From 0cbf1ac1b2dd02a5c022b38df9cb76a9733b1ef6 Mon Sep 17 00:00:00 2001 From: sneakers-the-rat Date: Wed, 3 Jul 2024 23:36:58 -0700 Subject: [PATCH] how come ide always misses the schema lol --- .../linkml/core/v2_2_0/core.nwb.base.yaml | 1 + .../linkml/core/v2_2_0/core.nwb.ecephys.yaml | 35 +++- .../linkml/core/v2_2_0/core.nwb.epoch.yaml | 38 ++++- .../linkml/core/v2_2_0/core.nwb.language.yaml | 9 - .../linkml/core/v2_2_0/core.nwb.misc.yaml | 1 + .../core/v2_2_0/core.nwb.retinotopy.yaml | 1 + .../linkml/core/v2_2_1/core.nwb.base.yaml | 1 + .../linkml/core/v2_2_1/core.nwb.ecephys.yaml | 35 +++- .../linkml/core/v2_2_1/core.nwb.epoch.yaml | 38 ++++- .../linkml/core/v2_2_1/core.nwb.language.yaml | 9 - .../linkml/core/v2_2_1/core.nwb.misc.yaml | 1 + .../core/v2_2_1/core.nwb.retinotopy.yaml | 1 + .../linkml/core/v2_2_2/core.nwb.base.yaml | 1 + .../linkml/core/v2_2_2/core.nwb.ecephys.yaml | 35 +++- .../linkml/core/v2_2_2/core.nwb.epoch.yaml | 38 ++++- .../linkml/core/v2_2_2/core.nwb.language.yaml | 9 - .../linkml/core/v2_2_2/core.nwb.misc.yaml | 1 + .../core/v2_2_2/core.nwb.retinotopy.yaml | 1 + .../linkml/core/v2_2_4/core.nwb.base.yaml | 1 + .../linkml/core/v2_2_4/core.nwb.ecephys.yaml | 35 +++- .../linkml/core/v2_2_4/core.nwb.epoch.yaml | 38 ++++- .../linkml/core/v2_2_4/core.nwb.language.yaml | 9 - .../linkml/core/v2_2_4/core.nwb.misc.yaml | 1 + .../linkml/core/v2_2_4/core.nwb.ophys.yaml | 80 ++++++++- .../core/v2_2_4/core.nwb.retinotopy.yaml | 1 + .../linkml/core/v2_2_5/core.nwb.base.yaml | 1 + .../linkml/core/v2_2_5/core.nwb.ecephys.yaml | 35 +++- .../linkml/core/v2_2_5/core.nwb.epoch.yaml | 38 ++++- .../linkml/core/v2_2_5/core.nwb.language.yaml | 9 - .../linkml/core/v2_2_5/core.nwb.misc.yaml | 1 + .../linkml/core/v2_2_5/core.nwb.ophys.yaml | 80 ++++++++- .../core/v2_2_5/core.nwb.retinotopy.yaml | 1 + .../linkml/core/v2_3_0/core.nwb.base.yaml | 1 + .../linkml/core/v2_3_0/core.nwb.ecephys.yaml | 35 +++- .../linkml/core/v2_3_0/core.nwb.epoch.yaml | 38 ++++- .../linkml/core/v2_3_0/core.nwb.language.yaml | 9 - .../linkml/core/v2_3_0/core.nwb.misc.yaml | 1 + .../linkml/core/v2_3_0/core.nwb.ophys.yaml | 80 ++++++++- .../core/v2_3_0/core.nwb.retinotopy.yaml | 1 + .../linkml/core/v2_4_0/core.nwb.base.yaml | 23 +++ .../linkml/core/v2_4_0/core.nwb.ecephys.yaml | 35 +++- .../linkml/core/v2_4_0/core.nwb.epoch.yaml | 38 ++++- .../linkml/core/v2_4_0/core.nwb.language.yaml | 9 - .../linkml/core/v2_4_0/core.nwb.misc.yaml | 1 + .../linkml/core/v2_4_0/core.nwb.ophys.yaml | 80 ++++++++- .../core/v2_4_0/core.nwb.retinotopy.yaml | 1 + .../linkml/core/v2_5_0/core.nwb.base.yaml | 23 +++ .../linkml/core/v2_5_0/core.nwb.ecephys.yaml | 35 +++- .../linkml/core/v2_5_0/core.nwb.language.yaml | 9 - .../linkml/core/v2_5_0/core.nwb.misc.yaml | 1 + .../linkml/core/v2_5_0/core.nwb.ophys.yaml | 80 ++++++++- .../core/v2_5_0/core.nwb.retinotopy.yaml | 1 + .../core/v2_6_0_alpha/core.nwb.base.yaml | 23 +++ .../core/v2_6_0_alpha/core.nwb.ecephys.yaml | 35 +++- .../core/v2_6_0_alpha/core.nwb.language.yaml | 9 - .../core/v2_6_0_alpha/core.nwb.misc.yaml | 1 + .../core/v2_6_0_alpha/core.nwb.ophys.yaml | 80 ++++++++- .../v2_6_0_alpha/core.nwb.retinotopy.yaml | 1 + .../v1_1_0/hdmf-common.nwb.language.yaml | 9 - .../hdmf_common/v1_1_0/hdmf-common.table.yaml | 1 + .../v1_1_2/hdmf-common.nwb.language.yaml | 9 - .../hdmf_common/v1_1_2/hdmf-common.table.yaml | 1 + .../v1_1_3/hdmf-common.nwb.language.yaml | 9 - .../hdmf_common/v1_1_3/hdmf-common.table.yaml | 1 + .../v1_5_0/hdmf-common.nwb.language.yaml | 9 - .../hdmf_common/v1_5_0/hdmf-common.table.yaml | 1 + .../hdmf-experimental.nwb.language.yaml | 9 - .../v0_1_0/hdmf-experimental.resources.yaml | 157 +++++++++++++++--- 68 files changed, 1248 insertions(+), 193 deletions(-) diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.base.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.base.yaml index 805820e..7b38c16 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.base.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.base.yaml @@ -292,6 +292,7 @@ classes: attributes: name: name: name + ifabsent: string(Images) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.ecephys.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.ecephys.yaml index ecaa563..f845d26 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.ecephys.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.ecephys.yaml @@ -139,6 +139,7 @@ classes: attributes: name: name: name + ifabsent: string(FeatureExtraction) identifier: true range: string required: true @@ -200,6 +201,7 @@ classes: attributes: name: name: name + ifabsent: string(EventDetection) identifier: true range: string required: true @@ -309,9 +311,38 @@ classes: name: position description: stereotaxic or common framework coordinates multivalued: false - range: AnyType + range: ElectrodeGroup__position required: false tree_root: true + ElectrodeGroup__position: + name: ElectrodeGroup__position + description: stereotaxic or common framework coordinates + attributes: + name: + name: name + ifabsent: string(position) + identifier: true + range: string + required: true + equals_string: position + x: + name: x + description: x coordinate + multivalued: false + range: float32 + required: false + y: + name: y + description: y coordinate + multivalued: false + range: float32 + required: false + z: + name: z + description: z coordinate + multivalued: false + range: float32 + required: false ClusterWaveforms: name: ClusterWaveforms description: DEPRECATED The mean waveform shape, including standard deviation, @@ -324,6 +355,7 @@ classes: attributes: name: name: name + ifabsent: string(ClusterWaveforms) identifier: true range: string required: true @@ -366,6 +398,7 @@ classes: attributes: name: name: name + ifabsent: string(Clustering) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.epoch.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.epoch.yaml index 5ac1f3c..0138682 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.epoch.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.epoch.yaml @@ -49,8 +49,9 @@ classes: timeseries: name: timeseries description: An index into a TimeSeries object. - multivalued: true - range: AnyType + multivalued: false + range: TimeIntervals__timeseries + required: false timeseries_index: name: timeseries_index description: Index for timeseries. @@ -70,6 +71,39 @@ classes: range: string required: true equals_string: tags_index + TimeIntervals__timeseries: + name: TimeIntervals__timeseries + description: An index into a TimeSeries object. + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(timeseries) + identifier: true + range: string + required: true + equals_string: timeseries + idx_start: + name: idx_start + description: Start index into the TimeSeries 'data' and 'timestamp' datasets + of the referenced TimeSeries. The first dimension of those arrays is always + time. + multivalued: false + range: int32 + required: false + count: + name: count + description: Number of data samples available in this time series, during + this epoch. + multivalued: false + range: int32 + required: false + timeseries: + name: timeseries + description: the TimeSeries that this index applies to. + multivalued: false + range: TimeSeries + required: false TimeIntervals__timeseries_index: name: TimeIntervals__timeseries_index description: Index for timeseries. diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.language.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.language.yaml index edba729..929628d 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.language.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.language.yaml @@ -140,15 +140,6 @@ enums: isodatetime: text: isodatetime classes: - Arraylike: - name: Arraylike - description: Container for arraylike information held in the dims, shape, and - dtype properties.this is a special case to be interpreted by downstream i/o. - this class has no slotsand is abstract by default.- Each slot within a subclass - indicates a possible dimension.- Only dimensions that are present in all the - dimension specifiers in the original schema are required.- Shape requirements - are indicated using max/min cardinalities on the slot. - abstract: true AnyType: name: AnyType description: Needed because some classes in hdmf-common are datasets without dtype diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.misc.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.misc.yaml index bc542e8..48634c8 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.misc.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.misc.yaml @@ -246,6 +246,7 @@ classes: attributes: name: name: name + ifabsent: string(Units) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.retinotopy.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.retinotopy.yaml index d717b32..c61cf8a 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.retinotopy.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_0/core.nwb.retinotopy.yaml @@ -106,6 +106,7 @@ classes: attributes: name: name: name + ifabsent: string(ImagingRetinotopy) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.base.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.base.yaml index 0e3f8dd..5482e00 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.base.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.base.yaml @@ -292,6 +292,7 @@ classes: attributes: name: name: name + ifabsent: string(Images) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.ecephys.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.ecephys.yaml index c84d7f5..8187359 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.ecephys.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.ecephys.yaml @@ -139,6 +139,7 @@ classes: attributes: name: name: name + ifabsent: string(FeatureExtraction) identifier: true range: string required: true @@ -200,6 +201,7 @@ classes: attributes: name: name: name + ifabsent: string(EventDetection) identifier: true range: string required: true @@ -309,9 +311,38 @@ classes: name: position description: stereotaxic or common framework coordinates multivalued: false - range: AnyType + range: ElectrodeGroup__position required: false tree_root: true + ElectrodeGroup__position: + name: ElectrodeGroup__position + description: stereotaxic or common framework coordinates + attributes: + name: + name: name + ifabsent: string(position) + identifier: true + range: string + required: true + equals_string: position + x: + name: x + description: x coordinate + multivalued: false + range: float32 + required: false + y: + name: y + description: y coordinate + multivalued: false + range: float32 + required: false + z: + name: z + description: z coordinate + multivalued: false + range: float32 + required: false ClusterWaveforms: name: ClusterWaveforms description: DEPRECATED The mean waveform shape, including standard deviation, @@ -324,6 +355,7 @@ classes: attributes: name: name: name + ifabsent: string(ClusterWaveforms) identifier: true range: string required: true @@ -366,6 +398,7 @@ classes: attributes: name: name: name + ifabsent: string(Clustering) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.epoch.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.epoch.yaml index b58cc4e..27f674b 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.epoch.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.epoch.yaml @@ -49,8 +49,9 @@ classes: timeseries: name: timeseries description: An index into a TimeSeries object. - multivalued: true - range: AnyType + multivalued: false + range: TimeIntervals__timeseries + required: false timeseries_index: name: timeseries_index description: Index for timeseries. @@ -70,6 +71,39 @@ classes: range: string required: true equals_string: tags_index + TimeIntervals__timeseries: + name: TimeIntervals__timeseries + description: An index into a TimeSeries object. + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(timeseries) + identifier: true + range: string + required: true + equals_string: timeseries + idx_start: + name: idx_start + description: Start index into the TimeSeries 'data' and 'timestamp' datasets + of the referenced TimeSeries. The first dimension of those arrays is always + time. + multivalued: false + range: int32 + required: false + count: + name: count + description: Number of data samples available in this time series, during + this epoch. + multivalued: false + range: int32 + required: false + timeseries: + name: timeseries + description: the TimeSeries that this index applies to. + multivalued: false + range: TimeSeries + required: false TimeIntervals__timeseries_index: name: TimeIntervals__timeseries_index description: Index for timeseries. diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.language.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.language.yaml index edba729..929628d 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.language.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.language.yaml @@ -140,15 +140,6 @@ enums: isodatetime: text: isodatetime classes: - Arraylike: - name: Arraylike - description: Container for arraylike information held in the dims, shape, and - dtype properties.this is a special case to be interpreted by downstream i/o. - this class has no slotsand is abstract by default.- Each slot within a subclass - indicates a possible dimension.- Only dimensions that are present in all the - dimension specifiers in the original schema are required.- Shape requirements - are indicated using max/min cardinalities on the slot. - abstract: true AnyType: name: AnyType description: Needed because some classes in hdmf-common are datasets without dtype diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.misc.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.misc.yaml index d04f85b..bf95ca9 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.misc.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.misc.yaml @@ -246,6 +246,7 @@ classes: attributes: name: name: name + ifabsent: string(Units) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.retinotopy.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.retinotopy.yaml index 1cf2daf..8873bfa 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.retinotopy.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_1/core.nwb.retinotopy.yaml @@ -106,6 +106,7 @@ classes: attributes: name: name: name + ifabsent: string(ImagingRetinotopy) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.base.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.base.yaml index a68fc43..6e691c3 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.base.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.base.yaml @@ -292,6 +292,7 @@ classes: attributes: name: name: name + ifabsent: string(Images) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.ecephys.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.ecephys.yaml index d3197fb..8126f97 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.ecephys.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.ecephys.yaml @@ -139,6 +139,7 @@ classes: attributes: name: name: name + ifabsent: string(FeatureExtraction) identifier: true range: string required: true @@ -200,6 +201,7 @@ classes: attributes: name: name: name + ifabsent: string(EventDetection) identifier: true range: string required: true @@ -309,9 +311,38 @@ classes: name: position description: stereotaxic or common framework coordinates multivalued: false - range: AnyType + range: ElectrodeGroup__position required: false tree_root: true + ElectrodeGroup__position: + name: ElectrodeGroup__position + description: stereotaxic or common framework coordinates + attributes: + name: + name: name + ifabsent: string(position) + identifier: true + range: string + required: true + equals_string: position + x: + name: x + description: x coordinate + multivalued: false + range: float32 + required: false + y: + name: y + description: y coordinate + multivalued: false + range: float32 + required: false + z: + name: z + description: z coordinate + multivalued: false + range: float32 + required: false ClusterWaveforms: name: ClusterWaveforms description: DEPRECATED The mean waveform shape, including standard deviation, @@ -324,6 +355,7 @@ classes: attributes: name: name: name + ifabsent: string(ClusterWaveforms) identifier: true range: string required: true @@ -366,6 +398,7 @@ classes: attributes: name: name: name + ifabsent: string(Clustering) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.epoch.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.epoch.yaml index 5f64174..442c85e 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.epoch.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.epoch.yaml @@ -49,8 +49,9 @@ classes: timeseries: name: timeseries description: An index into a TimeSeries object. - multivalued: true - range: AnyType + multivalued: false + range: TimeIntervals__timeseries + required: false timeseries_index: name: timeseries_index description: Index for timeseries. @@ -70,6 +71,39 @@ classes: range: string required: true equals_string: tags_index + TimeIntervals__timeseries: + name: TimeIntervals__timeseries + description: An index into a TimeSeries object. + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(timeseries) + identifier: true + range: string + required: true + equals_string: timeseries + idx_start: + name: idx_start + description: Start index into the TimeSeries 'data' and 'timestamp' datasets + of the referenced TimeSeries. The first dimension of those arrays is always + time. + multivalued: false + range: int32 + required: false + count: + name: count + description: Number of data samples available in this time series, during + this epoch. + multivalued: false + range: int32 + required: false + timeseries: + name: timeseries + description: the TimeSeries that this index applies to. + multivalued: false + range: TimeSeries + required: false TimeIntervals__timeseries_index: name: TimeIntervals__timeseries_index description: Index for timeseries. diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.language.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.language.yaml index edba729..929628d 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.language.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.language.yaml @@ -140,15 +140,6 @@ enums: isodatetime: text: isodatetime classes: - Arraylike: - name: Arraylike - description: Container for arraylike information held in the dims, shape, and - dtype properties.this is a special case to be interpreted by downstream i/o. - this class has no slotsand is abstract by default.- Each slot within a subclass - indicates a possible dimension.- Only dimensions that are present in all the - dimension specifiers in the original schema are required.- Shape requirements - are indicated using max/min cardinalities on the slot. - abstract: true AnyType: name: AnyType description: Needed because some classes in hdmf-common are datasets without dtype diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.misc.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.misc.yaml index 53d7a9c..96da1bd 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.misc.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.misc.yaml @@ -246,6 +246,7 @@ classes: attributes: name: name: name + ifabsent: string(Units) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.retinotopy.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.retinotopy.yaml index b0ba8c6..30360f0 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.retinotopy.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_2/core.nwb.retinotopy.yaml @@ -28,6 +28,7 @@ classes: attributes: name: name: name + ifabsent: string(ImagingRetinotopy) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.base.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.base.yaml index 14daf08..194fef6 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.base.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.base.yaml @@ -292,6 +292,7 @@ classes: attributes: name: name: name + ifabsent: string(Images) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.ecephys.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.ecephys.yaml index 8e03555..fa76144 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.ecephys.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.ecephys.yaml @@ -139,6 +139,7 @@ classes: attributes: name: name: name + ifabsent: string(FeatureExtraction) identifier: true range: string required: true @@ -200,6 +201,7 @@ classes: attributes: name: name: name + ifabsent: string(EventDetection) identifier: true range: string required: true @@ -309,9 +311,38 @@ classes: name: position description: stereotaxic or common framework coordinates multivalued: false - range: AnyType + range: ElectrodeGroup__position required: false tree_root: true + ElectrodeGroup__position: + name: ElectrodeGroup__position + description: stereotaxic or common framework coordinates + attributes: + name: + name: name + ifabsent: string(position) + identifier: true + range: string + required: true + equals_string: position + x: + name: x + description: x coordinate + multivalued: false + range: float32 + required: false + y: + name: y + description: y coordinate + multivalued: false + range: float32 + required: false + z: + name: z + description: z coordinate + multivalued: false + range: float32 + required: false ClusterWaveforms: name: ClusterWaveforms description: DEPRECATED The mean waveform shape, including standard deviation, @@ -324,6 +355,7 @@ classes: attributes: name: name: name + ifabsent: string(ClusterWaveforms) identifier: true range: string required: true @@ -366,6 +398,7 @@ classes: attributes: name: name: name + ifabsent: string(Clustering) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.epoch.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.epoch.yaml index 8c9a07e..89d7026 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.epoch.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.epoch.yaml @@ -49,8 +49,9 @@ classes: timeseries: name: timeseries description: An index into a TimeSeries object. - multivalued: true - range: AnyType + multivalued: false + range: TimeIntervals__timeseries + required: false timeseries_index: name: timeseries_index description: Index for timeseries. @@ -70,6 +71,39 @@ classes: range: string required: true equals_string: tags_index + TimeIntervals__timeseries: + name: TimeIntervals__timeseries + description: An index into a TimeSeries object. + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(timeseries) + identifier: true + range: string + required: true + equals_string: timeseries + idx_start: + name: idx_start + description: Start index into the TimeSeries 'data' and 'timestamp' datasets + of the referenced TimeSeries. The first dimension of those arrays is always + time. + multivalued: false + range: int32 + required: false + count: + name: count + description: Number of data samples available in this time series, during + this epoch. + multivalued: false + range: int32 + required: false + timeseries: + name: timeseries + description: the TimeSeries that this index applies to. + multivalued: false + range: TimeSeries + required: false TimeIntervals__timeseries_index: name: TimeIntervals__timeseries_index description: Index for timeseries. diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.language.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.language.yaml index edba729..929628d 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.language.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.language.yaml @@ -140,15 +140,6 @@ enums: isodatetime: text: isodatetime classes: - Arraylike: - name: Arraylike - description: Container for arraylike information held in the dims, shape, and - dtype properties.this is a special case to be interpreted by downstream i/o. - this class has no slotsand is abstract by default.- Each slot within a subclass - indicates a possible dimension.- Only dimensions that are present in all the - dimension specifiers in the original schema are required.- Shape requirements - are indicated using max/min cardinalities on the slot. - abstract: true AnyType: name: AnyType description: Needed because some classes in hdmf-common are datasets without dtype diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.misc.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.misc.yaml index 6177d09..cd058d7 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.misc.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.misc.yaml @@ -246,6 +246,7 @@ classes: attributes: name: name: name + ifabsent: string(Units) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.ophys.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.ophys.yaml index 3444dac..e8541b4 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.ophys.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.ophys.yaml @@ -187,8 +187,9 @@ classes: description: 'Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation' - multivalued: true - range: AnyType + multivalued: false + range: PlaneSegmentation__pixel_mask + required: false voxel_mask_index: name: voxel_mask_index description: Index into voxel_mask. @@ -200,8 +201,9 @@ classes: description: 'Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation' - multivalued: true - range: AnyType + multivalued: false + range: PlaneSegmentation__voxel_mask + required: false reference_images: name: reference_images description: Image stacks that the segmentation masks apply to. @@ -223,6 +225,38 @@ classes: range: string required: true equals_string: pixel_mask_index + PlaneSegmentation__pixel_mask: + name: PlaneSegmentation__pixel_mask + description: 'Pixel masks for each ROI: a list of indices and weights for the + ROI. Pixel masks are concatenated and parsing of this dataset is maintained + by the PlaneSegmentation' + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(pixel_mask) + identifier: true + range: string + required: true + equals_string: pixel_mask + x: + name: x + description: Pixel x-coordinate. + multivalued: false + range: uint32 + required: false + y: + name: y + description: Pixel y-coordinate. + multivalued: false + range: uint32 + required: false + weight: + name: weight + description: Weight of the pixel. + multivalued: false + range: float32 + required: false PlaneSegmentation__voxel_mask_index: name: PlaneSegmentation__voxel_mask_index description: Index into voxel_mask. @@ -235,6 +269,44 @@ classes: range: string required: true equals_string: voxel_mask_index + PlaneSegmentation__voxel_mask: + name: PlaneSegmentation__voxel_mask + description: 'Voxel masks for each ROI: a list of indices and weights for the + ROI. Voxel masks are concatenated and parsing of this dataset is maintained + by the PlaneSegmentation' + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(voxel_mask) + identifier: true + range: string + required: true + equals_string: voxel_mask + x: + name: x + description: Voxel x-coordinate. + multivalued: false + range: uint32 + required: false + y: + name: y + description: Voxel y-coordinate. + multivalued: false + range: uint32 + required: false + z: + name: z + description: Voxel z-coordinate. + multivalued: false + range: uint32 + required: false + weight: + name: weight + description: Weight of the voxel. + multivalued: false + range: float32 + required: false ImagingPlane: name: ImagingPlane description: An imaging plane and its metadata. diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.retinotopy.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.retinotopy.yaml index 5f4183f..dcae22d 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.retinotopy.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_4/core.nwb.retinotopy.yaml @@ -28,6 +28,7 @@ classes: attributes: name: name: name + ifabsent: string(ImagingRetinotopy) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.base.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.base.yaml index 466517d..513d03d 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.base.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.base.yaml @@ -292,6 +292,7 @@ classes: attributes: name: name: name + ifabsent: string(Images) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.ecephys.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.ecephys.yaml index 9c9a128..31df5a5 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.ecephys.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.ecephys.yaml @@ -139,6 +139,7 @@ classes: attributes: name: name: name + ifabsent: string(FeatureExtraction) identifier: true range: string required: true @@ -200,6 +201,7 @@ classes: attributes: name: name: name + ifabsent: string(EventDetection) identifier: true range: string required: true @@ -309,9 +311,38 @@ classes: name: position description: stereotaxic or common framework coordinates multivalued: false - range: AnyType + range: ElectrodeGroup__position required: false tree_root: true + ElectrodeGroup__position: + name: ElectrodeGroup__position + description: stereotaxic or common framework coordinates + attributes: + name: + name: name + ifabsent: string(position) + identifier: true + range: string + required: true + equals_string: position + x: + name: x + description: x coordinate + multivalued: false + range: float32 + required: false + y: + name: y + description: y coordinate + multivalued: false + range: float32 + required: false + z: + name: z + description: z coordinate + multivalued: false + range: float32 + required: false ClusterWaveforms: name: ClusterWaveforms description: DEPRECATED The mean waveform shape, including standard deviation, @@ -324,6 +355,7 @@ classes: attributes: name: name: name + ifabsent: string(ClusterWaveforms) identifier: true range: string required: true @@ -366,6 +398,7 @@ classes: attributes: name: name: name + ifabsent: string(Clustering) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.epoch.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.epoch.yaml index c4d07b5..4128406 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.epoch.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.epoch.yaml @@ -49,8 +49,9 @@ classes: timeseries: name: timeseries description: An index into a TimeSeries object. - multivalued: true - range: AnyType + multivalued: false + range: TimeIntervals__timeseries + required: false timeseries_index: name: timeseries_index description: Index for timeseries. @@ -70,6 +71,39 @@ classes: range: string required: true equals_string: tags_index + TimeIntervals__timeseries: + name: TimeIntervals__timeseries + description: An index into a TimeSeries object. + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(timeseries) + identifier: true + range: string + required: true + equals_string: timeseries + idx_start: + name: idx_start + description: Start index into the TimeSeries 'data' and 'timestamp' datasets + of the referenced TimeSeries. The first dimension of those arrays is always + time. + multivalued: false + range: int32 + required: false + count: + name: count + description: Number of data samples available in this time series, during + this epoch. + multivalued: false + range: int32 + required: false + timeseries: + name: timeseries + description: the TimeSeries that this index applies to. + multivalued: false + range: TimeSeries + required: false TimeIntervals__timeseries_index: name: TimeIntervals__timeseries_index description: Index for timeseries. diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.language.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.language.yaml index edba729..929628d 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.language.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.language.yaml @@ -140,15 +140,6 @@ enums: isodatetime: text: isodatetime classes: - Arraylike: - name: Arraylike - description: Container for arraylike information held in the dims, shape, and - dtype properties.this is a special case to be interpreted by downstream i/o. - this class has no slotsand is abstract by default.- Each slot within a subclass - indicates a possible dimension.- Only dimensions that are present in all the - dimension specifiers in the original schema are required.- Shape requirements - are indicated using max/min cardinalities on the slot. - abstract: true AnyType: name: AnyType description: Needed because some classes in hdmf-common are datasets without dtype diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.misc.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.misc.yaml index 056c439..85681bf 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.misc.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.misc.yaml @@ -246,6 +246,7 @@ classes: attributes: name: name: name + ifabsent: string(Units) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.ophys.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.ophys.yaml index ae0c707..74618fb 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.ophys.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.ophys.yaml @@ -187,8 +187,9 @@ classes: description: 'Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation' - multivalued: true - range: AnyType + multivalued: false + range: PlaneSegmentation__pixel_mask + required: false voxel_mask_index: name: voxel_mask_index description: Index into voxel_mask. @@ -200,8 +201,9 @@ classes: description: 'Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation' - multivalued: true - range: AnyType + multivalued: false + range: PlaneSegmentation__voxel_mask + required: false reference_images: name: reference_images description: Image stacks that the segmentation masks apply to. @@ -223,6 +225,38 @@ classes: range: string required: true equals_string: pixel_mask_index + PlaneSegmentation__pixel_mask: + name: PlaneSegmentation__pixel_mask + description: 'Pixel masks for each ROI: a list of indices and weights for the + ROI. Pixel masks are concatenated and parsing of this dataset is maintained + by the PlaneSegmentation' + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(pixel_mask) + identifier: true + range: string + required: true + equals_string: pixel_mask + x: + name: x + description: Pixel x-coordinate. + multivalued: false + range: uint32 + required: false + y: + name: y + description: Pixel y-coordinate. + multivalued: false + range: uint32 + required: false + weight: + name: weight + description: Weight of the pixel. + multivalued: false + range: float32 + required: false PlaneSegmentation__voxel_mask_index: name: PlaneSegmentation__voxel_mask_index description: Index into voxel_mask. @@ -235,6 +269,44 @@ classes: range: string required: true equals_string: voxel_mask_index + PlaneSegmentation__voxel_mask: + name: PlaneSegmentation__voxel_mask + description: 'Voxel masks for each ROI: a list of indices and weights for the + ROI. Voxel masks are concatenated and parsing of this dataset is maintained + by the PlaneSegmentation' + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(voxel_mask) + identifier: true + range: string + required: true + equals_string: voxel_mask + x: + name: x + description: Voxel x-coordinate. + multivalued: false + range: uint32 + required: false + y: + name: y + description: Voxel y-coordinate. + multivalued: false + range: uint32 + required: false + z: + name: z + description: Voxel z-coordinate. + multivalued: false + range: uint32 + required: false + weight: + name: weight + description: Weight of the voxel. + multivalued: false + range: float32 + required: false ImagingPlane: name: ImagingPlane description: An imaging plane and its metadata. diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.retinotopy.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.retinotopy.yaml index 9b7ae8c..b45f3d3 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.retinotopy.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_2_5/core.nwb.retinotopy.yaml @@ -28,6 +28,7 @@ classes: attributes: name: name: name + ifabsent: string(ImagingRetinotopy) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.base.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.base.yaml index b817010..6dc1690 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.base.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.base.yaml @@ -305,6 +305,7 @@ classes: attributes: name: name: name + ifabsent: string(Images) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.ecephys.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.ecephys.yaml index 5ff3db5..c5b188d 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.ecephys.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.ecephys.yaml @@ -149,6 +149,7 @@ classes: attributes: name: name: name + ifabsent: string(FeatureExtraction) identifier: true range: string required: true @@ -210,6 +211,7 @@ classes: attributes: name: name: name + ifabsent: string(EventDetection) identifier: true range: string required: true @@ -319,9 +321,38 @@ classes: name: position description: stereotaxic or common framework coordinates multivalued: false - range: AnyType + range: ElectrodeGroup__position required: false tree_root: true + ElectrodeGroup__position: + name: ElectrodeGroup__position + description: stereotaxic or common framework coordinates + attributes: + name: + name: name + ifabsent: string(position) + identifier: true + range: string + required: true + equals_string: position + x: + name: x + description: x coordinate + multivalued: false + range: float32 + required: false + y: + name: y + description: y coordinate + multivalued: false + range: float32 + required: false + z: + name: z + description: z coordinate + multivalued: false + range: float32 + required: false ClusterWaveforms: name: ClusterWaveforms description: DEPRECATED The mean waveform shape, including standard deviation, @@ -334,6 +365,7 @@ classes: attributes: name: name: name + ifabsent: string(ClusterWaveforms) identifier: true range: string required: true @@ -376,6 +408,7 @@ classes: attributes: name: name: name + ifabsent: string(Clustering) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.epoch.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.epoch.yaml index 502aa87..1fe1134 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.epoch.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.epoch.yaml @@ -49,8 +49,9 @@ classes: timeseries: name: timeseries description: An index into a TimeSeries object. - multivalued: true - range: AnyType + multivalued: false + range: TimeIntervals__timeseries + required: false timeseries_index: name: timeseries_index description: Index for timeseries. @@ -70,6 +71,39 @@ classes: range: string required: true equals_string: tags_index + TimeIntervals__timeseries: + name: TimeIntervals__timeseries + description: An index into a TimeSeries object. + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(timeseries) + identifier: true + range: string + required: true + equals_string: timeseries + idx_start: + name: idx_start + description: Start index into the TimeSeries 'data' and 'timestamp' datasets + of the referenced TimeSeries. The first dimension of those arrays is always + time. + multivalued: false + range: int32 + required: false + count: + name: count + description: Number of data samples available in this time series, during + this epoch. + multivalued: false + range: int32 + required: false + timeseries: + name: timeseries + description: the TimeSeries that this index applies to. + multivalued: false + range: TimeSeries + required: false TimeIntervals__timeseries_index: name: TimeIntervals__timeseries_index description: Index for timeseries. diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.language.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.language.yaml index edba729..929628d 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.language.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.language.yaml @@ -140,15 +140,6 @@ enums: isodatetime: text: isodatetime classes: - Arraylike: - name: Arraylike - description: Container for arraylike information held in the dims, shape, and - dtype properties.this is a special case to be interpreted by downstream i/o. - this class has no slotsand is abstract by default.- Each slot within a subclass - indicates a possible dimension.- Only dimensions that are present in all the - dimension specifiers in the original schema are required.- Shape requirements - are indicated using max/min cardinalities on the slot. - abstract: true AnyType: name: AnyType description: Needed because some classes in hdmf-common are datasets without dtype diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.misc.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.misc.yaml index ac1eb11..4a62445 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.misc.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.misc.yaml @@ -266,6 +266,7 @@ classes: attributes: name: name: name + ifabsent: string(Units) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.ophys.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.ophys.yaml index 42b638d..65f02e5 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.ophys.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.ophys.yaml @@ -187,8 +187,9 @@ classes: description: 'Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation' - multivalued: true - range: AnyType + multivalued: false + range: PlaneSegmentation__pixel_mask + required: false voxel_mask_index: name: voxel_mask_index description: Index into voxel_mask. @@ -200,8 +201,9 @@ classes: description: 'Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation' - multivalued: true - range: AnyType + multivalued: false + range: PlaneSegmentation__voxel_mask + required: false reference_images: name: reference_images description: Image stacks that the segmentation masks apply to. @@ -223,6 +225,38 @@ classes: range: string required: true equals_string: pixel_mask_index + PlaneSegmentation__pixel_mask: + name: PlaneSegmentation__pixel_mask + description: 'Pixel masks for each ROI: a list of indices and weights for the + ROI. Pixel masks are concatenated and parsing of this dataset is maintained + by the PlaneSegmentation' + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(pixel_mask) + identifier: true + range: string + required: true + equals_string: pixel_mask + x: + name: x + description: Pixel x-coordinate. + multivalued: false + range: uint32 + required: false + y: + name: y + description: Pixel y-coordinate. + multivalued: false + range: uint32 + required: false + weight: + name: weight + description: Weight of the pixel. + multivalued: false + range: float32 + required: false PlaneSegmentation__voxel_mask_index: name: PlaneSegmentation__voxel_mask_index description: Index into voxel_mask. @@ -235,6 +269,44 @@ classes: range: string required: true equals_string: voxel_mask_index + PlaneSegmentation__voxel_mask: + name: PlaneSegmentation__voxel_mask + description: 'Voxel masks for each ROI: a list of indices and weights for the + ROI. Voxel masks are concatenated and parsing of this dataset is maintained + by the PlaneSegmentation' + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(voxel_mask) + identifier: true + range: string + required: true + equals_string: voxel_mask + x: + name: x + description: Voxel x-coordinate. + multivalued: false + range: uint32 + required: false + y: + name: y + description: Voxel y-coordinate. + multivalued: false + range: uint32 + required: false + z: + name: z + description: Voxel z-coordinate. + multivalued: false + range: uint32 + required: false + weight: + name: weight + description: Weight of the voxel. + multivalued: false + range: float32 + required: false ImagingPlane: name: ImagingPlane description: An imaging plane and its metadata. diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.retinotopy.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.retinotopy.yaml index f44a870..f674437 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.retinotopy.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_3_0/core.nwb.retinotopy.yaml @@ -28,6 +28,7 @@ classes: attributes: name: name: name + ifabsent: string(ImagingRetinotopy) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.base.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.base.yaml index e1832c4..53e5c00 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.base.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.base.yaml @@ -34,9 +34,31 @@ classes: attributes: name: name: name + ifabsent: string(timeseries) identifier: true range: string required: true + idx_start: + name: idx_start + description: Start index into the TimeSeries 'data' and 'timestamp' datasets + of the referenced TimeSeries. The first dimension of those arrays is always + time. + multivalued: false + range: int32 + required: true + count: + name: count + description: Number of data samples available in this time series, during + this epoch + multivalued: false + range: int32 + required: true + timeseries: + name: timeseries + description: The TimeSeries that this index applies to + multivalued: false + range: TimeSeries + required: true tree_root: true Image: name: Image @@ -318,6 +340,7 @@ classes: attributes: name: name: name + ifabsent: string(Images) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.ecephys.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.ecephys.yaml index f6a0150..6b0a535 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.ecephys.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.ecephys.yaml @@ -149,6 +149,7 @@ classes: attributes: name: name: name + ifabsent: string(FeatureExtraction) identifier: true range: string required: true @@ -210,6 +211,7 @@ classes: attributes: name: name: name + ifabsent: string(EventDetection) identifier: true range: string required: true @@ -319,9 +321,38 @@ classes: name: position description: stereotaxic or common framework coordinates multivalued: false - range: AnyType + range: ElectrodeGroup__position required: false tree_root: true + ElectrodeGroup__position: + name: ElectrodeGroup__position + description: stereotaxic or common framework coordinates + attributes: + name: + name: name + ifabsent: string(position) + identifier: true + range: string + required: true + equals_string: position + x: + name: x + description: x coordinate + multivalued: false + range: float32 + required: false + y: + name: y + description: y coordinate + multivalued: false + range: float32 + required: false + z: + name: z + description: z coordinate + multivalued: false + range: float32 + required: false ClusterWaveforms: name: ClusterWaveforms description: DEPRECATED The mean waveform shape, including standard deviation, @@ -334,6 +365,7 @@ classes: attributes: name: name: name + ifabsent: string(ClusterWaveforms) identifier: true range: string required: true @@ -376,6 +408,7 @@ classes: attributes: name: name: name + ifabsent: string(Clustering) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.epoch.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.epoch.yaml index 88b0139..2903c11 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.epoch.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.epoch.yaml @@ -49,8 +49,9 @@ classes: timeseries: name: timeseries description: An index into a TimeSeries object. - multivalued: true - range: AnyType + multivalued: false + range: TimeIntervals__timeseries + required: false timeseries_index: name: timeseries_index description: Index for timeseries. @@ -70,6 +71,39 @@ classes: range: string required: true equals_string: tags_index + TimeIntervals__timeseries: + name: TimeIntervals__timeseries + description: An index into a TimeSeries object. + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(timeseries) + identifier: true + range: string + required: true + equals_string: timeseries + idx_start: + name: idx_start + description: Start index into the TimeSeries 'data' and 'timestamp' datasets + of the referenced TimeSeries. The first dimension of those arrays is always + time. + multivalued: false + range: int32 + required: false + count: + name: count + description: Number of data samples available in this time series, during + this epoch. + multivalued: false + range: int32 + required: false + timeseries: + name: timeseries + description: the TimeSeries that this index applies to. + multivalued: false + range: TimeSeries + required: false TimeIntervals__timeseries_index: name: TimeIntervals__timeseries_index description: Index for timeseries. diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.language.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.language.yaml index edba729..929628d 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.language.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.language.yaml @@ -140,15 +140,6 @@ enums: isodatetime: text: isodatetime classes: - Arraylike: - name: Arraylike - description: Container for arraylike information held in the dims, shape, and - dtype properties.this is a special case to be interpreted by downstream i/o. - this class has no slotsand is abstract by default.- Each slot within a subclass - indicates a possible dimension.- Only dimensions that are present in all the - dimension specifiers in the original schema are required.- Shape requirements - are indicated using max/min cardinalities on the slot. - abstract: true AnyType: name: AnyType description: Needed because some classes in hdmf-common are datasets without dtype diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.misc.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.misc.yaml index c56c722..ff90cbc 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.misc.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.misc.yaml @@ -266,6 +266,7 @@ classes: attributes: name: name: name + ifabsent: string(Units) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.ophys.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.ophys.yaml index 1e62ac5..8b3c3a1 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.ophys.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.ophys.yaml @@ -187,8 +187,9 @@ classes: description: 'Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation' - multivalued: true - range: AnyType + multivalued: false + range: PlaneSegmentation__pixel_mask + required: false voxel_mask_index: name: voxel_mask_index description: Index into voxel_mask. @@ -200,8 +201,9 @@ classes: description: 'Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation' - multivalued: true - range: AnyType + multivalued: false + range: PlaneSegmentation__voxel_mask + required: false reference_images: name: reference_images description: Image stacks that the segmentation masks apply to. @@ -223,6 +225,38 @@ classes: range: string required: true equals_string: pixel_mask_index + PlaneSegmentation__pixel_mask: + name: PlaneSegmentation__pixel_mask + description: 'Pixel masks for each ROI: a list of indices and weights for the + ROI. Pixel masks are concatenated and parsing of this dataset is maintained + by the PlaneSegmentation' + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(pixel_mask) + identifier: true + range: string + required: true + equals_string: pixel_mask + x: + name: x + description: Pixel x-coordinate. + multivalued: false + range: uint32 + required: false + y: + name: y + description: Pixel y-coordinate. + multivalued: false + range: uint32 + required: false + weight: + name: weight + description: Weight of the pixel. + multivalued: false + range: float32 + required: false PlaneSegmentation__voxel_mask_index: name: PlaneSegmentation__voxel_mask_index description: Index into voxel_mask. @@ -235,6 +269,44 @@ classes: range: string required: true equals_string: voxel_mask_index + PlaneSegmentation__voxel_mask: + name: PlaneSegmentation__voxel_mask + description: 'Voxel masks for each ROI: a list of indices and weights for the + ROI. Voxel masks are concatenated and parsing of this dataset is maintained + by the PlaneSegmentation' + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(voxel_mask) + identifier: true + range: string + required: true + equals_string: voxel_mask + x: + name: x + description: Voxel x-coordinate. + multivalued: false + range: uint32 + required: false + y: + name: y + description: Voxel y-coordinate. + multivalued: false + range: uint32 + required: false + z: + name: z + description: Voxel z-coordinate. + multivalued: false + range: uint32 + required: false + weight: + name: weight + description: Weight of the voxel. + multivalued: false + range: float32 + required: false ImagingPlane: name: ImagingPlane description: An imaging plane and its metadata. diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.retinotopy.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.retinotopy.yaml index 464e367..770824e 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.retinotopy.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_4_0/core.nwb.retinotopy.yaml @@ -28,6 +28,7 @@ classes: attributes: name: name: name + ifabsent: string(ImagingRetinotopy) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.base.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.base.yaml index 39857f8..7a22de1 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.base.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.base.yaml @@ -34,9 +34,31 @@ classes: attributes: name: name: name + ifabsent: string(timeseries) identifier: true range: string required: true + idx_start: + name: idx_start + description: Start index into the TimeSeries 'data' and 'timestamp' datasets + of the referenced TimeSeries. The first dimension of those arrays is always + time. + multivalued: false + range: int32 + required: true + count: + name: count + description: Number of data samples available in this time series, during + this epoch + multivalued: false + range: int32 + required: true + timeseries: + name: timeseries + description: The TimeSeries that this index applies to + multivalued: false + range: TimeSeries + required: true tree_root: true Image: name: Image @@ -345,6 +367,7 @@ classes: attributes: name: name: name + ifabsent: string(Images) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.ecephys.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.ecephys.yaml index 6c73e13..6d1f15f 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.ecephys.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.ecephys.yaml @@ -149,6 +149,7 @@ classes: attributes: name: name: name + ifabsent: string(FeatureExtraction) identifier: true range: string required: true @@ -210,6 +211,7 @@ classes: attributes: name: name: name + ifabsent: string(EventDetection) identifier: true range: string required: true @@ -319,9 +321,38 @@ classes: name: position description: stereotaxic or common framework coordinates multivalued: false - range: AnyType + range: ElectrodeGroup__position required: false tree_root: true + ElectrodeGroup__position: + name: ElectrodeGroup__position + description: stereotaxic or common framework coordinates + attributes: + name: + name: name + ifabsent: string(position) + identifier: true + range: string + required: true + equals_string: position + x: + name: x + description: x coordinate + multivalued: false + range: float32 + required: false + y: + name: y + description: y coordinate + multivalued: false + range: float32 + required: false + z: + name: z + description: z coordinate + multivalued: false + range: float32 + required: false ClusterWaveforms: name: ClusterWaveforms description: DEPRECATED The mean waveform shape, including standard deviation, @@ -334,6 +365,7 @@ classes: attributes: name: name: name + ifabsent: string(ClusterWaveforms) identifier: true range: string required: true @@ -376,6 +408,7 @@ classes: attributes: name: name: name + ifabsent: string(Clustering) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.language.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.language.yaml index edba729..929628d 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.language.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.language.yaml @@ -140,15 +140,6 @@ enums: isodatetime: text: isodatetime classes: - Arraylike: - name: Arraylike - description: Container for arraylike information held in the dims, shape, and - dtype properties.this is a special case to be interpreted by downstream i/o. - this class has no slotsand is abstract by default.- Each slot within a subclass - indicates a possible dimension.- Only dimensions that are present in all the - dimension specifiers in the original schema are required.- Shape requirements - are indicated using max/min cardinalities on the slot. - abstract: true AnyType: name: AnyType description: Needed because some classes in hdmf-common are datasets without dtype diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.misc.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.misc.yaml index 51b0078..6e9a263 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.misc.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.misc.yaml @@ -266,6 +266,7 @@ classes: attributes: name: name: name + ifabsent: string(Units) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.ophys.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.ophys.yaml index a205204..8f6e16a 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.ophys.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.ophys.yaml @@ -187,8 +187,9 @@ classes: description: 'Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation' - multivalued: true - range: AnyType + multivalued: false + range: PlaneSegmentation__pixel_mask + required: false voxel_mask_index: name: voxel_mask_index description: Index into voxel_mask. @@ -200,8 +201,9 @@ classes: description: 'Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation' - multivalued: true - range: AnyType + multivalued: false + range: PlaneSegmentation__voxel_mask + required: false reference_images: name: reference_images description: Image stacks that the segmentation masks apply to. @@ -223,6 +225,38 @@ classes: range: string required: true equals_string: pixel_mask_index + PlaneSegmentation__pixel_mask: + name: PlaneSegmentation__pixel_mask + description: 'Pixel masks for each ROI: a list of indices and weights for the + ROI. Pixel masks are concatenated and parsing of this dataset is maintained + by the PlaneSegmentation' + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(pixel_mask) + identifier: true + range: string + required: true + equals_string: pixel_mask + x: + name: x + description: Pixel x-coordinate. + multivalued: false + range: uint32 + required: false + y: + name: y + description: Pixel y-coordinate. + multivalued: false + range: uint32 + required: false + weight: + name: weight + description: Weight of the pixel. + multivalued: false + range: float32 + required: false PlaneSegmentation__voxel_mask_index: name: PlaneSegmentation__voxel_mask_index description: Index into voxel_mask. @@ -235,6 +269,44 @@ classes: range: string required: true equals_string: voxel_mask_index + PlaneSegmentation__voxel_mask: + name: PlaneSegmentation__voxel_mask + description: 'Voxel masks for each ROI: a list of indices and weights for the + ROI. Voxel masks are concatenated and parsing of this dataset is maintained + by the PlaneSegmentation' + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(voxel_mask) + identifier: true + range: string + required: true + equals_string: voxel_mask + x: + name: x + description: Voxel x-coordinate. + multivalued: false + range: uint32 + required: false + y: + name: y + description: Voxel y-coordinate. + multivalued: false + range: uint32 + required: false + z: + name: z + description: Voxel z-coordinate. + multivalued: false + range: uint32 + required: false + weight: + name: weight + description: Weight of the voxel. + multivalued: false + range: float32 + required: false ImagingPlane: name: ImagingPlane description: An imaging plane and its metadata. diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.retinotopy.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.retinotopy.yaml index 8562943..85a616b 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.retinotopy.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_5_0/core.nwb.retinotopy.yaml @@ -28,6 +28,7 @@ classes: attributes: name: name: name + ifabsent: string(ImagingRetinotopy) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.base.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.base.yaml index 053d845..b00ddb1 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.base.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.base.yaml @@ -34,9 +34,31 @@ classes: attributes: name: name: name + ifabsent: string(timeseries) identifier: true range: string required: true + idx_start: + name: idx_start + description: Start index into the TimeSeries 'data' and 'timestamp' datasets + of the referenced TimeSeries. The first dimension of those arrays is always + time. + multivalued: false + range: int32 + required: true + count: + name: count + description: Number of data samples available in this time series, during + this epoch + multivalued: false + range: int32 + required: true + timeseries: + name: timeseries + description: The TimeSeries that this index applies to + multivalued: false + range: TimeSeries + required: true tree_root: true Image: name: Image @@ -345,6 +367,7 @@ classes: attributes: name: name: name + ifabsent: string(Images) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.ecephys.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.ecephys.yaml index 97a5f08..d24123d 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.ecephys.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.ecephys.yaml @@ -149,6 +149,7 @@ classes: attributes: name: name: name + ifabsent: string(FeatureExtraction) identifier: true range: string required: true @@ -210,6 +211,7 @@ classes: attributes: name: name: name + ifabsent: string(EventDetection) identifier: true range: string required: true @@ -319,9 +321,38 @@ classes: name: position description: stereotaxic or common framework coordinates multivalued: false - range: AnyType + range: ElectrodeGroup__position required: false tree_root: true + ElectrodeGroup__position: + name: ElectrodeGroup__position + description: stereotaxic or common framework coordinates + attributes: + name: + name: name + ifabsent: string(position) + identifier: true + range: string + required: true + equals_string: position + x: + name: x + description: x coordinate + multivalued: false + range: float32 + required: false + y: + name: y + description: y coordinate + multivalued: false + range: float32 + required: false + z: + name: z + description: z coordinate + multivalued: false + range: float32 + required: false ClusterWaveforms: name: ClusterWaveforms description: DEPRECATED The mean waveform shape, including standard deviation, @@ -334,6 +365,7 @@ classes: attributes: name: name: name + ifabsent: string(ClusterWaveforms) identifier: true range: string required: true @@ -376,6 +408,7 @@ classes: attributes: name: name: name + ifabsent: string(Clustering) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.language.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.language.yaml index edba729..929628d 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.language.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.language.yaml @@ -140,15 +140,6 @@ enums: isodatetime: text: isodatetime classes: - Arraylike: - name: Arraylike - description: Container for arraylike information held in the dims, shape, and - dtype properties.this is a special case to be interpreted by downstream i/o. - this class has no slotsand is abstract by default.- Each slot within a subclass - indicates a possible dimension.- Only dimensions that are present in all the - dimension specifiers in the original schema are required.- Shape requirements - are indicated using max/min cardinalities on the slot. - abstract: true AnyType: name: AnyType description: Needed because some classes in hdmf-common are datasets without dtype diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.misc.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.misc.yaml index c349c6c..569f0c7 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.misc.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.misc.yaml @@ -266,6 +266,7 @@ classes: attributes: name: name: name + ifabsent: string(Units) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.ophys.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.ophys.yaml index 00d10b3..7cb07bb 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.ophys.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.ophys.yaml @@ -224,8 +224,9 @@ classes: description: 'Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation' - multivalued: true - range: AnyType + multivalued: false + range: PlaneSegmentation__pixel_mask + required: false voxel_mask_index: name: voxel_mask_index description: Index into voxel_mask. @@ -237,8 +238,9 @@ classes: description: 'Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation' - multivalued: true - range: AnyType + multivalued: false + range: PlaneSegmentation__voxel_mask + required: false reference_images: name: reference_images description: Image stacks that the segmentation masks apply to. @@ -260,6 +262,38 @@ classes: range: string required: true equals_string: pixel_mask_index + PlaneSegmentation__pixel_mask: + name: PlaneSegmentation__pixel_mask + description: 'Pixel masks for each ROI: a list of indices and weights for the + ROI. Pixel masks are concatenated and parsing of this dataset is maintained + by the PlaneSegmentation' + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(pixel_mask) + identifier: true + range: string + required: true + equals_string: pixel_mask + x: + name: x + description: Pixel x-coordinate. + multivalued: false + range: uint32 + required: false + y: + name: y + description: Pixel y-coordinate. + multivalued: false + range: uint32 + required: false + weight: + name: weight + description: Weight of the pixel. + multivalued: false + range: float32 + required: false PlaneSegmentation__voxel_mask_index: name: PlaneSegmentation__voxel_mask_index description: Index into voxel_mask. @@ -272,6 +306,44 @@ classes: range: string required: true equals_string: voxel_mask_index + PlaneSegmentation__voxel_mask: + name: PlaneSegmentation__voxel_mask + description: 'Voxel masks for each ROI: a list of indices and weights for the + ROI. Voxel masks are concatenated and parsing of this dataset is maintained + by the PlaneSegmentation' + is_a: VectorData + attributes: + name: + name: name + ifabsent: string(voxel_mask) + identifier: true + range: string + required: true + equals_string: voxel_mask + x: + name: x + description: Voxel x-coordinate. + multivalued: false + range: uint32 + required: false + y: + name: y + description: Voxel y-coordinate. + multivalued: false + range: uint32 + required: false + z: + name: z + description: Voxel z-coordinate. + multivalued: false + range: uint32 + required: false + weight: + name: weight + description: Weight of the voxel. + multivalued: false + range: float32 + required: false ImagingPlane: name: ImagingPlane description: An imaging plane and its metadata. diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.retinotopy.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.retinotopy.yaml index 364898f..0bde202 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.retinotopy.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/core/v2_6_0_alpha/core.nwb.retinotopy.yaml @@ -28,6 +28,7 @@ classes: attributes: name: name: name + ifabsent: string(ImagingRetinotopy) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_0/hdmf-common.nwb.language.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_0/hdmf-common.nwb.language.yaml index 2afd49a..d85e6fc 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_0/hdmf-common.nwb.language.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_0/hdmf-common.nwb.language.yaml @@ -140,15 +140,6 @@ enums: isodatetime: text: isodatetime classes: - Arraylike: - name: Arraylike - description: Container for arraylike information held in the dims, shape, and - dtype properties.this is a special case to be interpreted by downstream i/o. - this class has no slotsand is abstract by default.- Each slot within a subclass - indicates a possible dimension.- Only dimensions that are present in all the - dimension specifiers in the original schema are required.- Shape requirements - are indicated using max/min cardinalities on the slot. - abstract: true AnyType: name: AnyType description: Needed because some classes in hdmf-common are datasets without dtype diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_0/hdmf-common.table.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_0/hdmf-common.table.yaml index a6a3c01..d86161c 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_0/hdmf-common.table.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_0/hdmf-common.table.yaml @@ -84,6 +84,7 @@ classes: attributes: name: name: name + ifabsent: string(element_id) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_2/hdmf-common.nwb.language.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_2/hdmf-common.nwb.language.yaml index 2afd49a..d85e6fc 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_2/hdmf-common.nwb.language.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_2/hdmf-common.nwb.language.yaml @@ -140,15 +140,6 @@ enums: isodatetime: text: isodatetime classes: - Arraylike: - name: Arraylike - description: Container for arraylike information held in the dims, shape, and - dtype properties.this is a special case to be interpreted by downstream i/o. - this class has no slotsand is abstract by default.- Each slot within a subclass - indicates a possible dimension.- Only dimensions that are present in all the - dimension specifiers in the original schema are required.- Shape requirements - are indicated using max/min cardinalities on the slot. - abstract: true AnyType: name: AnyType description: Needed because some classes in hdmf-common are datasets without dtype diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_2/hdmf-common.table.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_2/hdmf-common.table.yaml index 9fb473d..e50fc1a 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_2/hdmf-common.table.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_2/hdmf-common.table.yaml @@ -84,6 +84,7 @@ classes: attributes: name: name: name + ifabsent: string(element_id) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_3/hdmf-common.nwb.language.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_3/hdmf-common.nwb.language.yaml index 2afd49a..d85e6fc 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_3/hdmf-common.nwb.language.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_3/hdmf-common.nwb.language.yaml @@ -140,15 +140,6 @@ enums: isodatetime: text: isodatetime classes: - Arraylike: - name: Arraylike - description: Container for arraylike information held in the dims, shape, and - dtype properties.this is a special case to be interpreted by downstream i/o. - this class has no slotsand is abstract by default.- Each slot within a subclass - indicates a possible dimension.- Only dimensions that are present in all the - dimension specifiers in the original schema are required.- Shape requirements - are indicated using max/min cardinalities on the slot. - abstract: true AnyType: name: AnyType description: Needed because some classes in hdmf-common are datasets without dtype diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_3/hdmf-common.table.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_3/hdmf-common.table.yaml index 452518d..8ac286c 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_3/hdmf-common.table.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_1_3/hdmf-common.table.yaml @@ -112,6 +112,7 @@ classes: attributes: name: name: name + ifabsent: string(element_id) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_5_0/hdmf-common.nwb.language.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_5_0/hdmf-common.nwb.language.yaml index 2afd49a..d85e6fc 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_5_0/hdmf-common.nwb.language.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_5_0/hdmf-common.nwb.language.yaml @@ -140,15 +140,6 @@ enums: isodatetime: text: isodatetime classes: - Arraylike: - name: Arraylike - description: Container for arraylike information held in the dims, shape, and - dtype properties.this is a special case to be interpreted by downstream i/o. - this class has no slotsand is abstract by default.- Each slot within a subclass - indicates a possible dimension.- Only dimensions that are present in all the - dimension specifiers in the original schema are required.- Shape requirements - are indicated using max/min cardinalities on the slot. - abstract: true AnyType: name: AnyType description: Needed because some classes in hdmf-common are datasets without dtype diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_5_0/hdmf-common.table.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_5_0/hdmf-common.table.yaml index fae9434..7efd118 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_5_0/hdmf-common.table.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_5_0/hdmf-common.table.yaml @@ -84,6 +84,7 @@ classes: attributes: name: name: name + ifabsent: string(element_id) identifier: true range: string required: true diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.nwb.language.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.nwb.language.yaml index 59a6caa..08b002e 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.nwb.language.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.nwb.language.yaml @@ -140,15 +140,6 @@ enums: isodatetime: text: isodatetime classes: - Arraylike: - name: Arraylike - description: Container for arraylike information held in the dims, shape, and - dtype properties.this is a special case to be interpreted by downstream i/o. - this class has no slotsand is abstract by default.- Each slot within a subclass - indicates a possible dimension.- Only dimensions that are present in all the - dimension specifiers in the original schema are required.- Shape requirements - are indicated using max/min cardinalities on the slot. - abstract: true AnyType: name: AnyType description: Needed because some classes in hdmf-common are datasets without dtype diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.resources.yaml b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.resources.yaml index 190f60e..7155a0f7 100644 --- a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.resources.yaml +++ b/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.resources.yaml @@ -30,46 +30,163 @@ classes: description: A table for storing user terms that are used to refer to external resources. multivalued: false - array: - dimensions: - - alias: num_rows - range: AnyType + range: ExternalResources__keys required: true entities: name: entities description: A table for mapping user terms (i.e., keys) to resource entities. multivalued: false - array: - dimensions: - - alias: num_rows - range: AnyType + range: ExternalResources__entities required: true resources: name: resources description: A table for mapping user terms (i.e., keys) to resource entities. multivalued: false - array: - dimensions: - - alias: num_rows - range: AnyType + range: ExternalResources__resources required: true objects: name: objects description: A table for identifying which objects in a file contain references to external resources. multivalued: false - array: - dimensions: - - alias: num_rows - range: AnyType + range: ExternalResources__objects required: true object_keys: name: object_keys description: A table for identifying which objects use which keys. multivalued: false - array: - dimensions: - - alias: num_rows - range: AnyType + range: ExternalResources__object_keys required: true tree_root: true + ExternalResources__keys: + name: ExternalResources__keys + description: A table for storing user terms that are used to refer to external + resources. + is_a: Data + attributes: + name: + name: name + ifabsent: string(keys) + identifier: true + range: string + required: true + equals_string: keys + key: + name: key + description: The user term that maps to one or more resources in the 'resources' + table. + multivalued: false + range: text + required: true + ExternalResources__entities: + name: ExternalResources__entities + description: A table for mapping user terms (i.e., keys) to resource entities. + is_a: Data + attributes: + name: + name: name + ifabsent: string(entities) + identifier: true + range: string + required: true + equals_string: entities + keys_idx: + name: keys_idx + description: The index to the key in the 'keys' table. + multivalued: false + range: uint + required: true + resources_idx: + name: resources_idx + description: The index into the 'resources' table + multivalued: false + range: uint + required: true + entity_id: + name: entity_id + description: The unique identifier entity. + multivalued: false + range: text + required: true + entity_uri: + name: entity_uri + description: The URI for the entity this reference applies to. This can be + an empty string. + multivalued: false + range: text + required: true + ExternalResources__resources: + name: ExternalResources__resources + description: A table for mapping user terms (i.e., keys) to resource entities. + is_a: Data + attributes: + name: + name: name + ifabsent: string(resources) + identifier: true + range: string + required: true + equals_string: resources + resource: + name: resource + description: The name of the resource. + multivalued: false + range: text + required: true + resource_uri: + name: resource_uri + description: The URI for the resource. This can be an empty string. + multivalued: false + range: text + required: true + ExternalResources__objects: + name: ExternalResources__objects + description: A table for identifying which objects in a file contain references + to external resources. + is_a: Data + attributes: + name: + name: name + ifabsent: string(objects) + identifier: true + range: string + required: true + equals_string: objects + object_id: + name: object_id + description: The UUID for the object. + multivalued: false + range: text + required: true + field: + name: field + description: The field of the object. This can be an empty string if the object + is a dataset and the field is the dataset values. + multivalued: false + range: text + required: true + ExternalResources__object_keys: + name: ExternalResources__object_keys + description: A table for identifying which objects use which keys. + is_a: Data + attributes: + name: + name: name + ifabsent: string(object_keys) + identifier: true + range: string + required: true + equals_string: object_keys + objects_idx: + name: objects_idx + description: The index to the 'objects' table for the object that holds the + key. + multivalued: false + range: uint + required: true + keys_idx: + name: keys_idx + description: The index to the 'keys' table for the key. + multivalued: false + range: uint + required: true