Skip to content

Latest commit

 

History

History
124 lines (111 loc) · 4.7 KB

changelog.mkd

File metadata and controls

124 lines (111 loc) · 4.7 KB
Raw

Changelog

All notable changes to the schema will be noted in this file. The format is based off Keep a Changelog.

This project adheres to Semantic Versioning.

Unreleased

Added

  • Added LncBook and LncRNAWiki as data providers
  • Added LncBook example
  • Added CRS as a data provider
  • Added CRS example
  • Added an ECO term for the SO term annotation. This will help track the evidence for a sequence being an example of the given SO term.
  • Add an inferredPhylogeny section. This is allow databases, like SILVA, that create their own phylogeny to provide it to RNAcentral.
  • Added tmRNA Website example
  • Added 5SRRNAdb as a data provider
  • Added 5SRRNAdb example
  • Added SnoDB example
  • Added host_gene relationship type
  • Added MirGeneDB example
  • Added ortholog relationship type
  • Added paralog relationship type
  • Added paralogue relationship type
  • Added SnoRNADB data provider
  • Added simple SGD example
  • Added ZFIN as a data provider

Changed

  • Require that all locations have at least one exon.
  • Updated modomics example to reflect modifications locations.
  • Renamed CRS -> CRW
  • Extend sequence validation regex to cover all of IUPAC
  • Reorder related sequences enum

Removed

  • Removed duplication modifications section from the top-level ncRNA entry.

[0.4.0] - 2018-09-24

Changed

  • Altered the validation script to display all errors.
  • Improved descriptions of sequence id fields to be clearer.
  • Changed doi reference pattern to start with DOI: to be consistent with PMID pattern.
  • Bug fix to re-enable secondary structure validation.
  • Bug fix validator to correctly get validator failure name.
  • Rename matureProduct to mature_product
  • Require all publications have at least one reference, either directly in publications or indirectly in metaData.publications.
  • Require chromosome in genomic locations.
  • Let database names be case insensitive in global ids.

Added

  • We now validate if the taxon ids are active or obsolete.
  • Added new type of related sequence, target_rna to represent the binding target of miRNA's and other ncRNA sequences.
  • Add new type of related sequence, target_protein to represent RNA's that interact with proteins.
  • Add an example for TarBase import
  • Add an evidence section to relatedSequences, to store information about the evidence for the relationship between sequences.
  • Validate PubMed Ids as being active.
  • Added ZWC as a new database.
  • Added genomicCoordinateSystem as a way of specifying how the coordinates in the JSON file are specified. This has been a point of confusion, so hopefully to allowing databases to specify this and supporting the two most common systems we can resolve the issues.

Removed

  • Removed the INSC_accession field. It isn't used and is unneeded in our current system.
  • Removed the ucsc_accession for genomicLocations. This is unused and unneeded.

[0.3.0] - 2018-05-22

Changed

  • Changed the meaning of assembly field to both be clearer as it's intended purpose as well as allow for more general utility.
  • Made INSC_accession optional. This isn't always easy available and we can probably get by without it.
  • Made the validation of the database name case insensitive.
  • Do not required geneId in the gene object.
  • Altered sequence constraint to allow for up to 10% of the nucleotides to be uncertain. This reflects the internal constraints on RNAcentral data.

Added

  • Added new databases for cross referencing:
    • ENTREZGENE
    • MICRORNA.ORG
    • MIRDB
    • TARGETMINER
    • TARGETSCANFISH
    • TARGETSCANFLY
    • TARGETSCANVERT
    • TARGETSCANWORM
  • Added coordinates field to relatedSequences. This is used to represent the relative coordinates of a related sequence.

[0.2.0] - 2018-02-07

Added

  • Added a description field to the schema (#2)
  • Automatically test all example files
  • Add examples for mirBase, LNCipedia and a minimal example
  • Added a locusTag, name, and url fields to gene
  • Added validation to check if a name for the transcript can be determined
  • Add symbol and symbolSynonyms to sections/ncrna.json
  • Add a section, relatedSequences, for generic related sequences
  • Add matureProduct as a type of related sequence
  • Add validation to check coordinate orientation

Changed

  • Allow colons in ids.
  • Limit publication references to DOI's and PubMed Ids
  • Made geneId required for genes
  • Rename sections/entry.json to sections/ncrna.json
  • name is no longer required for ncRNA's
  • version is no longer required for ncRNA's

Removed

  • Remove section precursorSequenceId in favor of the relatedSequences section