miaf-ontology

Medical image annotation framework Ontology. Use on SMIR.ch and in the VSD Framework to annotate medical imaging data. It consist of terms (incl. original IRI) from other existing ontolgies and MIAF terms. It is used to fill meta data in the VSD framework which is used by SICAS to host the SICAS Medical Image Repository.

Introduction

Goal: achieve u retrieve meta-data from a defined vocabular. For this reason, we have collected a specific vocabulary from different ontologies into a single ontology. but we also like to use a triple store for quering the meta-data. Therefore, this ontology consists of 3 parts needed for a triple store:

subject: an individual of an independent entity
predicate: an individual of internal entity >> Mapping
object : object property or text

Structure

Classes

SMIR classes

Domain entity -> Independent entity

Generic Object -> Object
File
Group
User

Internal classes

Domain entity -> Internal entity

Is used internal representation of VSD framework structures

Mapping
Status
Modificator

Objects classes

Domain entity -> Object property

Property values that are used to annotate an object with a predefined values. The terms are collected from various sources and its structure recreated. The last level (things to use to annotate) are most likely to be instances. Here a (incomplete) list of object property terms :

Gender (instances):
Title (honorific Prefix, classes)
License (Policy, instances):
Segmentation method (instances)
MR contrast (instances)
Mr sequences acronyms (instances)
Modalities (classes)
Ethnic group (instances)
Format (classes)
Dominance (Handedness)
Organism (classes)
Units (instances)
Anatomical region -> FMA

Properties

Object properties

if multiple instances are need or mappes other instances (value lists, icenses, modality etc.)

examples:

has_anatomical_region >> fma instance
has_gender >> gender instance
has_modality >> modality instance

Data properties

with a datatype string, integer, uri etc. most commonly used. But not applicable to classes. That means it is not a generic property of an Independent entity

Examples

age
lastname
rating

Annotation properties

It is either generic describe classes/properties, generic to all objects, or has a class as Range

** Example**

Label (generic)
Abbreviation (generic)
DisplayLabel (generic)
selfUrl (objects)

Extending

Look for already defined ontology classes:

** Make sure the new entity option is using the setting "use iri of active ontology" **

`Subjects`

Subjects dont have to be created as they are only needed in the triple store. However, MIAF contains some examples:

2 Object instances
1 file instance
1 user instance

Add `Object`

create the class (structure) to the Object property class using the external IRI
add the list as instance (using external IRI )
add Annotation properties

Label: Name of the object. Required
Abbreviation: If available
Comment: general comment
Description: description of the meaning of the term
DisplayLabel: The label that will be displayed

Add `Predicates` to object types

decide what typ of property (see above)

Object property
Data property
Annotation property

Create the property using the external IRI if available
Add Annotation properties

Label: Name of the object. Required
Abbreviation: If available
Comment: general comment
Description: description of the meaning of the term
DisplayLabel: The label that will be displayed

to define if a new predicate is default has_default_property or is standard has_property

has_default_property or has_property + the new predicate

Add Mapping

add instance of class Mapping
Add Annotation property

label: p_object_new_property
annotation property: MappingTo and add the correct Property

add property assertion has_property_modificator [user|system|file]

addon: default mappings for new object types

If you add a new object type, you can use the xml below to add it later in the owl file directly. change db7925ac_a8f1_47a8_860f_0cdb9ed18b5f to the desired indivdual (object type) and add it directly to the owl for a new object type

    <ObjectPropertyAssertion>
        <ObjectProperty IRI="#d88fc04d_8920_4f54_ad17_b9094e13865a"/>
        <NamedIndividual IRI="#db7925ac_a8f1_47a8_860f_0cdb9ed18b5f"/>
        <NamedIndividual IRI="#a4330bca_7b02_432d_8d89_787c0027cd0e"/>
    </ObjectPropertyAssertion>
    <ObjectPropertyAssertion>
        <ObjectProperty IRI="#d88fc04d_8920_4f54_ad17_b9094e13865a"/>
        <NamedIndividual IRI="#db7925ac_a8f1_47a8_860f_0cdb9ed18b5f"/>
        <NamedIndividual IRI="#ac1e9418_cf1e_471b_9e44_ea7f71069698"/>
    </ObjectPropertyAssertion>
    <ObjectPropertyAssertion>
        <ObjectProperty IRI="#d88fc04d_8920_4f54_ad17_b9094e13865a"/>
        <NamedIndividual IRI="#db7925ac_a8f1_47a8_860f_0cdb9ed18b5f"/>
        <NamedIndividual IRI="#b3081f13_637b_4319_befb_8a623de26b31"/>
    </ObjectPropertyAssertion>
    <ObjectPropertyAssertion>
        <ObjectProperty IRI="#d88fc04d_8920_4f54_ad17_b9094e13865a"/>
        <NamedIndividual IRI="#db7925ac_a8f1_47a8_860f_0cdb9ed18b5f"/>
        <NamedIndividual IRI="#cb25f8e6_95b0_4c23_b1d4_0128b7c337a5"/>
    </ObjectPropertyAssertion>
    <ObjectPropertyAssertion>
        <ObjectProperty IRI="#d88fc04d_8920_4f54_ad17_b9094e13865a"/>
        <NamedIndividual IRI="#db7925ac_a8f1_47a8_860f_0cdb9ed18b5f"/>
        <NamedIndividual IRI="#f63fc9ba_3ee2_4d3c_aaec_6d268bfd0097"/>
    </ObjectPropertyAssertion>
    <ObjectPropertyAssertion>
        <ObjectProperty IRI="#d88fc04d_8920_4f54_ad17_b9094e13865a"/>
        <NamedIndividual IRI="#db7925ac_a8f1_47a8_860f_0cdb9ed18b5f"/>
        <NamedIndividual IRI="#0e0500a5_2492_4f95_a055_1c969a6552fe"/>
    </ObjectPropertyAssertion>
    <ObjectPropertyAssertion>
        <ObjectProperty IRI="#d88fc04d_8920_4f54_ad17_b9094e13865a"/>
        <NamedIndividual IRI="#db7925ac_a8f1_47a8_860f_0cdb9ed18b5f"/>
        <NamedIndividual IRI="#10dcdaf9_6bdb_4b1f_bda7_2c46e5f1c29d"/>
    </ObjectPropertyAssertion>
    <ObjectPropertyAssertion>
        <ObjectProperty IRI="#d88fc04d_8920_4f54_ad17_b9094e13865a"/>
        <NamedIndividual IRI="#db7925ac_a8f1_47a8_860f_0cdb9ed18b5f"/>
        <NamedIndividual IRI="#213634ed_fec9_4f36_9e79_228f46642e87"/>
    </ObjectPropertyAssertion>
    <ObjectPropertyAssertion>
        <ObjectProperty IRI="#d88fc04d_8920_4f54_ad17_b9094e13865a"/>
        <NamedIndividual IRI="#db7925ac_a8f1_47a8_860f_0cdb9ed18b5f"/>
        <NamedIndividual IRI="#34127d03_aea2_4a24_871c_6f7e9ac72823"/>
    </ObjectPropertyAssertion>
    <ObjectPropertyAssertion>
        <ObjectProperty IRI="#d88fc04d_8920_4f54_ad17_b9094e13865a"/>
        <NamedIndividual IRI="#db7925ac_a8f1_47a8_860f_0cdb9ed18b5f"/>
        <NamedIndividual IRI="#57930446_dc48_4445_9615_d0e08f3a7dac"/>
    </ObjectPropertyAssertion>
    <ObjectPropertyAssertion>
        <ObjectProperty IRI="#d88fc04d_8920_4f54_ad17_b9094e13865a"/>
        <NamedIndividual IRI="#db7925ac_a8f1_47a8_860f_0cdb9ed18b5f"/>
        <NamedIndividual IRI="#8a20edb0_c831_4dbf_9e06_fec8c583a39e"/>
    </ObjectPropertyAssertion>
    <ObjectPropertyAssertion>
        <ObjectProperty IRI="#d88fc04d_8920_4f54_ad17_b9094e13865a"/>
        <NamedIndividual IRI="#db7925ac_a8f1_47a8_860f_0cdb9ed18b5f"/>
        <NamedIndividual IRI="#8bcdf331_a3e2_4764_bc44_40d0f22d856f"/>
    </ObjectPropertyAssertion>
    <ObjectPropertyAssertion>
        <ObjectProperty IRI="#d88fc04d_8920_4f54_ad17_b9094e13865a"/>
        <NamedIndividual IRI="#db7925ac_a8f1_47a8_860f_0cdb9ed18b5f"/>
        <NamedIndividual IRI="#8da83cb0_8c7f_4de3_8f33_53806f782f79"/>
    </ObjectPropertyAssertion>
    <ObjectPropertyAssertion>
        <ObjectProperty IRI="#d88fc04d_8920_4f54_ad17_b9094e13865a"/>
        <NamedIndividual IRI="#db7925ac_a8f1_47a8_860f_0cdb9ed18b5f"/>
        <NamedIndividual IRI="#859670b5_8337_4f2d_8473_a2761b49e09f"/>
    </ObjectPropertyAssertion>
    <ObjectPropertyAssertion>
        <ObjectProperty IRI="#d88fc04d_8920_4f54_ad17_b9094e13865a"/>
        <NamedIndividual IRI="#db7925ac_a8f1_47a8_860f_0cdb9ed18b5f"/>
        <NamedIndividual IRI="#908630bc_610b_47cd_9cc1_ad7b2e2a1e75"/>
    </ObjectPropertyAssertion>

Usage with VSD

Mapping file

create the mapping json: read sop-create-mapping-file.md file

Get the value list

if the list is has subcategories, use the subclasses and add Abbreviation to the terms that should appear in the list. -> example for sequence: Turbo Spin Echo (TSE)

find some queries here doc/miaf-queries.md

SICASFoundation/miaf-ontology