Field List

The ancillary information fields defined for the Trace Archive are listed below.

RED color designates fields that are required

GREEN color designates fields that may be required, depending upon the trace type and strategy employed.

A field may be mandatory, optional or not allowed for a given combination of strategy and trace type as indicated below.

Modifications/additions from the original RFC are in red if these changes affect either a field requirement, or the definition of a field. Slight changes to affect document clarity are not noted.

 ACCESSION - Genbank/EMBL/DDBJ accession number

Name: ACCESSION

Type: varchar(30)

Example: AC22227

The ACCESSION is assigned upon deposition to a public repository (GenBank/EMBL/DDBJ). This field will not be applicable to all trace types (primarily WGS). However, if this field contains a valid accession identifier correlation between the primary sequence data (in Trace) and the secondary sequence data (in the public repository) is facilitated.

 AMPLIFICATION_FORWARD - The forward amplification primer sequence

Name: AMPLIFICATION_FORWARD

Type: varchar(100)

Example: GGATTCTGACTAACGAGC

The AMPLIFICATION_FORWARD field is to allow submitters to define the primers used to amplify templates for sequencing. This field is required when TRACE_TYPE_CODE=PCR or RT-PCR.

 AMPLIFICATION_REVERSE - The reverse amplification primer sequence

Name: AMPLIFICATION_REVERSE

Type: varchar(100)

Example: GGATTCTGACTAACGAGC

The AMPLIFICATION_REVERSE field is to allow submitters to define the primers used to amplify templates for sequencing. This field is required when TRACE_TYPE_CODE=PCR or RT-PCR.

 AMPLIFICATION_SIZE - The expected amplification size for a pair of primers

Name: AMPLIFICATION_SIZE

Type: int

Example: 500

The AMPLIFICATION_SIZE field allows submitters to define the expected amplification size for a pair of primers (defined in the AMPLIFICATION_FORWARD and AMPLIFICATION_REVERSE fields). This number should be given in base pairs. If TRACE_TYPE_CODE=PCR, the amplification size is based on amplification of genomic DNA. If the TRACE_TYPE_CODE=RT-PCR, then the amplification size is based on amplification of transcript.

 ANONYMIZED_ID - Anonymous ID for an individual.

Name: ANONYMIZED_ID

Type: varchar(100)

Example: 2222anonym

Used in projects to maintain the anonymity of donors. In many cases, there my be a controlled access database that can map many anonymized_ids in the trace archive to a single individual id for which phenotypic information may be available.

 ATTEMPT - Number of times the sequencing project has been attempted by the center and/or submitted to the Trace Archive.

Name: ATTEMPT

Type: tinyint(1-255)

Example: 2

 BASE_FILE - File name with base calls

Name: BASE_FILE

Type: varchar(200)

Example: ./mytraces/123clone.fasta

Tracefiles which do not include the basecalls must provide this information in a separate file. The file designations are recorded in the BASE_FILE and QUAL_FILE fields of the TRACEINFO file. The actual bases are stored in the file designated in the BASE_FILE field. If base calls and quality scores are provided in separate files the information in these files will overwrite any information in the trace ( usually *.scf) file. If the base calls and quality scores that would be provided in the BASE_FILE and QUAL_FILE are the same as the information in the trace file DO NOT PROVIDE THE FILE. Providing redundant information complicates the loading process. However, it is important to note that if some formats do not include the quality scores, then these values must be provided as ancillary information. If the center provides the BASE_FILE and QUAL_FILE, then the peak index information should also be provided in a file called PEAK_FILE.

 CENTER_NAME - Name of the sequencing center.

Name: CENTER_NAME

Type: varchar(50)

Example: WUGSC

Sequencing centers wishing to submit data must contact the Trace Archive administrators () to determine a center abbreviation. This abbreviation is used in the CENTER_NAME field. This field has a controlled vocabulary. For the complete list of submitting centers see: http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=stat&f=xml_list_centers&m=obtain&s=center

 CENTER_PROJECT - Center defined project name

Name: CENTER_PROJECT

Type: varchar(100)

Example: HBBB

The CENTER_PROJECT reflects a sequencing center's internal designation for a specific sequencing project. This field can be useful for grouping related traces.

 CHEMISTRY - Description of the chemistry used in the sequencing reaction

Name: CHEMISTRY

Type: varchar(50)

Example: BIGDYEV3.0

 CHEMISTRY_TYPE - Type of chemistry used in the sequencing reaction

Name: CHEMISTRY_TYPE

Type: char(50)

Example: P

The CHEMISTRY_TYPE uses a controlled list. Accepted values are:

Primer
Terminator
p=primer
t=terminator

 CHROMOSOME - Chromosome to which the trace is assigned

Name: CHROMOSOME

Type: varchar(8)

Example: 11

The CHROMOSOME indicates to which chromosome a trace has been assigned. Gene names or cytogenetic positions are not appropriate substitutes for chromosome information.

 CLIP_QUALITY_LEFT - Left clip of the read, in base pairs, based on quality analysis

Name: CLIP_QUALITY_LEFT

Type: int

Example: 56

The CLIP_QUALITY_LEFT field indicates the base at the beginning of the sequence at which the read should be clipped due to poor quality sequence. The given value would be the first base of the high quality region of the trace.

 CLIP_QUALITY_RIGHT - Right clip of the read, in base pairs, based on quality analysis.

Name: CLIP_QUALITY_RIGHT

Type: int

Example: 256

The CLIP_QUALITY_RIGHT field indicates the base at the end of the sequence at which the read should be clipped due to poor quality sequence. The given value would be the last base of the high quality region of the trace.

 CLIP_VECTOR_LEFT - Left clip of the read, in base pairs, based on vector sequence.

Name: CLIP_VECTOR_LEFT

Type: int

Example: 75

The CLIP_VECTOR_LEFT field indicates the base at the beginning of the sequence at which the read should be clipped due to vector sequence. The given value would be the first base of non-vector sequence. This field is required for almost all combinations of STRATEGY and TRACE_TYPE_CODE. This information can be omitted if the INSERT_FLANK_LEFT field is populated or TRACE_TYPE_CODE is PCR or RT-PCR.

 CLIP_VECTOR_RIGHT - Right clip of the read, in base pairs, based on vector sequence.

Name: CLIP_VECTOR_RIGHT

Type: int

Example: 275

The CLIP_VECTOR_RIGHT field indicates the base at the end of the sequence at which the read should be clipped due to vector sequence. The given value would be the last non-vector sequence. This field is required for almost all combinations of STRATEGY and TRACE_TYPE_CODE. This information can be omitted if the INSERT_FLANK_RIGHT field is populated or TRACE_TYPE_CODE is PCR or RT-PCR.

NOTE: Many centers combine vector and quality analysis, and thus have only one set of clip values. In this case, the set of values should be placed in the CLIP_VECTOR_LEFT/CLIP_VECTOR_RIGHT fields.

NOTE: There have been some requests to make all of the clip value fields required. For various reasons, including the note above, this position has not been adopted. The decision was that either the CLIP_VECTOR_LEFT/CLIP_VECTOR_RIGHT fields should be required or the vector information (SVECTOR_ACCESSION field) should be supplied. However, since most centers use sequencing vectors that are not in GenBank/EMBL/DDBJ it seems more likely that the trim values will be given or INSERT_FLANK_RIGHT and INSERT_FLANK_LEFT fields are populated.

 CLONE_ID - The name of the clone from which the trace was derived

Name: CLONE_ID

Type: varchar(30)

Example: RP23-1123F10

The CLONE_ID field is used to store the identifier related to an individual clone, for example a BAC clone, PAC clone or cDNA clone. If the clone is registered with the clone registry (http://www.ncbi.nlm.nih.gov/genome/clone/), standard clone registry nomenclature (see http://www.ncbi.nih.gov/genome/clone/ nomenclature.shtml for more details) should be used. It is now proposed that this field would be required for the following combination of STRATEGY and TRACE_TYPE_CODE:

STRATEGY=cDNA; TRACE_TYPE_CODE=Any

STRATEGY=EST; TRACE_TYPE_CODE=Any

STRATEGY=CLONEEND; TRACE_TYPE_CODE=CLONEEND

STRATEGY=CLONE; TRACE_TYPE_CODE=Any

STRATEGY=ENCODE; TRACE_TYPE_CODE=SHOTGUN; PrimerWalk; CLONEEND

STRATEGY=FINISHING; TRACE_TYPE_CODE=Any

 CLONE_ID_LIST - Semi-colon delimited list of clones if the Strategy is PoolClone.

Name: CLONE_ID_LIST

Type: varchar(30)

Example: RP23-200A2;RP23-500P1

The CLONE_ID_LIST field is used only if STRATEGY =PoolClone. In this case, the list of clones is provided as a semicolon delimited list. If the clones are registered with the Clone Registry, standard clone registry nomenclature should be used (see CLONE_ID field).

Note: The list of clones is not limited, but the size of the individual clone within the list is limited to 30 bytes.

It is now proposed that this field would be required for the following combination of STRATEGY and TRACE_TYPE_CODE:

STRATEGY=PoolClone; TRACE_TYPE_CODE=Any

 COLLECTION_DATE - The full date, in "Mar 2 2006 12:00AM" format, on which an environmental sample was collected.

Name: COLLECTION_DATE

Type: datetime

Example: Mar 2 2006 12:00AM

The COLLECTION_DATE field is used to define the date and time on which an environmental sample was collected. This field would be required for the following combination of STRATEGY and TRACE_TYPE_CODE:

STRATEGY=Env Sample- Geo; TRACE_TYPE_CODE=Any

STRATEGY=Env Sample- Host; TRACE_TYPE_CODE=Any

 CVECTOR_ACCESSION - Repository ( GenBank/EMBL/DDBJ) accession identifier for the cloning vector.

Name: CVECTOR_ACCESSION

Type: varchar(50)

Example: AY451994

The CVECTOR_ACCESSION field holds the accession number for the cloning vector used. This cloning vector relates to the clone named in the CLONE_ID field.

 CVECTOR_CODE - Center defined code for the cloning vector

Name: CVECTOR_CODE

Type: varchar(50)

Example: PBACE3.6

The CVECTOR_CODE field holds the user defined identifier for the cloning vector. Submitters are encouraged to submit all vector sequence information to public repositories. However, it is understood that many sequencing centers sequence clones from libraries they did not prepare.

 DEPTH - Depth (in meters) at which an environmental sample was collected.

Name: DEPTH

Type: float

Example: 10M

The DEPTH field is applicable to water samples and earth samples. If the value of this field is NULL, it is anticipated the sample was taken from the surface of the environment. While this field is only applicable to environmental samples, it is not required.

 ELEVATION - Elevation (in meters) at which an environmental sample was collected

Name: ELEVATION

Type: float

Example: 500

If the value of this field is NULL it is assumed the data were obtained at sea level. The field ELEVATION is only applicable to some environmental sample data, but is not a required field.

 ENVIRONMENT_TYPE - Type of environment from which an environmental sample was collected.

Name: ENVIRONMENT_TYPE

Type: varchar(250)

Example: sea water

The ENVIRONMENT_TYPE field is used to describe the specific environment from which an environmental sample was taken. While the LATITUDE and LONGITUDE fields describe the location many types of environmental types could exist at this location (for example, soil, sludge, tree roots, etc). This field would be required for the following combination of STRATEGY and TRACE_TYPE_CODE:

STRATEGY=Env Sample - Geo; TRACE_TYPE_CODE=Any

 EXTENDED_DATA - Extra ancillary information wrapped around in a EXTENDED_DATA block, where actual values are provided with a special <field> tag

Name: EXTENDED_DATA

Type: varchar()

Example:

<extended_data>
    <field name='SamplingSiteMonthChlorophyllLevel'>1.4 mg_mm</field>
    <field name='SamplingSiteYearlyChlorophyllLevel'>1.12 mg_mm</field>
    <field name='SamplingSiteYearlyChlorophyllLevelStdError'>0.19 mg_mm</field>
</extended_data>
          

The '=' sign and the field separator character '|'should be excluded from names and their values. No other validity checks will be performed on the data. Although the number of <field> tags is not limited we are going to limit the total size of the block to 2 KB.

 FEATURE_ID_FILE - File describing the features and their locations on a chip.

Name: FEATURE_ID_FILE

Type: varchar(200)

Example: ./mytraces/chip2.cdf

The FEATURE_ID_FILE provides the location and sequence of the features for a given chip when TRACE_TYPE_CODE="CHIP".

 FEATURE_ID_FILE_NAME - Reference to a common FEATURE_ID_FILE which should be submitted first.

Name: FEATURE_ID_FILE_NAME

Type: varchar(200)

Example:

This field is required when TRACE_TYPE_CODE="CHIP".

 FEATURE_SIGNAL_FILE - File giving the signal and variance for features on a chip.

Name: FEATURE_SIGNAL_FILE

Type: varchar(200)

Example: ./mytraces/chip2.signal

The FEATURE_SIGNAL_FILE provides the signal and variance of signal for the features on a given chip when TRACE_TYPE_CODE="CHIP".

 FEATURE_SIGNAL_FILE_NAME - Reference to a common FEATURE_SIGNAL_FILE which should be submitted first.

Name: FEATURE_SIGNAL_FILE_NAME

Type: varchar(200)

Example:

This field is required when TRACE_TYPE_CODE="CHIP".

 GENE_NAME - Gene name or some other common identifier

Name: GENE_NAME

Type: varchar(100)

Example: transporter 1

Free text. Mainly this field would be for TRACE_TYPE_CODE='Re-sequencing' or 'ENCODE'. When a group is analyzing a particular gene, they may want to refer to that gene by it's name or some other common identifier. Gene names not in Entrez Gene can be used (for instance, Ensembl genes).

 HI_FILTER_SIZE - The largest filter used to stratify an environmental sample.

Name: HI_FILTER_SIZE

Type: varchar(50)

Example: 50 micron

The HI_FILTER_SIZE field is applicable only to environmental sample data but is not a required field.

 HOST_CONDITION - The condition of the host from which an environmental sample was obtained.

Name: HOST_CONDITION

Type: varchar(100)

Example: HIV-positive

The HOST_CONDITION field is only applicable to environmental sample data and is used to describe the condition (healthy, sick, etc) of the host from which a sample was taken.

 HOST_ID - Unique identifier for the specific host from which an environmental sample was taken.

Name: HOST_ID

Type: varchar(100)

Example: yerkes pedigree #C0479 'Clint'

The HOST_IDENTIFIER field is only applicable to environmental sample data and is used to capture the unique name for the specific host from which a sample was obtained. This field would be required for the following combination of STRATEGY and TRACE_TYPE_CODE:

STRATEGY=Env Sample- Host; TRACE_TYPE_CODE=Any

 HOST_LOCATION - Specific location on the host from which an environmental sample was collected.

Name: HOST_LOCATION

Type: varchar(100)

Example: rumen

The HOST_LOCATION field is only applicable to environmental sample data and is used to describe the specific part of the host from which the sample was obtained, for example: dental plaque, hindgut, root surfaces. This field would be required for the following combination of STRATEGY and TRACE_TYPE_CODE:

STRATEGY=Env Sample- Host; TRACE_TYPE_CODE=Any

 HOST_SPECIES - The host from which an environmental sample was obtained.

Name: HOST_SPECIES

Type: varchar(100)

Example: Pan troglodytes

The HOST_SPECIES field is only applicable to environmental sample data. This field would be required for the following combination of STRATEGY and TRACE_TYPE_CODE:

STRATEGY=Env Sample- Host; TRACE_TYPE_CODE=Any

 INDIVIDUAL_ID - Publicly available identifier to denote a specific individual or sample from which a trace was derived.

Name: INDIVIDUAL_ID

Type: varchar(100)

Example: NA12345

The INDIVIDUAL_ID field provides a center specific unique id that can associate a specific trace to an individual. This will be used primarily for population based studies.

 INSERT_FLANK_LEFT - Flanking sequence at the cloning junction.

Name: INSERT_FLANK_LEFT

Type: varchar(100)

Example: AAGGTGCGATGCAGTGGCAGTAGCAGTGTCGACGTGACGATTCGTCCGGA

The INSERT_FLANK_LEFT field should provide from 50 up to 100 bases of sequence (including linkers) to the left of the cloning junction. This information will allow users to perform their own vector trimming of reads. This field is required for almost all combinations of STRATEGY and TRACE_TYPE_CODE. This field can be omitted if CLIP_VECTOR_LEFT is populated. However, INSERT_FLANK_LEFT is the preferred choice. If there was no cloning step involved in the sequencing, please populate the field with 'NONE'.

 INSERT_FLANK_RIGHT - Flanking sequence at the cloning junction.

Name: INSERT_FLANK_RIGHT

Type: varchar(100)

Example: AAGGCGCGATGCAGTGAGCGAGGCTGACGTCGGCTAGCGTCGCGTCGGGT

The INSERT_FLANK_RIGHT field should provide from 50 up to 100 bases of sequence (including linkers) to the right of the cloning junction. This information will allow users to perform their own vector trimming of reads. This field is required for almost all combinations of STRATEGY and TRACE_TYPE_CODE. This field can be omitted if CLIP_VECTOR_RIGHT is populated. However, INSERT_FLANK_RIGHT is the preferred choice. If there was no cloning step involved in the sequencing, please populate the field with 'NONE'. It is anticipated that if INSERT_FLANK_LEFT is populated that INSERT_FLANK_RIGHT will also be populated. It is not anticipated that a mixture of clip values and junction sequence will be specified. (i.e. CLIP_VECTOR_LEFT and INSERT_FLANK_RIGHT populated for the same record.

 INSERT_SIZE - Expected size of the insert (referred to by the value in the TEMPLATE_ID field) in base pairs.

Name: INSERT_SIZE

Type: int

Example: 2000

The INSERT_SIZE field indicates the expected insert size of the clone that is sequenced. It is understood that this is an estimate based upon the average insert sizes found in a given library. However, this information is critical for certain experiments, such as whole genome assembly. This field would be required for the following combination of STRATEGY and TRACE_TYPE_CODE:

STRATEGY=Any; TRACE_TYPE_CODE=WGS

STRATEGY=Any; TRACE_TYPE_CODE=WCS

STRATEGY=cDNA; TRACE_TYPE_CODE=CLONEEND

STRATEGY=CLONEEND; TRACE_TYPE_CODE=CLONEEND

 INSERT_STDEV - Approximate standard deviation of value in INSERT_SIZE field

Name: INSERT_STDEV

Type: int

Example: 200

The INSERT_STDEV field reflects the approximate standard deviation of the insert size. It is understood that this information is an approximation and may change as better data is obtained. This field would be required for the following combination of STRATEGY and TRACE_TYPE_CODE:

STRATEGY=Any; TRACE_TYPE_CODE=WGS

STRATEGY=Any; TRACE_TYPE_CODE=WCS

STRATEGY=cDNA; TRACE_TYPE_CODE=CLONEEND

STRATEGY=CLONEEND; TRACE_TYPE_CODE=CLONEEND

 LATITUDE - The latitude measurement (using standard GPS notation) from which a sample was collected.

Name: LATITUDE

Type: float

Example: 54.736

The LATITUDE field is required to describe the collection of some environmental sample data. The latitude range is [-90,90] with the equator as 0 latitude and positive values of latitude are north of the equator. This field would be required for the following combination of STRATEGY and TRACE_TYPE_CODE: STRATEGY=Env Sample- Geo; TRACE_TYPE_CODE=Any

 LIBRARY_ID - The source of the clone identified in the CLONE_ID field

Name: LIBRARY_ID

Type: varchar(100)

Example: RP23

The LIBRARY_ID field documents the source library of the archival clone resource. Many genomic libraries have been registered with the Clone Registry ( http://www.ncbi.nlm.nih.gov/genome/clone/ ) and the standard nomenclature ( http://www.ncbi.nlm.nih.gov/genome/clone/clbrowse.cgi ) should be used for these libraries. This field would be required for the following combination of STRATEGY and TRACE_TYPE_CODE:

STRATEGY=cDNA; TRACE_TYPE_CODE=Any

STRATEGY=EST; TRACE_TYPE_CODE=Any

STRATEGY=CLONEEND; TRACE_TYPE_CODE=CLONEEND

STRATEGY=CLONE; TRACE_TYPE_CODE=Any

STRATEGY=ENCODE; TRACE_TYPE_CODE=SHOTGUN; PrimerWalk; CLONEEND

 LONGITUDE - The longitude measurement (using standard GPS notation) from which a sample was collected.

Name: LONGITUDE

Type: float

Example: -86.403

The LONGITUDE field is required to describe the collection of some environmental sample data. The longitude is ranging from 0° at the Prime Meridian to +180° eastward and −180° westward. This field would be required for the following combination of STRATEGY and TRACE_TYPE_CODE:

STRATEGY=Env Sample- Geo; TRACE_TYPE_CODE=Any

 LO_FILTER_SIZE - The smallest filter size used to stratify an environmental sample.

Name: LO_FILTER_SIZE

Type: varchar(50)

Example: 25 micron

The LO_FILTER_SIZE field is only applicable to environmental sample data but is not a required field.

 NCBI_PROJECT_ID - Project ID generated by the Genome Project database at NCBI/NLM/NIH

Name: NCBI_PROJECT_ID

Type: int

Example: 7

NCBI_PROJECT_ID field would allow to link traces to Genome Project database and easily retrieve sets of traces from each Project. Genome sequencing centers may register their project prior the submission of genomic sequence data. Submitters need not submit sequencing data at the time they register their project.

 ORGANISM_NAME - Description of species for BARCODE project from which trace is derived.

Name: ORGANISM_NAME

Type: varchar(100)

Example: Acanthocybium solandri

The ORGANISM_NAME field is used to classify the read by species for BARCODE data, using proper taxonomic name in accordance with Taxonomy Browser. SPECIES_CODE="BARCODE SPECIES" for all traces from this project. This field would be required for the STRATEGY=BARCODE.

 PEAK_FILE - Name of file that contains the list of peak values.

Name: PEAK_FILE

Type: varchar(200)

Example: ./mytraces/123clone.peak

Consult the BASE_FILE field description for more information.

 PH - The pH at which an environmental sample was collected.

Name: PH

Type: float

Example: 7.2

The PH field is only applicable to environmental sample data but is not a required field.

 PICK_GROUP_ID - Id to group traces picked at the same time.

Name: PICK_GROUP_ID

Type: int

Example: 939065

 PLACE_NAME - Country in which the biological sample was collected and/or common name for a given location.

Name: PLACE_NAME

Type: varchar(250)

Example: Octopus Springs

The PLACE_NAME field is applicable to environmental sample data, but is not required.

 PLATE_ID - Submitter defined plate id

Name: PLATE_ID

Type: varchar(32)

Example: 203

The PLATE_ID and WELL_ID fields are intended to identify the storage location of the sequencing template (not the library well coordinate of an archival clone named in the CLONE_ID field). This may enable flipped or contaminated trays to be easily identified. If a particular experiment did not require the use of a plate, please populate this field with '0'.

 POPULATION_ID - Center provided id to designate a population from which a trace (or group of traces) was derived.

Name: POPULATION_ID

Type: varchar(100)

Example: CEPH

The POPULATION_ID field is used to capture center specific designations of groups of individuals. This will likely only be useful in population studies (usually STRATEGY=SNP).

 PREP_GROUP_ID - ID that defines groups of traces prepared at the same time.

Name: PREP_GROUP_ID

Type: varchar(30)

Example: A2

 PRIMER - The primer sequence (used in the sequencing reaction)

Name: PRIMER

Type: varchar(200)

Example: GAATACCTACGATCGCC

The value of the PRIMER field is the actual base sequence of the sequencing primer used. If a center uses a primer extensively, the primer sequence can be entered into the list of primer codes and the PRIMER_CODE field can be used.

 PRIMER_CODE - Identifier for the sequencing primer used.

Name: PRIMER_CODE

Type: varchar(30)

Example: Sp6

 PRIMER_LIST - A ';' delimited list of primers used in a mapping experiment (such as AFLP)

Name: PRIMER_LIST

Type: varchar(100)

Example: AAGGTCTGCGCGTGTC;AGCTGCGTACGTAATCG;

This field is required if Strategy ="AFLP" and TRACE_TYPE_CODE ="PCR".

 PROGRAM_ID - The program used to create the trace file.

Name: PROGRAM_ID

Type: varchar(100)

Example: phred-19990722h

The PROGRAM_ID field is used to indicate the base calling program. This field is free text. Program name, version numbers or dates are very useful. More example values:

• phred-19980904e
• abi-3.1
• ATQA
• TraceTuner
• Licor
• Megabase
• Beckman

 PROJECT_NAME - Term by which to group traces from different centers based on a common project.

Name: PROJECT_NAME

Type: varchar(50)

Example: New Project

In this way sequencing centers that are working on the same large project can group all of the traces for this project using a common term. This field has a controlled vocabulary. Sequencing centers wishing to submit data must contact the Trace Archive administrators () to determine a name that all members of the project agree on.

 QUAL_FILE - Name of file containing the quality scores.

Name: QUAL_FILE

Type: varchar(200)

Example: ./mytraces/123clone.fasta.qs

See note associated with the BASE_FILE field.

 REFERENCE_ACCESSION - Reference accession (use accession and version to specify a particular instance of a sequence) used as the basis for a re-sequencing project. In case of Comparative strategy show the basis for primers design.

Name: REFERENCE_ACCESSION

Type: varchar(50)

Example: NT_029829.1

This field is required for the following combination of STRATEGY and TRACE_TYPE_CODE: STRATEGY=Re-sequencing; Comparative TRACE_TYPE_CODE=Any

 REFERENCE_ACC_MAX - Finish position for a particular amplicon in re-sequencing or comparative projects.

Name: REFERENCE_ACC_MAX

Type: int

Example: 30929

This field points to the finishing coordinate of the accession.version described in the REFERENCE_ACCESSION field. All coordinates should be in 1 base coordinates (i.e. sequences start at base 1, not base 0). This field is required for the following combination of STRATEGY and TRACE_TYPE_CODE: STRATEGY=Re-sequencing; TRACE_TYPE_CODE=SHOTGUN; PCR; RT-PCR

 REFERENCE_ACC_MIN - Start position for a particular amplicon in re-sequencing or comparative projects.

Name: REFERENCE_ACC_MIN

Type: int

Example: 29829

This field points to the starting coordinate of the accession.version described in the REFERENCE_ACCESSION field. All coordinates should be in 1 base coordinates (i.e. sequences start at base 1, not base 0). This field is required for the following combination of STRATEGY and TRACE_TYPE_CODE: STRATEGY=Re-sequencing; TRACE_TYPE_CODE=SHOTGUN; PCR; RT-PCR

 REFERENCE_OFFSET - Sequence offset of accession specified in REFERENCE_ACCESSION field to define the coordinate start position used as the basis for a re-sequencing project.

Name: REFERENCE_OFFSET

Type: int

Example: 1520899

This field points to the starting coordinate of the accession.version described in the REFERENCE_ACCESSION field. All coordinates should be in 1 base coordinates (i.e. sequences start at base 1, not base 0). This field is required for the following combination of STRATEGY and TRACE_TYPE_CODE: STRATEGY=Re-sequencing; TRACE_TYPE_CODE=CHIP

 REFERENCE_SET_MAX - Finish position for a entire re-sequencing region. This region may include several amplicons.

Name: REFERENCE_SET_MAX

Type: int

Example: 29829

This field points to the starting coordinate of the accession.version described in the REFERENCE_ACCESSION field for a entire re-sequencing region. All coordinates should be in 1 base coordinates (i.e. sequences start at base 1, not base 0). This field is required for The Cancer Genome Atlas (TCGA) project. The REFERENCE_ACC_[MIN|MAX] and REFERENCE_SET_[MIN|MAX] should refer to the same REFERENCE_ACC.

 REFERENCE_SET_MIN - Start position for a entire re-sequencing region. This region may include several amplicons.

Name: REFERENCE_SET_MIN

Type: int

Example: 29829

This field points to the starting coordinate of the accession.version described in the REFERENCE_ACCESSION field for a entire re-sequencing region. All coordinates should be in 1 base coordinates (i.e. sequences start at base 1, not base 0). This field is required for The Cancer Genome Atlas (TCGA) project. The REFERENCE_ACC_[MIN|MAX] and REFERENCE_SET_[MIN|MAX] should refer to the same REFERENCE_ACC.

 RUN_DATE - Date the sequencing reaction was run.

Name: RUN_DATE

Type: datetime

Example: 2000-10-28

 RUN_GROUP_ID - ID used to group traces run on the same machine.

Name: RUN_GROUP_ID

Type: varchar(30)

Example: group2

 RUN_LANE - Lane or capillary of the trace

Name: RUN_LANE

Type: int

Example: 1

The RUN_LANE documents the specific lane or capillary on which a trace was obtained.

 RUN_MACHINE_ID - ID of the specific sequencing machine on which a trace was obtained

Name: RUN_MACHINE_ID

Type: varchar(30)

Example: machine2

 RUN_MACHINE_TYPE - Type or model of machine on which a trace was obtained.

Name: RUN_MACHINE_TYPE

Type: varchar(30)

Example: ABI 310

 SALINITY - The salinity at which an environmental sample was collected measured in parts per thousand units (promille).

Name: SALINITY

Type: float

Example: 20‰

The SALINITY field is only applicable to environmental sample data but is not a required field.

 SEQ_LIB_ID - Center specified M13/PUC library that is actually sequenced.

Name: SEQ_LIB_ID

Type: varchar(255)

Example: 22194

The SEQ_LIB_ID field is the center identifier for the M13/PUC based clone that is actually sequenced. This will allow grouping of traces by the actual ligation event and is applicable to most projects. This value will be unique within a given center. This field would be required for the following combination of STRATEGY and TRACE_TYPE_CODE:

STRATEGY=Any; TRACE_TYPE_CODE=SHOTGUN

STRATEGY=Any; TRACE_TYPE_CODE=WGS/WCS

 SOURCE_TYPE - Source of the DNA

Name: SOURCE_TYPE

Type: varchar(50)

Example: GENOMIC DNA

The SOURCE_TYPE field consists of a code. Possible values are:

• G = Genomic DNA (includes PCR products from genomic DNA)
• N = Non Genomic DNA (EST, cDNA, RT-PCR, screened libraries)
• VIRAL RNA = Viral RNA
• SYNTHETIC = Synthetic DNA

Accepted values are G, N, GENOMIC, NON GENOMIC, VIRAL RNA, SYNTHETIC

 SPECIES_CODE - Description of species from which trace is derived

Name: SPECIES_CODE

Type: varchar(100)

Example: Homo sapiens

The SPECIES_CODE field is used to classify the read by species, using proper taxonomic names where possible. This field currently is maintained as a controlled vocabulary. For a list of species currently contained within the Trace Archive, see: http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=stat&f=xml_list_species&m=obtain&s=species To submit a new species, please contact us () prior to submission. For cases in which it is unclear of the taxonomic origin of a specific trace the taxonomic classification 'ENVIRONMENTAL SEQUENCE' can be used in a case of environmental samples or 'ARTIFICIAL SEQUENCE' in a case of artificial material. A second proposal for this field involves incorporating subspecies information into the species code identifier and making the field SUBSPECIES_ID obsolete.

 STRAIN - Strain from which a trace is derived.

Name: STRAIN

Type: varchar(50)

Example: C57BL/6J

Strain is required for Strategy = "SNP"

 STRATEGY - Experimental STRATEGY

Name: STRATEGY

Type: varchar(50)

Example: MODEL VERIFY

In the original RFC, the STRATEGY field was proposed to contain the sequencing STRATEGY used in obtaining the trace. This definition made this field largely redundant with the TRACE_TYPE_CODE field. The proposal in this new version of the RFC is to make this field reflective of the experimental STRATEGY used when obtaining the trace. In some cases, this may still be redundant with the TRACE_TYPE_CODE field. Some records in the Trace Archive already contain some values in this field that are reflective of this idea. For example, the STRATEGY 'MODEL VERIFY' was proposed for a group of traces that were obtained in the process of verifying proposed gene models. In addition to conveying some information as to the original purpose of the trace, it will likely be useful in retrieving groups of traces in batch sets. It is proposed that this would be a controlled vocabulary, but that submitters would contribute to this list as needed to define various experiments and projects.

Original values:

• CCS: Concatenated cDNA sequencing
• CLONE: Clone based sequencing
• ENCODE: Reads generated for the Encode project
• MODEL VERIFY: traces obtained to verify proposed gene models
• POOLCLONE: Pools of clones (BACs mostly)
• TRANSPOSON: Transposon based sequencing
• WCS: Whole Chromosome shotgun sequencing
• WGS: Whole Genome shotgun sequencing

Current values (this list would continually be expanding):

• AFLP: Amplified Fragment Length Polymorphism
• BARCODE: DNA sequence analysis of a uniform target gene to enable species identification
• CCS: Concatenated cDNA sequencing
• cDNA: Sequences generated in the process of sequencing cDNA clones
• CF-S: Cot-filtered single/low-copy genomic DNA
• CF-M: Cot-filtered moderately repetitive genomic DNA
• CF-H: Cot-filtered highly repetitive genomic DNA
• CF-T: Cot-filtered theoretical single-copy DNA
• CLONE: Genomic clone based (hierarchical) sequencing
• CLONEEND: Sequences generated from the end of a clone (BAC/PAC/Fosmid or cDNA)
• Comparative: Sequences obtained using primers design from related species
• CTS: Concatenated Tag Sequencing
• Env Sample-GEO: Geographically generated environmental sample
• Env Sample-Host: Environmental samples collected from a specific host
• EST: single pass sequencing of cDNA templates
• FINISHING: a read specifically made for finishing, could be either BAC finishing or Whole Genome Assembly (WGA) finishing
• MODEL VERIFY: Sequences obtained to verify proposed gene models
• PoolClone: Pools of clones (BACs mostly)
• SNP: Reads used for SNP identification
• TARGETED LOCUS: Sequences obtained from templates generated by primers designed to amplify a specific genetic locus
• Re-sequencing: Re-sequencing of targeted genomic regions
• RT-PCR: Sequences obtained using templates generated by Reverse Transcriptase Polymerase Chain Reaction
• WGA: Whole Genome Assembly

 SUBMISSION_TYPE - Type of submission

Name: SUBMISSION_TYPE

Type: varchar(50)

Example: NEW

The SUBMISSION_TYPE field allowed values:

• NEW – use to submit new data
• UPDATE – use to renew traces and their ancillary information. Previous data will be saved with their TI's; new traces with the same trace_name's will receive new TI's and they will become active
• UPDATEINFO – use to update or add ancillary information for already existing traces without re-submitting the entire package of data
• WITHDRAW – use to withdraw traces

 SVECTOR_ACCESSION - GenBank/EMBL/DDBJ accession of the sequencing vector.

Name: SVECTOR_ACCESSION

Type: varchar(50)

Example: X52325

 SVECTOR_CODE - Center defined code for the sequencing vector

Name: SVECTOR_CODE

Type: varchar(50)

Example: pBluescript SK(+)

 TEMPERATURE - The temperature (in ^oC) at which an environmental sample was collected.

Name: TEMPERATURE

Type: float

Example: 30

The TEMPERATURE field is only applicable to environmental sample data but it is not a required field.

 TEMPLATE_ID - Submitter defined identifier for the sequencing template.

Name: TEMPLATE_ID

Type: varchar(50)

Example: HBBBA2211

The TEMPLATE_ID field is used to uniquely identify the actual template that is sequenced. This field, in conjunction with the TRACE_END field, can be used to identify traces that should be marked as 'mate_pairs' because they come from opposite ends of the same clone.

 TRACE_END - Defines the end of the template contained in the read.

Name: TRACE_END

Type: varchar(50)

Example: F

The TRACE_END field can have the following values:

• F: FORWARD
• R: REVERSE
• N: UNKNOWN

 TRACE_FILE - Filename with the trace, relative to the top of the volume.

Name: TRACE_FILE

Type: varchar(200)?

Example: ./traces/TRACE001.scf

 TRACE_FORMAT - Format of the trace file.

Name: TRACE_FORMAT

Type: varchar(20)

Example: scf

The TRACE_FORMAT field can have the following values:

• SFF (new) - Standard Flowgram Format.
• SCF - A standard file format for data from DNA sequencing instruments.
• ZTR - The ZTR format is used for storing analogue chromatogram data from DNA sequencing instruments.
• ABI - A ABI-tracefile is a binary file including the tracedata and the sequence.

 TRACE_NAME - Center defined trace identifier.

Name: TRACE_NAME

Type: varchar(250)

Example: HBBBA1U2211

The TRACE_NAME field must be unique within a center, but is not required to be unique between centers. The combination of TRACE_NAME and CENTER_NAME act as a unique key within the Trace Archive.

 TRACE_TYPE_CODE - Sequencing strategy by which the trace was obtained.

Name: TRACE_TYPE_CODE

Type: varchar(50)

Example: wgs

The field TRACE_TYPE_CODE reflects the sequencing STRATEGY used to obtain the trace.

Original values:

• CLONEEND: BAC/PAC/fosmid end sequence
• EST: Expressed sequence tag sequencing- single pass sequencing of a cDNA template
• FINISHING: a read generated for finishing a BAC project
• GSS: Genome Survey Sequences
• PCR: Sequences obtained using templates generated by Polymerase Chain Reaction
• RT-PCR: Sequences obtained using templates generated by Reverse Transcriptase Polymerase Chain Reaction
• SHOTGUN: generally refers to BAC based shotgun sequencing
• WCS: Whole Chromosome Shotgun
• WGS: Whole Genome Shotgun

Current values:

• CHIP: Sequences obtained using microarrays (also called DNA chips or gene chips)
• CLONEEND: Sequences generated from the end of a large insert (BAC/PAC/Fosmid) or cDNA clone
• EST: Single Pass Expressed Sequence Tag
• HTP SELEX: High throughput SELEX
• OTHER: Other than PCR, PrimerWalk, SHOTGUN or TRANSPOSON for FINISHING STRATEGY
• PCR: Sequences obtained using templates generated by genomic Polymerase Chain Reaction
• PrimerWalk: Sequences generated through a primer walking step
• RT-PCR: Sequences obtained using templates generated by Reverse Transcriptase Polymerase Chain Reaction
• SHOTGUN: Shotgun sequencing of clones (genomic or cDNA)
• TRANSPOSON: Sequences obtained using templates generated by transposons
• WCS: Whole Chromosome Shotgun
• WGS: Whole Genome Shotgun

Obsolete values:

• 454: Sequences obtained using the 454 technology

 TRANSPOSON_ACC - GenBank/EMBL/DDBJ accession for transposon used in generating sequencing template.

Name: TRANSPOSON_ACC

Type: varchar(50)

Example: X00913

The TRANSPOSON_ACC would be required for the following combination of STRATEGY and TRACE_TYPE_CODE:

STRATEGY =Any; TRACE_TYPE_CODE =TRANSPOSON

 TRANSPOSON_CODE - Center defined code for transposon used in generating sequencing template.

Name: TRANSPOSON_CODE

Type: varchar(50)

Example: Mu transposon

This TRANSPOSON_CODE field would be required for the following combination of STRATEGY and TRACE_TYPE_CODE:

STRATEGY =Any; TRACE_TYPE_CODE =TRANSPOSON

 WELL_ID - Center defined well identifier for the sequencing reaction.

Name: WELL_ID

Type: varchar(50)

Example: A1

The field WELL_ID in combination with the field PLATE_ID, is used to define the storage location of the sequencing reaction (see note with the field WELL_ID). Typically, sequencing reactions are performed in standard microtiter dishes having either 96 or 384 wells. (see standard configurations below).
Standard 96 well microtiter configuration
Standard 384 well microtiter configuration

NEW and UPDATE submissions

NEW and UPDATE submissions should have the structure shown below:

Examples are available for download: ftp://ftp-private.ncbi.nlm.nih.gov/pub/TraceDB/misc/examples

The ancillary TRACEINFO file describes the submitted data as well as points to the location of the chromatograms. XML format is preferable, since it is easier for a human to read if necessary. The ancillary data requirements are in the Validation Table (Excel format) for specific combinations of STRATEGY and TRACE_TYPE_CODE. Both types of ancillary files can contain common fields section at the beginning of it. This section defines common for the submission values if any.

If the trace info is provided as an XML file the info fields will serve as the tags. To preserve the grouping, the trace_volume tag is used.

<?xml version="1.0" encoding="UTF-8"?>
<trace_volume>
   <common_fields>
      <center_name>CENTER NAME ACRONYM IS HERE</center_name>
      <submission_type>NEW</submission_type>
      <strategy>WGS</strategy>
      <trace_type_code>WGS</trace_type_code>
      <center_project>Gorilla WGS</center_project>
      <source_type>G</source_type>
      <species_code>Gorilla gorilla</species_code>
      <insert_size>1500</insert_size>
   </common_fields>
   <trace>
      <template_id>HBBAA1U0001</template_id>
      <trace_name>HBBAA1U0001</trace_name>
      <trace_file>traces/HBBA/HBBAA1U0001.scf</trace_file>
      <trace_format>scf</trace_format>
      <trace_end>R</trace_end>
      <clip_vector_left>56</clip_vector_left>
      <clip_vector_right>737</clip_vector_right>
      <run_machine_id>legrenzi</run_machine_id>
      <chemistry>BIGDYEV2</chemistry>
      <program_id>phred version=0.020425.c</program_id>
      <run_machine_type>ABI 3700</run_machine_type>
   </trace>
   <trace>
      <template_id>HBBAA1U0002</template_id>
      <trace_name>HBBAA1U0002</trace_name>
        ...more info...
    </trace>
</trace_volume>

 

Tabular file has the following format, and either has no extension at all, or its name is extended with '.txt' or '.tbl'. Data represents the actual values of the fields described in the header. It is also tab delimited

center_name     = CENTER NAME ACRONYM IS HERE
submission_type = NEW
strategy        = WGA
trace_type_code = WGS
center_project  = Gorilla WGS
source_type     = G
species_code    = Gorilla gorilla
insert_size     = 1500
template_id    trace_name    trace_file    trace_format    trace_end   clip_vector_left    clip_vector_right    run_machine_id    chemistry   program_id    run_machine_type
HBBAA1U0001    HBBAA1U0001    traces/HBBA/HBBAA1U0001.scf    scf    R   56   737    legrenzi    BIGDYEV2    phred version=0.020425.c   ABI 3700   s2SCF     scf    F    44    793    agricola    BIGDYEV2    phred version=0.020425.c    ABI 3700
HBBAA1U0002    HBBAA1U0002  ...
    ...

728018368a7820c50cbaad633bc608a1  TRACEINFO
0cbaad633bc608a1728018368a7820c5  traces/TRACE0001.scf
 

UPDATEINFO submission

An UPDATEINFO submission should have the structure shown below:

TOP_DIRECTORY/
TOP_DIRECTORY/TRACEINFO.txt
TOP_DIRECTORY/MD5
TOP_DIRECTORY/README
 

TRACEINFO file in this case has to have SUBMISSION_TYPE=UPDATEINFO, the unique keys to the traces(CENTER_NAME and TRACE_NAME) and fields with their values that you wish to update. These data will be uploaded into our database without changing the ti's and the rest information. This file can contain common fields section at the beginning of it. This section defines common for the submission values if any.

If the trace info is provided as an XML file the info fields will serve as the tags. To preserve the grouping, the trace_volume tag is used.

<?xml version="1.0"?>
<trace_volume>
    <common_fields>
        <center_name>CENTER NAME ACRONYM IS HERE</center_name>
        <submission_type>UPDATEINFO</submission_type>
        <trace_type_code>WGS</trace_type_code>
        <insert_size>40000</insert_size>
    </common_fields>
    <trace>
        <trace_name>HBBA0001</trace_name>
        <template_id>template_id_HBBA0001</template_id>
        ...more info...
    </trace>
    <trace>
        <trace_name>HBBA0002</trace_name>
        <template_id>template_id_HBBA0002</template_id>
        ...more info...
    </trace>
</trace_volume>
 

Tabular file has the following format, and either has no extension at all, or its name is extended with '.txt' or '.tbl'. Data represents the actual values of the fields described in the header. It is also tab delimited

SUBMISSION_TYPE=UPDATEINFO
CENTER_NAME=CENTER NAME ACRONYM IS HERE
trace_name   clip_vector_left    clip_vector_right     more fields (if necessary)... 
my_trace1     33   89    ...
my_trace2     19   80    ...
my_trace2     1    68    ...
more trace_name's...

728018368a7820c50cbaad633bc608a1  TRACEINFO
0cbaad633bc608a1728018368a7820c5  traces/TRACE0001.scf
 

WITHDRAW submission

To delete traces use SUBMISSION_TYPE =WITHDRAW

A WITHDRAW submission is a TRACEINFO file inside a tar file, just as any regular Trace Archive submission. It should have the structure shown below:

TOP_DIRECTORY/
TOP_DIRECTORY/TRACEINFO.txt
 

WITHDRAW type of submission is very similar to UPDATEINFO, except you do not have to supply extra fields but center_name, trace_name and submission_type=WITHDRAW

submission_type = WITHDRAW
center_name     = CENTER NAME ACRONYM IS HERE
trace_name	
my_trace1
my_trace2
my_trace2
   ...

Tracking Submissions

When a submission is loaded a log file is generated. This log file contains the ti and read name for passed reads and a list of the reads that were rejected.

If more than 5% of the reads from a particular submission fail, the entire submission will be rejected.

A tracking system has been implemented that will allow the tracking of individual submissions. Each FTP submission is given a unique tracking identifier (SID). Submissions can be tracked by name, SID, date or status. The submitting center will be notified via ftp when a submission has been processed.

After each submission has been processed log files documenting the load are placed on the FTP site.

There is an ability to track the submissions with query_tracedb Perl script. The output is in XML format.

Examples:

$ query_tracedb "track name='NISC_mkp_2006-09-22.tar.gz'"
$ query_tracedb "track sid=174661"
$ query_tracedb "track name in ('NISC_mkp_2006-09-22.tar.gz', 'NISC_jyp_2006-09-22.tar.gz')"
$ query_tracedb "track sid in (174661, 174657)"

If submission does not completely comply to the RFC it will be either rejected or a warning will be sent.

Some ancillary fields are mutually exclusive or not required for a particular type of submission. Please do not include redundant fields into the submission; it can be rejected because of this. For example, if no chromosome information is available for a read, the CHROMOSOME field should not be included.

If a read fails the reason of it failure will be documented in the log file. For example it can fail for the following reasons:

• Information in the ancillary information file, but no trace file
• Zero length trace file
• Number of bases does not match the number of quality values
• There is a trace file but no ancillary information
• If the SUBMISSION_TYPE field has the value 'NEW' but the values in the CENTER_NAME and TRACE_NAME fields are already in the database, the read will be rejected.
• If the same read name is found more than one time in the tar file all reads with that name are failed.