View source for HCLSIG BioRDF Subgroup/Tasks/Brain Atlas condition to scans

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'''Task''':  Create RDF to describe the brain scans in the [http://www.med.harvard.edu/AANLIB/home.html The Whole Brain Atlas]

'''Task Objectives''': 

# Find and use controlled vocabulary for disease/condition that will enable later linking of different content.
# Find and use controlled vocabulary of tissue types to clearly identify the tissues shown in the image.
# Generate RDF annotation suitable for inclusion on the home page and image pages, and for gathering into the BioRDF demo.

'''Participants''': 

'''Use case context''': RDF Annotation of clinical data related to neurological disorders.

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'''Problem statement for this use case''':  

One view of the semantic web is enabling the linking of diverse content based on explicitly represented properties. This resources is clearly valuable in the neurosciences domain - it shows brain images using a variety of technologies, in a variety of conditions starting with normal brains and showing brain scans of patients with a variety of different neuropathologies. However we would currently have no way to clearly relate this content to other resources that describe different aspects of these same pathologies, or to even identify these images as being of the brain as opposed to some other tissue. 

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'''Deliverables'''

# Informal proposal of what the content of the RDF will be, choice of pages to annotate. 
# For diseases listed on home page, RDF describing the connection between the condition being described and the pages which present the scans, without controlled vocabulary.
# Same for some selection of [http://www.med.harvard.edu/AANLIB/cases/caseM/case.html Top 100 Brain Structures], and some selection of the images of diseased brains.
# Proposal for which controlled ontology/controlled vocabulary to be used for annotation
# Version of RDF describing same using controlled vocabulary/ontology that might be suitable for later integration efforts
# Any artifacts generated in the process, scripts, spreadsheets etc.
# Lessons learned

'''Related resources''':

* [http://www.nlm.nih.gov/cgi/mesh/2006/MB_cgi?mode=&term=Mental+Disorders&field=entry#TreeF03 Mesh Terms for Mental disorders]
* [http://www.nlm.nih.gov/cgi/mesh/2006/MB_cgi?mode=&term=Central+Nervous+System+Diseases&field=entry#TreeC10.228 Mesh terms for Central nervous system diseases]
* [http://www.nlm.nih.gov/cgi/mesh/2006/MB_cgi?mode=&term=Central+Nervous+System&field=entry#TreeA08.186 Mesh terms for Central Nervous system anatomy]
* [http://sig.biostr.washington.edu/projects/fm/AboutFM.html Foundational model of anatomy]
* [http://obo.sourceforge.net/cgi-bin/detail.cgi?image OBO Biological imaging methods ontology]
* [http://obo.sourceforge.net/cgi-bin/detail.cgi?disease_ontology OBO Disease ontology]
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM OMIM], a catalog of human genes and genetic disorders.
* [http://www.fruitfly.org/~cjm/obo-download/ OBO ontologies in a variety of different formats, including RDF]
* [http://www.nbirn.net/ Biomedical Informatics Research Network]
* [http://smi.stanford.edu/projects/cbio/mwiki-internal/images/7/75/Gupta_disease_ontology.pdf Towards a formalization of disease-specific ontologies for neuroinformatics]
* [http://smi.stanford.edu/projects/cbio/mwiki-internal/index.php/Workshop_on_Ontology_of_Images Workshop on Ontology of Images] 

'''Task supports and dependencies''':

* 

'''Tools and Services''':

* 

'''Timeline for Task Completion'''

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* Stage 1  
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* Stage 2 
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''Categories:'' [[Category:Hclsig]] [[Category:HclsigTask]]