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Revision 1.27 - (download) (as text) (annotate)
Sun Jun 25 07:34:46 2006 UTC (13 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.26: +8 -0 lines
Added support for mapped synonym IDs.

<?xml version="1.0" encoding="utf-8" ?>
<Database>
    <Title>Sprout Genome and Subsystem Database</Title>
    <Entities>
        <Entity name="Genome" keyType="name-string">
            <Notes>A [i]genome[/i] contains the sequence data for a particular individual organism.</Notes>
            <Fields>
                <Field name="genus" type="name-string">
                    <Notes>Genus of the relevant organism.</Notes>
                    <DataGen pass="1">RandParam('streptococcus', 'staphyloccocus', 'felis', 'homo', 'ficticio', 'strangera', 'escherischia', 'carborunda')</DataGen>
                </Field>
                <Field name="species" type="name-string">
                    <Notes>Species of the relevant organism.</Notes>
                    <DataGen pass="1">StringGen('PKVKVKVKVKV')</DataGen>
                </Field>
                <Field name="unique-characterization" type="medium-string">
                    <Notes>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.</Notes>
                    <DataGen>StringGen('PKVKVK999')</DataGen>
                </Field>
                <Field name="access-code" type="key-string">
                    <Notes>The access code determines which users can look at the data relating to this genome.
                    Each user is associated with a set of access codes. In order to view a genome, one of
                    the user's access codes must match this value.</Notes>
                    <DataGen>RandParam('low','medium','high')</DataGen>
                </Field>
                <Field name="complete" type="boolean">
                    <Notes>TRUE if the genome is complete, else FALSE</Notes>
                </Field>
                <Field name="taxonomy" type="text">
                    <Notes>The taxonomy string contains the full 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).</Notes>
                    <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'),
                                                  ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen>
                </Field>
                <Field name="group-name" type="name-string" relation="GenomeGroups">
                    <Notes>The group identifies a special grouping of organisms that would be displayed on a particular
                    page or of particular interest to a research group or web site. A single genome can belong to multiple
                    such groups or none at all.</Notes>
                </Field>
            </Fields>
            <Indexes>
                <Index>
                    <Notes>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.</Notes>
                    <IndexFields>
                        <IndexField name="access-code" order="ascending" />
                        <IndexField name="genus" order="ascending" />
                        <IndexField name="species" order="ascending" />
                        <IndexField name="unique-characterization" order="ascending" />
                    </IndexFields>
                </Index>
                <Index Unique="false">
                    <Notes>This index allows the applications to find all genomes for a particular
                    species.</Notes>
                    <IndexFields>
                        <IndexField name="genus" order="ascending" />
                        <IndexField name="species" order="ascending" />
                        <IndexField name="unique-characterization" order="ascending" />
                    </IndexFields>
                </Index>
            </Indexes>
        </Entity>
        <Entity name="Source" keyType="medium-string">
            <Notes>A [i]source[/i] describes a place from which genome data was taken. This can be an organization
            or a paper citation.</Notes>
            <Fields>
                <Field name="URL" type="string" relation="SourceURL">
                    <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>
                    <DataGen>"http://www.conservativecat.com/Ferdy/TestTarget.php?Source=" . $this->{id}</DataGen>
                </Field>
                <Field name="description" type="text">
                    <Notes>Description the source. The description can be a street address or a citation.</Notes>
                    <DataGen>$this->{id} . ': ' . StringGen(IntGen(50,200))</DataGen>
                </Field>
            </Fields>
        </Entity>
        <Entity name="Contig" keyType="name-string">
            <Notes>A [i]contig[/i] 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.
            [p]A contig can contain over a million residues. For performance reasons, therefore,
            the contig is split into multiple pieces called [i]sequences[/i]. The sequences
            contain the characters that represent the residues as well as data on the quality of
            the residue identification.</Notes>
        </Entity>
        <Entity name="Sequence" keyType="name-string">
            <Notes>A [i]sequence[/i] is a continuous piece of a [i]contig[/i]. 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.</Notes>
            <Fields>
                <Field name="sequence" type="text">
                    <Notes>String consisting of the residues. Each residue is described by a single
                    character in the string.</Notes>
                    <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>
                </Field>
                <Field name="quality-vector" type="text">
                    <Notes>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 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 [b]unknown[/b].</Notes>
                    <DataGen>unknown</DataGen>
                </Field>
            </Fields>
        </Entity>
        <Entity name="Feature" keyType="id-string">
            <Notes>A [i]feature[/i] 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.</Notes>
            <Fields>
                <Field name="feature-type" type="string">
                    <Notes>Code indicating the type of this feature.</Notes>
                    <DataGen>RandParam('peg','rna')</DataGen>
                </Field>
                <Field name="alias" type="medium-string" relation="FeatureAlias">
                    <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>
                    <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>
                </Field>
                <Field name="translation" type="text" relation="FeatureTranslation">
                    <Notes>[i](optional)[/i] A translation of this feature's residues into character
                    codes, formed by concatenating the pieces of the feature together. For a
                    protein encoding group, this is the protein characters. For other types
                    it is the DNA characters.</Notes>
                    <DataGen testCount="0"></DataGen>
                </Field>
                <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
                    <Notes>Upstream sequence the feature. This includes residues preceding the feature as well as some of
                    the feature's initial residues.</Notes>
                    <DataGen testCount="0"></DataGen>
                </Field>
                <Field name="active" type="boolean">
                    <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>
                    <DataGen>1</DataGen>
                </Field>
                <Field name="link" type="text" relation="FeatureLink">
                    <Notes>Web hyperlink for this feature. A feature 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 [b]&lt;a href="[i]link[/i]"&gt;[i]text[/i]&lt;/a&gt;[/b] notation.</Notes>
                    <DataGen testCount="3">'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} .
                    "&amp;Number=" . IntGen(1,99)</DataGen>
                </Field>
            </Fields>
            <Indexes>
                <Index>
                    <Notes>This index allows the user to find the feature corresponding to
                    the specified alias name.</Notes>
                    <IndexFields>
                        <IndexField name="alias" order="ascending" />
                    </IndexFields>
                </Index>
            </Indexes>
        </Entity>
        <Entity name="SynonymGroup" keyType="id-string">
            <Notes>A [i]synonym group[/i] represents a group of features. Substantially identical features
            are mapped to the same synonym group, and this information is used to expand similarities.</Notes>
        </Entity>
        <Entity name="Role" keyType="string">
            <Notes>A [i]role[/i] 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.</Notes>
            <Fields>
                <Field name="EC" type="string" relation="RoleEC">
                    <Notes>EC code for this role.</Notes>
                    <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>
                </Field>
                <Field name="abbr" type="name-string">
                    <Notes>Abbreviated name for the role, generally non-unique, but useful
                    in column headings for HTML tables.</Notes>
                </Field>
            </Fields>
            <Indexes>
                <Index>
                    <Notes>This index allows the user to find the role corresponding to
                    an EC number.</Notes>
                    <IndexFields>
                        <IndexField name="EC" order="ascending" />
                    </IndexFields>
                </Index>
            </Indexes>
        </Entity>
        <Entity name="Annotation" keyType="name-string">
            <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations
            are currently the only objects that may be inserted directly into the database. All other
            information is loaded from data exported by the SEED.</Notes>
            <Fields>
                <Field name="time" type="date">
                    <Notes>Date and time of the annotation.</Notes>
                </Field>
                <Field name="annotation" type="text">
                    <Notes>Text of the annotation.</Notes>
                </Field>
            </Fields>
            <Indexes>
                <Index>
                    <Notes>This index allows the user to find recent annotations.</Notes>
                    <IndexFields>
                        <IndexField name="time" order="descending" />
                    </IndexFields>
                </Index>
            </Indexes>
        </Entity>
        <Entity name="Reaction" keyType="key-string">
            <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
            is generally a small number preceded by a letter.</Notes>
            <Fields>
                <Field name="url" type="string" relation="ReactionURL">
                    <Notes>HTML string containing a link to a web location that describes the
                    reaction. This field is optional.</Notes>
                </Field>
                <Field name="rev" type="boolean">
                    <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
                </Field>
            </Fields>
        </Entity>
        <Entity name="Compound" keyType="name-string">
            <Notes>A [i]compound[/i] is a chemical that participates in a reaction.
            All compounds have a unique ID and may also have one or more names.</Notes>
            <Fields>
                <Field name="name-priority" type="int" relation="CompoundName">
                    <Notes>Priority of a compound name. The name with the loweset
                    priority is the main name of this compound.</Notes>
                </Field>
                <Field name="name" type="name-string" relation="CompoundName">
                    <Notes>Descriptive name for the compound. A compound may
                    have several names.</Notes>
                </Field>
                <Field name="cas-id" type="name-string" relation="CompoundCAS">
                    <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>
                </Field>
                <Field name="label" type="name-string">
                    <Notes>Name used in reaction display strings.
                    It 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.</Notes>
                </Field>
            </Fields>
            <Indexes>
                <Index>
                    <Notes>This index allows the user to find the compound corresponding to
                    the specified name.</Notes>
                    <IndexFields>
                        <IndexField name="name" order="ascending" />
                    </IndexFields>
                </Index>
                <Index>
                    <Notes>This index allows the user to find the compound corresponding to
                    the specified CAS ID.</Notes>
                    <IndexFields>
                        <IndexField name="cas-id" order="ascending" />
                    </IndexFields>
                </Index>
                <Index>
                    <Notes>This index allows the user to access the compound names in
                    priority order.</Notes>
                    <IndexFields>
                        <IndexField name="id" order="ascending" />
                        <IndexField name="name-priority" order="ascending" />
                    </IndexFields>
                </Index>
            </Indexes>
        </Entity>
        <Entity name="Subsystem" keyType="string">
            <Notes>A [i]subsystem[/i] 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.</Notes>
            <Fields>
                <Field name="curator" type="string">
                    <Notes>Name of the person currently in charge of the subsystem.</Notes>
                </Field>
                <Field name="notes" type="text">
                    <Notes>Descriptive notes about the subsystem.</Notes>
                </Field>
            </Fields>
        </Entity>
        <Entity name="RoleSubset" keyType="string">
            <Notes>A [i]role subset[/i] 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.</Notes>
        </Entity>
        <Entity name="GenomeSubset" keyType="string">
            <Notes>A [i]genome subset[/i] 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.</Notes>
        </Entity>
        <Entity name="SSCell" keyType="hash-string">
            <Notes>Part of the process of locating and assigning features is creating a spreadsheet of
            genomes and roles to which features are assigned. A [i]spreadsheet cell[/i] represents one
            of the positions on the spreadsheet.</Notes>
        </Entity>
        <Entity name="SproutUser" keyType="name-string">
            <Notes>A [i]user[/i] is a person who can make annotations and view data in the database. The
            user object is keyed on the user's login name.</Notes>
            <Fields>
                <Field name="description" type="string">
                    <Notes>Full name or description of this user.</Notes>
                </Field>
                <Field name="access-code" type="key-string" relation="UserAccess">
                    <Notes>Access code possessed by this
                    user. A user can have many access codes; a genome is accessible to the user if its
                    access code matches any one of the user's access codes.</Notes>
                    <DataGen testCount="2">RandParam('low', 'medium', 'high')</DataGen>
                </Field>
            </Fields>
        </Entity>
        <Entity name="Property" keyType="int">
            <Notes>A [i]property[/i] 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.</Notes>
            <Fields>
                <Field name="property-name" type="name-string">
                    <Notes>Name of this property.</Notes>
                </Field>
                <Field name="property-value" type="string">
                    <Notes>Value associated with this property. For each property
                    name, there must by a property record for all of its possible
                    values.</Notes>
                </Field>
            </Fields>
            <Indexes>
                <Index>
                    <Notes>This index enables the application to find all values for a specified property
                    name, or any given name/value pair.</Notes>
                    <IndexFields>
                        <IndexField name="property-name" order="ascending" />
                        <IndexField name="property-value" order="ascending" />
                    </IndexFields>
                </Index>
            </Indexes>
        </Entity>
        <Entity name="Diagram" keyType="name-string">
            <Notes>A functional diagram describes the 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 indicate which roles belong to a particular
            map.</Notes>
            <Fields>
                <Field name="name" type="text">
                    <Notes>Descriptive name of this diagram.</Notes>
                </Field>
            </Fields>
        </Entity>
        <Entity name="ExternalAliasOrg" keyType="name-string">
            <Notes>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.</Notes>
                <Fields>
                    <Field name="org" type="text">
                        <Notes>Descriptive name of the target organism for this external alias.</Notes>
                    </Field>
                </Fields>
        </Entity>
        <Entity name="ExternalAliasFunc" keyType="name-string">
            <Notes>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.</Notes>
                <Fields>
                    <Field name="func" type="text">
                        <Notes>Functional role for this external alias.</Notes>
                    </Field>
                </Fields>
        </Entity>
        <Entity name="Coupling" keyType="hash-string">
            <Notes>A coupling is a relationship between two features. The features are
            physically close on the contig, and there is evidence that they generally
            belong together. The key of this entity is formed by combining the coupled
            feature IDs with a space.</Notes>
            <Fields>
                <Field name="score" type="int">
                    <Notes>A number based on the set of PCHs (pairs of close homologs). A PCH
                    indicates that two genes near each other on one genome are very similar to
                    genes near each other on another genome. The score only counts PCHs for which
                    the genomes are very different. (In other words, we have a pairing that persists
                    between different organisms.) A higher score implies a stronger meaning to the
                    clustering.</Notes>
                </Field>
            </Fields>
        </Entity>
        <Entity name="PCH" keyType="hash-string">
            <Notes>A PCH (physically close homolog) connects a clustering (which is a
            pair of physically close features on a contig) to a second pair of physically
            close features that are similar to the first. Essentially, the PCH is a
            relationship between two clusterings in which the first clustering's features
            are similar to the second clustering's features. The simplest model for
            this would be to simply relate clusterings to each other; however, not all
            physically close pairs qualify as clusterings, so we relate a clustering to
            a pair of features. The key is the clustering key followed by the IDs
            of the features in the second pair.</Notes>
            <Fields>
                <Field name="used" type="boolean">
                    <Notes>TRUE if this PCH is used in scoring the attached clustering,
                    else FALSE. If a clustering has a PCH for a particular genome and many
                    similar genomes are present, then a PCH will probably exist for the
                    similar genomes as well. When this happens, only one of the PCHs will
                    be scored: the others are considered duplicates of the same evidence.</Notes>
                </Field>
            </Fields>
        </Entity>
    </Entities>
    <Relationships>
        <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">
            <Notes>This relationship connects a feature to all the functional couplings
            in which it participates. A functional coupling is a recognition of the fact
            that the features are close to each other on a chromosome, and similar
            features in other genomes also tend to be close.</Notes>
            <Fields>
                <Field name="pos" type="int">
                    <Notes>Ordinal position of the feature in the coupling. Currently,
                    this is either "1" or "2".</Notes>
                </Field>
            </Fields>
            <ToIndex>
                <Notes>This index enables the application to view the features of
                a coupling in the proper order. The order influences the way the
                PCHs are examined.</Notes>
                <IndexFields>
                    <IndexField name="pos" order="ascending" />
                </IndexFields>
            </ToIndex>
        </Relationship>
        <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="1M">
            <Notes>This relation connects a synonym group to the features that make it
            up.</Notes>
        </Relationship>
        <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
            <Notes>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.</Notes>
            <Fields>
                <Field name="type" type="key-string">
                    <Notes>Feature type (eg. peg, rna)</Notes>
                </Field>
            </Fields>
            <ToIndex>
                <Notes>This index enables the application to view the features of a
                Genome sorted by type.</Notes>
                <IndexFields>
                    <IndexField name="type" order="ascending" />
                </IndexFields>
            </ToIndex>
        </Relationship>
        <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
            <Notes>This relationship connects a functional coupling to the physically
            close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>
        </Relationship>
        <Relationship name="UsesAsEvidence" from="PCH" to="Feature" arity="MM">
            <Notes>This relationship connects a PCH to the features that represent its
            evidence. Each PCH is connected to a parent coupling that relates two features
            on a specific genome. The PCH's evidence that the parent coupling is functional
            is the existence of two physically close features on a different genome that
            correspond to the features in the coupling. Those features are found on the
            far side of this relationship.</Notes>
            <Fields>
                <Field name="pos" type="int">
                    <Notes>Ordinal position of the feature in the coupling that corresponds
                    to our target feature. There is a one-to-one correspondence between the
                    features connected to the PCH by this relationship and the features
                    connected to the PCH's parent coupling. The ordinal position is used
                    to decode that relationship. Currently, this field is either "1" or
                    "2".</Notes>
                </Field>
            </Fields>
            <FromIndex>
                <Notes>This index enables the application to view the features of
                a PCH in the proper order.</Notes>
                <IndexFields>
                    <IndexField name="pos" order="ascending" />
                </IndexFields>
            </FromIndex>
        </Relationship>
        <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">
            <Notes>This relationship connects a genome to the contigs that contain the actual genetic
            information.</Notes>
        </Relationship>
        <Relationship name="ComesFrom" from="Genome" to="Source" arity="MM">
            <Notes>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.</Notes>
        </Relationship>
        <Relationship name="IsMadeUpOf" from="Contig" to="Sequence" arity="1M">
            <Notes>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.</Notes>
            <Fields>
                <Field name="len" type="int">
                    <Notes>Length of the sequence.</Notes>
                </Field>
                <Field name="start-position" type="int">
                    <Notes>Index (1-based) of the point in the contig where this
                    sequence starts.</Notes>
                </Field>
            </Fields>
            <FromIndex>
                <Notes>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.</Notes>
                <IndexFields>
                    <IndexField name="start-position" order="ascending" />
                    <IndexField name="len" order="ascending" />
                </IndexFields>
            </FromIndex>
        </Relationship>
        <Relationship name="IsTargetOfAnnotation" from="Feature" to="Annotation" arity="1M">
            <Notes>This relationship connects a feature to its annotations.</Notes>
        </Relationship>
        <Relationship name="MadeAnnotation" from="SproutUser" to="Annotation" arity="1M">
            <Notes>This relationship connects an annotation to the user who made it.</Notes>
        </Relationship>
        <Relationship name="ParticipatesIn" from="Genome" to="Subsystem" arity="MM">
            <Notes>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 [b]SSCell[/b] object.</Notes>
            <Fields>
                <Field name="variant-code" type="key-string">
                    <Notes>Code indicating the subsystem variant to which this
                    genome belongs. Each subsystem can have multiple variants. A variant
                    code of [b]-1[/b] indicates that the genome does not have a functional
                    variant of the subsystem. A variant code of [b]0[/b] indicates that
                    the genome's participation is considered iffy.</Notes>
                </Field>
            </Fields>
            <ToIndex>
                <Notes>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.</Notes>
                <IndexFields>
                    <IndexField name="variant-code" order="ascending" />
                </IndexFields>
            </ToIndex>
        </Relationship>
        <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
            <Notes>This relationship connects roles to the subsystems that implement them. </Notes>
            <Fields>
                <Field name="column-number" type="int">
                    <Notes>Column number for this role in the specified subsystem's
                    spreadsheet.</Notes>
                </Field>
            </Fields>
            <ToIndex>
                <Notes>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.</Notes>
                <IndexFields>
                    <IndexField name="column-number" order="ascending" />
                </IndexFields>
            </ToIndex>
        </Relationship>
        <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
            <Notes>This relationship connects a subsystem's spreadsheet cell to the
            genome for the spreadsheet column.</Notes>
        </Relationship>
        <Relationship name="IsRoleOf" from="Role" to="SSCell" arity="1M">
            <Notes>This relationship connects a subsystem's spreadsheet cell to the
            role for the spreadsheet row.</Notes>
        </Relationship>
        <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
            <Notes>This relationship connects a subsystem's spreadsheet cell to the
            features assigned to it.</Notes>
            <Fields>
                <Field name="cluster-number" type="int">
                    <Notes>ID of this feature's cluster. Clusters represent families of
                    related proteins participating in a subsystem.</Notes>
                </Field>
            </Fields>
        </Relationship>
        <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
            <Notes>This relationship connects a reaction to the compounds that participate
            in it.</Notes>
            <Fields>
                <Field name="product" type="boolean">
                    <Notes>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.</Notes>
                </Field>
                <Field name="stoichiometry" type="key-string">
                    <Notes>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.</Notes>
                </Field>
                <Field name="main" type="boolean">
                    <Notes>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.</Notes>
                </Field>
                <Field name="loc" type="key-string">
                    <Notes>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.</Notes>
                </Field>
                <Field name="discriminator" type="int">
                    <Notes>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.</Notes>
                </Field>
            </Fields>
            <ToIndex>
                <Notes>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.</Notes>
                <IndexFields>
                    <IndexField name="product" order="ascending" />
                    <IndexField name="loc" order="ascending" />
                    <IndexField name="main" order="descending" />
                </IndexFields>
            </ToIndex>
        </Relationship>
        <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
            <Notes>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.
            [p]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 [b]ABC[/b], 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.</Notes>
            <Fields>
                <Field name="locN" type="int">
                    <Notes>Sequence number of this segment.</Notes>
                </Field>
                <Field name="beg" type="int">
                    <Notes>Index (1-based) of the first residue in the contig that
                    belongs to the segment.</Notes>
                </Field>
                <Field name="len" type="int">
                    <Notes>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.</Notes>
                </Field>
                <Field name="dir" type="char">
                    <Notes>Direction of the segment: [b]+[/b] if it is forward and
                    [b]-[/b] if it is backward.</Notes>
                </Field>
            </Fields>
            <FromIndex Unique="false">
                <Notes>This index allows the application to find all the segments of a feature in
                the proper order.</Notes>
                <IndexFields>
                    <IndexField name="locN" order="ascending" />
                </IndexFields>
            </FromIndex>
            <ToIndex>
                <Notes>This index is the one used by applications to find all the feature
                segments that contain a specific residue.</Notes>
                <IndexFields>
                    <IndexField name="beg" order="ascending" />
                </IndexFields>
            </ToIndex>
        </Relationship>
        <Relationship name="IsBidirectionalBestHitOf" from="Feature" to="Feature" arity="MM">
            <Notes>This relationship is one of two that relate features to each other. It
            connects features that are very similar but on separate genomes. A
            bidirectional best hit relationship exists between two features [b]A[/b]
            and [b]B[/b] if [b]A[/b] is the best match for [b]B[/b] on [b]A[/b]'s genome
            and [b]B[/b] is the best match for [b]A[/b] on [b]B[/b]'s genome. </Notes>
            <Fields>
                <Field name="genome" type="name-string">
                    <Notes>ID of the genome containing the target (to) feature.</Notes>
                </Field>
                <Field name="sc" type="float">
                    <Notes>score for this relationship</Notes>
                </Field>
            </Fields>
            <FromIndex>
                <Notes>This index allows the application to find a feature's best hit for
                a specific target genome.</Notes>
                <IndexFields>
                    <IndexField name="genome" order="ascending" />
                </IndexFields>
            </FromIndex>
        </Relationship>
        <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
            <Notes>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.</Notes>
            <Fields>
                <Field name="evidence" type="text">
                    <Notes>URL or citation of the paper or
                    institution that reported evidence of the relevant feature possessing
                    the specified property value.</Notes>
                </Field>
            </Fields>
        </Relationship>
        <Relationship name="RoleOccursIn" from="Role" to="Diagram" arity="MM">
            <Notes>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.</Notes>
        </Relationship>
        <Relationship name="HasSSCell" from="Subsystem" to="SSCell" arity="1M">
            <Notes>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.</Notes>
        </Relationship>
        <Relationship name="IsTrustedBy" from="SproutUser" to="SproutUser" arity="MM">
            <Notes>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 [b]FIG[/b].</Notes>
        </Relationship>
        <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM">
            <Notes>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.</Notes>
        </Relationship>
        <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM">
            <Notes>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.</Notes>
        </Relationship>
        <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M">
            <Notes>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.</Notes>
        </Relationship>
        <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M">
            <Notes>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.</Notes>
        </Relationship>
        <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">
            <Notes>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.</Notes>
        </Relationship>
    </Relationships>
</Database>

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