From b574d622f5ed5427ee76c7fe3eb859fa9e9ea333 Mon Sep 17 00:00:00 2001 From: Alexander Terry Date: Thu, 25 Jul 2024 11:04:28 -0400 Subject: [PATCH 1/3] Added functional MRI acquisition sequence subclasses - BOLD/VASO/ASL fMRI acquisition sequences. - Added ASL fMRI acquisition sequence subclasses: continuous/pulsed/velocity selective/diffusion prepared pseudocontinuous ASL fMRI acquisition sequences. --- src/ontology/MRIO-edit.owl | 84 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 84 insertions(+) diff --git a/src/ontology/MRIO-edit.owl b/src/ontology/MRIO-edit.owl index aa0bee6..d5c2a25 100644 --- a/src/ontology/MRIO-edit.owl +++ b/src/ontology/MRIO-edit.owl @@ -4970,6 +4970,30 @@ The values often belong to a group of pixels or voxels that share the same chara + + + + + A functional MRI acquisition sequence that uses the vascular space occupancy signal to measure cerebral blood volume and detect metabolic activity in the brain. + + 2024-07-25T14:45:57Z + vascular space occupancy functional MRI acquisition sequence + + + + + + + + + A type of arterial spin labeling functional MRI acquisition sequence that utilizes the continuous arterial spin labeling technique to measure cerebral blood flow and detect metabolic activity in the brain. + + 2024-07-25T14:27:33Z + continuous arterial spin labeling functional MRI acquisition sequence + + + + @@ -4981,6 +5005,30 @@ The values often belong to a group of pixels or voxels that share the same chara + + + + + A type of arterial spin labeling functional MRI acquisition sequence that utilizes the diffusion prepared pseudocontinuous arterial spin labeling technique to measure cerebral blood flow and detect metabolic activity in the brain. + + 2024-07-25T14:40:25Z + diffusion prepared pseudocontinuous arterial spin labeling functional MRI acquisition sequence + + + + + + + + + A type of arterial spin labeling functional MRI acquisition sequence that utilizes the pulsed arterial spin labeling technique to measure cerebral blood flow and detect metabolic activity in the brain. + + 2024-07-25T14:39:45Z + pulsed arterial spin labeling functional MRI acquisition sequence + + + + @@ -4991,6 +5039,42 @@ The values often belong to a group of pixels or voxels that share the same chara + + + + + A type of arterial spin labeling functional MRI acquisition sequence that utilizes the velocity selective arterial spin labeling technique to measure cerebral blood flow and detect metabolic activity in the brain. + + 2024-07-25T14:40:05Z + velocity selective arterial spin labeling functional MRI acquisition sequence + + + + + + + + + A functional MRI acquisition sequence that uses the blood oxygenation level dependent signal to detect metabolic activity in the brain. + + 2024-07-25T14:47:05Z + blood oxygenation level dependent functional MRI acquisition sequence + + + + + + + + + A functional MRI acquisition sequence that uses the arterial spin labeling signal to measure cerebral blood flow and detect metabolic activity in the brain. + + 2024-07-25T14:27:03Z + arterial spin labeling functional MRI acquisition sequence + + + + From 12454100a79727ac4f65cc5946ec1afd8fcdff69 Mon Sep 17 00:00:00 2001 From: Alexander Terry Date: Thu, 15 Aug 2024 00:18:30 -0400 Subject: [PATCH 2/3] Made updates to existing terms Deleted ASL fMRI data set in order to avoid merge conflict. Term is already added on fMRI-terms-1 branch. Added synonym to fMRI acquisition sequence and added myself as a term editor. Added synonyms to all fMRI acquisition sequence subclasses. modified defs to include acronyms, and assigned ID's within the range (e.g. MRIO_1000000) for each term. --- src/ontology/MRIO-edit.owl | 160 ++++++++++++++++++++++++++----------- 1 file changed, 112 insertions(+), 48 deletions(-) diff --git a/src/ontology/MRIO-edit.owl b/src/ontology/MRIO-edit.owl index d5c2a25..6e9bdf7 100644 --- a/src/ontology/MRIO-edit.owl +++ b/src/ontology/MRIO-edit.owl @@ -3695,6 +3695,8 @@ The values often belong to a group of pixels or voxels that share the same chara Usually T2* sequence with same TE value throughout. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0009-0004-2155-902X + fMRI acquisition sequence NCIT:C17958 SCTID:241603006 functional MRI acquisition sequence @@ -4970,107 +4972,169 @@ The values often belong to a group of pixels or voxels that share the same chara - + - + + + + + + + + + + + + - A functional MRI acquisition sequence that uses the vascular space occupancy signal to measure cerebral blood volume and detect metabolic activity in the brain. + A functional MRI acquisition sequence that uses the arterial spin labeling signal (ASL) to measure cerebral blood flow and detect metabolic activity in the brain. - 2024-07-25T14:45:57Z - vascular space occupancy functional MRI acquisition sequence + 2024-07-25T14:27:03Z + ASL fMRI acquisition sequence + arterial spin labeling functional MRI acquisition sequence - + - - - A type of arterial spin labeling functional MRI acquisition sequence that utilizes the continuous arterial spin labeling technique to measure cerebral blood flow and detect metabolic activity in the brain. + + + A type of arterial spin labeling (ASL) functional MRI acquisition sequence that utilizes the continuous arterial spin labeling (CASL) technique to measure cerebral blood flow and detect metabolic activity in the brain. 2024-07-25T14:27:33Z + CASL fMRI acquisition sequence continuous arterial spin labeling functional MRI acquisition sequence - + - - + + + A type of arterial spin labeling (ASL) functional MRI acquisition sequence that utilizes the pulsed arterial spin labeling (PASL) technique to measure cerebral blood flow and detect metabolic activity in the brain. - 2024-07-24T16:37:31Z - arterial spin labeling functional magnetic resonance image data set + 2024-07-25T14:39:45Z + PASL fMRI acquisition sequence + pulsed arterial spin labeling functional MRI acquisition sequence + + + + + + + + + A type of arterial spin labeling (ASL) functional MRI acquisition sequence that utilizes the velocity selective arterial spin labeling (VSASL) technique to measure cerebral blood flow and detect metabolic activity in the brain. + + 2024-07-25T14:40:05Z + VSASL fMRI acquisition sequence + velocity selective arterial spin labeling functional MRI acquisition sequence - + - - - A type of arterial spin labeling functional MRI acquisition sequence that utilizes the diffusion prepared pseudocontinuous arterial spin labeling technique to measure cerebral blood flow and detect metabolic activity in the brain. + + + A type of arterial spin labeling (ASL) functional MRI acquisition sequence that utilizes the diffusion prepared pseudocontinuous arterial spin labeling (DP-pCASL) technique to measure cerebral blood flow and detect metabolic activity in the brain. 2024-07-25T14:40:25Z - diffusion prepared pseudocontinuous arterial spin labeling functional MRI acquisition sequence + DP-pCASL fMRI acquisition sequence + diffusion-prepared pseudocontinuous arterial spin labeling MRI acquisition sequence - + - - - A type of arterial spin labeling functional MRI acquisition sequence that utilizes the pulsed arterial spin labeling technique to measure cerebral blood flow and detect metabolic activity in the brain. + + + + + + + + + + + + + + A functional MRI acquisition sequence that uses the vascular space occupancy (VASO) signal to measure cerebral blood volume and detect metabolic activity in the brain. - 2024-07-25T14:39:45Z - pulsed arterial spin labeling functional MRI acquisition sequence + 2024-07-25T14:45:57Z + VASO fMRI acquisition sequence + vascular space occupancy functional MRI acquisition sequence - + - - - An image segmentation map where voxel intensity values encode the location of the lateral ventricles in the brain and voxels outside the lateral ventricles have an intensity value of zero. - lateral ventricle segmentation map + + + + + + + + + + + + + + A functional MRI acquisition sequence that uses the blood oxygenation level dependent (BOLD) signal to detect metabolic activity in the brain. + + 2024-07-25T14:47:05Z + BOLD fMRI acquisition sequence + blood oxygenation level dependent functional MRI acquisition sequence - + - - - A type of arterial spin labeling functional MRI acquisition sequence that utilizes the velocity selective arterial spin labeling technique to measure cerebral blood flow and detect metabolic activity in the brain. + + - 2024-07-25T14:40:05Z - velocity selective arterial spin labeling functional MRI acquisition sequence + 2024-08-09T22:05:39Z + arterial spin labeling functional magnetic resonance image data set - + - - - A functional MRI acquisition sequence that uses the blood oxygenation level dependent signal to detect metabolic activity in the brain. + + - 2024-07-25T14:47:05Z - blood oxygenation level dependent functional MRI acquisition sequence + 2024-08-09T22:05:03Z + blood oxygenation level dependent functional magnetic resonance image data set - + - - - A functional MRI acquisition sequence that uses the arterial spin labeling signal to measure cerebral blood flow and detect metabolic activity in the brain. + + - 2024-07-25T14:27:03Z - arterial spin labeling functional MRI acquisition sequence + 2024-08-09T22:04:39Z + vascular space occupancy functional magnetic resonance image data set + + + + + + + + + An image segmentation map where voxel intensity values encode the location of the lateral ventricles in the brain and voxels outside the lateral ventricles have an intensity value of zero. + lateral ventricle segmentation map From 548b7ac33a5503078248de34bb96fc0a094022f2 Mon Sep 17 00:00:00 2001 From: Alex Bartnik Date: Mon, 21 Oct 2024 16:07:47 -0400 Subject: [PATCH 3/3] Updated OBI import --- src/ontology/imports/obi_import.owl | 38 ++--------------------------- 1 file changed, 2 insertions(+), 36 deletions(-) diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl index d897344..ea40935 100644 --- a/src/ontology/imports/obi_import.owl +++ b/src/ontology/imports/obi_import.owl @@ -11,7 +11,7 @@ - 2024-05-29 + 2024-05-29 @@ -4785,40 +4785,6 @@ In regard to the statement that reagents are 'distinct' from the speci - - - - - resting state functional magnetic resonance image data set - An fMRI used for assessing functional connectivity of brain regions at rest. - - A type of functional MRI in which the participant is not given a task, but just rests during acquisision - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" - https://github.com/obi-ontology/obi/issues/1481 - resting state functional magnetic resonance image data set - - - - - - - - - task-based functional magnetic resonance image data set - fMRI type used for assessing brain activity while performing an action or in response to stimuli. - - A type of functional MRI in which the participant is given a task or tasks, which are timed with the acquisition - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" - https://github.com/obi-ontology/obi/issues/1481 - task-based functional magnetic resonance image data set - - - - @@ -10242,5 +10208,5 @@ realizes some 'host of immune response role' - +