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. A [[Genome]] contains the sequence data for a particular individual organism. Genus of the relevant organism. Species of the relevant organism. 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 for this genome, generally consisting of the genome ID followed by a period and a string of digits. The access code field is deprecated. Its function has been replaced by the account management system developed for the [[RapidAnnotationServer]]. TRUE if the genome is complete, else FALSE number of base pairs in the genome The taxonomy string contains the full [[Wikipedia:taxonomy]] of the organism, while 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). The primary NMPDR group for this organism. There is always exactly one NMPDR group per organism (either based on the organism name or the default value =Supporting=). In general, more data is kept on organisms in NMPDR groups than on supporting organisms. Number of contigs for this organism. Number of [[protein encoding genes]] for this organism Number of RNA features found for this organism. This index allows the applications to find all genomes associated with a specific access code, so that a complete list of the genomes users can view may be generated. This index allows the applications to find all genomes associated with a specific primary (NMPDR) group. This index allows the applications to find all genomes for a particular species. 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 [[http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml Conserved Domain Database]]. A CDD can occur on multiple features and a feature generally has multiple CDDs. A _source_ describes a place from which genome data was taken. This can be an organization or a paper citation. URL the paper cited or of the organization's web site. This field optional. Description of the source. The description can be a street address or a citation. 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 _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 consisting of the residues (base pairs). Each residue is described by a single character in the string. 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=. A _keyword_ is a word stem that can be used to search the feature table. This entity indicates how many features correspond to each word. Number of features that can be found by searching for the specified keyword. 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]]. 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. _(optional)_ A translation of this feature's residues into character codes, formed by concatenating the pieces of the feature together. For a [[protein encoding gene]], the translation contains protein characters. For other types it contains DNA characters. Upstream sequence for the feature. This includes residues preceding the feature as well as some of the feature's initial residues. Default functional assignment for this feature. (This field is deprecated.) TRUE if this feature is still considered valid, FALSE if it has been logically deleted. name of the user who made the functional assignment quality of the functional assignment, usually a space, but may be W (indicating weak) or X (indicating experimental) This is a list of search keywords for the feature. It includes the functional assignment, subsystem roles, and special properties. 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, using <a href="_link_">_text_</a> notation. _(optional)_ A number between 0 and 1 that indicates the degree to which this feature's DNA is conserved in related genomes. A value of 1 indicates perfect conservation. A value less than 1 is a reflection of the degree to which gap characters interfere in the alignment between the feature and its close relatives. 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. 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. The cello value specifies the expected location of the protein: cytoplasm, cell wall, inner membrane, and so forth. 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. 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. This index allows us to locate a feature by its CELLO value. 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. A _user_ is a person who can make annotations and view data in the database. The user object is keyed on the user's login name. Full name or description of this user. This field is deprecated. 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. 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. EC code for a role. 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. Date and time of the annotation. Text of the annotation. This index allows the user to find recent annotations. A _reaction_ is a chemical process catalyzed by a protein. The reaction ID is generally a small number preceded by a letter. HTML string containing a link to a web location that describes the reaction. This field is optional. TRUE if this reaction is reversible, else FALSE A _compound_ is a chemical that participates in a reaction. All compounds have a unique ID and may also have one or more names. 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. A _compound name_ is a common name for the chemical represented by a compound. This entity represents the [[http://www.cas.org/ Chemical Abstract Service]] ID for a compound. Each Compound has at most one CAS ID. 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. See also [[Subsystems Approach]] and [[Subsystem]]. Name of the person currently in charge of the subsystem. Descriptive notes about the subsystem. Description of the subsystem's function. Classification string, colon-delimited. This string organizes the subsystems into a hierarchy. 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. 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. Part of the process of [[SubsystemsApproach][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. 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. Name of this property. Value associated with this property. For each property name, there must by a property record for all of its possible values. This index enables the application to find all values for a specified property name, or any given name/value pair. A functional diagram describes a network 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. Descriptive name of this diagram. An external alias is a feature name for a functional assignment that is not a FIG ID. Functional assignments for external aliases are kept in a separate section of the database. This table contains a description of the relevant organism for an external alias functional assignment. Descriptive name of the target organism for this external alias. An external alias is a feature name for a functional assignment that is not a FIG ID. Functional assignments for external aliases are kept in a separate section of the database. This table contains the functional role for the external alias functional assignment. Functional role for this external alias. A _family_ (also called a [[FigFam]]) is a group of homologous features believed to have the same function. Families provide a mechanism for verifying the accuracy of functional assignments and are also used in [[Rapid Annotation]] and in determining phylogenetic trees. The functional assignment expected for all PEGs in this family. The number of proteins in this family. This may be larger than the number of PEGs included in the family, since the family may also contain external IDs. 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 [[http://www.rcsb.org PDB web site]]. The number of ligands that have been docked against this PDB. 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 [[http://zinc.docking.org ZINC database]]. Chemical name of this ligand. This relationship connects a feature to its CDD protein domains. The match score is included as intersection data. This is the match score between the feature and the CDD. A lower score is a better match. 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. Relates a role to its EC number. Every EC number is associated with a role, but not all roles have EC numbers. Connects an alias to the feature it represents. Every alias connects to at least 1 feature, and a feature connects to many aliases. Connects a compound to its names. A compound generally has several names Priority of this name, with 1 being the highest priority, 2 the next highest, and so forth. This index enables the application to view the names of a compound in priority order. Relates a PDB to features that produce highly similar proteins. Similarity score for the comparison between the feature and the PDB protein. A lower score indicates a better match. Starting location within the feature of the matching region. Ending location within the feature of the matching region. This index enables the application to view the PDBs of a feature in order from the closest match to the furthest. This index enables the application to view the features of a PDB in order from the closest match to the furthest. 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. 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. Name of the tool used to produce the docking result. Total energy required for the ligand to dock with the PDB protein, in kcal/mol. A negative value means energy is released. Docking energy in kcal/mol that results from the geometric fit (Van der Waals force) between the PDB and the ligand. Docking energy in kcal/mol that results from the movement of electrons (electrostatic force) between the PDB and the ligand. This index enables the application to view a PDB's docking results from the lowest energy (best docking) to highest energy (worst docking). This index enables the application to view a ligand's docking results from the lowest energy (best docking) to highest energy (worst docking). This relationship connects a protein family to all of its PEGs and connects each PEG to all of its protein families. This relation connects a synonym group to the features that make it up. 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. Feature type (eg. peg, rna) This index enables the application to view the features of a Genome sorted by type. This relationship connects a genome to the contigs that contain the actual genetic information. 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. 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. Length of the sequence. Index (1-based) of the point in the contig where this sequence starts. This index enables the application to find all of the sequences in a contig in order, and makes it easier to find a particular residue section. This relationship connects a feature to its annotations. This relationship connects an annotation to the user who made it. 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. This index enables the application to find all of the genomes using a subsystem in order by variant code, which is how we wish to display them in the spreadsheets. This relationship connects roles to the subsystems that implement them. Abbreviated name for the role, generally non-unique, but useful in column headings for HTML tables. Column number for this role in the specified subsystem's spreadsheet. This index enables the application to see the subsystem roles in column order. The ordering of the roles is usually significant, so it is important to preserve it. This relationship connects a subsystem's spreadsheet cell to the genome for the spreadsheet column. This relationship connects a subsystem's spreadsheet cell to the role for the spreadsheet row. This relationship connects a subsystem's spreadsheet cell to the features assigned to it. ID of this feature's cluster. Clusters represent families of related proteins participating in a subsystem. This relationship connects a reaction to the compounds that participate in it. 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. 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. 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. 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. 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. This index presents the compounds in the reaction in the order they should be displayed when writing it in chemical notation. All the substrates appear before all the products, and within that ordering, the main compounds appear first. 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. Sequence number of this segment. Index (1-based) of the first residue in the contig that belongs to the segment. 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. Direction of the segment: =+= if it is forward and =-= if it is backward. This index allows the application to find all the segments of a feature in the proper order. This index is the one used by applications to find all the feature segments that contain a specific residue. 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. URL or citation of the paper or institution that reported evidence of the relevant feature possessing the specified property value. 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. 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 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=. 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. 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 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 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 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 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. ID of the genome containing the feature Feature type (eg. peg, rna) This index enables the application to view the features of a subsystem sorted by genome and feature type.