Trace Archive RFC v.2.4…

                                               Trace Archive RFC v.2.4
                                                             7/22/2008
Preface
This is a revised version of the original Trace Archive RFC. The purpose of this
document is to specify a means of exchange of traces and their ancillary data. In the
four years that have elapsed since the Trace Archive was originally developed, the
scope and uses of the data have evolved. Revisions have been made this document will
clarify, and in some instances change, the contents that are to be submitted in specific
fields. To accommodate new data sources, additional fields need to be added and
specified. In addition, required data for specific trace types will be clarified. This
proposal covers:
· Goals
· Ancillary Information
· Submission Information
The biggest changes involve:
The addition of new fields to accommodate environmental sample data
· These additional fields allow the storage of experimental data related to the field. This
  is especially important as these sets of data do not fit into our normal taxonomic
  classification of traces.
Modification of the description of the STRATEGY and TRACE_TYPE_CODE fields
· Currently, STRATEGY and TRACE_TYPE_CODE fields are largely redundant. The
  proposal involves changing the description of the STRATEGY field to reflect the
  experimental strategy (rather than the sequencing strategy) used to produce a trace.
  This should not only better reflect the data, but also make retrieval of large sets of
  data easier.
Changing the SUBSPECIES_ID field to STRAIN field
· Most of the data in SUBSPECIES_ID field was actually related to STRAIN or cultivar
  information, so it makes some degree of sense to change the name of this field.
  Subspecies information can be related in the SPECIES_CODE field.
Addition of new requirements
· Currently, it is quite difficult to use certain data sets because there is not enough
  ancillary data associated with the trace. Initially, the trace archive had few restrictions
  because not every field is applicable to every TRACE_TYPE_CODE and STRATEGY
  combination. There is no change to the fields that are required for all submissions, but
  there now are fields that are required for specific combinations of STRATEGY and
  TRACE_TYPE_CODE. You may check requirements in the Validation Table
Accommodation of new sequencing technologies and data types
· As sequencing technology emerges, standard dideoxy sequencing is being
  supplemented with other sequencing technologies such as chip based resequencing
  technologies as well as synthesis based technologies like the 454 Life Sciences
  technology. We will also be accepting other data types, such as AFLP mapping data.
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  In order to accept these data we are adding new fields, and in some cases additional
  files, in order to fully capture the raw information

Goals
The original goal of the Trace Archive was largely related to data storage. However,
over the last three years, the scope of the Trace Archive has grown substantially. The
current goals of the Trace Archive are:
Archival data storage of sequence traces:
· Database storage
Easy retrieval of individual traces and groups of traces:
· Retrieval based on specific ancillary information
· Retrieval based on sequence comparison
The NCBI and Ensembl are collaborating to store all of the traces. There is an ongoing
effort to keep the two sites synchronized with respect to trace content.

Ancillary Information
For the Trace Archive to be a useful resource, the archive must contain information
describing the traces. Different sequencing centers have different naming schemes that
are not mutually exclusive and it is likely that the schemes can change over time. While
the name of the trace conveys some information, it is not sufficient for fully describing
the data. Sequencing centers generally use the trace name as a unique key within their
databases. The Trace Archive will use a combination of the center name and trace
name as a unique key. In addition, every trace will be assigned a unique trace identifier.
The trace identifier will be an integer value and can also function as a unique key. When
the actual trace for a particular record is updated, the current TI will be replaced by a
new TI. A change in TI will not occur for an update of ancillary information only. The
ancillary data information should be contained in a separate file. This file can be a tab
delimited text file or it can use XML format. The format of the TRACEINFO file is
described in the Submission Information.
The list of ancillary data fields are described below.

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.

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.




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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.


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.


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.


Name: EXTENDED_DATA
Type: varchar()
Example:
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  tags is not
limited we are going to limit the total size of the block to 2 KB.


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.


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 (
trace@ncbi.nlm.nih.gov ) to determine a name that all members of the project agree on.


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



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other common identifier. Gene names not in Entrez Gene can be used (for instance, Ensembl
genes).


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.


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.


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.


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.


Name: CENTER_NAME
Type: varchar(50)
Example: WUGSC
Sequencing centers wishing to submit data must contact the Trace Archive administrators (
trace@ncbi.nlm.nih.gov ) 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


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.


Name: CHEMISTRY


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Type: varchar(50)
Example: BIGDYEV3.0

Name: CHEMISTRY_TYPE
Type: char(50)
Example: P
The CHEMISTRY_TYPE uses a controlled list. Accepted values are:
Primer
Terminator
p=primer
t=terminator


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.


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.


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.


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.


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



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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.


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


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


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


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.


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



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understood that many sequencing centers sequence clones from libraries they did not prepare.


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.


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.


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


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".


Name: FEATURE_ID_FILE_NAME
Type: varchar(200)
Example:
This field is required when TRACE_TYPE_CODE="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".


Name: FEATURE_SIGNAL_FILE_NAME
Type: varchar(200)
Example:
This field is required when TRACE_TYPE_CODE="CHIP".


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.



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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.


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


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


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


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'.


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.



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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


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.


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


Name: ATTEMPT
Type: tinyint(1-255)
Example: 2

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


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.


Name: LONGITUDE
Type: float
Example: -86.403


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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


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


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.


Name: PEAK_FILE
Type: varchar(200)
Example: ./mytraces/123clone.peak
Consult the BASE_FILE field description for more information.


Name: PH
Type: float
Example: 7.2
The PH field is only applicable to environmental sample data but is not a required field.


Name: PICK_GROUP_ID
Type: int
Example: 939065

Name: PLACE_NAME
Type: varchar(250)
Example: Octopus Springs
The PLACE_NAME field is applicable to environmental sample data, but is not required.


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



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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'.


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).


Name: PREP_GROUP_ID
Type: varchar(30)
Example: A2

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.


Name: PRIMER_CODE
Type: varchar(30)
Example: Sp6

Name: PRIMER_LIST
Type: varchar(100)
Example: AAGGTCTGCGCGTGTC;AGCTGCGTACGTAATCG;
This field is required if Strategy ="AFLP" and TRACE_TYPE_CODE ="PCR".


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


Name: QUAL_FILE
Type: varchar(200)
Example: ./mytraces/123clone.fasta.qs
See note associated with the BASE_FILE field.


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



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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


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


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


Name: RUN_DATE
Type: datetime
Example: 2000-10-28

Name: RUN_GROUP_ID
Type: varchar(30)
Example: group2

Name: RUN_LANE
Type: int
Example: 1
The RUN_LANE documents the specific lane or capillary on which a trace was obtained.


Name: RUN_MACHINE_ID
Type: varchar(30)
Example: machine2

Name: RUN_MACHINE_TYPE
Type: varchar(30)
Example: ABI 310

Name: SALINITY
Type: float
Example: 20#
The SALINITY field is only applicable to environmental sample data but is not a required field.



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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


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


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 (trace@ncbi.nlm.nih.gov) 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.


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



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· 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: traces obtained to verify proposed gene models
· PoolClone: Pools of clones (BACs mostly)
· SNP: Reads used for SNP identification
· 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


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


Name: STRAIN
Type: varchar(50)
Example: C57BL/6J
Strain is required for Strategy = "SNP"


Name: SVECTOR_ACCESSION
Type: varchar(50)
Example: X52325

Name: SVECTOR_CODE
Type: varchar(50)
Example: pBluescript SK(+)

Name: TEMPERATURE
Type: float
Example: 30


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


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.


Name: TRACE_END
Type: varchar(50)
Example: F
The TRACE_END field can have the following values:
· F: FORWARD
· R: REVERSE
· N: UNKNOWN


Name: TRACE_FILE
Type: varchar(200)?
Example: ./traces/TRACE001.scf

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.


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.


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



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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


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


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


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).




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Standard 96 well microtiter configuration




Standard 384 well microtiter configuration


Internal Fields
Fields automatically assigned for each record as it is uploaded. Part of these fields is
available to the user either following the submitter provided ancillary information on the
webpage, or in the  block in the xml_info retrieval section.

Name: TI
Type: int
Example: 304753779
It is given for a record at the loading stage, and any record, or number of records can be obtain by
their identifiers. These numbers can be used to query the database, either in a list
"1,2,3,7,100003", through specifying a range "1-10" or in a combination of both "1,2, 5-10".


Name: BASES_20
Type: smallint


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Example: 50
These fields can be used in a query to limit retrieve for the quality traces only.
Example of query:
center_name = 'ABC' and BASES_20 > 100
Warning: There are some depositions that don't have quality scores. This is likely due to the
center submitting ABI files and not providing quality calls separately.


Name: BASES_40
Type: smallint
Example: 50
These fields can be used in a query to limit retrieve for the quality traces only.
Example of query:
center_name = 'BCM' and BASES_40 > 70
Warning: There are some depositions that don't have quality scores. This is likely due to the
center submitting ABI files and not providing quality calls separately.


Name: BASES_60
Type: smallint
Example: 50
These fields can be used in a query to limit retrieve for the quality traces only.
Example of query:
center_name = 'WIBR' and BASES_60 > 50
Warning: There are some depositions that don't have quality scores. This is likely due to the
center submitting ABI files and not providing quality calls separately.


Name: LOAD_DATE
Type: smalldatetime
Example: Jan 8 2001 11:59AM
This field helps to specify retrieve data by date.
Example of query:
species_code='MUS MUSCULUS' and load_date >= '12/11/2005'


Name: STATE
Type: varchar
Example: active
Possible values:
· active
· updated
· withdrawn


Name: REPLACED_BY
Type: int
Example: 304753779
This field points to the more recent data set. If trace was updated then the REPLACED_BY field
stores the TI for the new trace. If only ancillary information has been updated, then replaced_by=0
and is not shown.


Name: UPDATE_DATE
Type: smalldatetime
Example: Jul 19 2001 3:48PM
This field is used to store the date of the last update.


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Name: MATE_PAIR
Type: int
Example: 203682255
MATE PAIR is the pair of reads obtained from two ends of the same template (FORWARD and
REVERSE).


Name: TAXID
Type: int
Example: 10090
This field links Trace Archive with NCBI Taxonomy Browser.


Name: BASECALL_LENGTH
Type: int
Example: 396

Obsolete fields
Name: ASSEMBLY_ID
Type: varchar(50)
Example: NCBI Build 33
Please use REFERENCE_ACCESSION and REFERENCE_OFFSET


Name: CHROMOSOME_REGION
Type: varchar(50)
Example: 2:105000-106000
Please use REFERENCE_ACCESSION and REFERENCE_OFFSET.


Name: SUBSPECIES_ID
Type: varchar(50)
Example: Verus
Please use STRAIN and SPECIES_CODE. Subspecies information should be incorporated into the
SPECIES_CODE field.


Name: TRACE_DIRECTION
Type: varchar(50)
Example: FORWARD
Please use TRACE_END instead.


Submission Information
The submitting data should be placed on a provided by NCBI secure FTP site
(ftp-trace.ncbi.nih.gov). Contact trace@ncbi.nlm.nih.gov to obtain a secure FTP
account. Please have a contact information as well as a full center's name and the
center's acronym provided with the request.
All submissions made to NCBI via ftp are automatically picked up by Ensembl.
(http://trace.ensembl.org)
Submissions made to Ensembl are placed on NCBI FTP site to pick up and load.
Each submission is a single file in UNIX USTAR format compressed with "gzip" utility. It
is suggested to have the size of the submission file between 1 and 4 GB. It also is


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suggested to use unique names for the submissions and include the center's name and
the date into its name.
All submissions when extracted should have a top directory. The top directory may be
named similar to the submission's file. All ancillary files should be placed under that
directory. In case when the submission should contain trace files at least one more
directory should be introduced to the top directory and all trace files should be placed
under that directory.
Below is what should be placed under the top directory.
· TRACEINFO.xml or TRACEINFO.txt: either one must be present. This is the main file
   describing the submission. It contains ancillary data and references to trace files if
   necessary. It can be either in XML or tab delimited format.
· MD5: md5 hashes, suggested to be present.
· README: free text describing this volume and preparation.
Below are examples of the submission directory hierarchy and examples of
TRACEINFO ancillary files.
The trace files should not appear in the top level directory, but rather should be in a
subdirectory. It is suggested to use the name of the traces or the name of the project for
subdirectories. There may be subdirectories within and this is encouraged to group
traces.

NEW and UPDATE submissions
NEW and UPDATE submissions should have the structure shown below:


TOP_DIRECTORY/
TOP_DIRECTORY/TRACEINFO.txt
TOP_DIRECTORY/MD5
TOP_DIRECTORY/README
TOP_DIRECTORY/traces
TOP_DIRECTORY/traces/HBBA/
TOP_DIRECTORY/traces/HBBA/HBBAA1U0001.scf
TOP_DIRECTORY/traces/HBBA/HBBAA1U0002.scf
TOP_DIRECTORY/traces/HBBA/HBBAA1U0003.scf
...

Examples are available for download:
ftp://ftp.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.
TRACEINFO.xml example
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.


   
      CENTER NAME ACRONYM IS HERE
      NEW
      WGS
      WGS
      Gorilla WGS


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      G
      Gorilla gorilla
      1500
   
   
      HBBAA1U0001
      HBBAA1U0001
      traces/HBBA/HBBAA1U0001.scf
      scf
      R
      56
      737
      legrenzi
      BIGDYEV2
      phred version=0.020425.c
      ABI 3700
   
   
      HBBAA1U0002
      HBBAA1U0002
        ...more info...
    



TRACEINFO.txt example
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 ...
    ...
MD5 example
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


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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.
TRACEINFO.xml example
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.


    
        CENTER NAME ACRONYM IS HERE
        UPDATEINFO
        WGS
        40000
    
    
        HBBA0001
        template_id_HBBA0001
        ...more info...
    
    
        HBBA0002
        template_id_HBBA0002
        ...more info...
    


TRACEINFO.txt example
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...
MD5 example
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


TRACEINFO.txt example
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



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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.




NIH/NLM/NCBI                                                                    Page 23 of 23