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| 1 : | parrello | 1.1 | <?xml version='1.0' standalone='yes'?> |
| 2 : | <Database> | ||
| 3 : | <Title>Attributes Database</Title> | ||
| 4 : | <Entities> | ||
| 5 : | <Entity name="AttributeGroup" keyType="name-string"> | ||
| 6 : | parrello | 1.8 | <Notes>A _group_ is a named set of attribute keys. An attribute key can belong to |
| 7 : | parrello | 1.1 | many groups or none at all.</Notes> |
| 8 : | </Entity> | ||
| 9 : | <Entity name="AttributeKey" keyType="name-string"> | ||
| 10 : | parrello | 1.8 | <Notes>An _attribute key_ describes named values attached to a particular type of object. |
| 11 : | parrello | 1.1 | Each instance of this entity contains the attribute's description and its name. An attribute |
| 12 : | key name must consist of letters, numbers, periods, underscores, and hyphens.</Notes> | ||
| 13 : | <Fields> | ||
| 14 : | <Field name="description" type="text"> | ||
| 15 : | <Notes>Text describing the attribute. This should explain what the attribute means and | ||
| 16 : | what kinds of values are appropriate.</Notes> | ||
| 17 : | </Field> | ||
| 18 : | <Field name="data-type" type="name-string"> | ||
| 19 : | <Notes>ERDB data type for the attribute. This serves as documentation only, but | ||
| 20 : | that may change at some future point.</Notes> | ||
| 21 : | </Field> | ||
| 22 : | </Fields> | ||
| 23 : | </Entity> | ||
| 24 : | parrello | 1.2 | <Entity name="TargetObject" keyType="string"> |
| 25 : | parrello | 1.8 | <Notes>An _object_ represents a keyed thing to which an attribute can be assigned. |
| 26 : | parrello | 1.2 | In order to improve performance, this table has no data in it. It is simply required by |
| 27 : | the semantics of the database.</Notes> | ||
| 28 : | parrello | 1.1 | </Entity> |
| 29 : | parrello | 1.8 | <Entity name="EvidenceClass" keyType="name-string"> |
| 30 : | <Notes>An _evidence class_ describes a general type of evidence code. An actual evidence | ||
| 31 : | code consists of its class (e.g. =dlit=, =ff=) and an optional modifier. The modifier | ||
| 32 : | is contained in the relationship between the class and the target object.</Notes> | ||
| 33 : | <Fields> | ||
| 34 : | <Field name="format" keyType="string"> | ||
| 35 : | <Notes>The format string is an example showing how the modifier portion of the | ||
| 36 : | evidence code is formatted. It may contain HTML markup.</Notes> | ||
| 37 : | </Field> | ||
| 38 : | <Field name="short-description" type="string"> | ||
| 39 : | <Notes>The short description is a brief noun phrase explanation of the evidence class.</Notes> | ||
| 40 : | </Field> | ||
| 41 : | <Field name="description" type="text"> | ||
| 42 : | <Notes>The description is a long text description of the evidence class and its | ||
| 43 : | format string.</Notes> | ||
| 44 : | </Field> | ||
| 45 : | </Fields> | ||
| 46 : | </Entity> | ||
| 47 : | parrello | 1.1 | </Entities> |
| 48 : | <Relationships> | ||
| 49 : | parrello | 1.8 | <Relationship name="IsEvidencedBy" from="TargetObject" to="EvidenceClass" arity="MM"> |
| 50 : | <Notes>This relationship connects a feature (target object) to its evidence.</Notes> | ||
| 51 : | <Fields> | ||
| 52 : | <Field name="modifier" type="string"> | ||
| 53 : | <Notes>The modifier contains ancillary information about the evidence, including | ||
| 54 : | counts for clustering codes, pubmed IDs for literature codes, and so forth. | ||
| 55 : | The modifier contains its own punctuation, and the full code is computed by | ||
| 56 : | concatenating the modifier directly to the evidence class.</Notes> | ||
| 57 : | </Field> | ||
| 58 : | </Fields> | ||
| 59 : | </Relationship> | ||
| 60 : | parrello | 1.1 | <Relationship name="IsInGroup" from="AttributeKey" to="AttributeGroup" arity="MM"> |
| 61 : | <Notes>This relationship connects an attribute key to the groups of which it is a member.</Notes> | ||
| 62 : | </Relationship> | ||
| 63 : | parrello | 1.2 | <Relationship name="HasValueFor" from="AttributeKey" to="TargetObject" arity="MM"> |
| 64 : | <Notes>This relationship connects an attribute key to its objects. It contains the | ||
| 65 : | attribute values, and is therefore the primary data repository for the database.</Notes> | ||
| 66 : | <Fields> | ||
| 67 : | parrello | 1.5 | <Field name="subkey" type="string"> |
| 68 : | <Notes>Some attribute keys are split into two parts. The real key is controlled and | ||
| 69 : | must correspond to a key in the AttributeKey table. The second part of the key | ||
| 70 : | resides in this field. When the attribute value is presented to the user, the two | ||
| 71 : | parts of the key are joined together around the splitter value.</Notes> | ||
| 72 : | </Field> | ||
| 73 : | <Field name="value" type="text"> | ||
| 74 : | parrello | 1.2 | <Notes>This is the actual attribute value. Note that a single key/object pair may in fact |
| 75 : | have many values, and therefore many entries in this table.</Notes> | ||
| 76 : | </Field> | ||
| 77 : | </Fields> | ||
| 78 : | parrello | 1.5 | <FromIndex> |
| 79 : | <Notes>This index sorts all the values for a single attribute key by the subkey value.</Notes> | ||
| 80 : | <IndexFields> | ||
| 81 : | <IndexField name="subkey" order="ascending" /> | ||
| 82 : | </IndexFields> | ||
| 83 : | </FromIndex> | ||
| 84 : | parrello | 1.7 | <ToIndex> |
| 85 : | <Notes>This index sorts all the values for an object by attribute key and the subkey.</Notes> | ||
| 86 : | <IndexFields> | ||
| 87 : | <IndexField name="from-link" order="ascending" /> | ||
| 88 : | <IndexField name="subkey" order="ascending" /> | ||
| 89 : | </IndexFields> | ||
| 90 : | </ToIndex> | ||
| 91 : | parrello | 1.5 | <Indexes> |
| 92 : | <Index> | ||
| 93 : | <Notes>This index allows searching for an attribute value by its prefix.</Notes> | ||
| 94 : | <IndexFields> | ||
| 95 : | <IndexField name="value" order="ascending" /> | ||
| 96 : | </IndexFields> | ||
| 97 : | </Index> | ||
| 98 : | parrello | 1.6 | <Index> |
| 99 : | <Notes>This index allows searching for values within keys.</Notes> | ||
| 100 : | <IndexFields> | ||
| 101 : | <IndexField name="from-link" order="ascending" /> | ||
| 102 : | <IndexField name="value" order="ascending" /> | ||
| 103 : | </IndexFields> | ||
| 104 : | </Index> | ||
| 105 : | parrello | 1.7 | <Index> |
| 106 : | <Notes>This index sorts all the values for a single attribute key by the target object ID.</Notes> | ||
| 107 : | <IndexFields> | ||
| 108 : | <IndexField name="from-link" order="ascending" /> | ||
| 109 : | <IndexField name="to-link" order="ascending" /> | ||
| 110 : | </IndexFields> | ||
| 111 : | </Index> | ||
| 112 : | parrello | 1.5 | </Indexes> |
| 113 : | parrello | 1.1 | </Relationship> |
| 114 : | </Relationships> | ||
| 115 : | </Database> |
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