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Revision 1.1 - (download) (as text) (annotate)
Mon Jan 19 21:49:02 2009 UTC (10 years, 10 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, rast_rel_2014_0912, mgrast_dev_04082011, rast_rel_2010_0928, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, rast_rel_2009_05_18, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, mgrast_dev_04012011, rast_rel_2009_07_09, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, rast_rel_2009_03_26, mgrast_dev_10262011, HEAD
Tutorial examples.

<Database>
    <Title>Sample ERDB Database</Title>
    <Notes>This XML file defines a small genetic database that demonstrates the features of
    the ERDB database engine.</Notes>
    <Entities>
        <Entity name="Genome" keyType="string">
            <DisplayInfo theme="nmpdr" col="1" row="1" />
            <Notes>A Genome contains the sequence data for a particular individual organism.</Notes>
            <Fields>
                <Field name="scientific-name" type="string">
                    <Notes>Scientific name of this genome, usually consisting of the genus,
                    species, and unique characterization.</Notes>
                </Field>
                <Field name="version" type="string">
                    <Notes>Version string for this genome, generally consisting of the genome ID followed
                    by a period and a string of digits.</Notes>
                </Field>
                <Field name="pegs" type="int">
                    <Notes>Number of [[protein encoding genes]] for this organism</Notes>
                </Field>
                <Field name="rnas" type="int">
                    <Notes>Number of RNA features found for this organism.</Notes>
                </Field>
                <Field name="oxygen" type="string">
                    <Notes>Indication of this organism's behavior relating to environmental oxygen.</Notes>
                </Field>
                <Field name="pathogenic" type="semi-boolean">
                    <Notes>Y/N/? flag indicating whether or not this organism is pathogenic.</Notes>
                </Field>
            </Fields>
            <Indexes>
                <Index>
                    <Notes>This index allows the applications to search for genome by scientific
                    name.</Notes>
                    <IndexFields>
                        <IndexField name="scientific-name" order="ascending" />
                    </IndexFields>
                </Index>
            </Indexes>
        </Entity>
        <Entity name="Contig" keyType="string">
            <DisplayInfo theme="nmpdr" col="3" row="1" />
            <Notes>A contig is a contiguous run of base pairs. The contig's ID consists of the
            genome ID followed by a name that identifies which contig this is for the parent
            genome.</Notes>
            <Fields>
                <Field name="sequence" type="dna">
                    <Notes>String consisting of the base pairs.</Notes>
                </Field>
            </Fields>
        </Entity>
        <Entity name="Feature" keyType="string">
            <DisplayInfo theme="seed" col="2" row="3" />
            <Notes>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 FIG ID.</Notes>
            <Fields>
                <Field name="feature-type" type="string">
                    <Notes>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.</Notes>
                </Field>
                <Field name="translation" type="text" relation="FeatureTranslation">
                    <Notes>(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.</Notes>
                </Field>
                <Field name="assignment" type="text">
                    <Notes>Default functional assignment for this feature.</Notes>
                </Field>
                <Field name="assignment-maker" type="string">
                    <Notes>Name of the user who made the functional assignment</Notes>
                </Field>
                <Field name="assignment-quality" type="char">
                    <Notes>Quality of the functional assignment, usually a space, but may be
                    W (indicating weak) or X (indicating experimental)</Notes>
                </Field>
            </Fields>
        </Entity>
    </Entities>
    <Relationships>
        <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
            <DisplayInfo theme="seed" caption="Has" />
            <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="string">
                    <Notes>Feature type (eg. peg, rna)</Notes>
                </Field>
            </Fields>
            <FromIndex>
                <Notes>This index enables the application to view the features of a
                Genome sorted by type.</Notes>
                <IndexFields>
                    <IndexField name="type" order="ascending" />
                </IndexFields>
            </FromIndex>
        </Relationship>
        <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">
            <DisplayInfo caption="Consists Of" theme="nmpdr" />
            <Notes>This relationship connects a genome to the contigs that contain the actual genetic
            information.</Notes>
        </Relationship>
        <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
            <DisplayInfo caption="Is\nLocation\nOf" theme="seed" />
            <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.  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.</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: + if it is forward and
                    - if it is backward.</Notes>
                </Field>
            </Fields>
            <FromIndex>
                <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>
    </Relationships>
</Database>

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