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activities:theme3:projects:semantic-annotation:index 2015/01/20 14:33 activities:theme3:projects:semantic-annotation:index 2016/01/05 14:44 current
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  * [[members:xavier.morandi:index|Xavier Morandi]] - Medical expert   * [[members:xavier.morandi:index|Xavier Morandi]] - Medical expert
  * [[members:romuald.seizeur:index|Romuald Seizeur]] - Medical expert   * [[members:romuald.seizeur:index|Romuald Seizeur]] - Medical expert
 +  * [[:members:pierre-jean.lereste:index| Pierre-Jean Le Reste]] - Neurosurgeon
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====== General purpose ====== ====== General purpose ======
-This projet is in the continuity of [[:members:ammar.mechouche:index| Ammar Mechouche]]'s PhD on the semantic annotation of cortical structures.  The general objective remains to produce image annotations that enable to associate explicit semantics to anatomical  features extracted from anatomical MRI images and DTI images. Such features can be regions of interest (ROI) representing anatomical structures such as gyri or gyri parts, as well as fiber bundles extracted from DTI images. The annotations refer to ontologies, that provide a reference terminology and represent the common properties of the referred entities. In our vision, such an approach can be used for various purposes: (1) reasoning - e.g. spatial reasoning - about anatomical entities, especially in the context of surgery planning; (2) intelligent querying of image repositories, and (3) mediation for the integration of heterogeneous databases.+This projet is in the continuity of [[:members:ammar.mechouche:index| Ammar Mechouche]]'s PhD on the semantic annotation of cortical structures.  The general objective remains to produce image annotations that enable to associate explicit semantics to anatomical  features extracted from anatomical MRI images and Diffusion MRI images. Such features can be regions of interest (ROI) representing anatomical structures such as gyri or gyri parts, as well as fiber bundles extracted from Diffusion MRI images, using deterministic or probabilistic tractography methods. The annotations refer to ontologies, that provide a reference terminology and represent the common properties of the referred entities. In our vision, such an approach can be used for various purposes: (1) reasoning - e.g. spatial reasoning - about anatomical entities, especially in the context of surgery planning; (2) intelligent querying of image repositories, and (3) mediation for the integration of heterogeneous databases. 
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 + 
 +====== Keywords ====== 
 +connectomics, ontology, connectome, tractography, data sharing, neuroimaging, neuroanatomy, semantic web
====== Description ====== ====== Description ======
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-===== Semantic representation of connectomics data =====+===== Ontology-based approach for in vivo human connectomics: the medial Brodmann area 6 case study =====
In the following of the project we propose an ontology called "Human Connectomics Ontology" (HCO) and we show how it can be used to annotate in vivo human connectomics datasets. This ontology is an extension of the Foundational Model of Anatomy (FMA), specifically designed to represent structural connectivity imaged by diffusion tractography. It includes a subset of FMA, called Neuro-DL-FMA, built from several lists of brain anatomical structures: (1) the Freesurfer cortical regions (Desikan et al. 2006), (2) the white matter bundles of the JHU white matter tractography atlas (Wakana et al. 2007) and (3) a list of subcortical and hippocampal structures. In Neuro-DL-FMA, the original object properties (such as fma:regional_part_of and fma:constitutional_part_of) - originally represented at the individuals' level - were translated at the classes' level (using existential restriction axioms). In the following of the project we propose an ontology called "Human Connectomics Ontology" (HCO) and we show how it can be used to annotate in vivo human connectomics datasets. This ontology is an extension of the Foundational Model of Anatomy (FMA), specifically designed to represent structural connectivity imaged by diffusion tractography. It includes a subset of FMA, called Neuro-DL-FMA, built from several lists of brain anatomical structures: (1) the Freesurfer cortical regions (Desikan et al. 2006), (2) the white matter bundles of the JHU white matter tractography atlas (Wakana et al. 2007) and (3) a list of subcortical and hippocampal structures. In Neuro-DL-FMA, the original object properties (such as fma:regional_part_of and fma:constitutional_part_of) - originally represented at the individuals' level - were translated at the classes' level (using existential restriction axioms).
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{{:activities:theme3:projects:semantic-annotation:subject01-hco.owl.zip|"subject 1 annotation file"}} {{:activities:theme3:projects:semantic-annotation:subject01-hco.owl.zip|"subject 1 annotation file"}}
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{{:activities:theme3:projects:semantic-annotation:subject02-hco.owl.zip|"subject 2 annotation file"}} {{:activities:theme3:projects:semantic-annotation:subject02-hco.owl.zip|"subject 2 annotation file"}}
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{{:activities:theme3:projects:semantic-annotation:subject03-hco.owl.zip|"subject 3 annotation file"}} {{:activities:theme3:projects:semantic-annotation:subject03-hco.owl.zip|"subject 3 annotation file"}}
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{{:activities:theme3:projects:semantic-annotation:subject04-hco.owl.zip|"subject 4 annotation file"}} {{:activities:theme3:projects:semantic-annotation:subject04-hco.owl.zip|"subject 4 annotation file"}}
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{{:activities:theme3:projects:semantic-annotation:subject05-hco.owl.zip|"subject 5 annotation file"}} {{:activities:theme3:projects:semantic-annotation:subject05-hco.owl.zip|"subject 5 annotation file"}}
 +====== Publications ======
 +
 +<html>
 +<span id="halpublispm">
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 +<p><iframe width="99%" scrolling="no" height="2000" frameborder="0" src="
 +https://haltools.archives-ouvertes.fr/Public/afficheRequetePubli.php?annee_publideb=1996&collection_exp=LTSI%3BUNIV-RENNES1&solrQuery=%28authFullName_t%3A%22gibaud%22+AND+authFullName_t%3A%22moreau%22%29&CB_auteur=oui&CB_titre=oui&CB_article=oui&langue=Anglais&tri_exp=annee_publi&tri_exp2=typdoc&tri_exp3=date_publi& amp;ord re_aff=TA&Fen=Aff&css=https://halur1.univ-rennes1.fr/css/publis-HAL.css></iframe></p>
 +</span>
 +</html>
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