From 8d3bda334976aaff7d48299d4b3d668f2abc3892 Mon Sep 17 00:00:00 2001 From: Alexander Terry Date: Thu, 25 Jul 2024 10:10:55 -0400 Subject: [PATCH 1/2] Updated fMRI data set subclasses - Deleted task based fMRI data set, and resting state fMRI data set (they were replaced). - Added fMRI data set subclasses: BOLD fMRI data set, VASO fMRI data set, and ASL image data set. - Added BOLD/VASO/ASL fMRI data set subclasses: resting state BOLD/VASO/ASL fMRI data set, task-based BOLD/VASO/ASL fMRI data set. - Added BOLD/VASO/ASL task-based fMRI data set subclasses: BOLD/VASO/ASL event-related fMRI data set, BOLD/VASO/ASL block design fMRI data set, BOLD/VASO/ASL mixed event-related/block design fMRI data set. - Added BOLD/VASO/ASL event-related fMRI data set subclasses: BOLD/VASO/ASL rapid event-related fMRI data set. - Added defs to each new term. --- src/ontology/MRIO-edit.owl | 243 +++++++++++++++++++++++++++- src/ontology/imports/obi_import.owl | 38 +---- 2 files changed, 243 insertions(+), 38 deletions(-) diff --git a/src/ontology/MRIO-edit.owl b/src/ontology/MRIO-edit.owl index aa0bee6..45dfe7a 100644 --- a/src/ontology/MRIO-edit.owl +++ b/src/ontology/MRIO-edit.owl @@ -520,7 +520,6 @@ 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" - obsolete Resting state functional magnetic resonance image data set true @@ -534,7 +533,6 @@ 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" - obsolete Task-based functional magnetic resonance image data set true @@ -4970,10 +4968,59 @@ The values often belong to a group of pixels or voxels that share the same chara + + + + + A type of blood oxygenation level dependent task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli that alternate between structured blocks and randomized or semi-randomized order seperated by rest periods during the imaging acquisition. + + 2024-07-25T03:45:29Z + blood oxygenation level dependant mixed event-related/block design functional magnetic resonance image data set + + + + + + + + + A type of arterial spin labeling functional magnetic resonance imaging in which the participant is not given a task, but just rests during acquisition. + + 2024-07-24T23:50:47Z + arterial spin labeling resting state functional magnetic resonance image data set + + + + + + + + + A type of arterial spin labeling task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli that alternate between structured blocks and randomized or semi-randomized order seperated by rest periods during the imaging acquisition. + + 2024-07-25T13:56:33Z + arterial spin labeling mixed event-related/block design functional magnetic resonance image data set + + + + + + + + + A type of vascular space occupancy event-related functional magnetic resonance imaging where trials are closely spaced without allowing the hemodynamic response to return to baseline, and the resulting hemodynamic responses are deconvolved afterwards. + + 2024-07-25T03:26:42Z + vascular space occupancy rapid event-related functional magnetic resonance image data set + + + + + A functional magnetic resonance image data set that utilizes arterial spin labeling. 2024-07-24T16:37:31Z arterial spin labeling functional magnetic resonance image data set @@ -4981,6 +5028,78 @@ The values often belong to a group of pixels or voxels that share the same chara + + + + + A type of blood oxygenation level dependent event-related functional magnetic resonance imaging where trials are closely spaced without allowing the hemodynamic response to return to baseline, and the resulting hemodynamic responses are deconvolved afterwards. + + 2024-07-25T03:29:43Z + blood oxygenation level dependent rapid event-related functional magnetic resonance image data set + + + + + + + + + A type of arterial spin labeling task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli in structured blocks seperated by rest periods during the imaging acquisition. + + 2024-07-25T13:58:36Z + arterial spin labeling block design functional magnetic resonance image data set + + + + + + + + + A type of vascular space occupancy task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli in structured blocks seperated by rest periods during the imaging acquisition. + + 2024-07-25T13:59:05Z + vascular space occupancy block design functional magnetic resonance image data set + + + + + + + + + A type of arterial spin labeling task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli that are presented in a randomized or semi-randomized order seperated by rest periods during the imaging acquisition. Typically, after each trial, the hemodynamic response is allowed to return to baseline. + + 2024-07-25T03:27:23Z + arterial spin labeling event-related functional magnetic resonance image data set + + + + + + + + + A type of blood oxygenation level dependent functional magnetic resonance imaging in which the participant is not given a task, but just rests during acquisition. + + 2024-07-25T00:11:14Z + blood oxygenation level dependent resting state functional magnetic resonance image data set + + + + + + + + + A type of blood oxygenation level dependent task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli in structured blocks seperated by rest periods during the imaging acquisition. + + 2024-07-25T03:44:38Z + blood oxygenation level dependant block design functional magnetic resonance image data set + + + + @@ -4991,6 +5110,126 @@ The values often belong to a group of pixels or voxels that share the same chara + + + + + A type of vascular space occupancy functional magnetic resonance imaging in which the participant is given a task(s), which are timed with the acquisition. + + 2024-07-25T00:14:44Z + vascular space occupancy task-based functional magnetic resonance image data set + + + + + + + + + A type of blood oxygenation level dependent task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli that are presented in a randomized or semi-randomized order seperated by rest periods during the imaging acquisition. Typically, after each trial, the hemodynamic response is allowed to return to baseline. + + 2024-07-25T03:29:25Z + blood oxygenation level dependent event-related functional magnetic resonance image data set + + + + + + + + + A type of blood oxygenation level dependent functional magnetic resonance imaging in which the participant is given a task(s), which are timed with the acquisition. + + 2024-07-25T00:11:54Z + blood oxygenation level dependent task-based functional magnetic resonance image data set + + + + + + + + + A type of arterial spin labeling functional magnetic resonance imaging in which the participant is given a task(s), which are timed with the acquisition. + + 2024-07-24T23:53:17Z + arterial spin labeling task-based functional magnetic resonance image data set + + + + + + + + + A functional magnetic resonance image data set that utilizes blood oxygenation level dependent contrast. + + 2024-07-24T23:33:43Z + blood oxygenation level dependent functional magnetic resonance image data set + + + + + + + + + A type of vascular space occupancy task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli that alternate between structured blocks and randomized or semi-randomized order seperated by rest periods during the imaging acquisition. + + 2024-07-25T13:59:29Z + vascular space occupancy mixed event-related/block design functional magnetic resonance image data set + + + + + + + + + A type of arterial spin labeling event-related functional magnetic resonance imaging where trials are closely spaced without allowing the hemodynamic response to return to baseline, and the resulting hemodynamic responses are deconvolved afterwards. + + 2024-07-25T03:28:00Z + arterial spin labeling rapid event-related functional magnetic resonance image data set + + + + + + + + + A functional magnetic resonance image data set that utilizes vascular space occupancy contrast. + + 2024-07-24T23:33:06Z + vascular space occupancy functional magnetic resonance image data set + + + + + + + + + A type of vascular space occupancy functional magnetic resonance imaging in which the participant is not given a task, but just rests during acquisition. + + 2024-07-25T00:14:36Z + vascular space occupancy resting state functional magnetic resonance image data set + + + + + + + + + A type of vascular space occupancy task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli that are presented in a randomized or semi-randomized order seperated by rest periods during the imaging acquisition. Typically, after each trial, the hemodynamic response is allowed to return to baseline. + + 2024-07-25T03:25:21Z + vascular space occupancy event-related functional magnetic resonance image data set + + + + 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' - + From dbe8ab58fb7fee8f9dc8a3fb5f3220cc16a19e85 Mon Sep 17 00:00:00 2001 From: Alexander Terry Date: Thu, 15 Aug 2024 00:16:18 -0400 Subject: [PATCH 2/2] Updated BOLD/VASO/ASL fMRI data set subclasses Updated BOLD/VASO/ASL fMRI data set subclasses: Deleted BOLD/VASO/ASL mixed/event-related/rapid event-related/block design subclasses. Added synonyms to all fMRI image data set 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 | 299 ++++++++++++++++--------------------- 1 file changed, 128 insertions(+), 171 deletions(-) diff --git a/src/ontology/MRIO-edit.owl b/src/ontology/MRIO-edit.owl index 45dfe7a..c0f5e3d 100644 --- a/src/ontology/MRIO-edit.owl +++ b/src/ontology/MRIO-edit.owl @@ -365,6 +365,16 @@ + + + + + 2024-08-09T20:33:47Z + cognitive process + + + + @@ -4968,264 +4978,211 @@ The values often belong to a group of pixels or voxels that share the same chara - + - - - A type of blood oxygenation level dependent task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli that alternate between structured blocks and randomized or semi-randomized order seperated by rest periods during the imaging acquisition. + + - 2024-07-25T03:45:29Z - blood oxygenation level dependant mixed event-related/block design functional magnetic resonance image data set + 2024-08-09T19:59:31Z + arterial spin labeling functional MRI acquisition sequence - + - - - A type of arterial spin labeling functional magnetic resonance imaging in which the participant is not given a task, but just rests during acquisition. + + - 2024-07-24T23:50:47Z - arterial spin labeling resting state functional magnetic resonance image data set + 2024-08-09T19:59:51Z + vascular space occupancy functional MRI acquisition sequence - + - - - A type of arterial spin labeling task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli that alternate between structured blocks and randomized or semi-randomized order seperated by rest periods during the imaging acquisition. + + - 2024-07-25T13:56:33Z - arterial spin labeling mixed event-related/block design functional magnetic resonance image data set + 2024-08-09T20:00:10Z + blood oxygenation level dependent functional MRI acquisition sequence - + - - - A type of vascular space occupancy event-related functional magnetic resonance imaging where trials are closely spaced without allowing the hemodynamic response to return to baseline, and the resulting hemodynamic responses are deconvolved afterwards. - - 2024-07-25T03:26:42Z - vascular space occupancy rapid event-related functional magnetic resonance image data set - - - - - - - + + + + + + + + + + + + - A functional magnetic resonance image data set that utilizes arterial spin labeling. + A functional magnetic resonance image data set that utilizes arterial spin labeling (ASL). 2024-07-24T16:37:31Z + ASL functional magnetic resonance image data set arterial spin labeling functional magnetic resonance image data set - - - - - A type of blood oxygenation level dependent event-related functional magnetic resonance imaging where trials are closely spaced without allowing the hemodynamic response to return to baseline, and the resulting hemodynamic responses are deconvolved afterwards. - - 2024-07-25T03:29:43Z - blood oxygenation level dependent rapid event-related functional magnetic resonance image data set - - - - - + - - - A type of arterial spin labeling task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli in structured blocks seperated by rest periods during the imaging acquisition. + + + A type of arterial spin labeling (ASL) functional magnetic resonance imaging (fMRI) in which the participant is not given a task, but just rests during acquisition. - 2024-07-25T13:58:36Z - arterial spin labeling block design functional magnetic resonance image data set + 2024-07-24T23:50:47Z + ASL resting state functional magnetic resonance image data set + arterial spin labeling resting state functional magnetic resonance image data set - + - - - A type of vascular space occupancy task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli in structured blocks seperated by rest periods during the imaging acquisition. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A type of arterial spin labeling (ASL) functional magnetic resonance imaging (fMRI) in which the participant is given a task(s), which are timed with the acquisition. - 2024-07-25T13:59:05Z - vascular space occupancy block design functional magnetic resonance image data set + 2024-07-24T23:53:17Z + ASL task-based functional magnetic resonance image data set + arterial spin labeling task-based functional magnetic resonance image data set - + - - - A type of arterial spin labeling task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli that are presented in a randomized or semi-randomized order seperated by rest periods during the imaging acquisition. Typically, after each trial, the hemodynamic response is allowed to return to baseline. + + + A functional magnetic resonance image data set that utilizes blood oxygenation level dependent (BOLD) contrast. - 2024-07-25T03:27:23Z - arterial spin labeling event-related functional magnetic resonance image data set + 2024-07-24T23:33:43Z + BOLD functional magnetic resonance image data set + blood oxygenation level dependent functional magnetic resonance image data set - + - - - A type of blood oxygenation level dependent functional magnetic resonance imaging in which the participant is not given a task, but just rests during acquisition. + + + A type of blood oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI) in which the participant is not given a task, but just rests during acquisition. 2024-07-25T00:11:14Z + BOLD resting state functional magnetic resonance image data set blood oxygenation level dependent resting state functional magnetic resonance image data set - - - - - A type of blood oxygenation level dependent task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli in structured blocks seperated by rest periods during the imaging acquisition. - - 2024-07-25T03:44:38Z - blood oxygenation level dependant block design 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 - - - - - - - - - A type of vascular space occupancy functional magnetic resonance imaging in which the participant is given a task(s), which are timed with the acquisition. - - 2024-07-25T00:14:44Z - vascular space occupancy task-based functional magnetic resonance image data set - - - - - - - - - A type of blood oxygenation level dependent task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli that are presented in a randomized or semi-randomized order seperated by rest periods during the imaging acquisition. Typically, after each trial, the hemodynamic response is allowed to return to baseline. - - 2024-07-25T03:29:25Z - blood oxygenation level dependent event-related functional magnetic resonance image data set - - - - - + - - - A type of blood oxygenation level dependent functional magnetic resonance imaging in which the participant is given a task(s), which are timed with the acquisition. + + + A type of blood oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI) in which the participant is given a task(s), which are timed with the acquisition. 2024-07-25T00:11:54Z + BOLD task-based functional magnetic resonance image data set blood oxygenation level dependent task-based functional magnetic resonance image data set - - - - - A type of arterial spin labeling functional magnetic resonance imaging in which the participant is given a task(s), which are timed with the acquisition. - - 2024-07-24T23:53:17Z - arterial spin labeling task-based functional magnetic resonance image data set - - - - - + - + - A functional magnetic resonance image data set that utilizes blood oxygenation level dependent contrast. + A functional magnetic resonance image data set that utilizes vascular space occupancy (VASO) contrast. - 2024-07-24T23:33:43Z - blood oxygenation level dependent functional magnetic resonance image data set - - - - - - - - - A type of vascular space occupancy task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli that alternate between structured blocks and randomized or semi-randomized order seperated by rest periods during the imaging acquisition. - - 2024-07-25T13:59:29Z - vascular space occupancy mixed event-related/block design functional magnetic resonance image data set + 2024-07-24T23:33:06Z + VASO functional magnetic resonance image data set + vascular space occupancy functional magnetic resonance image data set - + - - - A type of arterial spin labeling event-related functional magnetic resonance imaging where trials are closely spaced without allowing the hemodynamic response to return to baseline, and the resulting hemodynamic responses are deconvolved afterwards. + + + A type of vascular space occupancy (VASO) functional magnetic resonance imaging (fMRI) in which the participant is not given a task, but just rests during acquisition. - 2024-07-25T03:28:00Z - arterial spin labeling rapid event-related functional magnetic resonance image data set + 2024-07-25T00:14:36Z + VASO resting state functional magnetic resonance image data set + vascular space occupancy resting state functional magnetic resonance image data set - + - - - A functional magnetic resonance image data set that utilizes vascular space occupancy contrast. + + + A type of vascular space occupancy (VASO) functional magnetic resonance imaging (fMRI) in which the participant is given a task(s), which are timed with the acquisition. - 2024-07-24T23:33:06Z - vascular space occupancy functional magnetic resonance image data set + 2024-07-25T00:14:44Z + VASO task-based functional magnetic resonance image data set + vascular space occupancy task-based functional magnetic resonance image data set - + - - - A type of vascular space occupancy functional magnetic resonance imaging in which the participant is not given a task, but just rests during acquisition. + + A type of blood oxygenation level dependent event-related functional magnetic resonance imaging where trials are closely spaced without allowing the hemodynamic response to return to baseline, and the resulting hemodynamic responses are deconvolved afterwards. - 2024-07-25T00:14:36Z - vascular space occupancy resting state functional magnetic resonance image data set + 2024-07-25T03:29:43Z + blood oxygenation level dependent rapid event-related functional magnetic resonance image data set - + - - - A type of vascular space occupancy task-based functional magnetic resonance imaging where the participant is given specific tasks or stimuli that are presented in a randomized or semi-randomized order seperated by rest periods during the imaging acquisition. Typically, after each trial, the hemodynamic response is allowed to return to baseline. - - 2024-07-25T03:25:21Z - vascular space occupancy event-related 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