Changes between Initial Version and Version 1 of XgapFormatReference


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Timestamp:
2010-10-01T23:38:13+02:00 (11 years ago)
Author:
trac
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  • XgapFormatReference

    v1 v1  
     1[[TOC()]]
     2
     3= XGAP TAB format reference =
     4This 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.
     5== xgap.core package ==
     6
     7Core entities.
     8
     9=== investigation.txt file ===
     10The file investigation.txt can have the following fields:
     11
     12||column name||type||required?||description||
     13||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     14||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     15||id||int||||automatically generated id-field||
     16||start||datetime||||The start point of the investigation. (n.b. removed null  constraint)||
     17||end||datetime||||The end point of the investigation. (n.b. removed null  constraint)||
     18
     19Note that values in  column id should unique.[[BR]]Note that values in column name should unique.[[BR]]
     20
     21=== protocolapplication.txt file ===
     22The file protocolapplication.txt can have the following fields:
     23
     24||column name||type||required?||description||
     25||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     26||activitydate||datetime||Y||When the protocol was applied.||
     27||protocol_name||xref||Y||Reference to a value in column 'name' in protocol.txt.||
     28||status||enum||Y||The status of this protocolapplication (inprocess = still working on it,  final = ready for further analysis).||
     29||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     30||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     31||id||int||||automatically generated id-field||
     32||inputdata_name||mref||||Reference to a value in column 'name' in data.txt. Multiple references  can be added separated by '|'.||
     33||protocoldeviation_id||xref||||Reference to a value in column 'id' in description.txt.||
     34||outputmaterials_name||mref||||Reference to a value in column 'name' in material.txt. Multiple  references can be added separated by '|'.||
     35||outputdata_name||mref||||Reference to a value in column 'name' in data.txt. Multiple references  can be added separated by  '|'.||
     36
     37Note that values in column  id should unique.[[BR]]Note that values in the combined columns (name,  investigation) should be unique.[[BR]]
     38
     39=== data.txt file ===
     40Generic structure for describing data matrices such as genotype result, gene  expression measurement, QTL calculation, etc. The file data.txt can have the  following fields:
     41
     42||column name||type||required?||description||
     43||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     44||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     45||rowtype||enum||Y||Type of the columns of this matrix. Each column refers to a Trait or Subject  (!DimensionElement).||
     46||coltype||enum||Y||Type of the rows of this matrix. Each row refers to a Trait or Subject  (!DimensionElement)||
     47||valuetype||enum||Y||Type of the values of this matrix. E.g. text strings or decimal  numbers.||
     48||totalrows||int||Y||!TotalRows||
     49||totalcols||int||Y||!TotalCols||
     50||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     51||id||int||||automatically generated id-field||
     52
     53Note that values in  column id should unique.[[BR]]Note that values in the combined columns (name,  investigation) should be unique.[[BR]]
     54
     55=== dimensionelement.txt file ===
     56Describes the biological material or subject which is being 'measured' by an  Data set. [[BR]]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). [[BR]]An !DimensionElement is always linked to a single one Investigation.  The file dimensionelement.txt can have the following fields:
     57
     58||column name||type||required?||description||
     59||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     60||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     61||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     62||id||int||||automatically generated id-field||
     63
     64Note that values in  column id should unique.[[BR]]Note that values in the combined columns (name,  investigation) should be unique.[[BR]]
     65
     66=== decimaldataelement.txt file ===
     67A !DataElement for storing decimal data. The file decimaldataelement.txt can  have the following fields:
     68
     69||column name||type||required?||description||
     70||data_name||xref||Y||Reference to a value in column 'name' in data.txt.||
     71||col_name||xref||Y||Reference to a value in column 'name' in dimensionelement.txt.||
     72||row_name||xref||Y||Reference to a value in column 'name' in dimensionelement.txt.||
     73||rowindex||int||Y||Row position in the matrix.||
     74||colindex||int||Y||Col position in the matrix.||
     75||id||int||||automatically generated id-field||
     76||value||decimal||||The value, e.g., correlation.||
     77
     78Note that values  in column id should unique.[[BR]]Note that values in the combined columns  (colindex, rowindex, data) should be unique.[[BR]]Note that values in the combined  columns (rowindex, colindex, data) should be unique.[[BR]]
     79
     80=== textdataelement.txt file ===
     81Store text data The file textdataelement.txt can have the following  fields:
     82
     83||column name||type||required?||description||
     84||data_name||xref||Y||Reference to a value in column 'name' in data.txt.||
     85||col_name||xref||Y||Reference to a value in column 'name' in dimensionelement.txt.||
     86||row_name||xref||Y||Reference to a value in column 'name' in dimensionelement.txt.||
     87||rowindex||int||Y||Row position in the matrix.||
     88||colindex||int||Y||Col position in the matrix.||
     89||id||int||||automatically generated id-field||
     90||value||text||||The value, e.g., genotype strings like AA, BA, BB.||
     91
     92Note that values in column  id should unique.[[BR]]Note that values in the combined columns (colindex,  rowindex, data) should be unique.[[BR]]Note that values in the combined columns  (rowindex, colindex, data) should be unique.[[BR]]
     93
     94== xgap.subject package ==
     95Subject variants.
     96
     97=== species.txt file ===
     98The file species.txt can have the following fields:
     99
     100||column name||type||required?||description||
     101||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     102||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     103||term||string||Y||The ontology term itself, also known as the local name in some  ontologies.||
     104||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).||
     105||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     106||id||int||||automatically generated id-field||
     107||ontologysource_name||xref||||Reference to a value in column 'name' in ontologysource.txt.||
     108||termpath||string||||EXTENSION. The Ontology Lookup Service path that contains this  term.||
     109||termcategory_name||xref||||Reference to a value in column 'name' in category.txt.||
     110
     111Note that values in column id  should unique.[[BR]]Note that values in the combined columns (name, investigation)  should be unique.[[BR]]
     112
     113=== datatype.txt file ===
     114The file datatype.txt can have the following fields:
     115
     116||column name||type||required?||description||
     117||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     118||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     119||term||string||Y||The ontology term itself, also known as the local name in some  ontologies.||
     120||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).||
     121||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     122||id||int||||automatically generated id-field||
     123||ontologysource_name||xref||||Reference to a value in column 'name' in ontologysource.txt.||
     124||termpath||string||||EXTENSION. The Ontology Lookup Service path that contains this  term.||
     125||termcategory_name||xref||||Reference to a value in column 'name' in category.txt.||
     126
     127Note that values in column id  should unique.[[BR]]Note that values in the combined columns (name, investigation)  should be unique.[[BR]]
     128
     129=== tissue.txt file ===
     130The file tissue.txt can have the following fields:
     131
     132||column name||type||required?||description||
     133||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     134||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     135||term||string||Y||The ontology term itself, also known as the local name in some  ontologies.||
     136||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).||
     137||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     138||id||int||||automatically generated id-field||
     139||ontologysource_name||xref||||Reference to a value in column 'name' in ontologysource.txt.||
     140||termpath||string||||EXTENSION. The Ontology Lookup Service path that contains this  term.||
     141||termcategory_name||xref||||Reference to a value in column 'name' in category.txt.||
     142
     143Note that values in column id  should unique.[[BR]]Note that values in the combined columns (name, investigation)  should be unique.[[BR]]
     144
     145=== samplelabel.txt file ===
     146The file samplelabel.txt can have the following fields:
     147
     148||column name||type||required?||description||
     149||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     150||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     151||term||string||Y||The ontology term itself, also known as the local name in some  ontologies.||
     152||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).||
     153||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     154||id||int||||automatically generated id-field||
     155||ontologysource_name||xref||||Reference to a value in column 'name' in ontologysource.txt.||
     156||termpath||string||||EXTENSION. The Ontology Lookup Service path that contains this  term.||
     157||termcategory_name||xref||||Reference to a value in column 'name' in category.txt.||
     158
     159Note that values in column id  should unique.[[BR]]Note that values in the combined columns (name, investigation)  should be unique.[[BR]]
     160
     161=== subject.txt file ===
     162The file subject.txt can have the following fields:
     163
     164||column name||type||required?||description||
     165||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     166||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     167||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     168||id||int||||automatically generated id-field||
     169||species_name||xref||||Reference to a value in column 'name' in species.txt.||
     170
     171Note that values in column id  should unique.[[BR]]Note that values in the combined columns (name, investigation)  should be unique.[[BR]]
     172
     173=== strain.txt file ===
     174A variant or subtype of animal, plant, virus or bacteria. The file strain.txt  can have the following fields:
     175
     176||column name||type||required?||description||
     177||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     178||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     179||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)||
     180||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     181||id||int||||automatically generated id-field||
     182||species_name||xref||||Reference to a value in column 'name' in species.txt.||
     183||founderstrains_name||mref||||Reference to a value in column 'name' in strain.txt. Multiple references  can be added separated by  '|'.||
     184
     185Note that values in column  id should unique.[[BR]]Note that values in the combined columns (name,  investigation) should be unique.[[BR]]
     186
     187=== individual.txt file ===
     188Biological individuals. The file individual.txt can have the following  fields:
     189
     190||column name||type||required?||description||
     191||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     192||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     193||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     194||id||int||||automatically generated id-field||
     195||species_name||xref||||Reference to a value in column 'name' in species.txt.||
     196||strain_name||xref||||Reference to a value in column 'name' in strain.txt.||
     197||mother_name||xref||||Reference to a value in column 'name' in individual.txt.||
     198||father_name||xref||||Reference to a value in column 'name' in individual.txt.||
     199
     200Note that values in column id  should unique.[[BR]]Note that values in the combined columns (name, investigation)  should be unique.[[BR]]
     201
     202=== sample.txt file ===
     203The file sample.txt can have the following fields:
     204
     205||column name||type||required?||description||
     206||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     207||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     208||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     209||id||int||||automatically generated id-field||
     210||species_name||xref||||Reference to a value in column 'name' in species.txt.||
     211||individual_name||xref||||Reference to a value in column 'name' in individual.txt.||
     212||tissue_name||xref||||Reference to a value in column 'name' in tissue.txt.||
     213
     214Note that values in column id  should unique.[[BR]]Note that values in the combined columns (name, investigation)  should be unique.[[BR]]
     215
     216=== pairedsample.txt file ===
     217A pair of samples labeled for a two-color microarray experiment. The file  pairedsample.txt can have the following fields:
     218
     219||column name||type||required?||description||
     220||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     221||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     222||subject1_name||xref||Y||Reference to a value in column 'name' in individual.txt.||
     223||subject2_name||xref||Y||Reference to a value in column 'name' in individual.txt.||
     224||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     225||id||int||||automatically generated id-field||
     226||species_name||xref||||Reference to a value in column 'name' in species.txt.||
     227||label1_name||xref||||Reference to a value in column 'name' in samplelabel.txt.||
     228||label2_name||xref||||Reference to a value in column 'name' in samplelabel.txt.||
     229
     230Note that values in column id  should unique.[[BR]]Note that values in the combined columns (name, investigation)  should be unique.[[BR]]
     231
     232== xgap.trait package ==
     233Trait variants.
     234
     235=== measurementunit.txt file ===
     236The file measurementunit.txt can have the following fields:
     237
     238||column name||type||required?||description||
     239||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     240||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     241||term||string||Y||The ontology term itself, also known as the local name in some  ontologies.||
     242||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).||
     243||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     244||id||int||||automatically generated id-field||
     245||ontologysource_name||xref||||Reference to a value in column 'name' in ontologysource.txt.||
     246||termpath||string||||EXTENSION. The Ontology Lookup Service path that contains this  term.||
     247||termcategory_name||xref||||Reference to a value in column 'name' in category.txt.||
     248
     249Note that values in column id  should unique.[[BR]]Note that values in the combined columns (name, investigation)  should be unique.[[BR]]
     250
     251=== trait.txt file ===
     252Traits 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:
     253
     254||column name||type||required?||description||
     255||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     256||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     257||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     258||id||int||||automatically generated id-field||
     259
     260Note that values in  column id should unique.[[BR]]Note that values in the combined columns (name,  investigation) should be unique.[[BR]]
     261
     262=== nmrbin.txt file ===
     263Shift of the NMR frequency due to the chemical environment. The file  nmrbin.txt can have the following fields:
     264
     265||column name||type||required?||description||
     266||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     267||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     268||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     269||id||int||||automatically generated id-field||
     270
     271Note that values in  column id should unique.[[BR]]Note that values in the combined columns (name,  investigation) should be unique.[[BR]]
     272
     273=== clone.txt file ===
     274BAC clone fragment. The file clone.txt can have the following fields:
     275
     276||column name||type||required?||description||
     277||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     278||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     279||chr||string||||chromosome name or number string (1, 2, .., x, y)||
     280||species_name||xref||||Reference to a value in column 'name' in species.txt.||
     281||cm||decimal||||genetic map position in centi morgan (cM).||
     282||bpstart||long||||numeric basepair postion (5') on the chromosome||
     283||bpend||long||||numeric basepair postion (3') on the chromosome||
     284||seq||text||||The FASTA text representation of the sequence.||
     285||symbol||text||||todo||
     286||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     287||id||int||||automatically generated id-field||
     288
     289Note that values in  column id should unique.[[BR]]Note that values in the combined columns (name,  investigation) should be unique.[[BR]]
     290
     291=== derived.txt file ===
     292Any meta trait, eg. false discovery rates, P-values, thresholds. The file  derived.txt can have the following fields:
     293
     294||column name||type||required?||description||
     295||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     296||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     297||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     298||id||int||||automatically generated id-field||
     299
     300Note that values in  column id should unique.[[BR]]Note that values in the combined columns (name,  investigation) should be unique.[[BR]]
     301
     302=== factor.txt file ===
     303Experimental conditions, such as temperature differences, batch effects etc.  The file factor.txt can have the following fields:
     304
     305||column name||type||required?||description||
     306||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     307||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     308||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     309||id||int||||automatically generated id-field||
     310
     311Note that values in  column id should unique.[[BR]]Note that values in the combined columns (name,  investigation) should be unique.[[BR]]
     312
     313=== gene.txt file ===
     314Trait annotations specific for genes. The file gene.txt can have the  following fields:
     315
     316||column name||type||required?||description||
     317||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     318||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     319||chr||string||||chromosome name or number string (1, 2, .., x, y)||
     320||species_name||xref||||Reference to a value in column 'name' in species.txt.||
     321||cm||decimal||||genetic map position in centi morgan (cM).||
     322||bpstart||long||||numeric basepair postion (5') on the chromosome||
     323||bpend||long||||numeric basepair postion (3') on the chromosome||
     324||seq||text||||The FASTA text representation of the sequence.||
     325||symbol||string||||Main symbol this gene is known by (not necessarily unique, in constrast to  'name')||
     326||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     327||id||int||||automatically generated id-field||
     328||aliases||string||||Alternative symbols this gene is known by, separated by ','||
     329||orientation||enum||||Orientation of the gene on the genome (F=forward, R=reverse)||
     330||control||bool||||Indicating whether this is a 'housekeeping' gene that can be used as  control.||
     331
     332Note that values in  column id should unique.[[BR]]Note that values in the combined columns (name,  investigation) should be unique.[[BR]]
     333
     334=== protein.txt file ===
     335Trait annotations specific for proteins. The file protein.txt can have the  following fields:
     336
     337||column name||type||required?||description||
     338||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     339||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     340||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     341||id||int||||automatically generated id-field||
     342||gene_name||xref||||Reference to a value in column 'name' in gene.txt.||
     343||sequence||text||||The aminoacid sequence.||
     344||mass||decimal||||The mass of this metabolite||
     345
     346Note that values in  column id should unique.[[BR]]Note that values in the combined columns (name,  investigation) should be unique.[[BR]]
     347
     348=== metabolite.txt file ===
     349Trait annotations specific for metabolites. The file metabolite.txt can have  the following fields:
     350
     351||column name||type||required?||description||
     352||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     353||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     354||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     355||id||int||||automatically generated id-field||
     356||formula||string||||The chemical formula of a metabolite.||
     357||mass||decimal||||The mass of this metabolite||
     358||structure||text||||The chemical structure of a metabolite (in SMILES  representation).||
     359
     360Note that  values in column id should unique.[[BR]]Note that values in the combined columns  (name, investigation) should be unique.[[BR]]
     361
     362=== phenotype.txt file ===
     363Trait annotations specific for classical phenotypes. The file phenotype.txt  can have the following fields:
     364
     365||column name||type||required?||description||
     366||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     367||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     368||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     369||id||int||||automatically generated id-field||
     370||category||string||||Category||
     371||description||string||||Description||
     372||molecule||string||||Molecule||
     373
     374Note that values  in column id should unique.[[BR]]Note that values in the combined columns (name,  investigation) should be unique.[[BR]]
     375
     376=== protocolelement.txt file ===
     377Quantitative treats that are part of a protocol. E.g. microarray probes,  marker set. The file protocolelement.txt can have the following fields:
     378
     379||column name||type||required?||description||
     380||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     381||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     382||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     383||id||int||||automatically generated id-field||
     384||protocol_name||xref||||Reference to a value in column 'name' in protocol.txt.||
     385
     386Note that values in column id  should unique.[[BR]]Note that values in the combined columns (name, investigation)  should be unique.[[BR]]
     387
     388=== marker.txt file ===
     389Trait annotations specific for markers. The file marker.txt can have the  following fields:
     390
     391||column name||type||required?||description||
     392||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     393||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     394||chr||string||||chromosome name or number string (1, 2, .., x, y)||
     395||species_name||xref||||Reference to a value in column 'name' in species.txt.||
     396||cm||decimal||||genetic map position in centi morgan (cM).||
     397||bpstart||long||||numeric basepair postion (5') on the chromosome||
     398||bpend||long||||numeric basepair postion (3') on the chromosome||
     399||seq||text||||The FASTA text representation of the sequence.||
     400||symbol||text||||todo||
     401||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     402||id||int||||automatically generated id-field||
     403||protocol_name||xref||||Reference to a value in column 'name' in protocol.txt.||
     404
     405Note that values in column id  should unique.[[BR]]Note that values in the combined columns (name, investigation)  should be unique.[[BR]]
     406
     407=== probe.txt file ===
     408A 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:
     409
     410||column name||type||required?||description||
     411||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     412||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     413||mismatch||bool||Y||Indicating whether the probe is a match||
     414||chr||string||||chromosome name or number string (1, 2, .., x, y)||
     415||species_name||xref||||Reference to a value in column 'name' in species.txt.||
     416||cm||decimal||||genetic map position in centi morgan (cM).||
     417||bpstart||long||||numeric basepair postion (5') on the chromosome||
     418||bpend||long||||numeric basepair postion (3') on the chromosome||
     419||seq||text||||The FASTA text representation of the sequence.||
     420||symbol||text||||todo||
     421||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     422||id||int||||automatically generated id-field||
     423||protocol_name||xref||||Reference to a value in column 'name' in protocol.txt.||
     424||probeset_name||xref||||Reference to a value in column 'name' in probeset.txt.||
     425
     426Note that values in column id  should unique.[[BR]]Note that values in the combined columns (name, investigation)  should be unique.[[BR]]
     427
     428=== spot.txt file ===
     429This is the spot on a microarray. [[BR]]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:
     430
     431||column name||type||required?||description||
     432||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     433||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     434||mismatch||bool||Y||Indicating whether the probe is a match||
     435||x||int||Y||Row||
     436||y||int||Y||Column||
     437||chr||string||||chromosome name or number string (1, 2, .., x, y)||
     438||species_name||xref||||Reference to a value in column 'name' in species.txt.||
     439||cm||decimal||||genetic map position in centi morgan (cM).||
     440||bpstart||long||||numeric basepair postion (5') on the chromosome||
     441||bpend||long||||numeric basepair postion (3') on the chromosome||
     442||seq||text||||The FASTA text representation of the sequence.||
     443||symbol||text||||todo||
     444||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     445||id||int||||automatically generated id-field||
     446||protocol_name||xref||||Reference to a value in column 'name' in protocol.txt.||
     447||probeset_name||xref||||Reference to a value in column 'name' in probeset.txt.||
     448||gridx||int||||Meta Row||
     449||gridy||int||||Meta Column||
     450
     451Note that  values in column id should unique.[[BR]]Note that values in the combined columns  (name, investigation) should be unique.[[BR]]Note that values in the combined  columns (protocol, x, y, gridx, gridy) should be unique.[[BR]]
     452
     453=== probeset.txt file ===
     454A set of Probes. E.g. Affymetrix probeset has multiple probes. The file  probeset.txt can have the following fields:
     455
     456||column name||type||required?||description||
     457||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     458||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     459||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     460||id||int||||automatically generated id-field||
     461||protocol_name||xref||||Reference to a value in column 'name' in protocol.txt.||
     462
     463Note that values in column id  should unique.[[BR]]Note that values in the combined columns (name, investigation)  should be unique.[[BR]]
     464
     465=== masspeak.txt file ===
     466A peak that has been selected within a mass spectrometry experiment. The file  masspeak.txt can have the following fields:
     467
     468||column name||type||required?||description||
     469||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     470||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     471||annotations_name||mref||||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     472||id||int||||automatically generated id-field||
     473||protocol_name||xref||||Reference to a value in column 'name' in protocol.txt.||
     474||mz||decimal||||Mass over charge ratio of this peak.||
     475||retentiontime||decimal||||The retention-time of this peak in minutes.||
     476
     477Note that values in  column id should unique.[[BR]]Note that values in the combined columns (name,  investigation) should be unique.
     478
     479== fuge.common package ==
     480
     481Common elements inherited from FuGE.
     482=== identifiable.txt file ===
     483Other 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:
     484
     485
     486||column name||type||required?||description||
     487||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     488||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     489||id||int|| ||automatically generated id-field||
     490
     491Note that values in  column id should unique.[[BR]]
     492=== describable.txt file ===
     493Abstract 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:
     494
     495
     496||column name||type||required?||description||
     497||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     498||id||int|| ||automatically generated id-field||
     499
     500Note that values in  column id should unique.[[BR]]
     501=== security.txt file ===
     502Permission information for an object as to ownership, write and read  permissions. The file security.txt can have the following fields:
     503
     504
     505||column name||type||required?||description||
     506||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     507||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     508||id||int|| ||automatically generated id-field||
     509||owners_name||mref|| ||Reference to a value in column 'name' in contact.txt. Multiple  references can be added separated by '|'.||
     510
     511Note that values in column  id should unique.[[BR]]
     512=== ontologyterm.txt file ===
     513A 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:
     514
     515
     516||column name||type||required?||description||
     517||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     518||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     519||term||string||Y||The ontology term itself, also known as the local name in some  ontologies.||
     520||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).||
     521||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     522||id||int|| ||automatically generated id-field||
     523||ontologysource_name||xref|| ||Reference to a value in column 'name' in ontologysource.txt.||
     524||termpath||string|| ||EXTENSION. The Ontology Lookup Service path that contains this  term.||
     525||termcategory_name||xref|| ||Reference to a value in column 'name' in category.txt.||
     526
     527Note that values in column id  should unique.[[BR]]Note that values in the combined columns (name, investigation)  should be unique.[[BR]]
     528=== category.txt file ===
     529EXTENSION for ontology plugin. The file category.txt can have the following  fields:
     530
     531
     532||column name||type||required?||description||
     533||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     534||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     535||id||int|| ||automatically generated id-field||
     536||description||string|| ||description||
     537
     538Note that  values in column id should unique.[[BR]]
     539=== uri.txt file ===
     540A 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:
     541
     542
     543||column name||type||required?||description||
     544||location||hyperlink||Y||The Uniform Resource Indicator for this object.||
     545||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     546||id||int|| ||automatically generated id-field||
     547
     548Note that values in  column id should unique.[[BR]]
     549=== bibliographicreference.txt file ===
     550Represents 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:
     551
     552
     553||column name||type||required?||description||
     554||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     555||authors||string||Y||The names of the authors of the reference.||
     556||publication||string||Y||The name of the journal, book etc.||
     557||publisher||string||Y||The publisher of the publication.||
     558||editor||string||Y||The editor(s) of the reference.||
     559||year||int||Y||The year of publication.||
     560||volume||string||Y||The volume name or number.||
     561||issue||string||Y||The issue name or number.||
     562||pages||string||Y||The page numbers.||
     563||title||string||Y||The title of the !BibliographicReference.||
     564||investigation_name||xref||Y||Reference to a value in column 'name' in investigation.txt.||
     565||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     566||id||int|| ||automatically generated id-field||
     567
     568Note that values in  column id should unique.[[BR]]Note that values in the combined columns (name,  investigation) should be unique.[[BR]]
     569=== ontologysource.txt file ===
     570The source ontology or controlled vocabulary list that ontology terms have  been obtained from. The file ontologysource.txt can have the following  fields:
     571
     572
     573||column name||type||required?||description||
     574||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     575||ontologyuri||hyperlink||Y||A URI that references the location of the ontology.||
     576||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     577||id||int|| ||automatically generated id-field||
     578
     579Note that values in  column id should unique.[[BR]]
     580=== contact.txt file ===
     581A contact is either a person or an organization. The file contact.txt can  have the following fields:
     582
     583
     584||column name||type||required?||description||
     585||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     586||address||string||Y||The address of the Contact.||
     587||phone||string||Y||The telephone number of the Contact including the suitable area  codes.||
     588||email||string||Y||The email address of the Contact.||
     589||fax||string||Y||The fax number of the Contact.||
     590||tollfreephone||string||Y||A toll free phone number for the Contact, including suitable area  codes.||
     591||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     592||id||int|| ||automatically generated id-field||
     593
     594Note that values in  column id should unique.[[BR]]
     595=== description.txt file ===
     596A free text description of an object. The file description.txt can have the  following fields:
     597
     598
     599||column name||type||required?||description||
     600||text||string||Y||The description.||
     601||describable_descriptions_id||xref||Y||Reference to a value in column 'id' in describable.txt.||
     602||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     603||id||int|| ||automatically generated id-field||
     604
     605Note that values in  column id should unique.[[BR]]
     606=== databasereference.txt file ===
     607A reference to a record in a database. The file databasereference.txt can  have the following fields:
     608
     609
     610||column name||type||required?||description||
     611||accession||string||Y||The identifier used to look up the record.||
     612||accessionversion||string||Y||The appropriate version of the accession (if applicable).||
     613||database_id_id||xref||Y||Reference to a value in column 'id' in databaseaddress.txt.||
     614||identifiablereferences_id||xref||Y||Reference to a value in column 'id' in identifiable.txt.||
     615||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     616||id||int|| ||automatically generated id-field||
     617
     618Note that values in  column id should unique.[[BR]]
     619=== databaseaddress.txt file ===
     620An address to a repository. The file databaseaddress.txt can have the  following fields:
     621
     622
     623||column name||type||required?||description||
     624||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     625||version||string||Y||The version of the Database.||
     626||dburi||hyperlink||Y||The location of the Database.||
     627||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     628||id||int|| ||automatically generated id-field||
     629
     630Note that values in  column id should unique.[[BR]]
     631=== fugeprotocolapplication.txt file ===
     632The 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:
     633
     634
     635||column name||type||required?||description||
     636||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     637||activitydate||datetime||Y||When the protocol was applied.||
     638||protocol_name||xref||Y||Reference to a value in column 'name' in protocol.txt.||
     639||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     640||id||int|| ||automatically generated id-field||
     641||inputdata_name||mref|| ||Reference to a value in column 'name' in data.txt. Multiple references  can be added separated by '|'.||
     642||protocoldeviation_id||xref|| ||Reference to a value in column 'id' in description.txt.||
     643||outputmaterials_name||mref|| ||Reference to a value in column 'name' in material.txt. Multiple  references can be added separated by '|'.||
     644||outputdata_name||mref|| ||Reference to a value in column 'name' in data.txt. Multiple references  can be added separated by  '|'.||
     645
     646Note that values in column  id should unique.[[BR]]
     647=== parameterizableapplication.txt file ===
     648The interface that is the use of a Parameterizable class. The file  parameterizableapplication.txt can have the following fields:
     649
     650
     651||column name||type||required?||description||
     652||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     653||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     654||id||int|| ||automatically generated id-field||
     655
     656Note that values in  column id should unique.[[BR]]
     657=== protocol.txt file ===
     658A 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:
     659
     660
     661||column name||type||required?||description||
     662||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     663||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     664||id||int|| ||automatically generated id-field||
     665||types_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     666||outputtypes_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     667||inputtypes_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     668||software_name||mref|| ||Reference to a value in column 'name' in software.txt. Multiple  references can be added separated by '|'.||
     669||equipment_name||mref|| ||Reference to a value in column 'name' in equipment.txt. Multiple  references can be added separated by '|'.||
     670
     671Note that values in column  id should unique.[[BR]]
     672=== parameterizable.txt file ===
     673The Parameterizable interface encapsulates the association of Parameters with  !ParameterValues. The file parameterizable.txt can have the following fields:
     674
     675
     676||column name||type||required?||description||
     677||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     678||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     679||id||int|| ||automatically generated id-field||
     680||types_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     681
     682Note that values in column  id should unique.[[BR]]
     683=== software.txt file ===
     684Software 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:
     685
     686
     687||column name||type||required?||description||
     688||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     689||version||string||Y||The version of Software used.||
     690||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     691||id||int|| ||automatically generated id-field||
     692||types_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     693||equipment_name||mref|| ||Reference to a value in column 'name' in equipment.txt. Multiple  references can be added separated by '|'.||
     694
     695Note that values in column  id should unique.[[BR]]
     696=== equipment.txt file ===
     697The 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:
     698
     699
     700||column name||type||required?||description||
     701||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     702||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     703||id||int|| ||automatically generated id-field||
     704||types_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     705||make_name||xref|| ||Reference to a value in column 'name' in ontologyterm.txt.||
     706||equipmentparts_name||mref|| ||Reference to a value in column 'name' in equipment.txt. Multiple  references can be added separated by '|'.||
     707||software_name||mref|| ||Reference to a value in column 'name' in software.txt. Multiple  references can be added separated by '|'.||
     708||model_name||xref|| ||Reference to a value in column 'name' in ontologyterm.txt.||
     709
     710Note that values in column id  should unique.[[BR]]
     711== fuge.bio package ==
     712Bio elements inherited from FuGE.
     713
     714
     715=== fugeinvestigation.txt file ===
     716An 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:
     717
     718
     719||column name||type||required?||description||
     720||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     721||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     722||id||int|| ||automatically generated id-field||
     723||start||datetime|| ||The start point of the investigation. (n.b. removed null  constraint)||
     724||end||datetime|| ||The end point of the investigation. (n.b. removed null  constraint)||
     725
     726Note that values in  column id should unique.[[BR]]
     727=== material.txt file ===
     728Material 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:
     729
     730
     731||column name||type||required?||description||
     732||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     733||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     734||id||int|| ||automatically generated id-field||
     735||components_name||mref|| ||Reference to a value in column 'name' in material.txt. Multiple  references can be added separated by '|'.||
     736||materialtype_name||xref|| ||Reference to a value in column 'name' in ontologyterm.txt.||
     737||characteristics_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     738||qualitycontrolstatistics_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     739
     740Note that values in column  id should unique.[[BR]]
     741=== higherlevelanalysis.txt file ===
     742A container for domain-specific analyses performed on data. Subclasses must  be created for different domains. The file higherlevelanalysis.txt can have the  following fields:
     743
     744
     745||column name||type||required?||description||
     746||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     747||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     748||id||int|| ||automatically generated id-field||
     749||conclusion_id||xref|| ||Reference to a value in column 'id' in description.txt.||
     750||supportingdata_name||mref|| ||Reference to a value in column 'name' in data.txt. Multiple references  can be added separated by '|'.||
     751||hypothesis_id||xref|| ||Reference to a value in column 'id' in description.txt.||
     752
     753Note that values in column id  should unique.[[BR]]
     754=== fugedata.txt file ===
     755Data 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:
     756
     757
     758||column name||type||required?||description||
     759||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     760||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     761||id||int|| ||automatically generated id-field||
     762
     763Note that values in  column id should unique.[[BR]]
     764=== fugedimensionelement.txt file ===
     765A single point within a parent dimension. This class should be extended. The  file fugedimensionelement.txt can have the following fields:
     766
     767
     768||column name||type||required?||description||
     769||name||string||Y||The potentially ambiguous common identifier, such as a human-readable name  for the instance.||
     770||annotations_name||mref|| ||Reference to a value in column 'name' in ontologyterm.txt. Multiple  references can be added separated by '|'.||
     771||id||int|| ||automatically generated id-field||
     772
     773Note that values in  column id should unique.