Tables that are used to define the Warehouse contents and its current state.
Tables that contain universally- or widely-accepted scientific data. These tables are independent
of any dataset.
Tables that represent the principal objects in the Warehouse.
All object tables have a WID column that is globally unique identifier,
and a DataSetWID column that refers to the DataSet row of the dataset that
loaded the object.
Tables that implement arbitrary relations among Warehouse objects.
Naming convention is to use /table/WID as a column name for any WID
referencing an object from /table/.
Tables that reference an untyped WID (one that could be from one of several object tables).
Naming convention is to use OtherWID as a column name for the untyped WID.
Tables that (only) link WIDs from two object tables.
These tables implement many-many relations between Warehouse objects.
Naming convention is /table1/WID/table2/WID.
Describes this version of the BioSPICE Warehouse.
This table contains exactly one row.
Numbered version of the warehouse schema that is loaded
Date that this schema was loaded
Maximum value allowed for SpecialWIDTable.PreviousWID / specialWID sequence
Maximum value allowed for reserved WIDs (regulard WIDs start above this WID number)
Free-form text as desired by the warehouse maintainers
INSERT INTO Warehouse (Version, LoadDate, MaxSpecialWID, MaxReservedWID)
VALUES (4.6, now(), 999, 999999);
INSERT INTO Warehouse (Version, LoadDate, MaxSpecialWID, MaxReservedWID)
VALUES (4.6, sysdate, 999, 999999);
Warehouse ID (WID) allocation --
Generate a unlimited sequence of unique numbers to do the bookkeeping for
Warehouse ID (WID) numbers, which serve as keys for all Warehouse entities.
WIDs 0 and 1 are reserved and not allocated.
Oracle dataset loaders use the following SQL for WID assignment:
SELECT WID_sequence.nextval FROM DUAL;
using an INTO clause in some APIs to store the result in a variable.
To allow for compatibility with RDBMS systems that do not support
sequences, this table may be used to store the last used WID.
MySQL dataset loaders use the following SQL for WID assignment:
DELETE FROM WIDTable;
INSERT INTO WIDTable VALUES ();
SELECT last_insert_id();
It may also be used in RDBMS systems that do not support auto-increment
of a counter; however additional protocol like table locking may be
needed to assure the integrity of WIDs during concurrent assignment.
This table contains exactly one row at any given time.
Last-used Warehouse identifier.
INSERT INTO WIDTable (PreviousWID) values (999999);
Generate a finite sequence of WIDs for use as special Warehouse entities,
including DataSet WIDs. These are small integers.
Special WIDs are low-valued WIDs, assigned to globally and frequently used
WIDs within a dataset, such as its DataSetWID. They are both more
mnemonic, and potentially more efficient to store. Warehouse.MaxSpecialWID
delimits special and regular WIDs.
Analogous to WIDTable, this table is used to allocate special WIDs.
MySQL dataset loaders use the following protocol for WID assignment:
DELETE FROM SpecialWIDTable;
INSERT INTO SpecialWIDTable VALUES ();
SELECT last_insert_id();
This table contains exactly one row at any given time.
Last-used special WID
INSERT INTO SpecialWIDTable (PreviousWID) values (1);
This table defines enumerated types used within the warehouse. Essentially,
enumerated types correspond to small controlled vocabularies used within
one or more warehouse tables. For example, the warehouse table Feature has
a column called Type that defines the type of a feature within an amino-acid
sequence. Examples types might be PHOS-RESIDUE and GLY-RESIDUE, corresponding
to residues in a protein that are phosphorylated and glycosylated, respectively.
Those two enumerated types would be entered into two rows of this Enumeration
table. Note that in some cases the values actually stored in the warehouse
table are numbers, which are stored in the Value field of the Enumeration table
as the string form of that number.
Table this enumeration is used in
Column this enumeration is used in
The enumeration value
A comment describing its meaning
Table whose rows define each dataset currently loaded into the warehouse.
Warehouse identifier for this entry.
Name of the database.
Version of the database described by this warehouse dataset; in practice, this can be
populated
with whatever the user chooses to put in it from the command line arguments
Date that the original database was first released.
Date that the load of this data set into the warehouse began.
Date of the last change to this dataset, or the date the load
completed if no changes have occurred. NULL means that the
is currently loading, or a fatal error occurred on the load.
NOTE: This feature is not supported by most loaders until version 4.0.
Web address of the home page of the original database.
A URL at which we can retrieve objects in this database via the WWW
by substituting the unique ID of the object we wish to retrieve for the
string "%s" in the query URL. An example URL is:
http://database.university.edu/get-object/5050%s
The name (or username) of the person who loaded this dataset.
NOTE: This feature is not supported by most loaders until
version 4.0. At that time, this column should be required.
The name of the application that created this dataset.
NOTE: This feature is not supported by most loaders until
version 4.0. At that time, this column should be required.
The version of the application that created this dataset.
NOTE: This feature is not supported by most loaders until
version 4.0. At that time, this column should be required.
Defines a dataset containment hierarchy.
If a dataset contains another, either directly or indirectly,
a row exists for that dataset pair in this table.
A dataset always contains itself; therefore each dataset is included in at least one row in this table.
A dataset may contain any number of datasets, and be contained in any number of datasets.
To query for an object in a containing dataset whose datasetwid is NN,
regardless of which contained dataset it is in, use a query like the following:
select wid from DataSetHierarchy h, Protein p
where h.superwid=NN and h.subwid=p.datasetwid
and p.name='some name'
Reference to the containing DataSet.
Reference to the contained DataSet.
Defines metadata describing a warehouse object.
Every warehouse object (that is, anything with a WID column) must have an associated Entry
row.
Warehouse ID of the entity
Date entity was stored in the warehouse
Date entity was created in its source dataset
Date that the entry was last modified, either
in the warehouse or in the source dataset
'T' if an error (eg. parse error on some field of the entry)
occured during loading of this entry into the warehouse, else 'F'.
Either line number or entry number from dataset source file
Message describing error, if any
The dataset the entity is from
MAGE gene expression data (BioDataCube)
This table definition may evolve as the requirements for gene expression data
are better understood. The MAGE OM currently allows 'any' type for the Value component
of the BioDataCube. We are investigating ways to make this table better accomodate
the variety of allowed datatypes. Please send suggestions to support@biowarehouse.org
BioAssay index
DesignElement index
Quantitation Type index
Data value. See associated QuantiatitationType obect for type information.
The BioAssayValues object the entity is from
The periodic table of elements
WID of this element
Long name (e.g. 'Oxygen')
Symbol (e.g. 'O')
Weighted average weight (e.g. 16.x)
Number of protons
Defines one or more valences for each element.
WID of the element
Number of valence electrons
Defines a light source, e.g., as produced by a scientific instrument.
Used by flow cytometry in describing the cytometry instrument.
Warehouse idetification number for this light source
Wavelength of the light emitted, in nanometers
Enumeration. Specifies the type of light source (arc lamp, a particular laser, etc.).
WID of the object representing the instrument producing the light.
For a flow cytometry experiment, this is typically
a reference to a Parameterizable row defining the cytometry instrument used.
This instrument is instantiated as a ParameterizableApplication row, and has
an associated ExperimentData row that defines the compensation parameter.
References the data set the entity came from
Defines an experimental sample prepared for use in a flow cytometry experiment.
A typical experiment consists of multiple samples X multiple readings
(forward/side scatter and using filters of various wavelengths),
with a vector of observations (one per cell of the BioSource)
for each sample/reading combination.
An ExperimentData row is defined for each observation; see that table for representation details.
An Experiment row is defined to associate each ExperimentData row with the experiment.
Warehouse idetification number for this flow cytometry sample
References the biological source of this sample.
References the probe used with this sample.
References a specification of the amount of the probe used.
References the Contact that describes the manufacturer of this sample.
References the data set the entity came from
Defines a material used to measure characteristics of a cell using flow cytometry.
If probe is a protein, a CrossReference may be defined to specify the protein;
in that case CrossReference.OtherWID refers to this FlowCytometryProbe.
Warehouse idetification number for this probe
Enumeration. Specifies the type of probe
Reference to the data set from which the entity came from
Defines a transcription unit, similar to an operon. There is a one-to-one
relationship between a promoter and a transcription unit. The transcription
unit includes the promoter, nearby site that regulate its activity, and downstream
genes and the terminator. Unlike operons, a transcription unit can contain a single
gene, and a transcription unit can contain only one promoter. For operons containing
multiple promoters, a different transcription unit would be created for each operon.
See TranscriptionUnitComponent for the types of components represented.
Warehouse identifier for this TranscriptionUnit
Name of the transcription unit
Reference to the data set from which the entity came from
Associates a TranscriptionUnit with its components. Components consist of
genes and/or features. A feature component may be either a promoter, a terminator or a DNA binding site
(transcription-factor binding site).
Enumeration. Specifies the type of component
Links to the TranscriptionUnit associated with this object.
WID of the Gene or Feature associated with the TranscriptionUnit
Defines small molecular weight chemical compounds.
Warehouse idetification number for this chemical
Common name of the chemical
'T' this is a class or family of related chemicals, else 'F'
The Beilstein name of this chemical
The systematic name for this chemical
The Chemical Abstract Service number
Charge of the chemical
The empirical formula of this chemical
Format: { ElementSymbol Integer }+
E.g. 'H2O1', 'C2H6O1', 'Na1Cl1'.
Molecular weight calculated from chemical formula.
Units: Daltons.
Molecular Weight determined through experimentation. Units: Daltons.
Octanol-water-partition coefficient
First ionization potential
Second ionization potential
Third ionization potential
'T' if soluble in water, else 'F'
Ascii representation of the chemical structure
Simplified Molecular Input Line Entry System
http://www.epa.gov/medatwrk/databases/smiles.html
Reference to the data set from which the entity came from
Defines a chemical reaction. The reaction could be enzyme catalyzed
or occur spontaneously. The reaction could involve small molecules, macromolecules,
or a combination of the two. Every reaction will be stored in the warehouse in
a given direction, for example, every reaction that has an assigned EC number is
written in a direction assigned by the enzyme commission. In physiological settings,
the reaction could occur in the direction the reaction is stored, the reverse direction,
or both directions.
Restrictions: Reaction only stores fully qualified EC numbers, e.g., NOT of the form
"X.Y.Z.-"
Warehouse ID for this entiry
Name of reaction
Delta G subzero prime value for this reaction
Official enzyme-commission-number.
Proposed enzyme-commission-number
'T' if the reaction occurs spontaneously, else 'F'
WID of the dataset the reaction is from
Defines a molecular interaction, such as two proteins observed to interact in a yeast-two-hybrid
experiement. The interaction could involve macromolecules, small molecules or both.
Warehouse ID for this interaction
Interaction type. It is recommended to use external controled vacabulary terms, such as PSI-MI
Interaction Type CV.
Name of the interaction.
WID of the dataset the interaction is from.
Defines a specific protein, that is, a real-world protein which was either purified and
isolated,
OR is reasonably inferred by genomic analysis or other means, such as enzymological
characterization.
The protein could be a monomer or a multimer. In the latter case, a sequence would not be stored for
such a record.
The warehouse ID of this protein
Common name of the protein, if it exists
Amino-acid sequence for this protein, if available
Length of the amino-acid sequence for this protein, if available
This value is not necessarily exact, as can be modified by LengthApproximate
Indicates that the Length is an approximate. It could be 'gt' for
greater than, 'lt' for less than and 'ne' to indicate that it is not
equal. This is a controlled vocabulary.
Charge of the chemical
'T' if protein is a fragment, else 'F'
Molecular weight calculated from sequence.
Units: kiloDaltons.
Molecular Weight determined through experimentation.
Units: kiloDaltons.
Isoelectric point (pI) calculated from its sequence.
Isoelectric point (pI) determined through experimentation.
WID of the dataset the protein is from
Features define regions or points of interest on the protein sequence or
nucleic acid sequence specified by SequenceWID.
Features are not used to describe objects such as Genes, BioSources, etc,
because attributes of those objects are described in their own tables.
Exceptions:
1. Since pseudogenes are not entered in the Gene table, they are listed as sequence features in
Feature
Warehouse identifier of this feature.
Textual description of this feature.
Type of feature. These type values come from the source dataset and
are not necessarily enumerated. Example: "Promoter CYZ".
Class of feature. Assigns our typology for types of features, or qualifiers
associated with features. These are our own enumerated type values, to allow us
to classify features without losing the original (author-provided) type values
stored in Type. Example: Class=promoter.
Enumeration (see also SequenceWID) that indicates whether the sequence
is protein or nucleic and how the sequence (if available) is represented:
If 'P', feature resides on a protein.
If 'S' or 'N', feature resides on a nucleic acid.
References the Protein or Subsequence containing the sequence on which we
are defining a feature:
SequenceType of 'S' implies SequenceWID is nonNULL and references a Subsequence-
sequence = Subsequence.Sequence (i.e., it is stored explicitly),
SequenceType of 'N' implies SequenceWID (if nonNULL) references a NucleicAcid-
sequence is the substring Subsequence.Sequence[StartPosition : EndPosition]
where Subsequence is the full Subsequence of the nucleic acid.
SequenceType of 'P' implies SequenceWID (if nonNULL) references a Protein-
sequence is the substring Protein.AASequence[StartPosition : EndPosition].
Amino-acid sequence for this protein, if available
Specifies whether this feature is specified with starting and ending coordinates
or with a single coordinate.
Only defined if RegionOrPoint='point'. Specifies where the feature is relative
to its location as encoded in StartPosition and EndPosition:
Start position of the feature within the NucleicAcid or Protein sequence.
If Feature.RegionOrPoint is 'point', StartPosition and EndPosition will
either be equal (location is exactly at a nucleotide or amino acid) or will differ by 1
(location is centered between two adjacent nucleotides or amino acids).
End position of the feature within the NucleicAcid or Protein sequence.
If Feature.RegionOrPoint is 'point', StartPosition and EndPosition will
either be equal (location is exactly at a nucleotide or amino acid) or will differ by 1
(location is between two adjacent nucleotides or amino acids).
Indicates that the Start position of the coding region is an approximate value
It could be 'gt' for greater than, 'lt' for less than and 'ne' to indicate that it is not
equal. This is a controlled vocabulary.
Indicates that the End position of the coding region is an approximate value.
It could be 'gt' for greater than, 'lt' for less than and 'ne' to indicate that it is not
equal. This is a controlled vocabulary.
'T' if the feature is supported by experimental evidence, else 'F'
'T' if the feature is supported by computational evidence, else 'F'
Reference to the data set from which the entity came from
Describes the non-enzymatic function(s) of proteins. That is,
this table should not be used to describe the enzymatic function of a protein whose enzymatic
function is described using the EnzymaticReaction table. Function names are stored as
strings with no particular format or interpretation.
Warehouse identifier for this function.
Name of this function.
Data set the entity came from
Defines an association between a reaction and an enzyme that catalyzes
that reaction (ProteinWID). In the case where we are defining an
association between a subunit of a larger enzyme complex, and a
reaction catalyzed by that subunit only when the subunit is part of
that larger complex, ComplexWID specifies that larger complex (assumes
that complex is in the warehouse).
This table requires a WID as it is referenced in multiple linking tables
to associate alternate compounds, cofactors, etc., to allow for multiple
valued attributes of the enzymatic reaction.
WID of this enzymatic reaction
WID of the catalyzed reaction
WID of the enzyme
WID of protein of which ProteinWID
must be a subunit of for this reaction
Reaction Direction Enumeration
WID of the dataset the reaction is from
Defines the genetic codes with a name, translation table and a start codon for each code.
See http://embryology.med.unsw.edu.au/DNA/Genetic_Codes.htm for more information.
Genbank ID is stored as DBID.XID, where DBID.OtherWID = GeneticCode.WID.
Warehouse ID for this GeneticCode.
1- or 2-digit ID assigned to this code. See URL above.
Genetic code name.
Translation table for this genetic code. See URL above for format.
Start Codon for this genetic code. See URL above for format
Reference to the data set from which the entity came from.
Stores the GenBank Division and the NCBI three letter code for records originating from GenBank.
NCBI uses Divisions to organize GenBank records according to two definitions: some divisions are based on
taxonomy (e.g., the "BCT" division), whereas other divisions exist purely for data organization reasons
(e.g., the "CON" division, whose records store instructions for the construction of large contigs).
Sequences from different GenBank divisions vary substantially in quality based upon the way they were
generated, e.g., single-pass genomic sequencing, ESTs (low quality, single-pass sequencing), cDNAs
(high coverage sequencing) and genomic sequencing (moderate coverage sequencing). All BioWarehouse
records associated with a GenBank dataset also have a record in the Division table.
Warehouse ID for this Division.
Genbank Division code (3 characters) which is an abbreviation for the GenBank Name.
Division name.
Reference to the data set from which the entity came from.
Defines a taxon, which could be a species, genus, family or some other rank.
These ranks are controlled vocabulary and are stored in the Enumeration table.
The taxon table associates a taxon with its parent, gives the name, division code and the
genetic code information for the taxon.
Warehouse ID for this Taxon
Warehouse ID of the parent of this taxon
Taxonomic Name of this taxon
Rank of this taxon (kingdom, superkingdom ..)
Warehouse ID of the division this taxon belongs to.
'T' if division is inherited from parent, else 'F'
Warehouse ID of the genetic code for this taxon.
'T' if gencode is inherited from parent, else 'F'
Warehouse ID of the mitochondrial genetic code for this taxon.
'T' if the mitochondrial gencode is inherited from parent, else 'F'
Reference to the data set from which the entity came from
Defines the biological source of an entry in the Protein,
NucleicAcid or Gene tables ("the object"), as well as other tables
eventually storing experimental data related to e.g., microarray or
proteomic experiments. For example, BioSource might be used to specify
the organism, organ, and tissue in which gene expression experiments
were performed. DEPENDENCIES: 1. As BioSource references Taxon.WID to
specify the species, the NCBI taxonomy dataset must have ALREADY been
loaded prior to populating BioSource. 2. BioSource stores subtype
information in BioSubtype via the BioSourceWIDBioSubtypeWID linking
table
Warehouse identifier for biological source.
Discriminator column specifies type of MAGE object this row represents (if needed)
Warehouse GUID identifying WID of Taxon entry for the species. Always
references species level or higher.
Informal name assigned to this source.
Ex. (CMR): 'Escherichia coli K12-MG1655'
Strain of organism from which object is derived, if applicable. This is a
subspecies taxonomic classification not supported by Taxon because it is not
a rigorous concept.
Strain is defined as a population of homogeneous organisms possessing a set of
defined characteristics. In bacteriology, the set of descendants that retains
the characteristics of the ancestor. Members of a strain that subsequently
differ from the original isolate are regarded as belonging either to a substrain
of the original strain, or to a new strain.
Organ of organism from which object is derived, if applicable.
Organ is defined as any part of the body exercising a specific function, such as
respiration, secretion, or digestion, if applicable.
Organelle of organism from which object is derived, if applicable.
Tissue of organism from which object is derived, if applicable. Can be used in
conjunction with Organ.
Tissue is defined as a collection of similar cells and the intercellular substances
surrounding them. Multiple tissues can be part of an Organ.
Cell type of organism from which object is derived, if applicable.
Cell type is defined as the type of an individual cell, e.g., "myoblast". This is a
cellular-level classification.
Cell line from which object is derived, if applicable
Cell line usually pertains to an immortalized version of a given cell type
Identifier assigned by ATCC.org to the cell.
'T' if source is diseased, else 'F'.
If source was diseased, describes the disease borne by it.
Stage of development associated with the object, if applicable
Sex of the organism from which object is derived, if
applicable Enumerated. Values=Male/Female/Hermaphrodite/Asexual/NULL
(NULL here means not provided by dataset)
The dataset this entity came from or is associated with
Describes idiosyncratic sub-species descriptions such as "serotype", "variety", etc.
These can be many to one (1 BioSource - many BioSubtypes) linked via
BioSourceWIDBioSubtypeWID
Warehouse GUID for this BioSubtype
Type of subtype, e.g., "serotype"
Value of the subtype, e.g., "O157"
The dataset this entity came from or is associated with
Defines a specific nucleic acid molecule, such as DNA or of RNA.
Entries in this table correspond to a real-world DNA or RNA molecules
which at one point were purified and isolated ("something you can point at"). A row in this
table
can define a complete molecule, a fragment of a molecule, or a molecule that has been
partially
sequenced in different regions.
This table will be used in several ways: (1) to associate a sequence with an entire
replicon, or a region of a replicon, when the sequence of that replicon is known; (2) to
associate
a DNA sequence with a single gene; (3) to define a DNA or RNA molecule that has not been
sequenced; (4) to define RNA molecules such as tRNAs.
Features on a NucleicAcid molecule (such as promoters or binding sites) can be defined using
the Feature table.
The Subsequence table contains zero or more full or partial sequences contents of this
molecule.
If one represents the full sequence of this molecule, Subsequence.FullSequence = 'T' where
Subsequence.NucleicAcidWID references this molecule. In this case, NucleicAcid.FullySequenced = 'T' as
well.
Warehouse identifier for this NucleicAcid.
Name or description of this molecule.
Ex: (CMR) 'Chromosome II Brucella melitensis 16M'.
Enumeration: 'DNA' 'RNA' or 'na'
Enumeration: describes the molecule as it exists in the organism; stores values such as RNA subtype
("pre-RNA", "mRNA"), replicon type (e.g., "chromosome", "plasmid")
Enumeration: 'circular', 'linear' or 'other'.
Enumeration indicating whether Nucleic Acid is single stranded, double stranded or mixed
stranded.
Enumeration describing how the sequence was generated
(e.g., from single clone, from assembly of sequences
from other sequence entries, collection of different clones, etc).
'T' if this is a fragment of a molecule,
'F' if this NucleicAcid describes an entire molecule.
'T' if the molecule is completely
sequenced within this dataset, else 'F'.
The length of the molecule, in nucleotides. This value is firm if FullySequenced is 'T';
otherwise,MoleculeLength is an approximation and is not necessarily equal to
CumulativeLength,
as the the molecule may not have been sequenced to completion.
This value is calculated if it is not explicitely stated in the source dataset
Enumeration; specifies whether MoleculeLength stores an approximate value:
'gt' for greater than,
'lt' for less than, or
'ne' for not equal.
The cumulative number of nucleotides for all Subsequences referenced by this NucleicAcid
entry,
whether contiguous or not. This value is a summation of the number of nucleotides for these
Subsequences.
If the molecule is completely sequenced, this value should be identical
to that of MoleculeLength, and both fields are populated.
Enumeration; specifies whether CumulativeLength how approximates actual total length:
'gt' for greater than,
'lt' for less than, or
'ne' for not equal.
References the genetic code of this molecule.
References the biological source of this molecule.
References the data set from which the entity came from
Contains a contiguous sequence of a nucleic acid molecule. Multiple Subsequences can make up a given
NucleicAcid entry.
Contains either the full or partial nucleotide sequence of the nucleic acid molecule stored in
NucleicAcid.
Todo: Currently the schema has no way of indicating an approximate position
of this Subsequence on the NucleicAcid as a whole.
Warehouse identifier for this Subsequence.
References the containing nucleic acid molecule.
'T' if this is the complete sequence of the nucleic acid molecule
referenced by NucleicAcidWID, else 'F'.
Nucleotide sequence of this Subsequence.
Number of nucleotides (and characters) in Sequence. This value
is calculated if it is not explicitely stated in the source
dataset
Enumeration; indicates that Length approximates actual Sequence length:
'gt' for greater than,
'lt' for less than, or
'ne' for not equal.
Percentage of Sequence nucleotides that are either guanine or cytosine.
This value is calculated if it is not explicitely stated in the source
dataset
Dataset-specific information to indicate the version of this Subsequence.
Reference to the data set from which the entity came from
Defines a notion of gene that is limited to procaryotic aspects of
genes. Later versions of the warehouse will expand this definition to include
eukaryotic aspects of genes. Separate tables define associations between a gene and
(1) its biological source(s),
(2) its protein product(s), if any, and
(3) its RNA product(s), if any.
Warehouse identifier this gene.
Name of the gene.
Reference to the NucleicAcid molecule (replicon) this gene resides upon.
Reference to the Subsequence containing the nucleotide sequence of this Gene.
Describes the type of molecule which is known to be *ultimately* produced by this gene
enumerated values (polypeptide, pre-mRNA, rRNA, tRNA, etc)
Unique ID assigned to this gene, such as by a genome project
Base position of start of coding region. Start is always less than End,
except for genes that wrap around the origin of a circular chromosome.
Base position of end of coding region.
Indexes the stop codon that terminates the gene.
Indicates that the Start position of the coding region is an approximate value.
It could be 'gt' for greater than, 'lt' for less than and 'ne' to indicate that it is not
equal. This is a controlled vocabulary.
Indicates that the End position of the coding region is an approximate value.
It could be 'gt' for greater than, 'lt' for less than and 'ne' to indicate that it is not
equal. This is a controlled vocabulary.
Direction of transcription as defined in the enumeration table
'T' if the gene is interrupted, else 'F'.
Reference to the data set from which the entity came from
Pathways are graphs of reactions, grouped together according to a
higher biological function they perform. Some pathways may be
"template", "reference", "model" or "sum of organisms" pathways. Those
pathways do not contain an BioSourceWID reference, and have the type
field set to "R" (Reference/Model/Theoretical). For real organisms,
the type is "O".
Warehouse ID for this pathway
Name of the pathway
Type of pathway (see comment above)
BioSource this pathway occurs in
WID of the dataset the pathway is from
A term is a controlled vocabulary term used within a particular dataset.
E.g. the keyword attached to proteins in SwissProt. Terms can be arranged
in a hierarchy (see the TermRelationship table).
Warehouse identifier for this term
Name for the term
Definition of the term
'T' if term is part of a hierarchy of terms
'T' if this term is at the top of a hierarchy
'T' if term is known to be obsolete
WID of the dataset the pathway is from
Defines a parameterized computation that has been performed on objects in the warehouse.
TODO: Parameters are specified in the Parameter table.
WID of this computation
Name of the algorithm, procedure, or program, e.g. 'BLAST'
Description of the computation performed
WID of the dataset the computation is from
Defines a literature citation.
Typically a citation is associated with one or more Warehouse objects via the CitationWIDOtherWID
table.
WID of this citation
Line of text containing the citation
Pubmed ID of the citation, if known
Title of the article
Author name(s)
Publication title
Publisher's name
Editor's name
Year of publication
Volume of publication
Issue number
Page number(s)
Publication URI
WID of the dataset the Citation is from
Defines an association between a warehouse entity and an external representation or depiction
of that entity in a well-defined format.
Can be used to store the contents itself, or to indicate that an archive is present at a URL.
Warehouse identifier for this entity
WID of entity archive is associated with
Storage/compression format used eg. 'zip' 'tar' 'tgz' 'jpeg'
Archive contents
Web address the archive is found at, ideally a specific file
The name of the tool or software kit the archive is used by
eg. 'MIAMExpress'
DataSet.WID this entity is associated with
Defines an experiment. Provides a context for associating experimental data with it.
Allows tree-structured experiments consisting of heterogeneous subexperiments,
subexperiments corresponding to time-series observations,
and repeated trials of identical experiments.
For a hierarchical experiment, data should be associated with the Experiment
at the appropriate level. For example, if data reflects results from averaging
numerous identically conducted trials, that data should be associated with the
Experiment representing the group of these trials.
A Comment table entry may be created to contain discussion of results, etc.
A DBID table entry may be created if the (sub)experiment has a unique name within its
DataSet.
SynonymTable table entries may be created to associate names with the (sub)experiment.
If published, a reference may be created in Citation table.
Warehouse identifier for this entity
Mnemonic for the general type of experiment, e.g. 'microarray'
Contact.WID for submitter/investigator
Archive.WID of external rep'n of experiment and its data.
Date+time experiment was started
Date+time experiment was completed
Description of this experiment
Experiment.WID defining the parent group of this subexperiment
Enumeration indicating type of any and all direct subexperiments
Exs: 'replicate' 'variant' 'step' 'time-series'
Number of child experiments loaded
Counter value identifying this experiment in a sequence or set
of subexperiments (eg. time-series). NULL if GroupWID is NULL.
Time offset indicating when associated observations in a
time-series experiment were conducted
Enumeration for units of TimePoint
DataSet.WID this entity is associated with
References the biological source of this experiment, if applicable.
Specifies a relationship between one data entity and an experiment in which it was
recorded as an observation or used in some other fashion.
Used in flow cytometry to represent both observations and filter wavelengths.
For an observation:
ExperimentData.Data contains the vector of observations
ExperimentData.MageData = NULL
ExperimentData.OtherWID = the FlowCytometrySample.WID of the sample,
ExperimentData.Role defines the reading ('forward scatter', 'side scatter', or 'filter'),
ExperimentData.Type = 'flow cytometry',
ExperimentData.Kind = 'O' (observation)
For a filter wavelength:
ExperimentData.Data = NULL
ExperimentData.MageData references a ParameterValue row for the wavelength
ExperimentData.Role = 'filter wavelength'
ExperimentData.Kind = 'P' (parameter)
ExperimentData.OtherWID = the ExperimentData.WID of the observation,
Warehouse identifier for this entity
Experiment entity
Data associated with experiment, in an unspecified format.
May be specified instead of or along with MageData.
Data associated with experiment using MAGE structure.
May be specified instead of or along with Data.
Describes how data is used in experiment
ex: 'green intensity', 'forward scatter', 'filter wavelength'
Characterizes relationship of data to experiment
When the observation was taken, the computation was performed, etc.
WID of entity this experiment data is associated with.
If Kind='O', it is typically the sample or specimen being observed.
If Kind='P', it is typically another ExperimentData or ParameterizableApplication
that is parameterized by this entity.
The data set this entity came from or is associated with
Describes the source and strength of evidence for individual facts in the warehouse.
This table is designed to allow different types of evidential support to be asserted for
different types of database assertions, such as using one set of evidence types for supporting
assertions about protein function, and another, possibly overlapping set of evidence types
for supporting assertions about protein existence.
Example use: Record that there are two sources of support for the function of a given
protein, one computational and one experimental. This table has a WID for use in the
CitationWIDOtherWID table.
WID of this support
WID of supported entity, e.g. Protein Function
Type: Identifies the type of assertion that this row pertains to.
EvidenceType: Defines the type of evidential support that this row pertains to.
0 < confidence <= 1.
The data set this entity came from or is associated with
CONSTRAINT CK_Support CHECK (Confidence > 0 AND Confidence <= 1)
The tables ChemicalAtom and ChemicalBond define the chemical bond structure of a chemical,
the
charge on the constituent atoms, and encodes a two or three dimensional representation of the
structure. It is implicit that ChemicalBonds are symmetric.
Atoms that are chiral centers are have a non-zero StereoParity field. Values for this field
are
defined in the Enumeration table, and are taken from MDL Molfile format defined in
http://www.mdli.com/downloads/ctfile/ctfile_subs.html . That specification is confusing
because
it appears to define two redundant ways (marking atoms and marking bonds) of defining stereo
configurations. Our theory is that the redundancy exists to allow different drawings of
stereo
configurations, and that for simply capturing a configuration, setting the StereoParity field
of an atom is sufficient. Also, setting the BondStereo field of a bond could simplify drawing
of chemical structures, and can allow different drawings of the same stereo configurations,
which can be desirable. But these two fields can be interpreted independently of one another.
See the appendix of the MDL specification for details on interpreting stereo configurations.
E.g. H2O could be encoded as:
ChemicalAtom (wid, 1, 'H', 0)
ChemicalAtom (wid, 2, 'O', 0)
ChemicalAtom (wid, 3, 'H', 0)
ChemicalBond (wid, 1, 2, 1)
ChemicalBond (wid, 2, 3, 1)
WID of the chemical
Order of the atoms within the structure,
starting from 1
Element symbol of the atom
Charge on the atom
X display coordinates for a drawing of the chemical structure
Y display coordinates for a drawing of the chemical structure
Z display coordinates for a drawing of the chemical structure
Defines parity of an atom that is a chiral center.
CONSTRAINT UN_ChemicalAtom UNIQUE (ChemicalWID, AtomIndex)
The tables ChemicalAtom and ChemicalBond define the chemical bond structure of a chemical, the charge
on
the constituent atoms, and encodes a two or three dimensional representation of the
structure.
It is implicit that ChemicalBonds are symmetric. BondTypes and BondStereo are defined in the
Enumeration table, and are taken from MDL Molfile format defined in
http://www.mdli.com/downloads/ctfile/ctfile_subs.html . That specification is confusing. See
documentation of ChemicalAtom table for more information.
E.g. H2O could be encoded as:
ChemicalAtom (wid, 1, 'H', 0)
ChemicalAtom (wid, 2, 'O', 0)
ChemicalAtom (wid, 3, 'H', 0)
ChemicalBond (wid, 1, 2, 1)
ChemicalBond (wid, 2, 3, 1)
WID of the chemical
Index of first atom bonded (from ChemicalAtom)
Index of second atom bonded
Type of bond enumeration, e.g., 1=Single, 2=Double, 3=Triple, 4=Aromatic.
Stereo information about bond, e.g., 0 = Not stereo.
Cofactors are chemicals that are required for the enzyme to catalyze
the reaction, but are left unchanged by the reaction. If multiple
cofactors are listed for a reaction, this is interpreted as a disjunction.
This table also encodes prosthetic groups.
EnzymaticReaction.WID of the Enzymatic Reaction
Chemical.WID of the compound
'T' if covalently/tightly bound to enzyme, else 'F'
Identifies a compound that is either an alternate substrate or an alternate cofactor
to a primary compound present in an enzymatic reaction.
EnzymaticReaction.WID of the Enzymatic Reaction
Chemical.WID of primary compound
Chemical.WID of alternate compound
'T' if this alternative is a cofactor, 'F' if it is a substrate
Associates an enzymatic reaction to the compounds that act as
inhibitors and activators for the reaction.
The mechanism of action is encoded in the Mechanism column.
EnzymaticReaction.WID of the Enzymatic Reaction
Chemical.WID or Protein.WID of the compound
Specifies whether the compound is an inhibitor or an activator.
Mechanism of inhibition or activation.
'T' if physiologically relevant, else 'F'
Defines one or more locations of a protein.
WID of the protein
Subcellular location of a protein.
This table allows us to state that two pathways are neighbors in
a biologically significant sense, because they share a substrate
in common. This link between two pathways is represented by the WIDs of the
interacting pathways, and of the chemical compound that they share.
WID of one of the linked pathways
WID of the other linked pathways
WID of the linking chemical
A pathway is defined as a set of reaction pairs or a collection of molecular interactions between
molecules.
This table stores not only the relationships between pathway and reactions, but also relationships between
molecular interaction network/pathway and interactions.
For each pair of reactions R1 and R2, R1 directly precedes R2 in the pathway.
Some reactions in a pathway may be considered hypothetical, probably because the presence of the enzyme
has not been demonstrated.
To specify an interaction is a part of a molecular interaction network/pathway, use R2 to represents
a molecular interaction, leave R1 blank.
WID of a pathway
WID of a reaction, R2, in the pathway
WID, R1, of a predecessor reaction of R2
'F' if R2 proven to exist, 'T' otherwise.
Associates a reaction with a chemical product of that reaction.
Warehouse identifier of the reaction that this reactant is part of.
Reference to the chemical or protein that is the reactant.
The number of molecules of this reactant used in the reaction.
Associates a reaction with a chemical that is consumed by the reaction.
Warehouse identifier of the reaction that this reactant is part of
Reference to the chemical or protein that is the reactant.
The amount of this reactant used in the reation
Associates an interaction with the entity that participates in the interaction.
Reference to the interaction that the entity is involved in.
Reference to the protein, nucletic acid, chemical that involves in the interaction.
The amount of this interaction participant involved in the interaction, if available.
Records a result of a computation of the degree of match between two sequences.
Sequences are either both Proteins or both Subsequences.
WID of the Protein or Subsequence being matched
WID of the Protein or Subsequence matched against QueryWID
WID of the Computation that describes the procedure used to determine the match
Roughly, the log-probability of this match occurring; see
http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html
1 - e^(-E), where E is EValue
Percentage of residues in the two molecules that are identical
Percentage of residues in the two molecules that are similar
Ordinal rank of Query molecule with other matches (1 is best)
The length of the match between the two molecules
Start of the matching region in Query
End of the matching region in Query
Start of the matching region in Match
End of the matching region in Match
Specifies that Subunit is a subunit of Complex. These subunit relationships could be
described in multiple levels. For example, this table can be used to describe multimeric
proteins,
or ribosomes.
Reference to the parent Protein
Reference to the child protein inside the parent Protein
Number of copies of the subunit within the complex
Pathways may be arranged in a hierarchy, i.e. containment within one or
more superpathways, as an abstraction mechanism.
WID of sub-pathway
WID of super-pathway
Defines a relationship between two terms.
Reference to a term.
The WID of the term the current term is related to.
Enumeration.
Defines a relationship between a term and another object.
For relationships between terms, TermRelationship is generally used.
Reference to a term.
The WID of the object associated with this term.
Enumeration.
Link from citations to the entities described in that citation. Enables one citation to
provide support for multiple entries in the warehouse.
WID of the object associated with this citation
WID of the Citation
This table allows for arbitrary association of (possibly lengthy) comments
with any object in the warehouse.
See the Description table for a more specific type of comment.
Warehouse id of an object
Comment about the object
This table is used to define (i) links between databases; (ii) links between objects within the same
dataset.
For case (i):
A row in this table defines a link between an object in the warehouse
(OtherWID) and an entry in another dataset that may or may not be loaded
into the warehouse. If it is not loaded, DatabaseName
(and XID, Type, and Version if available) will be nonnull.
For case (ii):
A row in this table defines a link between an object in the warehouse
(OtherWID) and an object in the same dataset for which the dataset specifies
an association between them not otherwise represented within the warehouse.
Such associations are currently (5/10/04) made between a gene described in one sequence (the root
Bioseq) and
another GenBank entry (the reference Bisoseq) which is being referenced and describes the gene
independently
of the first Bioseq. In such a case, CrossReference.OtherWID=Gene.WID.
In either case: if CrossWID is nonnull, the object linked to is
loaded into the warehouse; if it is null, it may or may not be loaded.
Note that if a loader does not know whether a referenced entry will be loaded,
it is free to fill in CrossWID at a later time.
Restrictions: CrossReference only stores keys that point to uniquely identified objects in the
referenced database.
Warehouse object we are linking FROM
Nonnull when the object we are linking TO resides in the warehouse
Unique id used in referenced database of object we are linking TO.
Enumeration: Describes the types of identifiers stored in
XID, namely 'GUID' or 'Accession': GUIDs: ID's of type GUID
(Globally Unique ID) are associated with database objects with one
or more invariant aspects, such as a specific DNA sequence. If the
invariant aspect of the database object is to change, a new GUID is
assigned, and the old GUID is retired. Example: NCBI GI numbers.
Accession: Database objects associated with IDs of type 'Accession'
(for Accession Numbers) can change, but the Accession Number remains
the same. Accession Numbers are often associated with a Version
number to reflect such changes. Example: Swiss-Prot's Primary
Accession Number See Enumeration table for further
details.
Further qualifies the values of identifiers stored in XID by
storing the version number of the identifier for datasets that
support multiple instances of the same object. For example,
NCBI Accession Numbers are associated with a version number,
which are REQUIRED for complete identification (w/o such,
different records can have the same accession number, albeit
with different version numbers)
A short description of the relationship between the objects identified by OtherWID and CrossWID
The object we are linking TO resides in an external database of this name
This table contains a textual description of a warehouse object.
An object will not have more than one description, and the description text
will typically define or otherwise characterize the object.
See the CommentTable table for a more general type of comment.
Warehouse id of an object
Name of Warehouse table containing OtherWID
Description of the object
Associates a warehouse entity with the identifier(s) used for that entity in its
source dataset. For example, if a protein is loaded from SwissProt into the
warehouse, this table can be used to store the SwissProt accession numbers for
the protein.
Restrictions: DBID only stores keys that point to uniquely identified objects in the referenced
database.
Reference to the warehouse entity uniquely identified by this entry
Unique identifier used in dataset of entity
Enumeration: Describes the types of identifiers stored in
XID, namely 'GUID' or 'Accession': GUIDs: ID's of type GUID
(Globally Unique ID) are associated with database objects with one
or more invariant aspects, such as a specific DNA sequence. If the
invariant aspect of the database object is to change, a new GUID is
assigned, and the old GUID is retired. Example: NCBI GI numbers.
Accession: Database objects associated with IDs of type 'Accession'
(for Accession Numbers) can change, but the Accession Number remains
the same. Accession Numbers are often associated with a Version
number to reflect such changes. Example: Swiss-Prot's Primary
Accession Number See Enumeration table for further
details.
Further qualifies the values of identifiers stored in XID by
storing the version number of the identifier for datasets that
support multiple instances of the same object. For example,
NCBI Accession Numbers are associated with a version number,
which are REQUIRED for complete identification (w/o such,
different records can have the same accession number, albeit
with different version numbers)
Defines one or more synonyms for a warehouse entity such as a protein, a
gene, a small molecule, or a pathway.
Warehouse ID of an entity
Another name for the entity
This table captures meta-data that does not have an interpretation in
the warehouse semantics, but is `hints' to various tools that may
operate on, or build pictorial representations of, core elements of the
schema. For example, it may give hints to a particular pathway viewing
tool on how to layout a pathway.
The entity to which this advice applies
The name of the tool
The advice
Linking table which links BioSource and BioSubtype
Links to the BioSource associated with this object.
Links to the BioSubtype associated with this object.
Associates a gene with those species, strains, tissues, etc, from which it was derived.
Reference to the BioSource that has this gene.
Reference to the Gene that is present in the organism.
Associates a protein with those species, strains, tissues, etc, from which it was derived.
Reference to the BioSource that has this protein.
Reference to the Protein that is present in the organism.
Associates a gene with its nucleic acid product(s).
Note that the nucleic acid (ie. replicon) containing the gene is referenced by
Gene.NucleicAcidWID,
not in this table.
Reference to the Gene that produces this nucleic acid.
Reference to the nucleic acid that has this gene.
Associates a gene with its protein product(s).
Reference to the Gene that produces this protein.
Reference to the protein that has this gene.
Associates a non-enzymatic function with a protein that has that function.
Reference to the protein that has this function.
Reference to the function for this protein.
Relates one experiment to another.
This table supports a many to many relationship.
Experiment entity
The WID of the experiment the current term is related to
Describes the location of a spot on a gel.
This tables maps spots to the one or more tables that they are found on.
Describes the X and Y coordinates on the Gel.
Information for the particular gel conditions that the spot was identified
on can be found in the Experiment table.
Warehouse identifier for this entity
The location record is for this spot.
The x-coordinate of the spot on the gel.
The y-coordinate of the spot on the gel.
Y or N.
A spot can be identified across multiple gels, so this columnn.
is used to indicate whether the X/Y coords of this particular gel was used to
determine the molecular weight and isolectric point for the spot.
Experiment entity
Describes the gel conditions for this particular record.
The dataset the entity is from
Associates a spot with a known protein.
Not all spots are associated with proteins since it is not necessarily
known what the protein is for a given spot.
This table supports the ability to have a spot linked to multiple protein,
or a protein linked to multiple spots.
Reference to the protein that has been mapped to this spot.
Reference to the Protein that is associated to this spot.
Describes a spot from a 2D Gel experiment.
A spot can be linked to one or more gels and the location on the gel. The
gel location information is stored in the ExperimentData table.
A spot can be identified to be a particluar protein in the protein table
and is associated to proteins via the ProteinWIDSpotWID table
The method used to identify the spot is contained in the SpotWIDSpotIDMethodWID
table and the SpotIDMethod table.
The growth conditions for the protein is found in the ExperimentData tableeh
The Spot Name/ID goes into the SpotId row, but additional names can be stored
as DBID table entry.
Warehouse identifier for this entity
Name of the spot
Can be null
Molecular weight estimated from migration on 2D gels.
Units: Daltons.
Isoelectric point (pI) estimated from migration on 2D gels.
The dataset the entity is from
Describes the method by which a spot was identified as
a particular (known) protein in the protein table.
Warehouse identifier for this entity
The name of the method
ex: Co-migration
More detailed description of method.
Ex: Co-migration with purified protein
A short abbreviation for the method name.
ex: C
The dataset the entity is from
Associates a spot with a SpotIdMethod,
which is the method used to identify a spot with a particular protein.
A spot can be identified as a particular protein by multiple methods,
so this table supports this many-to-many relationship.
Reference to the2A Spot record.
Reference to the method that was used to identify a spot as a
particular protein.