BIRN Ontology Task Force (Public Wiki) ( BIRN-OTF-Public.Home)

BIRN Ontology Task Force (Public Wiki)

BIRNLex Development Site
BIRNLex & the BIRN Mediator
Use Cases
Presentations

Only BIRN OTF members can edit this page *

BIRNLex Development Site

controlled lexicon for BIRN-wide data annotation

About BIRNLex
View BIRNLex
- We invite the community to view or download the current version of the BIRNLex. The OWL file can be accessed here. A more user-friendly interface for browsing and searching the BIRNLex is available through the NCBO BioPortal, or by launching the OntologEZ browser (requires Java Webstart). Please be advised that BIRNLex is under active development and subject to change, although the ID's assigned to BIRNLex classes are stable. Any changes to the ontology will be indicated by a change in version number. Comments and suggestions are welcome.
- OWL implementation
- Documentation - NOTE: this is a link to the OntologyEZ tool created by Steve Lamont of UCSD. It can take as long as a minute to load under slow Internet connections, but using a typical broadband or campus connection should load in approximately 20 seconds. This tool provides a simple means of navigating the BIRNLex hierarchy, searching for specific classes based on their preferred term, and viewing the many properties associated with a BIRNLex class.
- To view the most recent release of BIRNLex in the ontology editing tool Protege, follow the instructions listed here
BIRNLex Help
BIRNLex Development Practice

BIRNLex & the BIRN Mediator

BIRN Mediator-associated web services

Use Cases

required, BIRN-wide data management, retrieval, & analysis tasks

BIRN Task Force Use Cases
- BIRN OTF Use Cases

Testbed	Title	Author	Date	Description
Function BIRN	Multi-modal Complexity of Cognitive Paradigms	Jessica Turner	2006-07-08	Query for the federated database system: ?Find me all the subjects with fMRI data from a working memory task.? The mediator then has to search the ontology of behavioral paradigms to find out which tasks are working memory tasks, and go get those datasets. Ideally, every dataset has a concept ID annotating what behavioral task was used during its collection, that would then be the bottom node in a nice hierarchy of behavioral tasks. The mediator would start in the behavioral task hierarchy with the ?concept ID? for working memory tasks, find all the various working memory tasks below that in the hierarchy, and be off to the races. The tricky bit: Colloquially we know what a working memory task is. We currently have a dataset of 240 subjects who performed the Serial Item Recognition Paradigm (SIRP) while in the MRI. In the SIRP, subjects are shown a group of letters (targets) which they then have to remember, and then are shown other letters (probes), and they have to identify which were targets. Everyone recognizes that as a working memory task, which is a kind of memory task, which is a kind of behavioral paradigm. That?s a neat and tidy hierarchy. However, we are now collecting data using a different task: In this one, subjects still see words they have to remember; however, they then are shown pictures for a while, and only after that, they are shown probes and they have to indicate the targets. The pictures are sometimes nasty and sometimes not. This task is very rich, and we?re asking questions from it both about working memory, and about emotional processing, and about their interaction. This is a working memory task, but it is also an emotional processing task. So we end up with multiple parents for this task, in the previously sketched hierarchy of behavioral paradigms.
Morphometry BIRN	Determining whether the expression of cognitive dysfunctions like depresssion correlate with the eventual development of Alzheimer's disease	Christine Fennema-Notestine	2006-12-10	Example Queries: Find volumetric data/metadata from MRIs of humans with specific diagnosis(es): Which structures are decreased/increased in size relative to normal controls Which structures show structural differences across a variety of diagnoses Do any of these structural changes predict severity of diagnosis Are there difference in the structural changes across gender Given a structure which shows structural differences Which other structures are associated with it Do any of these associated structures show structural differences Do these other changed structures have commonalities (i.e. cell types, neurotransmitters, other afferent/efferent connections) What is the progression of the differences within these structures in relation to one another and the diagnosis What measures of structural change show the difference and are they correlated with one another Find volumetric metadata for humans with genotyping data for APOE status Are there any brain regions showing structural differences based on APOE status Find diffusion tensor/volumetric metadata for humans with genotyping data for APOE status Are there any regions showing differences in white/gray matter based on APOE status Do any brain areas show structural changes correlated with the severity of a specific disorder(s) in a population of human subjects Is the structural data able to classify the subjects regarding the disorder Given a new population of subjects can the structural data predict occurrence and the severity of the disorder in this new population Find observed structural changes in normal human subjects predictive of a future diagnosis

Testbed

Title

Author

Date

Description

Function BIRN

Multi-modal Complexity of Cognitive Paradigms

Jessica Turner

2006-07-08

Query for the federated database system: ?Find me all the subjects with fMRI data from a working memory task.? The mediator then has to search the ontology of behavioral paradigms to find out which tasks are working memory tasks, and go get those datasets. Ideally, every dataset has a concept ID annotating what behavioral task was used during its collection, that would then be the bottom node in a nice hierarchy of behavioral tasks. The mediator would start in the behavioral task hierarchy with the ?concept ID? for working memory tasks, find all the various working memory tasks below that in the hierarchy, and be off to the races.

The tricky bit: Colloquially we know what a working memory task is. We currently have a dataset of 240 subjects who performed the Serial Item Recognition Paradigm (SIRP) while in the MRI. In the SIRP, subjects are shown a group of letters (targets) which they then have to remember, and then are shown other letters (probes), and they have to identify which were targets. Everyone recognizes that as a working memory task, which is a kind of memory task, which is a kind of behavioral paradigm. That?s a neat and tidy hierarchy.

However, we are now collecting data using a different task: In this one, subjects still see words they have to remember; however, they then are shown pictures for a while, and only after that, they are shown probes and they have to indicate the targets. The pictures are sometimes nasty and sometimes not. This task is very rich, and we?re asking questions from it both about working memory, and about emotional processing, and about their interaction. This is a working memory task, but it is also an emotional processing task. So we end up with multiple parents for this task, in the previously sketched hierarchy of behavioral paradigms.

Morphometry BIRN

Determining whether the expression of cognitive dysfunctions like depresssion correlate with the eventual development of Alzheimer's disease

Christine Fennema-Notestine

2006-12-10

Example Queries:

Find volumetric data/metadata from MRIs of humans with specific diagnosis(es):
- Which structures are decreased/increased in size relative to normal controls
- Which structures show structural differences across a variety of diagnoses
- Do any of these structural changes predict severity of diagnosis
- Are there difference in the structural changes across gender
Given a structure which shows structural differences
- Which other structures are associated with it
- Do any of these associated structures show structural differences
- Do these other changed structures have commonalities (i.e. cell types, neurotransmitters, other afferent/efferent connections)
- What is the progression of the differences within these structures in relation to one another and the diagnosis
- What measures of structural change show the difference and are they correlated with one another
Find volumetric metadata for humans with genotyping data for APOE status
- Are there any brain regions showing structural differences based on APOE status
Find diffusion tensor/volumetric metadata for humans with genotyping data for APOE status
- Are there any regions showing differences in white/gray matter based on APOE status
Do any brain areas show structural changes correlated with the severity of a specific disorder(s) in a population of human subjects
- Is the structural data able to classify the subjects regarding the disorder
- Given a new population of subjects can the structural data predict occurrence and the severity of the disorder in this new population
Find observed structural changes in normal human subjects predictive of a future diagnosis

- BIRN XML Schema (XCEDE) TF Use Cases
BIRN Test Bed Use Cases
Other BIRN Use Cases
- Example of Simple Use Case resolved via the BIRN Infrastructure
  - this is a bit old (2002), but despite some of the technical details having changed a little, it gives a very nice overview of how solutions for such Use Cases are being implemented via the BIRN Infrastructural components.

Presentations

2nd FuGO Workshop (Wellcome Conference Centre, EBI, Hinxton, UK) - July 24 - 27
- BIRN OTF presentation (Bill Bug) BIRN-FuGO-20060724.ppt
- BIRNLex Experiment Terms BIRNLex-Experiment-Terms-20060704.xls

Version 1.71 last modified by Maryann Martone on 09/04/2008 at 19:46

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BIRN-FuGO-20060724.ppt 1.1

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