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Revision as of 10:18, 8 May 2012 by Jessica Severin (talk | contribs) (Experiment metadata)
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Basic structure

  • A simple tabdelimited text file.
  • Column order is flexible
  • Lines starting with '#' are comments.
  • Lines starting with '##' are attributes or metadata of the table. (See 'Metadata' section below)
  • The first line after the comments/metadata (see below) is a header line, which indicate column names of the table.
  • All the comment and attribute lines should appear above the header line
  • The first column should describe a 'key' (unique in many cases, but not necessarily) of the data, and the column name should be 'id'
  • If a cell needs to include multiple values, comma(',') is recommended to be used as a separator.
  • All the columns should be described in Metadata (See 'Metadata' section below)

Metadata ('##' lines)

The basic structure is '##qualifier = value'.
Required metadata: FileFormat, Date, ProtocolREF, ColumnVariable, ContactName, ContactEmail

'genome_assembly' for parameter value is required, when using


Required (mandatory) metadata


describes file format of this file.

##FileFormat = OSCtable1.1


describes the date when the data file is generated

##Date = 20090602


describes the protocol used to generate the data file.

##ProtocolREF = CAGEmappingv1.0


describes ALL the columns used in the data file

##ColumnVariable[start] = this is a start position of the genomic coordinate
##ColumnVariable[end] = this is a stop position of the genomic coordinate
##ColumnVariable[norm.THP10h] = this is TPM normalized value with 10h
##ColumnVariable[entrez_gene_id] = Entrez gene ID, which is assigned to the cluster


describes the contact name about the data file.

##ContactName = Hideya Kawaji


describes the contact address about the data file

##ContactEmai = kawaji@gsc.riken.jp

Optional metadata


describes the file(s) used to generate the data file

##InputFile = lane1.fa
##InputFile = lane2.fa


describes the parameter(s) used to generate the data file in the protocol
the parameter(s) should be consistent with the protocol description

##ParameterValue[alignment_program] = BWA
##ParamterValue[aligment_program_version] = 1.3.5
##ParameterValue[UCSC_gene_tracks] = RefSeq
##ParameterValue[UCSC_gene_tracks] = ENSEMBL transcript


describes the name space for the column names. See below (NameSpace)


Column Name Spaces

  • A set of column names (and parameters) to be used for a specific purpose or context.
  • The same column names with the same name space are recognized as the same (equivalent) meaning.
  • Supported name space: genomic_coordinate, expression


  • column names are: chrom, start.0base, start.1base, end, strand
  • parameter value: genome_assembly
    • chrom: chromosome name used in the genome assembly. For example, chr1, chr2, chr3, ... chrM for the UCSC hg18 genome assembly.
    • start.0base: start position (bp) on the chromosome in 0start coordinate system (BED, PSL, BLAT, exonerate, and nexAlign style)
    • start.1base: start position (bp) on the chromosome in 1start coordinate system (conventional coordinate system; adopted in GFF as well)
    • end: end position (bp) on the chromosome
    • strand: strand on the chromosome; optional
    • Note:
      • All of the above columns are not necessarily required. For example, start.0base would not be required if you have start.1base, and strand would not be required if the annotation do not have strand distinction
      • 'genome_assembly' for parameter value is required.


generic expression tags
  • column names are: raw.ZZZ, norm.ZZZ, or exp.YYY.ZZZ
    • raw.ZZZ : for raw value of expression such as raw_counts and raw signal intensities.
    • norm.ZZZ : for normalized value.
    • ZZZ indicates the experiment (cell conditions, RNAs, etc) of the expressions
    • YYY should not include dot (.), and indicates the type of expression.
'mapcount' tag

To specify that alignments may be be mapped on more than one location, you can either use...

ZENBU interpretation of OSCtable files

OSCtable is one of the main interchange formats for ZENBU. It allows all possible mapping of data into the ZENBU data model. Since the OSCtable specification is highly flexible, it was possible for the ZENBU OSCtable parser to have an extended vocabulary of metadata directives and column name spaces. In addition, the ZENBU OSCtable parser is able to parse both tab-separated and space-separated files.


While the official OSCtable specification include mandatory metadata elements, the ZENBU OSCtable parser relaxes this requirement. All ## metadata lines are parsed as optional metadata. Even ##ColumnVariable[] directives are consider as optional metadata. The only requirement for a valid OSCtable for ZENBU is the column header line.

Experiment metadata

The original OSCtable specification works very well with single experiment data files, but does not provide enough fine control of assigning metadata in a multi-experiment data file. To alleviate this, ZENBU added an additional metadata directive to the OSCtable specification

  • ##ExperimentMetadata[experiment-name][key] = value

experiment-name is the same as the ZZZ in the expression column header descriptions. By referencing to the experiment-name it is possible to have the same experiment used in multiple columns with different datatypes.

Example (please note that the text is wrapped)

##ParameterValue[filetype] = osc
##ParameterValue[genome] = mm9
##ColumnVariable[eedb:chrom] = chromosome name
##ColumnVariable[eedb:start.0base] = chromosome start in 0base coordinate system
##ColumnVariable[eedb:end] = chromosome end
##ColumnVariable[eedb:strand] = chromosome strand
##ColumnVariable[eedb:score] = score or significance of the feature
##ColumnVariable[exp.tagcount.Mouse_Embryoid_Body_RNAseq_exonic] = tagcount Mouse_Embryoid_Body_RNAseq_exonic
##ExperimentMetadata[Mouse_Embryoid_Body_RNAseq_exonic][eedb:display_name] = Mouse_Embryoid_Body_RNAseq_exonic
##ExperimentMetadata[Mouse_Embryoid_Body_RNAseq_exonic][eedb:platform] = SQRL_RNAseq
##ExperimentMetadata[Mouse_Embryoid_Body_RNAseq_exonic][description] = This is the exon junction signal for RNAseq of Mouse Embryoid body cells after 4 days of differentiation to the 'primitive streak stage' (see PMID:17286599 , and should contain expression of brachyury, mixl1, tbx6, and flk1) carried out at the IMB on Applied Biosystems SOLiD system (PMID: 18516046). Mouse strain: SV129. Mapping: published version.
##ExperimentMetadata[Mouse_Embryoid_Body_RNAseq_exonic][strain] = SV129
##ExperimentMetadata[Mouse_Embryoid_Body_RNAseq_exonic][tissue] = Mouse Embryoid body
##ColumnVariable[exp.tagcount.Mouse_Embryonic_Stem_Cell_RNAseq_exonic_signal] = tagcount Mouse_Embryonic_Stem_Cell_RNAseq_exonic_signal
##ExperimentMetadata[Mouse_Embryonic_Stem_Cell_RNAseq_exonic_signal][eedb:display_name] = Mouse_Embryonic_Stem_Cell_RNAseq_exonic_signal
##ExperimentMetadata[Mouse_Embryonic_Stem_Cell_RNAseq_exonic_signal][eedb:platform] = SQRL_RNAseq
##ExperimentMetadata[Mouse_Embryonic_Stem_Cell_RNAseq_exonic_signal][description] = Description: This is the exonic signal for RNAseq of Mouse Embryonic Stem Cells carried out at the IMB on Applied Biosystems SOLiD system (PMID: 18516046). Mouse strain: SV129. Mapping: published version
##ExperimentMetadata[Mouse_Embryonic_Stem_Cell_RNAseq_exonic_signal][strain] = SV129
##ExperimentMetadata[Mouse_Embryonic_Stem_Cell_RNAseq_exonic_signal][tissue] = Mouse Embryonic Stem Cells
eedb:chrom	eedb:start.0base	eedb:end	eedb:name	eedb:score	eedb:strand	exp.tagcount.Mouse_Embryoid_Body_RNAseq_exonic	exp.tagcount.Mouse_Embryonic_Stem_Cell_RNAseq_exonic_signal	exp.tpm.Mouse_Embryoid_Body_RNAseq_exonic	exp.tpm.Mouse_Embryonic_Stem_Cell_RNAseq_exonic_signal
chr7	52253690	52253691	block_chr7:52253691..52253691+	186.00	+	84.00	102.00	8.40	10.20
chr7	52253691	52253692	block_chr7:52253692..52253692+	184.00	+	83.00	101.00	8.30	10.10
chr7	52253692	52253693	block_chr7:52253693..52253693+	185.00	+	83.00	102.00	8.30	10.20
chr7	52253693	52253694	block_chr7:52253694..52253694+	180.00	+	81.00	99.00	8.10	9.90
chr7	52253694	52253695	block_chr7:52253695..52253695+	174.00	+	77.00	97.00	7.70	9.70

Column name spaces

This section is in reference to the names of columns in the header line.

official OSCtable column names

The official OSCtable specification has very few predefined column names

  • chrom -- chromosome name
  • start.0base -- chromosome start in a 0base coordinate system
  • start.1base -- chromosome start in a 1base coordinate system
  • end -- chromosome end location
  • strand -- chromosome strand
  • ID -- interpreted as the name of the Feature

While ZENBU uses a 1-based-inclusive coordinate space internally, it can automatically handle the conversion between coordinate spaces at load time.

ZENBU additional column namespaces

  • eedb:name -- the name of the Feature
  • eedb:score -- is stored in the Feature significance.
  • bed::blockCount, bed::blockSizes, bed::blockStarts -- are taken from the BED file specification. These three columns work together and are interpreted into SubFeatures on the primary Feature. Each of these SubFeatures are created with a FeatureSource category of block.
  • bed:thickStart and bed::thickEnd -- are taken from the BED file specification.
    • if bed::thickStart is not equal to start then the region from start to bed:thickStart is interpreted into a SubFeature of category 5utr
    • if bed:thickEnd is not equal to end then the region from bed:thickEnd to end is interpreted into a SubFeature of category 3utr

Aliased column names

Several column names have aliases to other column name spaces

  • name -- same as eedb:name
  • score -- same as eedb:score
  • eedb::chrom -- same as chrom
  • eedb:start.0base -- same as start.0base
  • eedb:start.1base -- same as start.1base
  • eedb:end -- same as end'
  • eedb:strand -- same as strand

ignoring columns

The OSCtable allows for easy wrapping of any tab-texted file into an OSCtable by simply pre-pending a header with the appropriate column names. But sometimes these original files contain columns which one might not really need. To simplify the process of loading, ZENBU added a special column-name

  • ignore.xxxx -- ignore this column, where xxxx would be the original column name

If a column is labeled as such, on loading this column will be stripped from the data file and thrown away. This can simplify the process for bioinformatician and avoid un-needed data-scripting to munge data prior to loading.

feature metadata columns

Any column with an unknown name is mapped into the Metadata of the Feature. The column name becomes the key of the metadata.

Wrapping external file formats with OSCtable headers

With the extended vocabulary of the ZENBU OSCtable parser, it is possible to wrap external file formats very easily with an OSCtable header and load them into ZENBU. In fact the ZENBU upload support for BED, SAM, GTF and GFF are done through wrapping predefined OSCtable column headers onto these files.

BED oscheader

Here is the column header line to wrap a BED file

eedb:chrom	eedb:start.0base	eedb:end	eedb:name	eedb:score	eedb:strand