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Published 20 hours ago • verified publisher icon phenopackets

Encouraging journal endorsement of PXF via FAIRsharing

Open mylesaxton opened this issue 4 years ago • 1 comments

Hi Chris,

Are there any plans to update PXF at FAIRsharing? https://fairsharing.org/10.25504/FAIRsharing.9xsgcr For example, the schema is not listed but rather found at https://github.com/phenopackets/phenopacket-schema

  1. What databases have implemented the exchange format? It is difficult for journals to endorse a database-database exchange format without an implementing database to refer from the publication to the phenotypic records.

  2. What licenses are associated with PXF records? How would licensing affect the export of full phenotypic records for publication?

  3. Is it possible to export PXF records from a hosting database into JSON format in order to replicate the record in a published work?

With all best wishes,

Myles

Myles Axton PhD -- Editor-in-Chief

Genetics & Genomics Next

https://onlinelibrary.wiley.com/journal/26416573

[email protected]

https://orcid.org/0000-0002-8042-4131

Wiley, Inc., Hoboken, NJ 07030

mylesaxton avatar Jan 08 '20 19:01 mylesaxton

@mylesaxton Thanks for these suggestions and sorry for the late feedback. This year we have been working on extensions for cancer and common disease and treatment, and we are now anticipating finalizing the v2 phenopackets early next year. We are also in the process of creating an API for the creation of phenopackets and we would love to move forward.

Answers

  1. FAIRSharing -- we need to update this entry. @cmungall @mellybelly let's make an entry for Monarch and GA4GH here?
  2. Databases -- there is a chicken/egg problem, but we have had promising discussions with mygene2 and ClinGen and plan to define concrete options early 2021
  3. License -- ultimately, the license would be decided by the group that makes the phenopacket, but we would promote open licensing, eg., CC-BY or CC-zero. The schema itself is BSD3 (https://github.com/phenopackets/phenopacket-schema/blob/master/LICENSE)
  4. We now have funding to help with software to work with phenopackets and would be happy to support any reasonable requirement. It is trivial to export as JSON.

pnrobinson avatar Dec 16 '20 21:12 pnrobinson