XGAP TAB format reference

This document describes what columns will be parsed by the xgap CsvImport and CsvExport programs, as well as the upload options in the user interface. Note that next to the files below, data matrix files and contant.properties files are also parsed. See XgapFormatTutorial.

xgap.core package

Core entities.

investigation.txt file

The file investigation.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
start	datetime	The start point of the investigation. (n.b. removed null constraint)
end	datetime	The end point of the investigation. (n.b. removed null constraint)

Note that values in column id should unique.
Note that values in column name should unique.

protocolapplication.txt file

The file protocolapplication.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
activitydate	datetime	Y	When the protocol was applied.
protocol_name	xref	Y	Reference to a value in column 'name' in protocol.txt.
status	enum	Y	The status of this protocolapplication (inprocess = still working on it, final = ready for further analysis).
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
inputdata_name	mref	Reference to a value in column 'name' in data.txt. Multiple references can be added separated by '|'.
protocoldeviation_id	xref	Reference to a value in column 'id' in description.txt.
outputmaterials_name	mref	Reference to a value in column 'name' in material.txt. Multiple references can be added separated by '|'.
outputdata_name	mref	Reference to a value in column 'name' in data.txt. Multiple references can be added separated by '|'.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

data.txt file

Generic structure for describing data matrices such as genotype result, gene expression measurement, QTL calculation, etc. The file data.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
rowtype	enum	Y	Type of the columns of this matrix. Each column refers to a Trait or Subject (DimensionElement).
coltype	enum	Y	Type of the rows of this matrix. Each row refers to a Trait or Subject (DimensionElement)
valuetype	enum	Y	Type of the values of this matrix. E.g. text strings or decimal numbers.
totalrows	int	Y	TotalRows
totalcols	int	Y	TotalCols
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

dimensionelement.txt file

Describes the biological material or subject which is being 'measured' by an Data set.
For example an 'Sample' extends from Item, which makes it possible that a microarray-assay Data set such sample (as DataElement can reference any Item).
An DimensionElement is always linked to a single one Investigation. The file dimensionelement.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

decimaldataelement.txt file

A DataElement for storing decimal data. The file decimaldataelement.txt can have the following fields:

column name	type	required?	description
data_name	xref	Y	Reference to a value in column 'name' in data.txt.
col_name	xref	Y	Reference to a value in column 'name' in dimensionelement.txt.
row_name	xref	Y	Reference to a value in column 'name' in dimensionelement.txt.
rowindex	int	Y	Row position in the matrix.
colindex	int	Y	Col position in the matrix.
id	int	automatically generated id-field
value	decimal	The value, e.g., correlation.

Note that values in column id should unique.
Note that values in the combined columns (colindex, rowindex, data) should be unique.
Note that values in the combined columns (rowindex, colindex, data) should be unique.

textdataelement.txt file

Store text data The file textdataelement.txt can have the following fields:

column name	type	required?	description
data_name	xref	Y	Reference to a value in column 'name' in data.txt.
col_name	xref	Y	Reference to a value in column 'name' in dimensionelement.txt.
row_name	xref	Y	Reference to a value in column 'name' in dimensionelement.txt.
rowindex	int	Y	Row position in the matrix.
colindex	int	Y	Col position in the matrix.
id	int	automatically generated id-field
value	text	The value, e.g., genotype strings like AA, BA, BB.

Note that values in column id should unique.
Note that values in the combined columns (colindex, rowindex, data) should be unique.
Note that values in the combined columns (rowindex, colindex, data) should be unique.

xgap.subject package

Subject variants.

species.txt file

The file species.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
term	string	Y	The ontology term itself, also known as the local name in some ontologies.
termaccession	string	Y	The accession number assigned to the ontology term in the source ontology. If there is no explicit accession assigned, then the term (localname) must be repeated (i.e. the term is the unique accession).
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
ontologysource_name	xref	Reference to a value in column 'name' in ontologysource.txt.
termpath	string	EXTENSION. The Ontology Lookup Service path that contains this term.
termcategory_name	xref	Reference to a value in column 'name' in category.txt.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

datatype.txt file

The file datatype.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
term	string	Y	The ontology term itself, also known as the local name in some ontologies.
termaccession	string	Y	The accession number assigned to the ontology term in the source ontology. If there is no explicit accession assigned, then the term (localname) must be repeated (i.e. the term is the unique accession).
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
ontologysource_name	xref	Reference to a value in column 'name' in ontologysource.txt.
termpath	string	EXTENSION. The Ontology Lookup Service path that contains this term.
termcategory_name	xref	Reference to a value in column 'name' in category.txt.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

tissue.txt file

The file tissue.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
term	string	Y	The ontology term itself, also known as the local name in some ontologies.
termaccession	string	Y	The accession number assigned to the ontology term in the source ontology. If there is no explicit accession assigned, then the term (localname) must be repeated (i.e. the term is the unique accession).
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
ontologysource_name	xref	Reference to a value in column 'name' in ontologysource.txt.
termpath	string	EXTENSION. The Ontology Lookup Service path that contains this term.
termcategory_name	xref	Reference to a value in column 'name' in category.txt.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

samplelabel.txt file

The file samplelabel.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
term	string	Y	The ontology term itself, also known as the local name in some ontologies.
termaccession	string	Y	The accession number assigned to the ontology term in the source ontology. If there is no explicit accession assigned, then the term (localname) must be repeated (i.e. the term is the unique accession).
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
ontologysource_name	xref	Reference to a value in column 'name' in ontologysource.txt.
termpath	string	EXTENSION. The Ontology Lookup Service path that contains this term.
termcategory_name	xref	Reference to a value in column 'name' in category.txt.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

subject.txt file

The file subject.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
species_name	xref	Reference to a value in column 'name' in species.txt.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

strain.txt file

A variant or subtype of animal, plant, virus or bacteria. The file strain.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
straintype	enum	Y	Indicate the type of Strain (Natural=wild type, Parental=parents of a cross, F1=First generation of cross, RCC=Recombinant congenic, CSS=chromosome substitution)
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
species_name	xref	Reference to a value in column 'name' in species.txt.
founderstrains_name	mref	Reference to a value in column 'name' in strain.txt. Multiple references can be added separated by '|'.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

individual.txt file

Biological individuals. The file individual.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
species_name	xref	Reference to a value in column 'name' in species.txt.
strain_name	xref	Reference to a value in column 'name' in strain.txt.
mother_name	xref	Reference to a value in column 'name' in individual.txt.
father_name	xref	Reference to a value in column 'name' in individual.txt.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

sample.txt file

The file sample.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
species_name	xref	Reference to a value in column 'name' in species.txt.
individual_name	xref	Reference to a value in column 'name' in individual.txt.
tissue_name	xref	Reference to a value in column 'name' in tissue.txt.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

pairedsample.txt file

A pair of samples labeled for a two-color microarray experiment. The file pairedsample.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
subject1_name	xref	Y	Reference to a value in column 'name' in individual.txt.
subject2_name	xref	Y	Reference to a value in column 'name' in individual.txt.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
species_name	xref	Reference to a value in column 'name' in species.txt.
label1_name	xref	Reference to a value in column 'name' in samplelabel.txt.
label2_name	xref	Reference to a value in column 'name' in samplelabel.txt.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

xgap.trait package

Trait variants.

measurementunit.txt file

The file measurementunit.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
term	string	Y	The ontology term itself, also known as the local name in some ontologies.
termaccession	string	Y	The accession number assigned to the ontology term in the source ontology. If there is no explicit accession assigned, then the term (localname) must be repeated (i.e. the term is the unique accession).
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
ontologysource_name	xref	Reference to a value in column 'name' in ontologysource.txt.
termpath	string	EXTENSION. The Ontology Lookup Service path that contains this term.
termcategory_name	xref	Reference to a value in column 'name' in category.txt.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

trait.txt file

Traits that are being measured. Traits can be very diverse. The specifics of these traits can be added, as for example in a "Gene" (Gene extends Trait). The file trait.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

nmrbin.txt file

Shift of the NMR frequency due to the chemical environment. The file nmrbin.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

clone.txt file

BAC clone fragment. The file clone.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
chr	string	chromosome name or number string (1, 2, .., x, y)
species_name	xref	Reference to a value in column 'name' in species.txt.
cm	decimal	genetic map position in centi morgan (cM).
bpstart	long	numeric basepair postion (5') on the chromosome
bpend	long	numeric basepair postion (3') on the chromosome
seq	text	The FASTA text representation of the sequence.
symbol	text	todo
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

derived.txt file

Any meta trait, eg. false discovery rates, P-values, thresholds. The file derived.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

factor.txt file

Experimental conditions, such as temperature differences, batch effects etc. The file factor.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

gene.txt file

Trait annotations specific for genes. The file gene.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
chr	string	chromosome name or number string (1, 2, .., x, y)
species_name	xref	Reference to a value in column 'name' in species.txt.
cm	decimal	genetic map position in centi morgan (cM).
bpstart	long	numeric basepair postion (5') on the chromosome
bpend	long	numeric basepair postion (3') on the chromosome
seq	text	The FASTA text representation of the sequence.
symbol	string	Main symbol this gene is known by (not necessarily unique, in constrast to 'name')
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
aliases	string	Alternative symbols this gene is known by, separated by ','
orientation	enum	Orientation of the gene on the genome (F=forward, R=reverse)
control	bool	Indicating whether this is a 'housekeeping' gene that can be used as control.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

protein.txt file

Trait annotations specific for proteins. The file protein.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
gene_name	xref	Reference to a value in column 'name' in gene.txt.
sequence	text	The aminoacid sequence.
mass	decimal	The mass of this metabolite

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

metabolite.txt file

Trait annotations specific for metabolites. The file metabolite.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
formula	string	The chemical formula of a metabolite.
mass	decimal	The mass of this metabolite
structure	text	The chemical structure of a metabolite (in SMILES representation).

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

phenotype.txt file

Trait annotations specific for classical phenotypes. The file phenotype.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
category	string	Category
description	string	Description
molecule	string	Molecule

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

protocolelement.txt file

Quantitative treats that are part of a protocol. E.g. microarray probes, marker set. The file protocolelement.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
protocol_name	xref	Reference to a value in column 'name' in protocol.txt.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

marker.txt file

Trait annotations specific for markers. The file marker.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
chr	string	chromosome name or number string (1, 2, .., x, y)
species_name	xref	Reference to a value in column 'name' in species.txt.
cm	decimal	genetic map position in centi morgan (cM).
bpstart	long	numeric basepair postion (5') on the chromosome
bpend	long	numeric basepair postion (3') on the chromosome
seq	text	The FASTA text representation of the sequence.
symbol	text	todo
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
protocol_name	xref	Reference to a value in column 'name' in protocol.txt.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

probe.txt file

A piece of sequence that reports for the expression of a gene, typically spotted onto a microarray. The file probe.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
mismatch	bool	Y	Indicating whether the probe is a match
chr	string	chromosome name or number string (1, 2, .., x, y)
species_name	xref	Reference to a value in column 'name' in species.txt.
cm	decimal	genetic map position in centi morgan (cM).
bpstart	long	numeric basepair postion (5') on the chromosome
bpend	long	numeric basepair postion (3') on the chromosome
seq	text	The FASTA text representation of the sequence.
symbol	text	todo
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
protocol_name	xref	Reference to a value in column 'name' in protocol.txt.
probeset_name	xref	Reference to a value in column 'name' in probeset.txt.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

spot.txt file

This is the spot on a microarray.
Note: We don't distinquish between probes (the sequence) and spots (the sequence as spotted on the array). The file spot.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
mismatch	bool	Y	Indicating whether the probe is a match
x	int	Y	Row
y	int	Y	Column
chr	string	chromosome name or number string (1, 2, .., x, y)
species_name	xref	Reference to a value in column 'name' in species.txt.
cm	decimal	genetic map position in centi morgan (cM).
bpstart	long	numeric basepair postion (5') on the chromosome
bpend	long	numeric basepair postion (3') on the chromosome
seq	text	The FASTA text representation of the sequence.
symbol	text	todo
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
protocol_name	xref	Reference to a value in column 'name' in protocol.txt.
probeset_name	xref	Reference to a value in column 'name' in probeset.txt.
gridx	int	Meta Row
gridy	int	Meta Column

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.
Note that values in the combined columns (protocol, x, y, gridx, gridy) should be unique.

probeset.txt file

A set of Probes. E.g. Affymetrix probeset has multiple probes. The file probeset.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
protocol_name	xref	Reference to a value in column 'name' in protocol.txt.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

masspeak.txt file

A peak that has been selected within a mass spectrometry experiment. The file masspeak.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
annotations_name	mref	Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int	automatically generated id-field
protocol_name	xref	Reference to a value in column 'name' in protocol.txt.
mz	decimal	Mass over charge ratio of this peak.
retentiontime	decimal	The retention-time of this peak in minutes.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

fuge.common package

Common elements inherited from FuGE.

identifiable.txt file

Other classes in the model can be specified as sub-classes, inheriting from Identifiable. Identifiable gives classes a unique identifier within the scope and a name that need not be unique. Identifiable also provides a mechanism for annotating objects with BibliographicReference(s) and DatabaseEntry(s). The file identifiable.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field

Note that values in column id should unique.

describable.txt file

Abstract class that allows subclasses to inherit associations that enable objects to be given a text description, additional annotations as Ontology entries, a URI, associations to Audit for tracking changes, and the association to Security for indicating permissions. The URI, Annotations, PropertySets and Descriptions associations inherited from Describable should only be used to capture additional information where the model contains no other structures that could be used to capture the information. The file describable.txt can have the following fields:

column name	type	required?	description
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field

Note that values in column id should unique.

security.txt file

Permission information for an object as to ownership, write and read permissions. The file security.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field
owners_name	mref		Reference to a value in column 'name' in contact.txt. Multiple references can be added separated by '|'.

Note that values in column id should unique.

ontologyterm.txt file

A single entry from an ontology or a controlled vocabulary. If it is a simple controlled vocabulary, there may be no formal accession for the term. In these cases the local name should be repeated in both term and termAccession. If the term has a value, the OntologyIndividual will have a single DataProperty whose value was the value for the property. For instance, for an OntologyIndividual based on the MO ontology the attributes might be: The term would be what is usually called the local name in the Ontology, for instance 'Age'; The termAccession could be 'http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Age' or a an arbitrary accession if one exists; The identifier is a unique identifier for individuals in the scope of the FuGE instance; The inherited name attribute should not be used; The ontologyURI of OntologySource could be 'http://mged.sourceforge.net/ontologies/MGEDOntology.owl". The OntologyTerm subclasses are instances of Ontology classes and properties, not the actual terms themselves. An OntologyIndividual, if based on an existing Ontology, can be considered a statement that can be validated against the referenced ontology. The subclasses and their associations are based on the Ontology Definition Model, ad/2005-04-13, submitted to the OMG as a response to RFP ad/2003-03-40, Copyright © 2005 DSTC Pty Ltd. Copyright © 2005 IBM Copyright © 2005 Sandpiper Software, Inc under the standard OMG license terms. The file ontologyterm.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
term	string	Y	The ontology term itself, also known as the local name in some ontologies.
termaccession	string	Y	The accession number assigned to the ontology term in the source ontology. If there is no explicit accession assigned, then the term (localname) must be repeated (i.e. the term is the unique accession).
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field
ontologysource_name	xref		Reference to a value in column 'name' in ontologysource.txt.
termpath	string		EXTENSION. The Ontology Lookup Service path that contains this term.
termcategory_name	xref		Reference to a value in column 'name' in category.txt.

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

category.txt file

EXTENSION for ontology plugin. The file category.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field
description	string		description

Note that values in column id should unique.

uri.txt file

A URI is short for Uniform Resource Identifier. A URI is a compact sequence of characters that identifies an abstract or physical resource. The file uri.txt can have the following fields:

column name	type	required?	description
location	hyperlink	Y	The Uniform Resource Indicator for this object.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field

Note that values in column id should unique.

bibliographicreference.txt file

Represents bibliographic references, including the most common attributes. Note that because a BibliographicReference is Identifiable, a DatabaseEntry can also be specified. The file bibliographicreference.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
authors	string	Y	The names of the authors of the reference.
publication	string	Y	The name of the journal, book etc.
publisher	string	Y	The publisher of the publication.
editor	string	Y	The editor(s) of the reference.
year	int	Y	The year of publication.
volume	string	Y	The volume name or number.
issue	string	Y	The issue name or number.
pages	string	Y	The page numbers.
title	string	Y	The title of the BibliographicReference.
investigation_name	xref	Y	Reference to a value in column 'name' in investigation.txt.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field

Note that values in column id should unique.
Note that values in the combined columns (name, investigation) should be unique.

ontologysource.txt file

The source ontology or controlled vocabulary list that ontology terms have been obtained from. The file ontologysource.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
ontologyuri	hyperlink	Y	A URI that references the location of the ontology.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field

Note that values in column id should unique.

contact.txt file

A contact is either a person or an organization. The file contact.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
address	string	Y	The address of the Contact.
phone	string	Y	The telephone number of the Contact including the suitable area codes.
email	string	Y	The email address of the Contact.
fax	string	Y	The fax number of the Contact.
tollfreephone	string	Y	A toll free phone number for the Contact, including suitable area codes.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field

Note that values in column id should unique.

description.txt file

A free text description of an object. The file description.txt can have the following fields:

column name	type	required?	description
text	string	Y	The description.
describable_descriptions_id	xref	Y	Reference to a value in column 'id' in describable.txt.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field

Note that values in column id should unique.

databasereference.txt file

A reference to a record in a database. The file databasereference.txt can have the following fields:

column name	type	required?	description
accession	string	Y	The identifier used to look up the record.
accessionversion	string	Y	The appropriate version of the accession (if applicable).
database_id_id	xref	Y	Reference to a value in column 'id' in databaseaddress.txt.
identifiablereferences_id	xref	Y	Reference to a value in column 'id' in identifiable.txt.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field

Note that values in column id should unique.

databaseaddress.txt file

An address to a repository. The file databaseaddress.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
version	string	Y	The version of the Database.
dburi	hyperlink	Y	The location of the Database.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field

Note that values in column id should unique.

fugeprotocolapplication.txt file

The use of a protocol with the requisite Parameters and ParameterValues. ProtocolApplications can take Material or Data (or both) as input and produce Material or Data (or both) as output. ProtocolApplication is abstract and should be subclassed in the development of modular formats. The subclass GenericProtocolApplication can be used without extension. The file fugeprotocolapplication.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
activitydate	datetime	Y	When the protocol was applied.
protocol_name	xref	Y	Reference to a value in column 'name' in protocol.txt.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field
inputdata_name	mref		Reference to a value in column 'name' in data.txt. Multiple references can be added separated by '|'.
protocoldeviation_id	xref		Reference to a value in column 'id' in description.txt.
outputmaterials_name	mref		Reference to a value in column 'name' in material.txt. Multiple references can be added separated by '|'.
outputdata_name	mref		Reference to a value in column 'name' in data.txt. Multiple references can be added separated by '|'.

Note that values in column id should unique.

parameterizableapplication.txt file

The interface that is the use of a Parameterizable class. The file parameterizableapplication.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field

Note that values in column id should unique.

protocol.txt file

A Protocol is a parameterizable description of a method. ProtocolApplication is used to specify the ParameterValues of its Protocol's Parameters. Protocol should be extended in data formats. For cases where no extension is developed, the subclass of Protocol, GenericProtocol, should be used to capture experimental protocols. The file protocol.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field
types_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
outputtypes_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
inputtypes_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
software_name	mref		Reference to a value in column 'name' in software.txt. Multiple references can be added separated by '|'.
equipment_name	mref		Reference to a value in column 'name' in equipment.txt. Multiple references can be added separated by '|'.

Note that values in column id should unique.

parameterizable.txt file

The Parameterizable interface encapsulates the association of Parameters with ParameterValues. The file parameterizable.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field
types_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.

Note that values in column id should unique.

software.txt file

Software used in the Protocol. Examples of Software include: feature extraction software, clustering software, etc... Software is abstract and should either be extended by subclassing or the GenericSoftware class, a functional version of Software, should be used without extension. The file software.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
version	string	Y	The version of Software used.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field
types_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
equipment_name	mref		Reference to a value in column 'name' in equipment.txt. Multiple references can be added separated by '|'.

Note that values in column id should unique.

equipment.txt file

The equipment (hardware) used in the Protocol. Examples include: computers, scanners, wash stations etc... Equipment is abstract and should either be extended by subclassing or the GenericEquipment class, a functional version of Equipment, should be used. The file equipment.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field
types_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
make_name	xref		Reference to a value in column 'name' in ontologyterm.txt.
equipmentparts_name	mref		Reference to a value in column 'name' in equipment.txt. Multiple references can be added separated by '|'.
software_name	mref		Reference to a value in column 'name' in software.txt. Multiple references can be added separated by '|'.
model_name	xref		Reference to a value in column 'name' in ontologyterm.txt.

Note that values in column id should unique.

fuge.bio package

Bio elements inherited from FuGE.

fugeinvestigation.txt file

An Investigation is a self-contained unit of study that contains one or more types of 'omics technology. The file fugeinvestigation.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field
start	datetime		The start point of the investigation. (n.b. removed null constraint)
end	datetime		The end point of the investigation. (n.b. removed null constraint)

Note that values in column id should unique.

material.txt file

Material represents any kind of substance used in an experimental workflow, such as whole organisms, cells, DNA, solutions, compounds and experimental substances (gels, arrays etc.). The Material class can be extended by adding subclasses to model domain specific properties, or the relationships to OntologyIndividual can be used to describe the characteristics and type of Material. Materials can be related to other materials through a directed acyclic graph (represented by ProtocolApplication(s)). Sub-component materials can be represented by the self-association on Material (e.g. Wells within a array). These associations are abstract and should be extended to represent these semantics for extensions of ProtocolApplication and Material. The file material.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field
components_name	mref		Reference to a value in column 'name' in material.txt. Multiple references can be added separated by '|'.
materialtype_name	xref		Reference to a value in column 'name' in ontologyterm.txt.
characteristics_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
qualitycontrolstatistics_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.

Note that values in column id should unique.

higherlevelanalysis.txt file

A container for domain-specific analyses performed on data. Subclasses must be created for different domains. The file higherlevelanalysis.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field
conclusion_id	xref		Reference to a value in column 'id' in description.txt.
supportingdata_name	mref		Reference to a value in column 'name' in data.txt. Multiple references can be added separated by '|'.
hypothesis_id	xref		Reference to a value in column 'id' in description.txt.

Note that values in column id should unique.

fugedata.txt file

Data can be an input to or an output from a ProtocolApplication. Data may be produced from a Material (data acquisition) or from another Data object (data transformation). Examples of Data are gene expression measurements, or phenotypes associated with genetic manipulations. The file fugedata.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field

Note that values in column id should unique.

fugedimensionelement.txt file

A single point within a parent dimension. This class should be extended. The file fugedimensionelement.txt can have the following fields:

column name	type	required?	description
name	string	Y	The potentially ambiguous common identifier, such as a human-readable name for the instance.
annotations_name	mref		Reference to a value in column 'name' in ontologyterm.txt. Multiple references can be added separated by '|'.
id	int		automatically generated id-field

Note that values in column id should unique.