rnacentral / rnacentral-data-schema Goto Github PK

Thanks to everyone's feedback, the JSON schema has improved a lot since we first created it. I think it is just about ready for a v1.0.0 and want a chance to get everyone's feedback as well as highlight one important change I just made.

I have just added one field which I want to ensure everyone knows about. In the metaData section you can now specify the coordinate system you are using. Either 0-based, half-open (the current default and used in BED files) or the 1-based, fully-closed. UCSC has some useful details on these systems at:

http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/

I think there has been confusion over how the coordinates are specified so hopefully adding an field helps. I'm also willing to change what the default assumed system is if people would prefer. Ideally no one has to change anything about their files, but I want to make sure everyone knows!

Other than that, I think the format is ready for a 1.0.0 version. This will be a version which is stable and supported by RNAcentral for the foreseeable future. Any major changes from this will require a new major version but we will continue to support v1.0.0 afterwards. If you have any suggestions for the schema please let me know. My plan is to have a v1.0.0 shortly after the consortium meeting on Oct 19th. Hopefully this gives everyone a chance to suggest any changes.

For all the (many) details on the changes you can read the changelog at:

https://github.com/RNAcentral/rnacentral-data-schema/blob/master/changelog.mkd

Thanks for working with us on this schema!

It would be nice to have an example file with nothing but required fields.

• description

• add tests that validate example files
• integrate with TravisCI so that tests are run on every commit

• miRBase
• LNCipedia