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WIP: BIDS to JSON-LD #3

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WIP: BIDS to JSON-LD #3

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15bf8c2
json context for bids documents only
natachaperez Aug 7, 2019
9f9e3f3
json context for bids documents only
natachaperez Aug 7, 2019
78ae846
Wrap up BIDS/ NIDM-Experiment
natachaperez Aug 7, 2019
78be24c
Wrap up BIDS NIDM-Experiment
natachaperez Aug 8, 2019
8f1ab0c
Delete BIDS to JSON-LD.ipynb
natachaperez Aug 8, 2019
042ded4
Delete BIDS to NIDM-E.ipynb
natachaperez Aug 8, 2019
4cb08d2
Merge pull request #1 from natachaperez/Jupyter-Notebook
natachaperez Aug 8, 2019
8cfc09a
jupyter notebook
natachaperez Aug 8, 2019
ee7d265
common bids and nidm attributes added to bids_context.json & update i…
natachaperez Aug 8, 2019
764f4bf
update on bids to jsonld
natachaperez Aug 13, 2019
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209 changes: 209 additions & 0 deletions BIDS2JSONLD.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# BIDS dataset to a JSON-LD BIDS dataset"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"This document illustrates an example showing how to go from a bids dataset to a JSON-LD BIDS dataset. More specifically, one wants to : \n",
"- add gently context into existing json files : T1w.json, taskxxx.json\n",
"- create an other JSON file with attached JSON-LD context to store metadata only present in the BIDS directory (bids_context.json findable at that location: https://github.com/incf-nidash/bids-ld/pull/1)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"1st step : we review existing JSON files with the metadata types in BIDS and compare them to the NIDM-Experiment data. \n",
"--> we list the bids attributes, the path to bids terms, the nidm attributes and their links to nidm objects. \n",
"\n",
"2st step : we create a context file only for bids terms labelled 'bids_context.json'.\n",
"--> At this time there is still no URIs for BIDS, so one must create one with the following prefix: \n",
" \"bids\": \"https://bids.neuroimaging.io#\"\n",
" Then to describe bids attributes : \n",
" \"Name\" : \"https://bids.neuroimaging.io#Name\"\n",
" \n",
"3rd step : we add this gently context into existing json files. "
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{\r\n",
" \"@context\": {\r\n",
" \"@version\": 1.1,\r\n",
" \"records\": {\r\n",
" \"@id\": \"@graph\",\r\n",
" \"@container\": \"@type\"\r\n",
" },\r\n",
" \"bids\": \"https://bids.neuroimaging.io#\",\r\n",
" \"BIDSVersion\": \"https://bids.neuroimaging.io#BIDSVersion\",\r\n",
" \"Name\": \"https://bids.neuroimaging.io#Name\",\r\n",
" \"Acquisition Matrix\": \"https://bids.neuroimaging.io#AcquisitionMatrix\",\r\n",
" \"Coil Combination Method\": \"https://bids.neuroimaging.io#CoilCombinationMethod\",\r\n",
" \"Echo Time\": \"https://bids.neuroimaging.io#EchoTime\",\r\n",
" \"Field of View Dimensions\": \"https://bids.neuroimaging.io#FieldOfViewDimensions\", \r\n",
" \"Field of View Shape\": \"https://bids.neuroimaging.io#FieldOfViewShape\",\r\n",
" \"Flip Angle\": \"https://bids.neuroimaging.io#FlipAngle\",\r\n",
" \"Gradient Set Type\": \"https://bids.neuroimaging.io#GradientSetType\",\r\n",
" \"Inversion Time\": \"https://bids.neuroimaging.io#InversionTime\",\r\n",
" \"MatrixCoilMode\": \"https://bids.neuroimaging.io#MatrixCoilMode\",\r\n",
" \"Negative Contrast\": \"https://bids.neuroimaging.io#NegativeContrast\", \r\n",
" \"Number Of Slices\": \"https://bids.neuroimaging.io#NumberOfSlices\", \r\n",
" \"Number Shots\": \"https://bids.neuroimaging.io#NumberShots\",\r\n",
" \"Parallel Acquisition\": \"https://bids.neuroimaging.io#ParallelAcquisition\",\r\n",
" \"Parallel Acquisition Technique\": \"https://bids.neuroimaging.io#ParallelAcquisitionTechnique\",\r\n",
" \"Parallel Reduction Factor In-plane\": \"https://bids.neuroimaging.io#ParallelReductionFactorIn-plane\",\r\n",
" \"Phase Encoding Direction\": \"https://bids.neuroimaging.io#PhaseEncodingDirection\",\r\n",
" \"Pixel Bandwidth\": \"https://bids.neuroimaging.io#PixelBandwidth\",\r\n",
" \"Plane Orientation Sequence\": \"https://bids.neuroimaging.io#PlaneOrientationSequence\",\r\n",
" \"Receive Coil Type\": \"https://bids.neuroimaging.io#ReceiveCoilType\",\r\n",
" \"Receive Coil Name\": \"https://bids.neuroimaging.io#ReceiveCoilName\",\r\n",
" \"Scan Options\": \"https://bids.neuroimaging.io#ScanOptions\",\r\n",
" \"Scanning Sequence\": \"https://bids.neuroimaging.io#ScanningSequence\",\r\n",
" \"Sequence Name\": \"https://bids.neuroimaging.io#SequenceName\",\r\n",
" \"Sequence Variant\": \"https://bids.neuroimaging.io#SequenceVariant\",\r\n",
" \"Slice Acquisition Order\": \"https://bids.neuroimaging.io#SliceAcquisitionOrder\",\r\n",
" \"Slice Encoding Direction\": \"https://bids.neuroimaging.io#SliceEncodingDirection\",\r\n",
" \"Slice Thickness\": \"https://bids.neuroimaging.io#SliceThickness\",\r\n",
" \"Slice Timing\": \"https://bids.neuroimaging.io#SliceTiming\",\r\n",
" \"Spacing Between Slices\": \"https://bids.neuroimaging.io#SpacingBetweenSlices\",\r\n",
" \"Total Readout Time\": \"https://bids.neuroimaging.io#TotalReadoutTime\",\r\n",
" \"Manufacturer\": \"https://bids.neuroimaging.io#Manufacturer\",\r\n",
" \"Manufacturers Model Name\": \"https://bids.neuroimaging.io#ManufacturersModelName\",\r\n",
" \"Magnetic Field Strength\": \"https://bids.neuroimaging.io#MagneticFieldStrength\",\r\n",
" \"Device Serial Number\": \"https://bids.neuroimaging.io#DeviceSerialNumber\",\r\n",
" \"Software Versions\": \"https://bids.neuroimaging.io#SoftwareVersions\",\r\n",
" \"MR Transmit Coil Sequence\": \"https://bids.neuroimaging.io#MRTransmitCoilSequence\",\r\n",
" \"Partial Fourier\": \"https://bids.neuroimaging.io#PartialFourier\",\r\n",
" \"Partial Fourier Direction\": \"https://bids.neuroimaging.io#PartialFourierDirection\",\r\n",
" \"Effective Echo Spacing\": \"https://bids.neuroimaging.io#EffectiveEchoSpacing\",\r\n",
" \"Receive Coil Active Elements\": \"https://bids.neuroimaging.io#ReceiveCoilActiveElements\",\r\n",
" \"Non Linear Gradient Correction\": \"https://bids.neuroimaging.io#NonLinearGradientCorrection\",\r\n",
" \"Dwell Time\": \"https://bids.neuroimaging.io#DwellTime\",\r\n",
" \"Multiband Acceleration Factor\": \"https://bids.neuroimaging.io#MultibandAccelerationFactor\",\r\n",
" \"Anatomical Landmark Coordinates\": \"https://bids.neuroimaging.io#AnatomicalLandmarkCoordinates\",\r\n",
" \"Institution Name\": \"https://bids.neuroimaging.io#InstitutionName\",\r\n",
" \"Institution Address\": \"https://bids.neuroimaging.io#Institution Address\",\r\n",
" \"Institutional Department Name\": \"https://bids.neuroimaging.io#InstitutionalDepartmentName\",\r\n",
" \"Author\": \"https://bids.neuroimaging.io#Author\",\r\n",
" \"License\": \"https://bids.neuroimaging.io#License\",\r\n",
" \"Description\": \"https://bids.neuroimaging.io#Description\",\r\n",
" \"Age\": \"https://bids.neuroimaging.io#Age\",\r\n",
" \"Ethnicity\": \"https://bids.neuroimaging.io#Ethnicity\",\r\n",
" \"Family Name\": \"https://bids.neuroimaging.io#FamilyName\",\r\n",
" \"Handedness\": \"https://bids.neuroimaging.io#Handedness\",\r\n",
" \"Sex\": \"https://bids.neuroimaging.io#Sex\",\r\n",
" \"Race\": \"https://bids.neuroimaging.io#Race\",\r\n",
" \"Participant Id\": \"https://bids.neuroimaging.io#ParticipantId\",\r\n",
" \"Sampling Frequency\": \"https://bids.neuroimaging.io#SamplingFrequency\",\r\n",
" \"Trigger\": \"https://bids.neuroimaging.io#Trigger\",\r\n",
" \"Angiography\": \"https://bids.neuroimaging.io#Angiography\",\r\n",
" \"Combined Proton Density/T2\": \"https://bids.neuroimaging.io#CombinedProtonDensityT2\",\r\n",
" \"FLAIR\": \"https://bids.neuroimaging.io#FLAIR\",\r\n",
" \"FLASH\": \"https://bids.neuroimaging.io#FLASH\",\r\n",
" \"Proton Density Map\": \"https://bids.neuroimaging.io#ProtonDensityMap\",\r\n",
" \"T1 Map\": \"https://bids.neuroimaging.io#T1Map\",\r\n",
" \"T1 Rho Map\": \"https://bids.neuroimaging.io#T1RhoMap\",\r\n",
" \"T2 Map\": \"https://bids.neuroimaging.io#T2Map\",\r\n",
" \"Inplane T1\": \"https://bids.neuroimaging.io#InplaneT1\",\r\n",
" \"Inplane T2\": \"https://bids.neuroimaging.io#InplaneT2\",\r\n",
" \"Duration\": \"https://bids.neuroimaging.io#Duration\",\r\n",
" \"Onset\": \"https://bids.neuroimaging.io#Onset\",\r\n",
" \"Sample\": \"https://bids.neuroimaging.io#Sample\",\r\n",
" \"Response Time\": \"https://bids.neuroimaging.io#ResponseTime\",\r\n",
" \"Value\": \"https://bids.neuroimaging.io#Value\",\r\n",
" \"Trial Type\": \"https://bids.neuroimaging.io#TrialType\",\r\n",
" \"Acquisition Duration\": \"https://bids.neuroimaging.io#AcquisitionDuration\",\r\n",
" \"BOLD\": \"https://bids.neuroimaging.io#BOLD\",\r\n",
" \"Delay After Trigger\": \"https://bids.neuroimaging.io#DelayAfterTrigger\",\r\n",
" \"Delay Time\": \"https://bids.neuroimaging.io#DelayTime\",\r\n",
" \"Instructions\": \"https://bids.neuroimaging.io#Instructions\",\r\n",
" \"Number Of Volumes Discarded By Scanner\": \"https://bids.neuroimaging.io#NumberOfVolumesDiscardedByScanner\",\r\n",
" \"Number Of Volumes Discarded By User\": \"https://bids.neuroimaging.io#NumberOfVolumesDiscardedByUser\",\r\n",
" \"Phase\": \"https://bids.neuroimaging.io#Phase\",\r\n",
" \"Repetition Time\": \"https://bids.neuroimaging.io#RepetitionTime\",\r\n",
" \"Task Description\": \"https://bids.neuroimaging.io#TaskDescription\",\r\n",
" \"Task Name\": \"https://bids.neuroimaging.io#TaskName\",\r\n",
" \"Volume Timing\": \"https://bids.neuroimaging.io#VolumeTiming\",\r\n",
" \"CBV\": \"https://bids.neuroimaging.io#CBV\",\r\n",
" \"Cog Atlas ID\": \"https://bids.neuroimaging.io#CogAtlasID\",\r\n",
" \"CogPO ID\": \"https://bids.neuroimaging.io#CogPOID\",\r\n",
" \"b-value\": \"https://bids.neuroimaging.io#b-ValueFile\",\r\n",
" \"b-vector\": \"https://bids.neuroimaging.io#b-VectorFile\", \r\n",
" \"Cardiac\": \"https://bids.neuroimaging.io#HeartRateMonitor\",\r\n",
" \"Diffusion Tensor\": \"https://bids.neuroimaging.io#DiffusionTensor\",\r\n",
" \"Diffusion Weighted\": \"https://bids.neuroimaging.io#DiffusionWeighted\",\r\n",
" \"Gender\": \"https://bids.neuroimaging.io#Gender\",\r\n",
" \"Proton Density\": \"https://bids.neuroimaging.io#ProtonDensityWeighted\", \r\n",
" \"Respiratory\": \"https://bids.neuroimaging.io#RespirationRateMonitor\",\r\n",
" \"Session\": \"https://bids.neuroimaging.io#Session\",\r\n",
" \"Stimulus Response File\": \"https://bids.neuroimaging.io#StimulusResponseFile\",\r\n",
" \"T1 Weighted\": \"https://bids.neuroimaging.io#T1Weighted\",\r\n",
" \"T2-Star Weighted\": \"https://bids.neuroimaging.io#T2StarWeighted\",\r\n",
" \"T2 Weighted\": \"https://bids.neuroimaging.io#T2Weighted\",\r\n",
" \"Pulse Sequence Details\": \"https://bids.neuroimaging.io#PulseSequence\",\r\n",
" \"Pulse Sequence Type\": \"https://bids.neuroimaging.io#PulseType\",\r\n",
" \"Title\": \"https://bids.neuroimaging.io#title\",\r\n",
" \"Group\": \"https://bids.neuroimaging.io#Group\",\r\n",
" } \r\n",
"}\r\n",
"\r\n"
]
}
],
"source": [
"cat bids_context.json\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"At that point, some bids terms present in the bids specification also appear in the nidm-experiment ontology such as: \"b-value\", \"b-vector\", \"T1 Weighted\" or \"Gender\" etc. We decided to not consider the existing prefixes, to avoid ambiguity. "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"WIP: to adapt the code in BIDSMRI2NIDM.py to add properly the information from the json files. "
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.1"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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