Changeset 2413


Ignore:
Timestamp:
11/04/09 15:49:56 (2 years ago)
Author:
erikroos
Message:
 
File:
1 edited

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  • molgenis4animaldb/molgenis4animal_db.xml

    r2398 r2413  
    1 <?xml version="1.0" encoding="UTF-8"?>  
    2 <!--DOCTYPE molgenis PUBLIC "MOLGENIS 1.0" "http://molgenis.sourceforge.net/dtd/molgenis_v_1_0.dtd"--> 
    3 <molgenis name="example" label="My First MOLGENIS"> 
     1<?xml version="1.0" encoding="UTF-8"?> 
     2        <!-- 
     3                DOCTYPE molgenis PUBLIC "MOLGENIS 1.0" 
     4                "http://molgenis.sourceforge.net/dtd/molgenis_v_1_0.dtd" 
     5        --> 
     6<molgenis name="animaldb" label="AnimalDB"> 
     7 
    48        <description>This is an minimal example database to show how 
    5                 MOLGENIS works. The purpose of this example database is to 
    6                 administrate experiment, samples, traits and measurements. The 
    7                 name='example' will result in a Java package 'example' being 
    8                 generated.</description> 
     9                AnimalDB works in combination with Molgenis. The purpose of 
     10                this example database is to administrate animals, groups, 
     11                locations, events and event types. The name='example' will 
     12                result in a Java package 'example' being generated.</description> 
     13 
    914        <!-- abstract data types --> 
     15 
    1016        <entity name="Identifiable" abstract="true"> 
    1117                <description>For modeling purposes only (denoted by 
    12                         abstract='true', this entity defines fields id and name centrally. 
     18                        abstract='true', 
     19                        this entity defines fields id and name centrally. 
    1320                </description> 
    14                 <field name="Id" type="autoid" description="autogenerated id number (autoid)" /> 
    15                 <field name="Name" unique="true" readonly="true" 
    16                         description="unique, user provided name string" /> 
     21                <field name="id" type="autoid" description="autogenerated id number (autoid)" /> 
     22                <field name="name" unique="true" description="unique, user provided name string" label="Name"/> 
    1723        </entity> 
    18         <!-- experiment structure --> 
    19         <entity name="Experiment" implements="Identifiable" xref_label="Name"> 
    20                 <description>Summary of an experiment.</description> 
    21                 <field name="Description" type="text" nillable="true" 
    22                         description="Optional description text" /> 
    23                 <field name="Date" type="date" auto="true" 
    24                         description="Creation date, with an automatic default to 'today'" /> 
     24 
     25        <!-- event structure --> 
     26 
     27        <entity name="Event" implements="Identifiable" xref_label="id" label="Events"> 
     28                <description>Summary of an event</description> 
     29                <field name="animalid" type="xref" xref_field="Animal.id" 
     30                        xref_label="name" label="Animal"/> 
     31                <field name="eventtypeid" type="xref" xref_field="Event_type.id" 
     32                        xref_label="name" label="Type of event"/> 
     33                <field name="locationid" type="xref" xref_field="Location.id" 
     34                        xref_label="name" label="Location"/> 
     35                <field name="date" type="date" auto="true" 
     36                        description="Creation date, with an automatic default to 'today'" label="Date"/> 
    2537        </entity> 
    26         <!-- sample description structure --> 
    27         <entity name="Sample" implements="Identifiable"> 
    28                 <description>Samples that are part of an experiment. 
    29                 </description> 
    30                 <field name="Species" default="Arabidopsis thaliana" 
    31                         description="Species, default to Arabidopsis" /> 
    32                 <field name="Tissue" nillable="true" description="Optional specification of tissue" /> 
    33                 <field name="Sex" type="enum" enum_options="[male,female,unknown]" 
    34                         description="Fixed choice on Sex" /> 
    35                 <field name="Experiment" type="xref" xref_field="Experiment.Id" 
    36                         description="Samples are part-of one experiment (by cross reference to Experiment.id)" /> 
    37                 <field name="SampleTime" type="datetime"/> 
     38 
     39        <entity name="Animal" implements="Identifiable" xref_label="name" label="Animals"> 
     40                <description>Summary of an animal</description> 
     41                <field name="locationid" type="xref" xref_field="Location.id" 
     42                        xref_label="name" label="Location"/> 
     43                <field name="animalgroupid" type="xref" xref_field="Animal_group.id" 
     44                        xref_label="name" nillable="true" label="Group"/> 
     45                <field name="species" label="Species"/> 
    3846        </entity> 
    39         <entity name="SpecialSample" extends="Sample"> 
    40                 <field name="detail" /> 
     47         
     48        <entity name="Animal_group" implements="Identifiable" xref_label="name" label="Groups"> 
     49                <description>Summary of a group of animals</description> 
    4150        </entity> 
    42         <!-- trait description structure --> 
    43         <entity name="Trait" implements="Identifiable"> 
    44                 <description>Traits that are studied in this experiment. 
    45                 </description> 
    46                 <field name="Molcular" type="bool" 
    47                         description="Indication whether this is a molecular trait" /> 
    48                 <field name="Experiment" type="xref" xref_field="Experiment.Id" 
    49                         xref_label="Name" 
    50                         description="Traits are defined per experiment (by cross reference to Experiment.id)" /> 
     51         
     52        <entity name="Location" implements="Identifiable" xref_label="name" label="Locations"> 
     53                <description>Summary of a location</description> 
    5154        </entity> 
    52         <!-- trait description structure --> 
    53         <entity name="Measurement" implements="Identifiable"> 
    54                 <description>Measurements (i.e. set of trait observations 
    55                         per sample) that are part of an experiment.</description> 
    56                 <field name="Experiment" type="xref" xref_field="Experiment.Id" 
    57                         xref_label="Name" description="Measurements are part-of one experiment" /> 
    58                 <field name="DataFile" type="file" 
    59                         description="A file attachment that summarizes the results" /> 
     55         
     56        <entity name="Event_type" implements="Identifiable" xref_label="name" label="Types of events"> 
     57                <description>Summary of a type of event</description> 
    6058        </entity> 
    61         <entity name="Data"> 
    62                 <description>Data values (observations) of a measurement. Note: 
    63                         Data doesn't inherit from Identifiable because it has no unique name. 
    64                 </description> 
    65                 <field name="Id" type="autoid" description="autogenerated id number" /> 
    66                 <field name="Measurement" type="xref" xref_field="Measurement.id" 
    67                         xref_label="Name" description="Data values are part-of one Measurement" /> 
    68                 <field name="Sample" type="xref" xref_field="Sample.Id" 
    69                         xref_label="Name" description="The sample this measurement is on" /> 
    70                 <field name="Trait" type="xref" xref_field="Trait.Id" 
    71                         xref_label="Name" description="The trait this measurement is on" /> 
    72                 <field name="Value" description="The value measured/calculated" /> 
    73                 <unique fields="Measurement,Sample,Trait" description="There can be only one value per Sample X Trait" /> 
    74         </entity> 
     59 
    7560</molgenis> 
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