work was discussed and implemented in #39 #119 #139 and #307. Egon Willighagen and the Bioschemas team did some work at ELIXIR Biohackathon 2020 as reported in this slide https://docs.google.com/presentation/d/1TKa9ItF3hZ1O_yU0YhewZt56KdsFcJSmvIYTOQHf8yk/edit#slide=id.gc52fa3201e_0_6 (Slide 20 in https://doi.org/10.5281/zenodo.5549916) using the BMuse scraper https://bioschemas.org/software.html , see also the https://bedroesb.github.io/bioschemas.github.io/liveDeploys Yours, Steffen

[sneumann]

Hi, as the BMUSE liveDeploys are currently down, Alisdair Gray suggested to use https://github.com/HW-SWeL/BMUSE/tree/dev and build a local Java client to scrape from https://massbank.eu/MassBank/sitemapindex.xml Yours, Steffen

[sneumann]

At the https://www.denbi.de/de-nbi-events/1454-biohackathon-germany @bhavin2897 and I successfully worked to harvest the schema.org DataSet and MolecularEntity from the (test) OAI provider at https://msbi.ipb-halle.de/oai/ into the nfdi4chem search service. Todo: find a regular process together with MassBank releases to create JSON+LD (Data Dumps ?) and update some OAI-PMH provider (maybe at FIZ Karlsruhe ?) Yours, Steffen