Opened 2 months ago

Closed 7 weeks ago

#1616 closed enhancement (fixed)

Implement support for new annotation type categories

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Reggie v5.4
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

BASE 3.20 has a new feature where more than one annotation type category can be linked to a given subtype where an annotation can be used to discriminate between them. See ​https://base.thep.lu.se/ticket/2329.

As an example we can divide the AlignedSequences subtype into 3 different categories with the help of the Pipeline annotation: RNAseq, WGS and sRNAseq where each category only contains the annotation types that are relevant for the given pipeline.

For other item types we can make similar sub-categories.

Change History (18)

comment:1 by Nicklas Nordborg, 2 months ago

In 7876:

References #1616: Implement support for new annotation type categories

Added Pipeline as the subcategory annotation type to AlignedSequences.

comment:2 by Nicklas Nordborg, 2 months ago

In 7877:

References #1616: Implement support for new annotation type categories

Added sub-categories for AlignedSequences. There are five different with some variations in annotations.

  • RNAseq: Pipeline=RNAseq/Hisat/StringTie
  • RNAseq/2023: Pipeline=RNAseq/Hisat/2023
  • RNAseq/Legacy: Pipeline=RNAseq/Legacy
  • WGS: Pipeline=DNA/Tumor/WGS, DNA/Normal/WGS
  • sRNA: Pipeline=sRNAseq

comment:3 by Nicklas Nordborg, 2 months ago

In 7879:

References #1616: Implement support for new annotation type categories

Added sub-categories for MergedSequences. There are three different with some variations in annotations.

  • RNAseq: Pipeline=RNAseq
  • WGS: Pipeline=DNA/Tumor/WGS, DNA/Normal/WGS
  • sRNA: Pipeline=sRNAseq


Also moved the category for MaskedSequences to the new system. It us only used by the RNAseq pipeline and they are all the same so a single category will do.

comment:4 by Nicklas Nordborg, 2 months ago

In 7881:

References #1616: Implement support for new annotation type categories

Added sub-categories for DemuxedSequences. There are four different with some variations in annotations.

  • RNAseq: Pipeline=RNAseq
  • RNAseq/External: Pipeline=RNAseq/External
  • WGS: Pipeline=DNA/Tumor/WGS, DNA/Normal/WGS
  • sRNA: Pipeline=sRNAseq


The RNAseq/External value is a new option for the Pipeline annotation and should be used when we import FASTQ files from external operator (eg. CMD). Existing DemuxedSequences need to be manually updated with a batch import.

comment:5 by Nicklas Nordborg, 2 months ago

In 7882:

References #1616: Implement support for new annotation type categories

Added sub-category for SequencingRun. There are almost no differences so we only use a single category.

The RNAseq/External value is a new option for the Pipeline annotation and should be used when we import FASTQ files from external operator (eg. CMD). Existing SequencingRun need to be manually updated with a batch import.

comment:6 by Nicklas Nordborg, 2 months ago

In 7884:

References #1616: Implement support for new annotation type categories

Added sub-categories for gene expression.

comment:7 by Nicklas Nordborg, 2 months ago

In 7886:

References #1616: Implement support for new annotation type categories

Added short name to annotation type categories.

comment:8 by Nicklas Nordborg, 2 months ago

In 7887:

References #1616: Implement support for new annotation type categories

Added sub-categories for variant call.

comment:9 by Nicklas Nordborg, 2 months ago

In 7889:

References #1616: Implement support for new annotation type categories

Added sub-categories for rest of derived bioassay types:

  • Methylation
  • Copy number
  • Genotyping
  • Imputed genotypes
  • Scan
  • Panel-of-normals

comment:10 by Nicklas Nordborg, 2 months ago

In 7891:

References #1616: Implement support for new annotation type categories

Added sub-categories for physical bioassays:

  • Flow cell
  • Bead chip

comment:11 by Nicklas Nordborg, 2 months ago

In 7892:

References #1616: Implement support for new annotation type categories

Added sub-categories for biosource and samples:

  • Patient
  • Retract
  • RetroNo
  • Case
  • Blood
  • Specimen
  • NoSpecimen
  • TMASpecimen
  • Histology
  • Stained
  • Sample handling


comment:12 by Nicklas Nordborg, 2 months ago

In 7898:

References #1616: Implement support for new annotation type categories

Added sub-categories for extracts:

  • Lysate
  • RNA
  • Normalized RNA
  • DNA
  • Normalized DNA
  • Flow through
  • Blood DNA
  • Small RNA
  • Extraction (protocol)
  • RNA and DNA normalization (protocol)
  • mRNA
  • cDNA
  • Library (with sub-categories for: RNAseq, WGS and sRNAseq)
  • Pooled library
  • Barcode
  • Library protocol

comment:13 by Nicklas Nordborg, 2 months ago

In 7899:

References #1616: Implement support for new annotation type categories

Categories for hardware, software, protocols, and files.

comment:14 by Nicklas Nordborg, 2 months ago

In 7900:

References #1616: Implement support for new annotation type categories

Added descriptions to all categories.

comment:15 by Nicklas Nordborg, 2 months ago

In 7901:

References #1616: Implement support for new annotation type categories

Fragment size annotations should be in WGS category.

comment:16 by Nicklas Nordborg, 2 months ago

In 7902:

References #1616: Implement support for new annotation type categories

Histology work lists should be assigned to Histology subtype.

comment:17 by Nicklas Nordborg, 2 months ago

In 7905:

References #1616: Implement support for new annotation type categories

The release exporter now export information about annotation type categories.

comment:18 by Nicklas Nordborg, 7 weeks ago

Resolution: → fixed
Status: new → closed
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