The Sprout database contains 34.6 billion characters of data and and additional 2.8 gigabytes of search indexes. The main tables are shown in the diagram below. Rectangles represent entities (sometimes also called objects) and diamonds represent relationships. Ovals represent external data servers. Hold the mouse over a shape to see a short description. A thick connecting line indicates a multiply-occurring relationship in that direction; a thin one indicates a singly-occurring relationship in that direction. Clicking on most shapes will take you to more detailed information.
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The Sprout database contains the genetic data for all complete organisms in the SeedEnvironment. The data that is not in Sprout-- attributes, similarities, couplings-- is stored on external servers available to the Sprout software. The Sprout database is reloaded approximately once per month. There is significant redundancy in the Sprout database because it has been optimized for searching. In particular, the Feature table contains an extra copy of the feature's functional role and a list of possible search terms.
Data Types
Type
Indexable
Sort
Pos
Format
Description
boolean
yes
numeric
1
scalar
Boolean value (0 or 1).
char
yes
alphabetic
1
scalar
Single-character value.
counter
yes
numeric
1
scalar
Large, unsigned integer, ranging from 0 to 9 quintillion.
date
yes
numeric
1
scalar
Date and time stamp, in seconds since 1970.
dna
no
alphabetic
5
scalar
Long DNA sequence, compressed
float
yes
numeric
1
scalar
Floating-point number, approximately 15 significant digits, from 10^-308 to 10^+308.
hash-string
yes
alphabetic
1
scalar
A Base64 Digest MD5 code.
int
yes
numeric
1
scalar
Standard signed integers, ranging from approximately -2 billion to 2 billion.
link
prefix
alphabetic
3
HyperLink
Short character string, with optional associated URL.
long-string
yes
alphabetic
4
scalar
Character string, up to approximately 500 characters long, fully indexable.
semi-boolean
yes
alphabetic
1
scalar
Ternary boolean value-- Y, N, or ?.
string
yes
alphabetic
2
scalar
Short character string, from 0 to approximately 250 characters.
text
prefix
alphabetic
4
scalar
Long character string, from 0 to approximately 16 million characters, not generally indexable.
Entities
Annotation
An annotation contains supplementary information about a feature. The most important type of annotation is the assignment of a functional role; however, other types of annotations are also possible.
A CDD is a protein domain designator. It represents the shape of a molecular unit on a feature's protein. The ID is six-digit string assigned by the public Conserved Domain Database. A CDD can occur on multiple features and a feature generally has multiple CDDs.
Name used in reaction display strings. This is the same as the name possessing a priority of 1, but it is placed here to speed up the query used to create the display strings.
CompoundCAS
This entity represents the Chemical Abstract Service ID for a compound. Each Compound has at most one CAS ID.
A contig is a contiguous run of residues. The contig's ID consists of the genome ID followed by a name that identifies which contig this is for the parent genome. As is the case with all keys in this database, the individual components are separated by a period. A contig can contain over a million residues. For performance reasons, therefore, the contig is split into multiple pieces called sequences. The sequences contain the characters that represent the residues as well as data on the quality of the residue identification.
A functional diagram describes a network of chemical reactions, often comprising a single subsystem. A diagram is identified by a short name and contains a longer descriptive name. The actual diagram shows which functional roles guide the reactions along with the inputs and outputs; the database, however, only indicates which roles belong to a particular diagram's map.
An external database identifies a biological database surveyed by PIR International as part of an effort to determine which features are essentially identical between bioinformatics organizations. Each feature in the database will have zero or more corresponding IDs that are captured from the PIR data. Each corresponding ID is represented in a relationship between an external database and the feature itself.
A feature (sometimes also called a "gene" is a part of a genome that is of special interest. Features may be spread across multiple contigs of a genome, but never across more than one genome. Features can be assigned to roles via spreadsheet cells, and are the targets of annotation. Each feature in the database has a unique FigId.
name of the user who made the functional assignment
assignment-quality
char
quality of the functional assignment, usually a space, but may be W (indicating weak) or X (indicating experimental)
conserved-neighbors
int
number of coupled features
feature-type
string
Code indicating the type of this feature. Among the codes currently supported are "peg" for a protein encoding gene, "bs" for a binding site, "opr" for an operon, and so forth.
in-genbank
boolean
TRUE if a feature can be found in GenBank, else FALSE
isoelectric-point
float
pH in the surrounding medium at which the charge on a protein is neutral. If the pH of the medium is lower than this value, the protein will have a net positive charge. If the pH of the medium is higher, then the protein will have a net negative charge.
keywords
text
This is a list of search keywords for the feature. It includes the functional assignment, subsystem roles, and special properties.
location-string
text
Location of the feature, expressed as a comma-delimited list of Sprout location strings. This gives us a fast mechanism for extracting the feature location. Otherwise, we have to painstakingly paste together the IsLocatedIn records, which are themselves designed to help look for features in a particular region rather than to find the location of a feature.
locked
boolean
TRUE if a feature's assignment is locked. A locked feature's functional role cannot be changed by automated programs.
molecular-weight
float
Molecular weight of this feature's protein, in daltons. A weight of 0 indicates that no protein is created.
sequence-length
counter
Number of base pairs in this feature.
signal-peptide
string
The signal peptide location for this feature. This is expressed as start and end numbers with a hyphen for the relevant amino acids. So, "1-22" would indicate a signal peptide at the beginning of the feature's protein and extending through 22 amino acid positions. An empty string means no signal peptide is present.
similar-to-human
boolean
TRUE if this feature generates a protein that is similar to one found in humans, else FALSE
transmembrane-domain-count
int
number of sections in the feature's protein that become embedded in the cell membrane
transmembrane-map
text
A map indicating which sections of a protein will be embedded in a membrane. This is expressed as a comma-separated list of as start and end numbers with hyphens for the relevant amino acids. So, "10-12, 40-60" would indicate that there are two sections of the protein that become embedded in a membrane: the 10th through 12th amino acids, and the 40th through the 60th. An empty string means no transmembrane regions are known.
ec
string array
An EC number associated with this feature.
essential
link array
A value indicating the essentiality of the feature, coded as HTML. In most cases, this will be a word describing whether the essentiality is confirmed (essential) or potential (potential-essential), hyperlinked to the document from which the essentiality was curated. If a feature is not essential, this field will have no values; otherwise, it may have multiple values.
iedb
link array
A value indicating whether or not the feature can be found in the Immune Epitope Database. If the feature has not been matched to that database, this field will have no values. Otherwise, it will have an epitope name and/or sequence, hyperlinked to the database.
link
text array
Web hyperlink for this feature. A feature can have no hyperlinks or it can have many. The links are to other websites that have useful about the gene that the feature represents, and are coded as raw HTML.
translation
text array
(optional) A translation of this feature's residues into protein character codes, formed by concatenating the pieces of the feature together. Only protein encoding genes have translations.
upstream-sequence
text array
Upstream sequence for the feature. This includes residues preceding the feature as well as some of the feature's initial residues.
virulent
link array
A value indicating the virulence of the feature, coded as HTML. In most cases, this will be a phrase or SA number hyperlinked to the document from which the virulence information was curated. If the feature is not virulent, this field will have no values; otherwise, it may have multiple values.
FeatureAlias
Alternative names for features. A feature can have many aliases. In general, each alias corresponds to only one feature, but there are many exceptions to this rule.
Y/N/? flag indicating whether or not this organism produces endospores.
gc-content
float
Percentage of the genome that consists of G and C base pairs.
genus
string
Genus of the relevant organism.
gram-stain
semi-boolean
Gram stain behaviour of organism-- positive, negative, or unknown.
habitat
string
Preferred habitat of organism.
motility
semi-boolean
Y/N/? flag indicating whether or not this organism can move under its own power.
optimal-temperature-range
string
Indication of this organism's behavior relating to environmental temperature.
oxygen
string
Indication of this organism's behavior relating to environmental oxygen.
pathogenic
semi-boolean
Y/N/? flag indicating whether or not this organism is pathogenic.
pegs
int
Number of protein encoding genes for this organism
primary-group
string
The primary NMPDR group for this organism. There is always exactly one NMPDR group per organism (either based on the organism name or a default value for supporting genomes). In general, more data is kept on organisms in NMPDR groups than on supporting organisms.
rnas
int
Number of RNA features found for this organism.
salinity
string
Indication of this organism's behavior relating to environmental salinity.
scientific-name
string
Scientific name of this genome, usually consisting of the genus, species, and unique characterization.
species
string
Species of the relevant organism.
taxonomy
text
The taxonomy string contains the full taxonomy of the organism, with individual elements separated by semi-colons (and optional white space), starting with the domain and ending with the disambiguated genus and species (which is the organism's scientific name plus an identifying string).
temperature-max
float
Maximum optimal temperature for this organism, in degrees Celsius.
temperature-min
float
Minimum optimal temperature for this organism, in degrees Celsius.
unique-characterization
string
The unique characterization identifies the particular organism instance from which the genome is taken. It is possible to have in the database more than one genome for a particular species, and every individual organism has variations in its DNA.
version
string
Version string for this genome, generally consisting of the genome ID followed by a period and a string of digits.
GenomeSubset
A genome subset is a named collection of genomes that participate in a particular subsystem. The subset names are generally very short, non-unique strings. The ID of the parent subsystem is prefixed to the subset ID in order to make it unique.
A keyword is a word that can be used to search the feature table. This entity contains the keyword's stem, its phonetic form, and the number of features that can be found by searching for the word.
Name
Type
Notes
id
string
Unique identifier for this Keyword.
phonex
string
A phonex is a string that identifies the phonetic characteristics of the word stem. This can be used to find alternative spellings if an matching word is not present.
stem
string
The stem of a keyword is a normalized form that is independent of parts of speech. The actual keywords stored in the database search index are stems.
Ligand
A Ligand is a chemical of interest in computing docking energies against a PDB. The ID of the ligand is an 8-digit ID number in the ZINC database.
A PDB is a protein data bank entry containing information that can be used to determine the shape of the protein and the energies required to dock with it. The ID is the four-character name used on the PDB web site.
The number of ligands that have been docked against this PDB.
Property
A property is a type of assertion that could be made about the properties of a particular feature. Each property instance is a key/value pair and can be associated with many different features. Conversely, a feature can be associated with many key/value pairs, even some that notionally contradict each other. For example, there can be evidence that a feature is essential to the organism's survival and evidence that it is superfluous.
Value associated with this property. For each property name, there must by a property record for all of its possible values.
ProteinFamily
A protein family represents a group of proteins with related functions. Some protein families are downloaded from the PFAM database and some are FIGfams. The protein family keys all begin with the letters PF and the FIGfams with the letters FIG.
HTML string containing a link to a web location that describes the reaction. This field is optional.
Role
A role describes a biological function that may be fulfilled by a feature. One of the main goals of the database is to record the roles of the various features.
A role subset is a named collection of roles in a particular subsystem. The subset names are generally very short, non-unique strings. The ID of the parent subsystem is prefixed to the subset ID in order to make it unique.
Part of the process of subsystem annotation of features is creating a spreadsheet of genomes and roles to which features are assigned. A spreadsheet cell represents one of the positions on the spreadsheet.
Column number of this cell. This value is put here to improve the performance of an essential query.
Scenario
A scenario used to verify the validity of subsystem assignments. Each scenario converrts input compounds to output compounds using reactions. The scenario may use all of the reactions controlled by a subsystem or only some, and may also incorporate additional reactions.
A sequence is a continuous piece of a contig. Contigs are split into sequences so that we don't have to have the entire contig in memory when we are manipulating it. The key of the sequence is the contig ID followed by the index of the begin point.
String describing the quality data for each base pair. Individual values will be separated by periods. The value represents negative exponent of the probability of error. Thus, for example, a quality of 30 indicates the probability of error is 10^-30. A higher quality number indicates a better chance of a correct match. It is possible that the quality data is not known for a sequence. If that is the case, the quality vector will contain the string "unknown".
sequence
dna
String consisting of the residues (base pairs). Each residue is described by a single character in the string.
Source
A source describes a place from which genome data was taken. This can be an organization or a paper citation.
A subsystem is a collection of roles that work together in a cell. Identification of subsystems is an important tool for recognizing parallel genetic features in different organisms.
Name of the person currently in charge of the subsystem.
description
text
Description of the subsystem's function in the cell.
notes
text
Descriptive notes about the subsystem.
version
int
Version number for the subsystem. This value is incremented each time the subsystem is backed up.
classification
string array
Classification string, colon-delimited. This string organizes the subsystems into a hierarchy.
hope-curation-notes
text array
Text description of how the scenarios were curated.
SynonymGroup
A synonym group represents a group of features. Features that represent substantially identical proteins or DNA sequences are mapped to the same synonym group, and this information is used to expand similarities.
This relationship connects a role to the reactions it catalyzes. The purpose of a role is to create proteins that trigger certain chemical reactions. A single reaction can be triggered by many roles, and a role can trigger many reactions.
This relationship connects a genome to the sources that mapped it. A genome can come from a single source or from a cooperation among multiple sources.
This relationship connects a subset to the genomes that it covers. A subset is, essentially, a named group of genomes participating in a specific subsystem, and this relationship effects that. Note that while a genome may belong to many subsystems, a subset belongs to only one subsystem, and all genomes in the subset must have that subsystem in common.
This relationship connects a role subset to the roles that it covers. A subset is, essentially, a named group of roles belonging to a specific subsystem, and this relationship effects that. Note that will a role may belong to many subsystems, a subset belongs to only one subsystem, and all roles in the subset must have that subsystem in common.
Indicates that a docking result exists between a PDB and a ligand. The docking result describes the energy required for the ligand to dock with the protein described by the PDB. A lower energy indicates the ligand has a good chance of disabling the protein. At the current time, only the best docking results are kept.
Name
Type
Notes
electrostatic-energy
float
Docking energy in kcal/mol that results from the movement of electrons (electrostatic force) between the PDB and the ligand.
Indication of the reason for determining the docking result. A value of Random indicates the docking was attempted as a part of a random survey used to determine the docking characteristics of the PDB. A value of Rich indicates the docking was attempted because a low-energy docking result was predicted for the ligand with respect to the PDB.
This relationship connects a genome to all of its features. This relationship is redundant in a sense, because the genome ID is part of the feature ID; however, it makes the creation of certain queries more convenient because you can drag in filtering information for a feature's genome.
This relationship connects a subsystem to its constituent genome subsets. Note that some genomes in a subsystem may not belong to a subset, so the relationship between genomes and subsystems cannot be derived from the relationships going through the subset.
This relationship connects a feature to its known property values. The relationship contains text data that indicates the paper or organization that discovered evidence that the feature possesses the property. So, for example, if two papers presented evidence that a feature is essential, there would be an instance of this relationship for both.
Name
Type
Notes
evidence
text
URL or citation of the paper or institution that reported evidence of the relevant feature possessing the specified property value.
This relationship connects a feature to the subsystems in which it participates. This is technically redundant information, but it is used so often that it gets its own table for performance reasons.
This relationship connects a subsystem to its constituent role subsets. Note that some roles in a subsystem may not belong to a subset, so the relationship between roles and subsystems cannot be derived from the relationships going through the subset.
This relationship connects a subsystem to the spreadsheet cells used to analyze and display it. The cells themselves can be thought of as a grid with Roles on one axis and Genomes on the other. The various features of the subsystem are then assigned to the cells.
This relationship connects a reaction to the compounds that participate in it.
Name
Type
Notes
discriminator
int
A unique ID for this record. The discriminator does not provide any useful data, but it prevents identical records from being collapsed by the SELECT DISTINCT command used by ERDB to retrieve data.
An optional character string that indicates the relative position of this compound in the reaction's chemical formula. The location affects the way the compounds present as we cross the relationship from the reaction side. The product/substrate flag comes first, then the value of this field, then the main flag. The default value is an empty string; however, the empty string sorts first, so if this field is used, it should probably be used for every compound in the reaction.
main
boolean
TRUE if this compound is one of the main participants in the reaction, else FALSE. It is permissible for none of the compounds in the reaction to be considered main, in which case this value would be FALSE for all of the relevant compounds.
product
boolean
TRUE if the compound is a product of the reaction, FALSE if it is a substrate. When a reaction is written on paper in chemical notation, the substrates are left of the arrow and the products are to the right. Sorting on this field will cause the substrates to appear first, followed by the products. If the reaction is reversible, then the notion of substrates and products is not at intuitive; however, a value here of FALSE still puts the compound left of the arrow and a value of TRUE still puts it to the right.
stoichiometry
string
Number of molecules of the compound that participate in a single instance of the reaction. For example, if a reaction produces two water molecules, the stoichiometry of water for the reaction would be two. When a reaction is written on paper in chemical notation, the stoichiometry is the number next to the chemical formula of the compound.
Each Feature relates to multiple ExternalDatabases.
Each ExternalDatabase relates to multiple Features
This relationship connects a feature to external databases that contain essentially identical features. The name used in the external database is stored in the relationship as intersection data.
Name
Type
Notes
alias
string
ID of the feature in the specified external database.
Relates a compound's CAS ID to the compound itself. Every CAS ID is associated with a compound, and some are associated with two compounds, but not all compounds have CAS IDs.
This relationship connects a feature to the contig segments that work together to effect it. The segments are numbered sequentially starting from 1. The database is required to place an upper limit on the length of each segment. If a segment is longer than the maximum, it can be broken into smaller bits. The upper limit enables applications to locate all features that contain a specific residue. For example, if the upper limit is 100 and we are looking for a feature that contains residue 234 of contig ABC, we can look for features with a begin point between 135 and 333. The results can then be filtered by direction and length of the segment.
Name
Type
Notes
beg
int
Index (1-based) of the first residue in the contig that belongs to the segment.
dir
char
Direction of the segment: + if it is forward and - if it is backward.
Number of residues in the segment. A length of 0 identifies a specific point between residues. This is the point before the residue if the direction is forward and the point after the residue if the direction is backward.
A contig is stored in the database as an ordered set of sequences. By splitting the contig into sequences, we get a performance boost from only needing to keep small portions of a contig in memory at any one time. This relationship connects the contig to its constituent sequences.
This relationship connects a feature with the various places in a cell that the feature might be found. The confidence factor is included as intersection data.
Name
Type
Notes
confidence
float
Confidence that the protein will be found in this location, expressed as a value from 0 to 10.
This relationship connects a genome to its representative. Genomes are partitioned into multiple sets of close strains, each having a single representative. In certain situations, it is desirable to analyze only representative genomes rather than the full suite.
This relationship identifies the users trusted by each particular user. When viewing functional assignments, the assignment displayed is the most recent one by a user trusted by the current user. The current user implicitly trusts himself. If no trusted users are specified in the database, the user also implicitly trusts the user FIG.
A description of the status of a role in relation to the reactions it produces as determined by the scenarios. If present, will indicate if the role has been determined to be auxiliary, if it has been examined to verify an automatic assignment, and so forth.
This relationship connects subsystems to the genomes that use it. If the subsystem has been curated for the genome, then the subsystem's roles will also be connected to the genome features through the SSCell object.
Code indicating the subsystem variant to which this genome belongs. Each subsystem can have multiple variants. A variant code of -1 indicates that the genome does not have a functional variant of the subsystem. A variant code of 0 indicates that the genome's participation is considered iffy.
RoleOccursIn
Each Role relates to multiple Diagrams.
Each Diagram relates to multiple Roles
This relationship connects a role to the diagrams on which it appears. A role frequently identifies an enzyme, and can appear in many diagrams. A diagram generally contains many different roles.
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