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FAIR Projector Builder

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Quickly re-publish CSV/TSV files from existing repositories as FAIR Data with just a few mouse clicks!

You select the columns to "project" as Linked Data, and the associated ontology terms. The FAIR Projector Builder will create a FAIR Projector for you: a Triple Pattern Fragment server to provide the Linked Data; a published DCAT Distribution containing metadata about those triples and their source; and an RML model (syntactic and semantic of the triples, to aid in third-party discovery of this novel projection.

(current status - first prototype, not ready for public consumption)

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Thanks to the NBDC/DBCLS for sponsoring the hackathon series.

MDW also funded by Ministerio de Economía y Competitividad grant number TIN2014-55993-RM

Published in: Internet
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FAIR Projector Builder

  1. 1. Activity Update: FAIR Projector Builder Mark D Wilkinson CBGP UPM-INIA Madrid http://tinyurl.com/FAIRProjectorBuilder
  2. 2. http://identifiers.org/uniprot/P06213
  3. 3. http://snpeffect.switchlab.org/uniprot/INSR_HUMAN
  4. 4. What do we do today? 1. Download the file 2. Write a custom script (probably) to transform it to triples 3. Use the triples a. Load them into our local triplestore... b. or refer to the local file in our SPARQL query 4. Throw the triples in the wastebasket 5. Throw the script in the wastebasket
  5. 5. The next person who needs triples...
  6. 6. The next person who needs triples... 1. Download the file 2. Write a custom script (probably) to transform it to triples 3. Use the triples a. Load them into our local triplestore... b. or refer to the local file in our SPARQL query 4. Throw the triples in the wastebasket 5. Throw the script in the wastebasket
  7. 7. RE
  8. 8. FAIR Projection Goal: Transform non-Linked-Data to Linked Data…. ● In a way that makes it findable ● In a way that makes it accessible ● In a way that makes it reusable
  9. 9. FAIR Projection Goal: Transform non-Linked-Data to Linked Data…. ● In a way that makes it findable ● In a way that makes it accessible ● In a way that makes it reusable
  10. 10. The first few lines of the file, with columns numbered
  11. 11. How many lines are headers? (in this case, one)
  12. 12. Column 1 http:// identifiers.org /uniprot/{ } rdf:type EDAM 2291 (UniProt ID)
  13. 13. Column 2 http://snpeffect. switchlab.org/u niprot/{ } rdf:type SIO Phenotype
  14. 14. (If you know what you want this all takes about 1 minute)
  15. 15. The URL to your triples (Includes Triple Pattern Fragments hypermedia controls)
  16. 16. The metadata published with those triples follows the guidelines of a FAIR Accessor (DCAT; LDP Compliant)
  17. 17. A syntactic and semantic description of those triples using RML (used for discovery of these data by others)
  18. 18. A syntactic and semantic description of those triples using RML (used for discovery of these data by others)
  19. 19. Your triples are a new DCAT Distribution of https://zenodo.org/ record/890267/files/ dataoutput.csv In three possible formats
  20. 20. The Plack server configuration file that created the FAIR Projector service (Just for interest)
  21. 21. curl -H "Accept: text/turtle" http://linkeddata.systems:3002/fragments ?predicate=http%3A%2F%2Fsemanticscience.org %2Fresource%2FSIO_001279
  22. 22. SPARQL over those triples...
  23. 23. ldf-client - a node.js SPARQL query resolver that “speaks TPF” Written by Ruben Verborgh ldf-client http://linkeddata.systems:3002/fragments query.sparql select * where { ?s a ?st . ?s <http://semanticscience.org/resource/SIO_001279> ?o . ?o a ?ot } query.sparql
  24. 24. Query Response
  25. 25. Current Status: not ready for public consumption… I will send a message to the BIoHack community when it is ready for others to beta-test it.
  26. 26. Thank You to NBDC/DBCLS and especially to Toshiaki-san for 10 years of amazing Hackathons!!
  27. 27. Additional funding for Mark Wilkinson Thanks to: Ministerio de Economía y Competitividad grant number TIN2014-55993-RM

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