The TAMBIS Ontology (TaO)

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CKML Base Ontology
Miscellany
TaO Theories

Figure 1 : The TaO top levels

Overview

Here we model the TAMBIS ontology (TaO) in Simple CKML. TaO has recently been described in the paper “An Ontology for bioinformatics application” by Patricia Baker, et al, that appeared in Bioinformatics, Volume 15, number 6, pages 510–520, 1999. Simple CKML is Simple OML extended with IF theories. Figure 1 shows the top levels of TaO annotated with the corresponding elements of CKML. According to Carole Goble, the top levels of the TaO are based on the top levels of the GALEN project's CORE ontology shown in Figure 2, which was originally developed by Prof. Alan Rector and heavily influenced by John Sowa's works. See the paper “The GALEN high level ontology” by A. Rector et al presented at Medical Informatics in Europe 1996, for more detail on GALEN.

Figure 2: The GALEN Core Ontology top levels

CKML

Ontology

at location http://www.tambis.org/ontology/ (fictitious)

<CKML>

<Ontology>

<extend ontology=“http://www.ontologos.org/ontology/CKML/”/> /* default namespace */

<extend theory=“http://www.tambis.org/theory/Generalized_Structure/” prefix=“Struc”/>

<extend theory=“http://www.tambis.org/theory/Generalized_Substance/” prefix=“Sub”/>

<extend theory=“http://www.tambis.org/theory/Generalized_Process/” prefix=“Proc”/>

<extend theory=“http://www.tambis.org/theory/Generalized_Function/” prefix=“Func”/>

</Ontology>

</CKML>

Theories

Generalized Structure

at location http://www.tambis.org/theory/Generalized_Structure/ (fictitious)

<CKML>

<Theory>

<Type.Object name=“Generalized Structure”>

<comment>Discrete abstract or physical things independent of time</comment>

<partition>

<li type=“Abstract Structure”/>

<li type=“Physical Structure”/>

</partition>

</Type.Object>

<Type.Object name=“Abstract Structure”>

<partition>

<li type=“protocol”/>

<li type=“method”/>

<li type=“classification”/>

<li type=“reaction”/>

<li type=“pathway”/>

<li type=“information source”/>

</partition>

</Type.Object>

<Type.Object name=“protocol”/>

<Type.Object name=“method”>

<comment>alignment method, comparison method</comment>

</Type.Object>

<Type.Object name=“classification”>

<comment>

taxonomic classification (NCBI), structural classification

</comment>

</Type.Object>

<Type.Object name=“reaction”>

<comment>enzymic reaction</comment>

</Type.Object>

<Type.Object name=“pathway”>

<comment>metabolic pathway</comment>

</Type.Object>

<Type.Object name=“information source”>

<comment>database, user</comment>

</Type.Object>

<Type.Object name=“Physical Structure”>

<partition>

<li type=“solid structure”/>

<li type=“biomolecular structure”/>

<li type=“component of biomolecular structure”/>

<li type=“chemical”/>

</partition>

</Type.Object>

<Type.Object name=“solid structure”>

<comment>cell, organelle, liver</comment>

</Type.Object>

<Type.Object name=“biomolecular structure”>

<comment>secondary structure, tertiary structure</comment>

</Type.Object>

<Type.Object name=“component of biomolecular structure”>

<comment>motif, domain, site</comment>

</Type.Object>

<Type.Object name=“chemical”>

<comment>protein, nucleic acid, sodium, drug</comment>

</Type.Object>

</Theory>

</CKML>

Generalized Substance

at location http://www.tambis.org/theory/Generalized_Substance/ (fictitious)

<CKML>

<Theory>

<Type.Object name=“Generalized Substance”>

<comment>Continous abstract or physical things independent of time</comment>

<partition>

<li type=“Body Substance”/>

<li type=“Cellular Substance”/>

</partition>

</Type.Object>

<Type.Object name=“Body Substance”>

<partition>

<li type=“body fluid”/>

<li type=“tissue”/>

</partition>

</Type.Object>

<Type.Object name=“body fluid”>

<comment>blood</comment>

</Type.Object>

<Type.Object name=“tissue”>

<comment>muscle, liver</comment>

</Type.Object>

<Type.Object name=“Cellular Substance”>

<comment>cytoplasm</comment>

</Type.Object>

</Theory>

</CKML>

Generalized Process

at location http://www.tambis.org/theory/Generalized_Process/ (fictitious)

<CKML>

<Theory>

<Type.Object name=“Generalized Process”>

<comment>Transformations that occur over time</comment>

</Type.Object>

<subtype specific=“Biological Process” generic=“Generalized Process”/>

<Type.Object name=“Biological Process”>

<partition>

<li type=“body process”/>

<li type=“biomolecular process”/>

</partition>

</Type.Object>

<Type.Object name=“body process”>

<comment>disease process, clotting</comment>

</Type.Object>

<Type.Object name=“biomolecular process”>

<comment>transcription, cleavage, metabolism</comment>

</Type.Object>

</Theory>

</CKML>

Generalized Function

at location http://www.tambis.org/theory/Generalized_Function/ (fictitious)

<CKML>

<Theory>

<Type.Object name=“Generalized Function”>

<comment>Roles or purposes independent of time</comment>

</Type.Object>

<subtype specific=“Biological Function” generic=“Generalized Function”/>

<Type.Object name=“Biological Function”>

<partition>

<li type=“MolecularModification”/>

<li type=“Binding”/>

<li type=“DNA Replication and Repair”/>

<li type=“Transport”/>

<li type=“Maintenance of Structure”/>

<li type=“Cellular Growth and Proliferation”/>

<li type=“Signal Transduction”/>

<li type=“Enzymic Function”/>

<li type=“Receptor”/>

<li type=“Hormone”/>

<li type=“Toxin”/>

<li type=“Inhibitor”/>

<li type=“Targetting”/>

<li type=“Stress”/>

</partition>

</Type.Object>

<Type.Object name=“MolecularModification”>

<comment>cleavage, glycosylation</comment>

</Type.Object>

<Type.Object name=“Binding”>

<comment>nucleic acid binding</comment>

</Type.Object>

<Type.Object name=“DNA Replication and Repair”/>

<Type.Object name=“Transport”>

<comment>transmembrane transport, electron transport</comment>

</Type.Object>

<Type.Object name=“Maintenance of Structure”/>

<Type.Object name=“Cellular Growth and Proliferation”/>

<Type.Object name=“Signal Transduction”/>

<Type.Object name=“Enzymic Function”>

<comment>transferase</comment>

</Type.Object>

<Type.Object name=“Receptor”/>

<Type.Object name=“Hormone”/>

<Type.Object name=“Toxin”/>

<Type.Object name=“Inhibitor”/>

<Type.Object name=“Targetting”/>

<Type.Object name=“Stress”/>

</Theory>

</CKML>

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Please send questions, comments and suggestions about this page to: Robert E. Kent rekent@ontologos.org

Copyright © 1999 TOC (The Ontology Consortium). All rights reserved.