SRA XML 1.3T (transitional) metadata format

The SRA 1.3T (transitional) XML will replace SRA 1.3 XML in March/April 2012. The SRA 1.3T XML contains a large number of simplifications in the form of removed fields. Submitters are adviced to stop using these fields; only minor adaptations to submissions pipelines are expected as most of the removed fields are rarely used. If these fields are used after the introduction of SRA 1.3T they are automatically removed by the SRA REST submission system.

For examples how to prepare the SRA XMLs please refer to Preparing SRA XML metadata.

Changes to Common XSD

• SpotDescriptorType: Remove READ_SPEC/CYCLE_COORD.
• SpotDescriptorType: Remove already deprecated 'SPOT_DECODE_METHOD' element (effected retospectively in SRA 1.3 XML).
• SpotDescriptorType: Remove already deprecated 'NUMBER_OF_READS_PER_SPOT' element.
• PlatformType: Remove optional SEQUENCE_LENGTH from ILLUMINA and ABI_SOLID platforms.
• PlatformType: Remove optional FLOW_COUNT from LS454, HELICOS platforms.
• PlatformType: Remove deprecated CYCLE_COUNT element from ILLUMINA and ABI_SOLID platforms.
• PlatformType: Remove optional CYCLE_SEQUENCE element from ILLUMINA platform. 
• PlatformType: Remove optional KEY_SEQUENCE and FLOW_SEQUENCE element from LS454 platform and FLOW_SEQUENCE from HELICOS platform.
• PlatformType: Remove optional COLOR_MATRIX and COLOR_MATRIX_CODE from ABI_SOLID platform.
• SpotDescriptorType: Remove EXPECTED_BASECALL element (use EXPECTED_BASECALL_TABLE instead).
• SpotDescriptorType: Remove ADAPTER_SPEC element. 

Changes to Submission XSD

• Make 'schema' attribute mandatory for MODIFY action.
• Remove 'target' attribute in MODIFY action.
• Remove 'HoldForPeriod' attribute from HOLD action.
• Remove 'CLOSE' action.
• Remove 'notes' attribute from ADD, MODIFY, SUPPRESS, HOLD, RELEASE, VALIDATE actions.
• Remove CONTACT element.

Changes to Experiment XSD

• Remove optional attribute 'expected_number_runs'.
• Remove already deprecated attributes 'expected_number_spots' and 'expected_number_reads'.
• Remove PROCESSING/BASE_CALLS element.
• Remove PROCESSING/QUALITY_SCORES element.

Changes to Run XSD (effected retrospectively in SRA 1.3 XML)

• Remove already deprecated 'instrument_model' attribute (effected retrospectively in SRA 1.3 XML).
• Remove already deprecated 'run_file' and 'total_data_blocks' attributes (effected retrospectively in SRA 1.3 XML).
• Remove 'total_spots', 'total_reads', 'number_channels', 'format_code' deprecated attributes form DATA_BLOCK element (effected retrospectively in SRA 1.3 XML).
• Remove 'serial' attribute from DATA_BLOCK (effected retrospectively in SRA 1.3 XML).
• Remove FILE/DATA_SERIES_LABEL element (effected retrospectively in SRA 1.3 XML).
• Remove 'name', 'sector', 'region' attributes from DATA_BLOCK (effected retrospectively in SRA 1.3 XML).
• Add REFERENCE_ALIGNMENT element to capture reference sequence and assembly details for BAM files  (effected retrospectively in SRA 1.3 XML).

Changes to Study XSD

• Remove deprecated DESCRIPTOR/CENTER_NAME element.
• Restrict the study types:
  • Whole Genome Sequencing (<- Re-sequencing) 
  • Transcriptome Sequencing (<- RNASeq)
  • Transcriptome Analysis (<- Gene Regulation Study)
  • Exome Sequencing

  • Metagenomics

  • Synthetic Genomics
  • Cancer Genomics

  • Epigenetics
  • Population Genomics
  • Pooled Clone Sequencing

  • Other (<- Forensic and Paleogenomics)

Changes to Analysis XSD

• Remove DATA_BLOCK while keeping FILES element.
• Rename SEQUENCE_REF element to SEQUENCE.
• Rename ASSEMBLY_REF elementto ASSEMBLY.
• Replace SAMPLE_LABEL element with sample_label attribute.
• Replace SEQUENCE_LABEL element with sequence_label attribute.
• Removed RUN_LABEL element.

Changes to Project XSD

• Remove OTHER_PROJECT element.
• Remove maps objective. 
• Remove peptides, chemical, map, sample materials.
• Remove ORGANISM_PROJECT element.
• Remove RELATED_ASSEMBLIES element.
• Remove RELATED_CHROMOSOMES element.