# col_desc

table_name: submission
field_name: alias
type: varchar
sradb_updated: 2011-10-28 18:15:41
description:
Sbmitter supplied name or id for the submission.  This value can be used by the submitterto track a submission without waiting for the Archive to assign an accession.


table_name: study
field_name: alias
type: varchar
sradb_updated: 2011-10-28 18:15:41
description:
Submitter designated name of the SRA document of this type.  At minimum alias should be unique throughout the submission of this document type.  If center_name is specified, the name should be unique in all submissions from that center of this document type.


table_name: study
field_name: study_type
type: varchar
description: The STUDY_TYPE presents a controlled vocabulary for expressing the overall purpose of the study.
sradb_updated: 2011-10-28 18:15:41
value_list:
Whole Genome Sequencing, Exome Sequencing, Resequencing, Cancer Genomics, Population Genomics, Pooled Clone Sequencing, Metagenomics, Epigenetics, Transcriptome Analysis, RNASeq, Gene Regulation Study, Synthetic Genomics, Forensic or Paleo-genomics, Other


table_name: study
field_name: study_abstract
type: text
sradb_updated: 2011-10-28 18:15:41
description:
Briefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication.


table_name: study
field_name: center_project_name
type: varchar
sradb_updated: 2011-10-28 18:15:41
description:
Submitter defined project name. This field is intended for backward tracking of the study record to the submitter's LIMS.


table_name: study
field_name: related_studies
type: text
sradb_updated: 2011-10-28 18:15:41
description:
Related study or project record from a list of supported databases. The study's information is derived from this project record rather than stored as first class information.


table_name: study
field_name: entrez_link
type: text
sradb_updated: 2011-10-28 18:15:41
description:
NCBI controlled vocabulary of permitted cross references. Please see http://www.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi? .


table_name: study
field_name: study_attribute
type: text
sradb_updated: 2011-10-28 18:15:41
description:
Properties and attributes of the study. These can be entered as free-form tag-value pairs. For certain studies, submitters may be asked to follow a community established ontology when describing the work.


table_name: sample
field_name: alias
type: varchar
sradb_updated: 2011-10-28 18:15:41
description:
Submitter designated name of the SRA document of this type. At minimum alias should be unique throughout the submission of this document type. If center_name is specified, the name should be unique in all submissions from that center of this document type.


table_name: sample
field_name: taxon_id
type: int
sradb_updated: 2011-10-28 18:15:41
description:
NCBI Taxonomy Identifier. This is appropriate for individual organisms and some environmental samples.


table_name: sample
field_name: scientific_name
type: varchar
sradb_updated: 2011-10-28 18:15:41
description:
Scientific name of sample that distinguishes its taxonomy.  Please use a name or synonym that is tracked in the INSDC Taxonomy database. Also, this field can be used to confirm the TAXON_ID setting.


table_name: sample
field_name: individual_name
type: varchar
sradb_updated: 2011-10-28 18:15:41
description:
Individual name of the sample.  This field can be used to identify the individual identity of a sample where appropriate (this is usually NOT appropriate for human subjects).  Example: "Glennie" the platypus.


table_name: sample
field_name: sample_attribute
type: text
sradb_updated: 2011-10-28 18:15:41
description:
Properties and attributes of a sample. These can be entered as free-form tag-value pairs. For certain studies, submitters may be asked to follow a community established ontology when describing the work.


table_name: experiment
field_name: center_name
type: varchar
sradb_updated: 2011-10-28 18:15:41
description:
Owner authority of this document and namespace for submitter's name of this document. If not provided, then the submitter is regarded as 'Individual' and document resolution can only happen within the submission.


table_name: experiment
field_name: title
type: varchar
sradb_updated: 2011-10-28 18:15:41
description:
Short text that can be used to call out experiment records in searches or in displays. This element is technically optional but should be used for all new records.


table_name: experiment
field_name: library_strategy
type: varchar
description: Sequencing technique intended for this library.
sradb_updated: 2011-10-28 18:15:41
value_list:
WGS,WCS,WXS,CLONE,CLONEEND,POOLCLONE,FINISHING,AMPLICON,RNA-Seq,EST,FL-cDNA,CTS,ChIP-Seq,MNase-Seq,Dase-Hypersensitivity,Bisulfite-Seq,MRE-Seq,MeDIP-Seq,MBD-Seq,Other


table_name: experiment
field_name: library_selection
type: varchar
description: Whether any method was used to select and/or enrich the material being sequenced.
sradb_updated: 2011-10-28 18:15:41
value_list:
RANDOM, PCR, RANDOM PCR, RT-PCR, HMPR, MF, CF-S, CF-M, CF-H, CF-T, MSLL, cDNA, ChIP, MNase, DNAse, Hybrid Selection, Reduced Representation, other, unspecified


table_name: experiment
field_name: library_layout
type: varchar
value_list: SINGLE or PAIRED
sradb_updated: 2011-10-28 18:15:41
description:
LIBRARY_LAYOUT specifies whether to expect single, paired, or other configuration of reads. In the case of paired reads, information about the relative distance and orientation is specified.


table_name: experiment
field_name: adapter_spec
type: varchar
sradb_updated: 2011-10-28 18:15:41
description:
Some technologies will require knowledge of the sequencing adapter or the last base of the adapter in order to decode the spot.


table_name: experiment
field_name: read_spec
type: text
value_list: READ_TYPE: Forward, Reverse, Adapter, Primer, Linker, BarCode, Other
sradb_updated: 2011-10-28 18:15:41
description:
Contains READ_INDEX, READ_LABEL, READ_CLASS, READ_TYPE, BASE_COORD, RELATIVE_ORDER, CYCLE_COORD, EXPECTED_BASECALL, EXPECTED_BASECALL_TABLE, BASECALL


table_name: experiment
field_name: platform
type: varchar
value_list: LS454, ILLUMINA, HELICOS, ABI_SOLID, COMPLETE_GENOMICS, PACBIO_SMRT
sradb_updated: 2011-10-28 18:15:41
description:
The PLATFORM record selects which sequencing platform and platform-specific runtime parameters. This will be determined by the Center.


table_name: experiment
field_name: instrument_model
type: varchar
description: Instrument model for a platform.
sradb_updated: 2011-10-28 18:15:41
value_list:
LS454: 454 GS, 454 GS 20, 454 GS FLX, 454 Titanium, GS 20, GS FLX, unspecified; ILLUMINA: Solexa 1G Genome Analyzer, Illumina Genome Analyzer, Illumina Genome Analyzer II, unspecified; ABI_SOLID: AB SOLiD System, AB SOLiD System 2.0, AB SOLiD System 3.0, unspecified


table_name: run
field_name: run_file
type: text
sradb_updated: 2011-10-28 18:15:41
description:
DEPRECATED. Name of the submission file containing the run. This file may have included multiple runs.


table_name: run
field_name: run_attribute
type: text
sradb_updated: 2011-10-28 18:15:41
description:
Properties and attributes of a RUN. These can be entered as free-form tag-value pairs. For certain studies, submitters may be asked to follow a community established ontology when describing the work.


table_name: data_block
field_name: name
type: varchar
sradb_updated: 2011-10-28 18:15:41
description:
The plate/slide/flowcell name for this data block. (454) plate name (Illumina) flowcell name (SOLiD) slide name (Helicos) flowcell


table_name: data_block
field_name: sector
type: int
sradb_updated: 2011-10-28 18:15:41
description:
Higher level partition of run data to which this data block pertains. (454) not used (Illumina) Lane number (SOLiD) slide (Helicos) channel


table_name: data_block
field_name: region
type: int
sradb_updated: 2011-10-28 18:15:41
description:
Lower level partition of run data to which this data block pertains, typically the field of view for the imaging camera. (454) 0 if whole plate is used, 1..16 for gasket partition. (Illumina) Tile number (1..200+), or use 0 if file contains all tiles. (SOLiD) Panel number (1..4096), or use 0 if file contains all panels.


table_name: data_block
field_name: files
type: varchar
sradb_updated: 2011-10-28 18:15:41
description:
Actual run data are contained in one of the files listed in the submission manifest. Each data block is represented by one SRF file, one SFF file, one compressed fastq file, or one compressed tar archive file.

value_list:
File Tpes: sra, srf, sff, fastq, tab, _seq.txt, _prb.txt, _sig2.txt, _qhg.txt, 454_native, 454_native_seq, 454_native_qual, Helicos_native, Illumina_native, Illumina_native_seq, Illumina_native_prb, Illumina_native_int, Illumina_native_qseq, Illumina_native_fastq, Illumina_native_scarf, SOLiD_native, SOLiD_native_csfasta, SOLiD_native_qual


