diff --git a/.gitignore b/.gitignore index e110be5..e98734c 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,7 @@ /docs/ /project/docs/ /tmp/ +/Testing # Byte-compiled / optimized / DLL files __pycache__/ diff --git a/LinkML/overall_schema.json b/LinkML/overall_schema.json deleted file mode 100644 index 638d3fa..0000000 --- a/LinkML/overall_schema.json +++ /dev/null @@ -1,895 +0,0 @@ -{ - "$defs": { - "Acquisition": { - "additionalProperties": false, - "description": "", - "properties": { - "Beamshift": { - "$ref": "#/$defs/Beamshift", - "description": "Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad." - }, - "Beamtilt": { - "$ref": "#/$defs/Beamtilt", - "description": "Another way to move the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad." - }, - "Beamtiltgroups": { - "description": "Number of Beamtilt groups present in this dataset - for optimized processing split dataset into groups of same tilt angle. Despite its name Beamshift is often used to achive this result.", - "type": "integer" - }, - "Binning_camera": { - "description": "Level of binning on the images applied during data collection", - "type": "number" - }, - "Calibrated_defocus": { - "$ref": "#/$defs/CalibratedDefocus", - "description": "Machine estimated defocus, min and max values in \u00b5m. Has a tendency to be off." - }, - "Calibrated_magnification": { - "description": "Calculated magnification, no unit", - "type": "integer" - }, - "Cryogen": { - "description": "Cryogen used in cooling the instrument and sample, usually nitrogen", - "type": "string" - }, - "Datetime": { - "description": "Time and date of the data acquisition", - "format": "date-time", - "type": "string" - }, - "Detector": { - "description": "Make and model of the detector used", - "type": "string" - }, - "Detector_mode": { - "description": "Operating mode of the detector", - "type": "string" - }, - "Dose_per_movie": { - "description": "Average dose per image/movie/tilt - given in electrons per square Angstrom", - "type": "number" - }, - "Energy_filter": { - "$ref": "#/$defs/EnergyFilter", - "description": "Wether an energy filter was used and its specifics." - }, - "Exposure_time": { - "description": "Time of data acquisition per movie/tilt - in s", - "type": "number" - }, - "Frames_per_movie": { - "description": "Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors", - "type": "integer" - }, - "GainRef_FlipRotate": { - "description": "Whether and how you have to flip or rotate the gainref in order to align with your acquired images", - "type": "string" - }, - "Grids_imaged": { - "description": "Number of grids imaged for this project - here with qualifier during this data acquisition", - "type": "integer" - }, - "Holder": { - "description": "Speciman holder model", - "type": "string" - }, - "Holder_cryogen": { - "description": "Type of cryogen used in the holder - if the holder is cooled seperately", - "type": "string" - }, - "Image_size": { - "$ref": "#/$defs/ImageSize", - "description": "The size of the image in pixels, height and width given." - }, - "Images_generated": { - "description": "Number of images generated total for this data collection - might need a qualifier for tilt series to determine whether full series or individual tilts are counted", - "type": "integer" - }, - "Imageshift": { - "description": "Movement of the Beam below the image in order to shift the image on the detector. Given in \u00b5m." - }, - "Microscope_software": { - "description": "Software used for instrument control,", - "type": "string" - }, - "Nominal_defocus": { - "$ref": "#/$defs/NominalDefocus", - "description": "Target defocus set, min and max values in \u00b5m." - }, - "Nominal_magnification": { - "description": "Magnification level as indicated by the instrument, no unit", - "type": "integer" - }, - "Pixel_size": { - "description": "Pixel size, in Angstrom", - "type": "number" - }, - "Specialist_Optics": { - "$ref": "#/$defs/SpecialistOptics", - "description": "Any type of special optics, such as a phaseplate" - }, - "Temperature": { - "$ref": "#/$defs/Temperature", - "description": "Temperature during data collection, in K with min and max values." - }, - "TiltAxisAngle": { - "description": "The tilt axis angle of a tomography series", - "type": "number" - }, - "Tilt_angle": { - "$ref": "#/$defs/TiltAngle", - "description": "The min, max and increment of the tilt angle in a tomography session. Unit is degree." - } - }, - "required": [ - "Detector", - "Dose_per_movie", - "Datetime", - "Binning_camera", - "Pixel_size" - ], - "title": "Acquisition", - "type": "object" - }, - "Author": { - "additionalProperties": false, - "description": "A class representing an author", - "properties": { - "Country": { - "description": "Country of the author's institution", - "type": "string" - }, - "Email": { - "description": "Email address of the author", - "type": "string" - }, - "Name": { - "$ref": "#/$defs/Name", - "description": "Full name of the author" - }, - "ORCID": { - "description": "ORCID of the author, a type of unique identifier", - "type": "string" - }, - "Organization": { - "$ref": "#/$defs/Organization", - "description": "The organization the author is affiliated with" - }, - "Phone": { - "description": "Phone number of the author", - "type": "string" - }, - "role": { - "description": "Role of the author, i.e., principal investigator", - "type": "string" - } - }, - "required": [ - "Name", - "Email", - "Phone", - "ORCID", - "Organization", - "Country" - ], - "title": "Author", - "type": "object" - }, - "Base": { - "additionalProperties": false, - "description": "", - "properties": { - "Acquisition": { - "$ref": "#/$defs/Acquisition" - } - }, - "title": "Base", - "type": "object" - }, - "Baseline": { - "additionalProperties": false, - "description": "", - "properties": { - "Acquisition": { - "$ref": "#/$defs/Acquisition" - }, - "Instrument": { - "$ref": "#/$defs/Instrument" - }, - "oscemsample": { - "$ref": "#/$defs/OSCEMSample" - } - }, - "required": [ - "Acquisition", - "Instrument", - "oscemsample" - ], - "title": "Baseline", - "type": "object" - }, - "Beamshift": { - "additionalProperties": false, - "description": "", - "properties": { - "X_max": { - "type": "number" - }, - "X_min": { - "type": "number" - }, - "Y_max": { - "type": "number" - }, - "Y_min": { - "type": "number" - } - }, - "title": "Beamshift", - "type": "object" - }, - "Beamtilt": { - "additionalProperties": false, - "description": "", - "properties": { - "X_max": { - "type": "number" - }, - "X_min": { - "type": "number" - }, - "Y_max": { - "type": "number" - }, - "Y_min": { - "type": "number" - } - }, - "title": "Beamtilt", - "type": "object" - }, - "CalibratedDefocus": { - "additionalProperties": false, - "description": "", - "properties": { - "Maximal": { - "description": "Minimal value of a given dataset property", - "type": "number" - }, - "Minimal": { - "description": "Minimal value of a given dataset property", - "type": "number" - } - }, - "title": "CalibratedDefocus", - "type": "object" - }, - "ChromaticAberrationCorrector": { - "additionalProperties": false, - "description": "", - "properties": { - "Type": { - "description": "Details of a given specialist instrument", - "type": "string" - }, - "Used": { - "description": "whether a specific instrument was used during data acquisition", - "type": "boolean" - } - }, - "required": [ - "Used", - "Type" - ], - "title": "ChromaticAberrationCorrector", - "type": "object" - }, - "EnergyFilter": { - "additionalProperties": false, - "description": "", - "properties": { - "Model": { - "description": "Make and model of a specilized device", - "type": "string" - }, - "Used": { - "description": "whether a specific instrument was used during data acquisition", - "type": "boolean" - }, - "Width": { - "description": "The width of a given item - unit depends on item", - "type": "integer" - } - }, - "required": [ - "Used", - "Width" - ], - "title": "EnergyFilter", - "type": "object" - }, - "Grant": { - "additionalProperties": false, - "description": "A class representing a grant", - "properties": { - "Funding_agency": { - "description": "The organization responsible for the funding of this research", - "type": "string" - }, - "Grant_ID": { - "description": "Unique identifier for the grant, often a number and letter code", - "type": "string" - } - }, - "required": [ - "Grant_ID", - "Funding_agency" - ], - "title": "Grant", - "type": "object" - }, - "Grid": { - "additionalProperties": false, - "description": "A class representing a grid", - "properties": { - "Film_material": { - "description": "Type of material the support film is made of", - "type": "string" - }, - "Film_support": { - "description": "Whether a support film was used", - "type": "boolean" - }, - "Film_thickness": { - "description": "Thickness of the support film", - "type": "string" - }, - "Film_topology": { - "description": "Topology of the support film", - "type": "string" - }, - "Manufacturer": { - "description": "Grid manufacturer", - "type": "string" - }, - "Material": { - "description": "Material out of which the grid is made", - "type": "string" - }, - "Mesh": { - "description": "Grid mesh in lines per inch" - }, - "Pretreatment_atmosphere": { - "description": "Atmospheric conditions in the chamber during pretreatment, i.e., addition of specific gases, etc.", - "type": "string" - }, - "Pretreatment_pressure": { - "description": "Pressure of the chamber during pretreatment, in Pa" - }, - "Pretreatment_time": { - "description": "Length of time of the pretreatment in s" - }, - "Pretreatment_type": { - "description": "Type of pretreatment of the grid, i.e., glow discharge", - "type": "string" - } - }, - "title": "Grid", - "type": "object" - }, - "ImageSize": { - "additionalProperties": false, - "description": "", - "properties": { - "Height": { - "description": "The height of a given item - unit depends on item", - "type": "integer" - }, - "Width": { - "description": "The width of a given item - unit depends on item", - "type": "integer" - } - }, - "title": "ImageSize", - "type": "object" - }, - "Imagehift": { - "additionalProperties": false, - "description": "", - "properties": { - "X_max": { - "type": "number" - }, - "X_min": { - "type": "number" - }, - "Y_max": { - "type": "number" - }, - "Y_min": { - "type": "number" - } - }, - "title": "Imagehift", - "type": "object" - }, - "Instrument": { - "additionalProperties": false, - "description": "Instrument values, mostly constant across a data collection.", - "properties": { - "Acceleration_Voltage": { - "description": "Voltage used for the electron acceleration, in kV", - "type": "integer" - }, - "C2_Aperture": { - "description": "C2 aperture size used in data acquisition, in \u00b5m", - "type": "integer" - }, - "CS": { - "description": "Spherical aberration of the instrument, in mm", - "type": "number" - }, - "Electron_source": { - "description": "Type of electron source used in the microscope, such as FEG", - "type": "string" - }, - "Illumination": { - "description": "Mode of illumination used during data collection", - "type": "string" - }, - "Imaging": { - "description": "Mode of imaging used during data collection", - "type": "string" - }, - "Microscope": { - "description": "Name/Type of the Microscope", - "type": "string" - } - }, - "required": [ - "Microscope", - "Illumination", - "Imaging", - "Electron_source", - "Acceleration_Voltage", - "CS" - ], - "title": "Instrument", - "type": "object" - }, - "Ligand": { - "additionalProperties": false, - "description": "A class representing a ligand", - "properties": { - "Present": { - "description": "Whether the model contains any ligands", - "type": "boolean" - }, - "reference": { - "description": "Link to a reference of your ligand, i.e., CCD, PubChem, etc.", - "type": "string" - }, - "smile": { - "description": "Provide a valid SMILE string of your ligand", - "type": "string" - } - }, - "required": [ - "Present" - ], - "title": "Ligand", - "type": "object" - }, - "Molecule": { - "additionalProperties": false, - "description": "A class representing a molecule", - "properties": { - "Class": { - "$ref": "#/$defs/MoleculeClassEnum", - "description": "Class of the molecule" - }, - "Expression_system": { - "description": "Scientific name of the organism used to produce the molecule of interest", - "type": "string" - }, - "Gene_name": { - "description": "Name of the gene of interest", - "type": "string" - }, - "Name": { - "description": "Name of an individual molecule (often protein) in the sample", - "type": "string" - }, - "Natural_source": { - "description": "Scientific name of the natural host organism", - "type": "string" - }, - "Sequence": { - "description": "Full sequence of the sample as in the data, i.e., cleaved tags should also be removed from sequence here", - "type": "string" - }, - "Taxonomy_ID_expression": { - "description": "Taxonomy ID of the expression system organism", - "type": "string" - }, - "Taxonomy_ID_source": { - "description": "Taxonomy ID of the natural source organism", - "type": "string" - }, - "Type": { - "description": "Description of the overall supramolecular type, i.e., a complex", - "type": "string" - } - }, - "required": [ - "Name", - "Type", - "Class", - "Sequence", - "Natural_source", - "Taxonomy_ID_source", - "Expression_system", - "Taxonomy_ID_expression" - ], - "title": "Molecule", - "type": "object" - }, - "MoleculeClassEnum": { - "description": "", - "enum": [ - "Antibiotic", - "Carbohydrate", - "Chimera", - "None of these" - ], - "title": "MoleculeClassEnum", - "type": "string" - }, - "Name": { - "additionalProperties": false, - "description": "A class representing the name of an author", - "properties": { - "FirstName": { - "description": "Given name of the author", - "type": "string" - }, - "LastName": { - "description": "Surname of the author", - "type": "string" - } - }, - "required": [ - "FirstName", - "LastName" - ], - "title": "Name", - "type": "object" - }, - "NominalDefocus": { - "additionalProperties": false, - "description": "", - "properties": { - "Maximal": { - "description": "Minimal value of a given dataset property", - "type": "number" - }, - "Minimal": { - "description": "Minimal value of a given dataset property", - "type": "number" - } - }, - "title": "NominalDefocus", - "type": "object" - }, - "OSCEMSample": { - "additionalProperties": false, - "description": "Main class for OSCEM sample schema", - "properties": { - "Author": { - "description": "List of authors associated with the project", - "items": { - "$ref": "#/$defs/Author" - }, - "type": "array" - }, - "Grant": { - "description": "List of grants associated with the project", - "items": { - "$ref": "#/$defs/Grant" - }, - "type": "array" - }, - "Sample": { - "$ref": "#/$defs/Sample", - "description": "Sample information" - } - }, - "required": [ - "Grant", - "Author", - "Sample" - ], - "title": "OSCEMSample", - "type": "object" - }, - "Organization": { - "additionalProperties": false, - "description": "A class representing an organization", - "properties": { - "Name_org": { - "description": "Name of the organization", - "type": "string" - }, - "Type_org": { - "$ref": "#/$defs/OrganizationTypeEnum", - "description": "Type of organization, academic, commercial, governmental, etc." - } - }, - "required": [ - "Type_org" - ], - "title": "Organization", - "type": "object" - }, - "OrganizationTypeEnum": { - "description": "", - "enum": [ - "Academic", - "Commercial", - "Government", - "Other" - ], - "title": "OrganizationTypeEnum", - "type": "string" - }, - "OverallMolecule": { - "additionalProperties": false, - "description": "A class representing the overall molecule", - "properties": { - "Molecular_weight": { - "description": "Molecular weight in Da" - }, - "Name": { - "description": "Name of the full sample", - "type": "string" - }, - "Source": { - "description": "Where the sample was taken from, i.e., natural host, recombinantly expressed, etc.", - "type": "string" - }, - "Type": { - "description": "Description of the overall supramolecular type, i.e., a complex", - "type": "string" - } - }, - "required": [ - "Type", - "Name", - "Source" - ], - "title": "OverallMolecule", - "type": "object" - }, - "Phaseplate": { - "additionalProperties": false, - "description": "", - "properties": { - "Type": { - "description": "Details of a given specialist instrument", - "type": "string" - }, - "Used": { - "description": "whether a specific instrument was used during data acquisition", - "type": "boolean" - } - }, - "required": [ - "Used", - "Type" - ], - "title": "Phaseplate", - "type": "object" - }, - "Sample": { - "additionalProperties": false, - "description": "A class representing a sample", - "properties": { - "Grid": { - "$ref": "#/$defs/Grid", - "description": "Description of the grid used" - }, - "Ligands": { - "description": "List of ligands associated with the sample", - "items": { - "$ref": "#/$defs/Ligand" - }, - "type": "array" - }, - "Molecule": { - "description": "List of molecule associated with the sample", - "items": { - "$ref": "#/$defs/Molecule" - }, - "type": "array" - }, - "Overall_Molecule": { - "$ref": "#/$defs/OverallMolecule", - "description": "Description of the overall molecule" - }, - "Specimen": { - "$ref": "#/$defs/Specimen", - "description": "Description of the specimen" - } - }, - "required": [ - "Overall_Molecule", - "Molecule", - "Specimen" - ], - "title": "Sample", - "type": "object" - }, - "SpecialistOptics": { - "additionalProperties": false, - "description": "", - "properties": { - "Chromatic_Aberration_Corrector": { - "$ref": "#/$defs/ChromaticAberrationCorrector", - "description": "Specialist device to correct for chromatic aberration of the microscope lenses" - }, - "Phaseplate": { - "$ref": "#/$defs/Phaseplate", - "description": "Phaseplate is a special optics device that can be used to enhance contrast" - }, - "Spherical_Aberration_Corrector": { - "$ref": "#/$defs/SphericalAberrationCorrector", - "description": "Specialist device to correct for spherical aberration of the microscope lenses" - } - }, - "title": "SpecialistOptics", - "type": "object" - }, - "Specimen": { - "additionalProperties": false, - "description": "A class representing a specimen", - "properties": { - "Buffer": { - "description": "Name/composition of the (chemical) sample buffer during grid preparation", - "type": "string" - }, - "Concentration": { - "description": "Concentration of the (supra)molecule in the sample, in M" - }, - "Embedding": { - "description": "Whether the sample was embedded", - "type": "boolean" - }, - "Humidity": { - "description": "Environmental humidity just before vitrification, in %" - }, - "Shadowing": { - "description": "Whether the sample was shadowed", - "type": "boolean" - }, - "Staining": { - "description": "Whether the sample was stained", - "type": "boolean" - }, - "Temperature": { - "description": "Environmental temperature just before vitrification, in K" - }, - "Vitrification": { - "description": "Whether the sample was vitrified", - "type": "boolean" - }, - "Vitrification_cryogen": { - "description": "Which cryogen was used for vitrification", - "type": "string" - }, - "pH": { - "description": "pH of the sample buffer" - } - }, - "required": [ - "pH", - "Vitrification", - "Vitrification_cryogen", - "Staining", - "Embedding", - "Shadowing" - ], - "title": "Specimen", - "type": "object" - }, - "SphericalAberrationCorrector": { - "additionalProperties": false, - "description": "", - "properties": { - "Type": { - "description": "Details of a given specialist instrument", - "type": "string" - }, - "Used": { - "description": "whether a specific instrument was used during data acquisition", - "type": "boolean" - } - }, - "required": [ - "Used", - "Type" - ], - "title": "SphericalAberrationCorrector", - "type": "object" - }, - "Temperature": { - "additionalProperties": false, - "description": "", - "properties": { - "Maximal": { - "description": "Minimal value of a given dataset property", - "type": "number" - }, - "Minimal": { - "description": "Minimal value of a given dataset property", - "type": "number" - } - }, - "title": "Temperature", - "type": "object" - }, - "Testschema": { - "additionalProperties": false, - "description": "", - "properties": { - "Instrument": { - "$ref": "#/$defs/Instrument" - } - }, - "title": "Testschema", - "type": "object" - }, - "TiltAngle": { - "additionalProperties": false, - "description": "", - "properties": { - "Increment": { - "type": "number" - }, - "Maximal": { - "description": "Minimal value of a given dataset property", - "type": "number" - }, - "Minimal": { - "description": "Minimal value of a given dataset property", - "type": "number" - } - }, - "title": "TiltAngle", - "type": "object" - } - }, - "$id": "http://example.org/oscem_1", - "$schema": "https://json-schema.org/draft/2019-09/schema", - "additionalProperties": true, - "description": "", - "metamodel_version": "1.7.0", - "properties": { - "Acquisition": { - "$ref": "#/$defs/Acquisition" - }, - "Instrument": { - "$ref": "#/$defs/Instrument" - }, - "oscemsample": { - "$ref": "#/$defs/OSCEMSample" - } - }, - "required": [ - "Acquisition", - "Instrument", - "oscemsample" - ], - "title": "OSCEM_test", - "type": "object", - "version": null -} diff --git a/LinkML/package.json b/LinkML/package.json deleted file mode 100644 index 4508e7b..0000000 --- a/LinkML/package.json +++ /dev/null @@ -1,16 +0,0 @@ -{ - "name": "testschema", - "version": "1.0.0", - "description": "", - "main": "test.js", - "scripts": { - "test": "echo \"Error: no test specified\" && exit 1" - }, - "keywords": [], - "author": "", - "license": "ISC", - "dependencies": { - "ajv": "^8.16.0", - "json-schema-validator": "^1.1.0" - } -} diff --git a/LinkML/schema_sample.json b/LinkML/schema_sample.json deleted file mode 100644 index 37c6526..0000000 --- a/LinkML/schema_sample.json +++ /dev/null @@ -1,412 +0,0 @@ -{ - "$defs": { - "Author": { - "additionalProperties": false, - "description": "A class representing an author", - "properties": { - "Country": { - "description": "Country of the author's institution", - "type": "string" - }, - "Email": { - "description": "Email address of the author", - "type": "string" - }, - "Name": { - "$ref": "#/$defs/Name", - "description": "Full name of the author" - }, - "ORCID": { - "description": "ORCID of the author, a type of unique identifier", - "type": "string" - }, - "Organization": { - "$ref": "#/$defs/Organization", - "description": "The organization the author is affiliated with" - }, - "Phone": { - "description": "Phone number of the author", - "type": "string" - }, - "role": { - "description": "Role of the author, i.e., principal investigator", - "type": "string" - } - }, - "required": [ - "Name", - "Email", - "Phone", - "ORCID", - "Organization", - "Country" - ], - "title": "Author", - "type": "object" - }, - "Grant": { - "additionalProperties": false, - "description": "A class representing a grant", - "properties": { - "Funding_agency": { - "description": "The organization responsible for the funding of this research", - "type": "string" - }, - "Grant_ID": { - "description": "Unique identifier for the grant, often a number and letter code", - "type": "string" - } - }, - "required": [ - "Grant_ID", - "Funding_agency" - ], - "title": "Grant", - "type": "object" - }, - "Grid": { - "additionalProperties": false, - "description": "A class representing a grid", - "properties": { - "Film_material": { - "description": "Type of material the support film is made of", - "type": "string" - }, - "Film_support": { - "description": "Whether a support film was used", - "type": "boolean" - }, - "Film_thickness": { - "description": "Thickness of the support film", - "type": "string" - }, - "Film_topology": { - "description": "Topology of the support film", - "type": "string" - }, - "Manufacturer": { - "description": "Grid manufacturer", - "type": "string" - }, - "Material": { - "description": "Material out of which the grid is made", - "type": "string" - }, - "Mesh": { - "description": "Grid mesh in lines per inch" - }, - "Pretreatment_atmosphere": { - "description": "Atmospheric conditions in the chamber during pretreatment, i.e., addition of specific gases, etc.", - "type": "string" - }, - "Pretreatment_pressure": { - "description": "Pressure of the chamber during pretreatment, in Pa" - }, - "Pretreatment_time": { - "description": "Length of time of the pretreatment in s" - }, - "Pretreatment_type": { - "description": "Type of pretreatment of the grid, i.e., glow discharge", - "type": "string" - } - }, - "title": "Grid", - "type": "object" - }, - "Ligand": { - "additionalProperties": false, - "description": "A class representing a ligand", - "properties": { - "Present": { - "description": "Whether the model contains any ligands", - "type": "boolean" - }, - "reference": { - "description": "Link to a reference of your ligand, i.e., CCD, PubChem, etc.", - "type": "string" - }, - "smile": { - "description": "Provide a valid SMILE string of your ligand", - "type": "string" - } - }, - "required": [ - "Present" - ], - "title": "Ligand", - "type": "object" - }, - "Molecule": { - "additionalProperties": false, - "description": "A class representing a molecule", - "properties": { - "Class": { - "$ref": "#/$defs/MoleculeClassEnum", - "description": "Class of the molecule" - }, - "Expression_system": { - "description": "Scientific name of the organism used to produce the molecule of interest", - "type": "string" - }, - "Gene_name": { - "description": "Name of the gene of interest", - "type": "string" - }, - "Name": { - "description": "Name of an individual molecule (often protein) in the sample", - "type": "string" - }, - "Natural_source": { - "description": "Scientific name of the natural host organism", - "type": "string" - }, - "Sequence": { - "description": "Full sequence of the sample as in the data, i.e., cleaved tags should also be removed from sequence here", - "type": "string" - }, - "Taxonomy_ID_expression": { - "description": "Taxonomy ID of the expression system organism", - "type": "string" - }, - "Taxonomy_ID_source": { - "description": "Taxonomy ID of the natural source organism", - "type": "string" - }, - "Type": { - "description": "Description of the overall supramolecular type, i.e., a complex", - "type": "string" - } - }, - "required": [ - "Name", - "Type", - "Class", - "Sequence", - "Natural_source", - "Taxonomy_ID_source", - "Expression_system", - "Taxonomy_ID_expression" - ], - "title": "Molecule", - "type": "object" - }, - "MoleculeClassEnum": { - "description": "", - "enum": [ - "Antibiotic", - "Carbohydrate", - "Chimera", - "None of these" - ], - "title": "MoleculeClassEnum", - "type": "string" - }, - "Name": { - "additionalProperties": false, - "description": "A class representing the name of an author", - "properties": { - "FirstName": { - "description": "Given name of the author", - "type": "string" - }, - "LastName": { - "description": "Surname of the author", - "type": "string" - } - }, - "required": [ - "FirstName", - "LastName" - ], - "title": "Name", - "type": "object" - }, - "OSCEMSample": { - "additionalProperties": false, - "description": "Main class for OSCEM sample schema", - "properties": { - "Author": { - "description": "List of authors associated with the project", - "items": { - "$ref": "#/$defs/Author" - }, - "type": "array" - }, - "Grant": { - "description": "List of grants associated with the project", - "items": { - "$ref": "#/$defs/Grant" - }, - "type": "array" - }, - "Sample": { - "$ref": "#/$defs/Sample", - "description": "Sample information" - } - }, - "required": [ - "Grant", - "Author", - "Sample" - ], - "title": "OSCEMSample", - "type": "object" - }, - "Organization": { - "additionalProperties": false, - "description": "A class representing an organization", - "properties": { - "Name_org": { - "description": "Name of the organization", - "type": "string" - }, - "Type_org": { - "$ref": "#/$defs/OrganizationTypeEnum", - "description": "Type of organization, academic, commercial, governmental, etc." - } - }, - "required": [ - "Type_org" - ], - "title": "Organization", - "type": "object" - }, - "OrganizationTypeEnum": { - "description": "", - "enum": [ - "Academic", - "Commercial", - "Government", - "Other" - ], - "title": "OrganizationTypeEnum", - "type": "string" - }, - "OverallMolecule": { - "additionalProperties": false, - "description": "A class representing the overall molecule", - "properties": { - "Molecular_weight": { - "description": "Molecular weight in Da" - }, - "Name": { - "description": "Name of the full sample", - "type": "string" - }, - "Source": { - "description": "Where the sample was taken from, i.e., natural host, recombinantly expressed, etc.", - "type": "string" - }, - "Type": { - "description": "Description of the overall supramolecular type, i.e., a complex", - "type": "string" - } - }, - "required": [ - "Type", - "Name", - "Source" - ], - "title": "OverallMolecule", - "type": "object" - }, - "Sample": { - "additionalProperties": false, - "description": "A class representing a sample", - "properties": { - "Grid": { - "$ref": "#/$defs/Grid", - "description": "Description of the grid used" - }, - "Ligands": { - "description": "List of ligands associated with the sample", - "items": { - "$ref": "#/$defs/Ligand" - }, - "type": "array" - }, - "Molecule": { - "description": "List of molecule associated with the sample", - "items": { - "$ref": "#/$defs/Molecule" - }, - "type": "array" - }, - "Overall_Molecule": { - "$ref": "#/$defs/OverallMolecule", - "description": "Description of the overall molecule" - }, - "Specimen": { - "$ref": "#/$defs/Specimen", - "description": "Description of the specimen" - } - }, - "required": [ - "Overall_Molecule", - "Molecule", - "Specimen" - ], - "title": "Sample", - "type": "object" - }, - "Specimen": { - "additionalProperties": false, - "description": "A class representing a specimen", - "properties": { - "Buffer": { - "description": "Name/composition of the (chemical) sample buffer during grid preparation", - "type": "string" - }, - "Concentration": { - "description": "Concentration of the (supra)molecule in the sample, in M" - }, - "Embedding": { - "description": "Whether the sample was embedded", - "type": "boolean" - }, - "Humidity": { - "description": "Environmental humidity just before vitrification, in %" - }, - "Shadowing": { - "description": "Whether the sample was shadowed", - "type": "boolean" - }, - "Staining": { - "description": "Whether the sample was stained", - "type": "boolean" - }, - "Temperature": { - "description": "Environmental temperature just before vitrification, in K" - }, - "Vitrification": { - "description": "Whether the sample was vitrified", - "type": "boolean" - }, - "Vitrification_cryogen": { - "description": "Which cryogen was used for vitrification", - "type": "string" - }, - "pH": { - "description": "pH of the sample buffer" - } - }, - "required": [ - "pH", - "Vitrification", - "Vitrification_cryogen", - "Staining", - "Embedding", - "Shadowing" - ], - "title": "Specimen", - "type": "object" - } - }, - "$id": "http://example.org/oscem_sample", - "$schema": "https://json-schema.org/draft/2019-09/schema", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "OSCEMSample", - "type": "object", - "version": null -} diff --git a/LinkML/schema_sample_forajv.json b/LinkML/schema_sample_forajv.json deleted file mode 100644 index 3eb4a28..0000000 --- a/LinkML/schema_sample_forajv.json +++ /dev/null @@ -1,410 +0,0 @@ -{ - "$defs": { - "Author": { - "additionalProperties": false, - "description": "A class representing an author", - "properties": { - "Country": { - "description": "Country of the author's institution", - "type": "string" - }, - "Email": { - "description": "Email address of the author", - "type": "string" - }, - "Name": { - "$ref": "#/$defs/Name", - "description": "Full name of the author" - }, - "ORCID": { - "description": "ORCID of the author, a type of unique identifier", - "type": "string" - }, - "Organization": { - "$ref": "#/$defs/Organization", - "description": "The organization the author is affiliated with" - }, - "Phone": { - "description": "Phone number of the author", - "type": "string" - }, - "role": { - "description": "Role of the author, i.e., principal investigator", - "type": "string" - } - }, - "required": [ - "Name", - "Email", - "Phone", - "ORCID", - "Organization", - "Country" - ], - "title": "Author", - "type": "object" - }, - "Grant": { - "additionalProperties": false, - "description": "A class representing a grant", - "properties": { - "Funding_agency": { - "description": "The organization responsible for the funding of this research", - "type": "string" - }, - "Grant_ID": { - "description": "Unique identifier for the grant, often a number and letter code", - "type": "string" - } - }, - "required": [ - "Grant_ID", - "Funding_agency" - ], - "title": "Grant", - "type": "object" - }, - "Grid": { - "additionalProperties": false, - "description": "A class representing a grid", - "properties": { - "Film_material": { - "description": "Type of material the support film is made of", - "type": "string" - }, - "Film_support": { - "description": "Whether a support film was used", - "type": "boolean" - }, - "Film_thickness": { - "description": "Thickness of the support film", - "type": "string" - }, - "Film_topology": { - "description": "Topology of the support film", - "type": "string" - }, - "Manufacturer": { - "description": "Grid manufacturer", - "type": "string" - }, - "Material": { - "description": "Material out of which the grid is made", - "type": "string" - }, - "Mesh": { - "description": "Grid mesh in lines per inch" - }, - "Pretreatment_atmosphere": { - "description": "Atmospheric conditions in the chamber during pretreatment, i.e., addition of specific gases, etc.", - "type": "string" - }, - "Pretreatment_pressure": { - "description": "Pressure of the chamber during pretreatment, in Pa" - }, - "Pretreatment_time": { - "description": "Length of time of the pretreatment in s" - }, - "Pretreatment_type": { - "description": "Type of pretreatment of the grid, i.e., glow discharge", - "type": "string" - } - }, - "title": "Grid", - "type": "object" - }, - "Ligand": { - "additionalProperties": false, - "description": "A class representing a ligand", - "properties": { - "Present": { - "description": "Whether the model contains any ligands", - "type": "boolean" - }, - "reference": { - "description": "Link to a reference of your ligand, i.e., CCD, PubChem, etc.", - "type": "string" - }, - "smile": { - "description": "Provide a valid SMILE string of your ligand", - "type": "string" - } - }, - "required": [ - "Present" - ], - "title": "Ligand", - "type": "object" - }, - "Molecule": { - "additionalProperties": false, - "description": "A class representing a molecule", - "properties": { - "Class": { - "$ref": "#/$defs/MoleculeClassEnum", - "description": "Class of the molecule" - }, - "Expression_system": { - "description": "Scientific name of the organism used to produce the molecule of interest", - "type": "string" - }, - "Gene_name": { - "description": "Name of the gene of interest", - "type": "string" - }, - "Name": { - "description": "Name of an individual molecule (often protein) in the sample", - "type": "string" - }, - "Natural_source": { - "description": "Scientific name of the natural host organism", - "type": "string" - }, - "Sequence": { - "description": "Full sequence of the sample as in the data, i.e., cleaved tags should also be removed from sequence here", - "type": "string" - }, - "Taxonomy_ID_expression": { - "description": "Taxonomy ID of the expression system organism", - "type": "string" - }, - "Taxonomy_ID_source": { - "description": "Taxonomy ID of the natural source organism", - "type": "string" - }, - "Type": { - "description": "Description of the overall supramolecular type, i.e., a complex", - "type": "string" - } - }, - "required": [ - "Name", - "Type", - "Class", - "Sequence", - "Natural_source", - "Taxonomy_ID_source", - "Expression_system", - "Taxonomy_ID_expression" - ], - "title": "Molecule", - "type": "object" - }, - "MoleculeClassEnum": { - "description": "", - "enum": [ - "Antibiotic", - "Carbohydrate", - "Chimera", - "None of these" - ], - "title": "MoleculeClassEnum", - "type": "string" - }, - "Name": { - "additionalProperties": false, - "description": "A class representing the name of an author", - "properties": { - "FirstName": { - "description": "Given name of the author", - "type": "string" - }, - "LastName": { - "description": "Surname of the author", - "type": "string" - } - }, - "required": [ - "FirstName", - "LastName" - ], - "title": "Name", - "type": "object" - }, - "OSCEMSample": { - "additionalProperties": false, - "description": "Main class for OSCEM sample schema", - "properties": { - "Author": { - "description": "List of authors associated with the project", - "items": { - "$ref": "#/$defs/Author" - }, - "type": "array" - }, - "Grant": { - "description": "List of grants associated with the project", - "items": { - "$ref": "#/$defs/Grant" - }, - "type": "array" - }, - "Sample": { - "$ref": "#/$defs/Sample", - "description": "Sample information" - } - }, - "required": [ - "Grant", - "Author", - "Sample" - ], - "title": "OSCEMSample", - "type": "object" - }, - "Organization": { - "additionalProperties": false, - "description": "A class representing an organization", - "properties": { - "Name_org": { - "description": "Name of the organization", - "type": "string" - }, - "Type_org": { - "$ref": "#/$defs/OrganizationTypeEnum", - "description": "Type of organization, academic, commercial, governmental, etc." - } - }, - "required": [ - "Type_org" - ], - "title": "Organization", - "type": "object" - }, - "OrganizationTypeEnum": { - "description": "", - "enum": [ - "Academic", - "Commercial", - "Government", - "Other" - ], - "title": "OrganizationTypeEnum", - "type": "string" - }, - "OverallMolecule": { - "additionalProperties": false, - "description": "A class representing the overall molecule", - "properties": { - "Molecular_weight": { - "description": "Molecular weight in Da" - }, - "Name": { - "description": "Name of the full sample", - "type": "string" - }, - "Source": { - "description": "Where the sample was taken from, i.e., natural host, recombinantly expressed, etc.", - "type": "string" - }, - "Type": { - "description": "Description of the overall supramolecular type, i.e., a complex", - "type": "string" - } - }, - "required": [ - "Type", - "Name", - "Source" - ], - "title": "OverallMolecule", - "type": "object" - }, - "Sample": { - "additionalProperties": false, - "description": "A class representing a sample", - "properties": { - "Grid": { - "$ref": "#/$defs/Grid", - "description": "Description of the grid used" - }, - "Ligands": { - "description": "List of ligands associated with the sample", - "items": { - "$ref": "#/$defs/Ligand" - }, - "type": "array" - }, - "Molecule": { - "description": "List of molecule associated with the sample", - "items": { - "$ref": "#/$defs/Molecule" - }, - "type": "array" - }, - "Overall_Molecule": { - "$ref": "#/$defs/OverallMolecule", - "description": "Description of the overall molecule" - }, - "Specimen": { - "$ref": "#/$defs/Specimen", - "description": "Description of the specimen" - } - }, - "required": [ - "Overall_Molecule", - "Molecule", - "Specimen" - ], - "title": "Sample", - "type": "object" - }, - "Specimen": { - "additionalProperties": false, - "description": "A class representing a specimen", - "properties": { - "Buffer": { - "description": "Name/composition of the (chemical) sample buffer during grid preparation", - "type": "string" - }, - "Concentration": { - "description": "Concentration of the (supra)molecule in the sample, in M" - }, - "Embedding": { - "description": "Whether the sample was embedded", - "type": "boolean" - }, - "Humidity": { - "description": "Environmental humidity just before vitrification, in %" - }, - "Shadowing": { - "description": "Whether the sample was shadowed", - "type": "boolean" - }, - "Staining": { - "description": "Whether the sample was stained", - "type": "boolean" - }, - "Temperature": { - "description": "Environmental temperature just before vitrification, in K" - }, - "Vitrification": { - "description": "Whether the sample was vitrified", - "type": "boolean" - }, - "Vitrification_cryogen": { - "description": "Which cryogen was used for vitrification", - "type": "string" - }, - "pH": { - "description": "pH of the sample buffer" - } - }, - "required": [ - "pH", - "Vitrification", - "Vitrification_cryogen", - "Staining", - "Embedding", - "Shadowing" - ], - "title": "Specimen", - "type": "object" - } - }, - "$id": "http://example.org/oscem_sample", - "$schema": "https://json-schema.org/draft/2019-09/schema", - "additionalProperties": true, - "title": "OSCEMSample", - "type": "object" -} diff --git a/LinkML/test_ajv.js b/LinkML/test_ajv.js deleted file mode 100755 index e833bb3..0000000 --- a/LinkML/test_ajv.js +++ /dev/null @@ -1,18 +0,0 @@ -const Ajv = require('ajv/dist/2019'); -const fs = require('fs'); - - -const data = JSON.parse(fs.readFileSync('data_valid_sample.json', 'utf8')) -//console.log(data); -const mySchema = JSON.parse(fs.readFileSync('schema_sample_forajv.json', 'utf8')) -//console.log(mySchema); -const ajv = new Ajv() - -const validate = ajv.compile(mySchema); -const valid = validate(data); - -if (valid) { - console.log('Data is valid!'); -} else { - console.error('Data is invalid:', validate.errors); -} diff --git a/LinkML/test_pythonlib_jsonschema.py b/LinkML/test_pythonlib_jsonschema.py deleted file mode 100644 index 17fcaa3..0000000 --- a/LinkML/test_pythonlib_jsonschema.py +++ /dev/null @@ -1,20 +0,0 @@ -import json -import jsonschema -from jsonschema import validate - -# Load the schema from a file -with open('draft-2019-09-schema.json', 'r') as schema_file: - schema = json.load(schema_file) - -with open('data_valid_sample.json', 'r') as data_file: - data = json.load(data_file) - -with open('overall_schema.json', 'r') as myschema_file: - myschema = json.load(myschema_file) - -# Validate the data -try: - validate(instance=data, schema=myschema) - print("Data is valid!") -except jsonschema.exceptions.ValidationError as err: - print("Data is invalid:", err.message) \ No newline at end of file diff --git a/LinkML/tomo_example.json b/LinkML/tomo_example.json deleted file mode 100644 index 87a5cbe..0000000 --- a/LinkML/tomo_example.json +++ /dev/null @@ -1,525 +0,0 @@ -{ - "$defs": { - "Acquisition": { - "additionalProperties": false, - "description": "", - "properties": { - "Beamshift": { - "$ref": "#/$defs/Beamshift", - "description": "Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad." - }, - "Beamtilt": { - "$ref": "#/$defs/Beamtilt", - "description": "Another way to move the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad." - }, - "Beamtiltgroups": { - "description": "Number of Beamtilt groups present in this dataset - for optimized processing split dataset into groups of same tilt angle. Despite its name Beamshift is often used to achive this result.", - "type": "integer" - }, - "Binning_camera": { - "description": "Level of binning on the images applied during data collection", - "type": "number" - }, - "Calibrated_defocus": { - "$ref": "#/$defs/CalibratedDefocus", - "description": "Machine estimated defocus, min and max values in \u00b5m. Has a tendency to be off." - }, - "Calibrated_magnification": { - "description": "Calculated magnification, no unit", - "type": "integer" - }, - "Cryogen": { - "description": "Cryogen used in cooling the instrument and sample, usually nitrogen", - "type": "string" - }, - "Datetime": { - "description": "Time and date of the data acquisition", - "format": "date-time", - "type": "string" - }, - "Detector": { - "description": "Make and model of the detector used", - "type": "string" - }, - "Detector_mode": { - "description": "Operating mode of the detector", - "type": "string" - }, - "Dose_per_movie": { - "description": "Average dose per image/movie/tilt - given in electrons per square Angstrom", - "type": "number" - }, - "Energy_filter": { - "$ref": "#/$defs/EnergyFilter", - "description": "Wether an energy filter was used and its specifics." - }, - "Exposure_time": { - "description": "Time of data acquisition per movie/tilt - in s", - "type": "number" - }, - "Frames_per_movie": { - "description": "Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors", - "type": "integer" - }, - "GainRef_FlipRotate": { - "description": "Whether and how you have to flip or rotate the gainref in order to align with your acquired images", - "type": "string" - }, - "Grids_imaged": { - "description": "Number of grids imaged for this project - here with qualifier during this data acquisition", - "type": "integer" - }, - "Holder": { - "description": "Speciman holder model", - "type": "string" - }, - "Holder_cryogen": { - "description": "Type of cryogen used in the holder - if the holder is cooled seperately", - "type": "string" - }, - "Image_size": { - "$ref": "#/$defs/ImageSize", - "description": "The size of the image in pixels, height and width given." - }, - "Images_generated": { - "description": "Number of images generated total for this data collection - might need a qualifier for tilt series to determine whether full series or individual tilts are counted", - "type": "integer" - }, - "Imageshift": { - "description": "Movement of the Beam below the image in order to shift the image on the detector. Given in \u00b5m." - }, - "Microscope_software": { - "description": "Software used for instrument control,", - "type": "string" - }, - "Nominal_defocus": { - "$ref": "#/$defs/NominalDefocus", - "description": "Target defocus set, min and max values in \u00b5m." - }, - "Nominal_magnification": { - "description": "Magnification level as indicated by the instrument, no unit", - "type": "integer" - }, - "Pixel_size": { - "description": "Pixel size, in Angstrom", - "type": "number" - }, - "Specialist_Optics": { - "$ref": "#/$defs/SpecialistOptics", - "description": "Any type of special optics, such as a phaseplate" - }, - "Temperature": { - "$ref": "#/$defs/Temperature", - "description": "Temperature during data collection, in K with min and max values." - } - }, - "required": [ - "Detector", - "Dose_per_movie", - "Datetime", - "Binning_camera", - "Pixel_size" - ], - "title": "Acquisition", - "type": "object" - }, - "Base": { - "additionalProperties": false, - "description": "", - "properties": { - "Acquisition": { - "$ref": "#/$defs/Acquisition" - } - }, - "title": "Base", - "type": "object" - }, - "Beamshift": { - "additionalProperties": false, - "description": "", - "properties": { - "X_max": { - "type": "number" - }, - "X_min": { - "type": "number" - }, - "Y_max": { - "type": "number" - }, - "Y_min": { - "type": "number" - } - }, - "title": "Beamshift", - "type": "object" - }, - "Beamtilt": { - "additionalProperties": false, - "description": "", - "properties": { - "X_max": { - "type": "number" - }, - "X_min": { - "type": "number" - }, - "Y_max": { - "type": "number" - }, - "Y_min": { - "type": "number" - } - }, - "title": "Beamtilt", - "type": "object" - }, - "CalibratedDefocus": { - "additionalProperties": false, - "description": "", - "properties": { - "Maximal": { - "description": "Maximal value of a given dataset property", - "type": "number" - }, - "Minimal": { - "description": "Minimal value of a given dataset property", - "type": "number" - } - }, - "title": "CalibratedDefocus", - "type": "object" - }, - "ChromaticAberrationCorrector": { - "additionalProperties": false, - "description": "", - "properties": { - "Type": { - "description": "Details of a given specialist instrument", - "type": "string" - }, - "Used": { - "description": "whether a specific instrument was used during data acquisition", - "type": "boolean" - } - }, - "required": [ - "Used", - "Type" - ], - "title": "ChromaticAberrationCorrector", - "type": "object" - }, - "EnergyFilter": { - "additionalProperties": false, - "description": "", - "properties": { - "Model": { - "description": "Make and model of a specilized device", - "type": "string" - }, - "Used": { - "description": "whether a specific instrument was used during data acquisition", - "type": "boolean" - }, - "Width": { - "description": "The width of a given item - unit depends on item", - "type": "integer" - } - }, - "required": [ - "Used", - "Width" - ], - "title": "EnergyFilter", - "type": "object" - }, - "ImageSize": { - "additionalProperties": false, - "description": "", - "properties": { - "Height": { - "description": "The height of a given item - unit depends on item", - "type": "integer" - }, - "Width": { - "description": "The width of a given item - unit depends on item", - "type": "integer" - } - }, - "title": "ImageSize", - "type": "object" - }, - "Imagehift": { - "additionalProperties": false, - "description": "", - "properties": { - "X_max": { - "type": "number" - }, - "X_min": { - "type": "number" - }, - "Y_max": { - "type": "number" - }, - "Y_min": { - "type": "number" - } - }, - "title": "Imagehift", - "type": "object" - }, - "NominalDefocus": { - "additionalProperties": false, - "description": "", - "properties": { - "Maximal": { - "description": "Maximal value of a given dataset property", - "type": "number" - }, - "Minimal": { - "description": "Minimal value of a given dataset property", - "type": "number" - } - }, - "title": "NominalDefocus", - "type": "object" - }, - "Phaseplate": { - "additionalProperties": false, - "description": "", - "properties": { - "Type": { - "description": "Details of a given specialist instrument", - "type": "string" - }, - "Used": { - "description": "whether a specific instrument was used during data acquisition", - "type": "boolean" - } - }, - "required": [ - "Used", - "Type" - ], - "title": "Phaseplate", - "type": "object" - }, - "SpecialistOptics": { - "additionalProperties": false, - "description": "", - "properties": { - "Chromatic_Aberration_Corrector": { - "$ref": "#/$defs/ChromaticAberrationCorrector", - "description": "Specialist device to correct for chromatic aberration of the microscope lenses" - }, - "Phaseplate": { - "$ref": "#/$defs/Phaseplate", - "description": "Phaseplate is a special optics device that can be used to enhance contrast" - }, - "Spherical_Aberration_Corrector": { - "$ref": "#/$defs/SphericalAberrationCorrector", - "description": "Specialist device to correct for spherical aberration of the microscope lenses" - } - }, - "title": "SpecialistOptics", - "type": "object" - }, - "SphericalAberrationCorrector": { - "additionalProperties": false, - "description": "", - "properties": { - "Type": { - "description": "Details of a given specialist instrument", - "type": "string" - }, - "Used": { - "description": "whether a specific instrument was used during data acquisition", - "type": "boolean" - } - }, - "required": [ - "Used", - "Type" - ], - "title": "SphericalAberrationCorrector", - "type": "object" - }, - "Temperature": { - "additionalProperties": false, - "description": "", - "properties": { - "Maximal": { - "description": "Maximal value of a given dataset property", - "type": "number" - }, - "Minimal": { - "description": "Minimal value of a given dataset property", - "type": "number" - } - }, - "title": "Temperature", - "type": "object" - }, - "TiltAngle": { - "additionalProperties": false, - "description": "The min, max and increment of the tilt angle in a tomography session. Unit is degree.", - "properties": { - "Increment": { - "type": "number" - }, - "Maximal": { - "description": "Maximal value of a given dataset property", - "type": "number" - }, - "Minimal": { - "description": "Minimal value of a given dataset property", - "type": "number" - } - }, - "title": "TiltAngle", - "type": "object" - }, - "Tomoacquisition": { - "additionalProperties": false, - "description": "", - "properties": { - "Beamshift": { - "$ref": "#/$defs/Beamshift", - "description": "Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad." - }, - "Beamtilt": { - "$ref": "#/$defs/Beamtilt", - "description": "Another way to move the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad." - }, - "Beamtiltgroups": { - "description": "Number of Beamtilt groups present in this dataset - for optimized processing split dataset into groups of same tilt angle. Despite its name Beamshift is often used to achive this result.", - "type": "integer" - }, - "Binning_camera": { - "description": "Level of binning on the images applied during data collection", - "type": "number" - }, - "Calibrated_defocus": { - "$ref": "#/$defs/CalibratedDefocus", - "description": "Machine estimated defocus, min and max values in \u00b5m. Has a tendency to be off." - }, - "Calibrated_magnification": { - "description": "Calculated magnification, no unit", - "type": "integer" - }, - "Cryogen": { - "description": "Cryogen used in cooling the instrument and sample, usually nitrogen", - "type": "string" - }, - "Datetime": { - "description": "Time and date of the data acquisition", - "format": "date-time", - "type": "string" - }, - "Detector": { - "description": "Make and model of the detector used", - "type": "string" - }, - "Detector_mode": { - "description": "Operating mode of the detector", - "type": "string" - }, - "Dose_per_movie": { - "description": "Average dose per image/movie/tilt - given in electrons per square Angstrom", - "type": "number" - }, - "Energy_filter": { - "$ref": "#/$defs/EnergyFilter", - "description": "Wether an energy filter was used and its specifics." - }, - "Exposure_time": { - "description": "Time of data acquisition per movie/tilt - in s", - "type": "number" - }, - "Frames_per_movie": { - "description": "Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors", - "type": "integer" - }, - "GainRef_FlipRotate": { - "description": "Whether and how you have to flip or rotate the gainref in order to align with your acquired images", - "type": "string" - }, - "Grids_imaged": { - "description": "Number of grids imaged for this project - here with qualifier during this data acquisition", - "type": "integer" - }, - "Holder": { - "description": "Speciman holder model", - "type": "string" - }, - "Holder_cryogen": { - "description": "Type of cryogen used in the holder - if the holder is cooled seperately", - "type": "string" - }, - "Image_size": { - "$ref": "#/$defs/ImageSize", - "description": "The size of the image in pixels, height and width given." - }, - "Images_generated": { - "description": "Number of images generated total for this data collection - might need a qualifier for tilt series to determine whether full series or individual tilts are counted", - "type": "integer" - }, - "Imageshift": { - "description": "Movement of the Beam below the image in order to shift the image on the detector. Given in \u00b5m." - }, - "Microscope_software": { - "description": "Software used for instrument control,", - "type": "string" - }, - "Nominal_defocus": { - "$ref": "#/$defs/NominalDefocus", - "description": "Target defocus set, min and max values in \u00b5m." - }, - "Nominal_magnification": { - "description": "Magnification level as indicated by the instrument, no unit", - "type": "integer" - }, - "Pixel_size": { - "description": "Pixel size, in Angstrom", - "type": "number" - }, - "Specialist_Optics": { - "$ref": "#/$defs/SpecialistOptics", - "description": "Any type of special optics, such as a phaseplate" - }, - "Temperature": { - "$ref": "#/$defs/Temperature", - "description": "Temperature during data collection, in K with min and max values." - }, - "TiltAxisAngle": { - "description": "The tilt axis angle of a tomography series", - "type": "number" - }, - "Tilt_angle": { - "$ref": "#/$defs/TiltAngle", - "description": "The min, max and increment of the tilt angle in a tomography session. Unit is degree." - } - }, - "required": [ - "TiltAxisAngle", - "Tilt_angle", - "Detector", - "Dose_per_movie", - "Datetime", - "Binning_camera", - "Pixel_size" - ], - "title": "Tomoacquisition", - "type": "object" - } - }, - "$id": "http://example.org/oscem_acquisition", - "$schema": "https://json-schema.org/draft/2019-09/schema", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "OSCEMSample", - "type": "object", - "version": null -} diff --git a/conversions.csv b/conversions.csv deleted file mode 100644 index a26ab12..0000000 --- a/conversions.csv +++ /dev/null @@ -1,134 +0,0 @@ -OSCEM,,,,from XML,From MDOC,from EMD,for PRZ,in PDBx/mmCIF,type,Ontology suggestions,comments -,,,,,,,,,,, -Instrument,Microscope,,,MicroscopeImage.microscopeData.instrument.InstrumentModel,,"Instrument.InstrumentClass, Instrument.InstrumentId, Instrument.InstrumentModel, Instrument.Manufacturer",,_em_imaging.microscope_model,string,, -Instrument,Illumination,,,MicroscopeImage.microscopeData.optics.IlluminationMode,,Optics.IlluminationMode,,_em_imaging.illumination_mode ,string,, -Instrument,Imaging,,,MicroscopeImage.microscopeData.optics.ColumnOperatingTemSubMode,ImagingMode,Optics.TemOperatingSubMode,,_em_imaging.mode,string,, -Instrument,Electron_source,,,MicroscopeImage.microscopeData.gun.Sourcetype,Source,Acquisition.SourceType,,_em_imaging.electron_source ,string,https://purls.helmholtz-metadaten.de/emg/EMG_00000045, -Instrument,Acceleration_Voltage,,,MicroscopeImage.microscopeData.gun.AccelerationVoltage,Voltage,Optics.AccelerationVoltage,,_em_imaging.accelerating_voltage ,int,https://purls.helmholtz-metadaten.de/emg/EMG_00000004, -Instrument,C2_Aperture,,,Aperture[C2].Name,,CustomProperties.Aperture[C2].Name.value,,_em_imaging.c2_aperture_diameter,int,, -Instrument,CS,,,,CS,,,_em_imaging.nominal_cs ,float,, -,,,,,,,,,,, -Instrument,Nominal_defocus,Minimal,,AppliedDefocus_min,TargetDefocus_min,Optics.Defocus,,_em_imaging.nominal_defocus_min,float,,EMD: Only one Defocus value. No min and max. No calibrated value. -Instrument,Nominal_defocus,Maximal,,AppliedDefocus_max,TargetDefocus_max,Optics.Defocus,,_em_imaging.nominal_defocus_max,float,,EMD: Only one Defocus value. No min and max. No calibrated value. -,,,,,,,,,,, -Instrument,Calibrated_defocus,Minimal,,MicroscopeImage.microscopeData.optics.Defocus_min,Defocus_min,Optics.Defocus,,_em_imaging.calibrated_defocus_min,float,,EMD: Only one Defocus value. No min and max. No calibrated value. -Instrument,Calibrated_defocus,Maximal,,MicroscopeImage.microscopeData.optics.Defocus_max,Defocus_max,Optics.Defocus,,_em_imaging.calibrated_defocus_max,float,,EMD: Only one Defocus value. No min and max. No calibrated value. -Instrument,Nominal_magnification,,,MicroscopeImage.microscopeData.optics.TemMagnification.NominalMagnification,Magnification,,,_em_imaging.nominal_magnification ,int,, -Instrument,Calibrated_magnification,,,,,,,_em_imaging.calibrated_magnification,int,, -Instrument,Holder,,,,,Stage.HolderType,,_em_imaging.specimen_holder_model,string,, -Instrument,Holder_cryogen,,,,,,,,string,, -,,,,,,,,,,, -Instrument,Temperature,Minimal,,,,CustomProperties.Detectors[x].Temperature,,_em_imaging.recording_temperature_minimum,float,,EMD: One Temperature value per Detector. No min and max. -Instrument,Temperature,Maximal,,,,CustomProperties.Detectors[x].Temperature,,_em_imaging.recording_temperature_maximum,float,,EMD: One Temperature value per Detector. No min and max. -Instrument,Alignment_procedure,,,,,,,_em_imaging.alignment_procedure ,string,, -Instrument,Software,,,MicroscopeImage.microscopeData.core.ApplicationSoftware,Software,Instrument.ControlSoftwareVersion,,_em_software.category ['IMAGE ACQUISITION'],string,, -Instrument,Detector,,,DetectorCommercialName,CameraUsed,"BinaryResult.Detector, BinaryResult.DetectorIndex, DetectorMetadata, Detectors","Acquisition_instrument.TEM.Detector, camera.detector_size",_em_image_recording.film_or_detector_model,string,,EMD: Potential overlap between Detector and DetectorMode. Multiple Detectors / PRZ: Acquisition_instrument.TEM.Detector does not always exist. If it doesnt then the only information about the Detector is the size. -Instrument,Detector_mode,,,,,"BinaryResult.Detector, BinaryResult.DetectorIndex, DetectorMetadata, Detectors",,_em_image_recording.detector_mode ,string,,EMD: Potential overlap between Detector and DetectorMode. Multiple Detectors -Instrument,Dose_per_image,,,DoseOnCamera_max,ExposureDose_max_max,,,_em_image_recording.avg_electron_dose_per_image,float,, -,,,,,,,,,,, -Instrument,Energy_filter,Used,,MicroscopeImage.microscopeData.optics.EnergyFilter.EnergySelectionSlitInserted,EnergyFilterUsed,EnergyFilter,,,boolean,, -Instrument,Energy_filter,Model,,,,,,_em_imaging_optics.energyfilter_name,string,, -Instrument,Energy_filter,Width,,MicroscopeImage.microscopeData.optics.EnergyFilter.EnergySelectionSlitWidth,EnergyFilterSlitWidth,,filter.energy_offset,_em_imaging_optics.energyfilter_slit_width,float,, -,,,,,,,,,,, -Instrument,Image_size,Height,,MicroscopeImage.microscopeData.acquisition.camera.ReadoutArea.height,ImageDimensions_Y,,image_size[0],,int,, -Instrument,Image_size,Width,,MicroscopeImage.microscopeData.acquisition.camera.ReadoutArea.width,ImageDimensions_X,,image_size[1],,int,, -Instrument,Datetime,,,MicroscopeImage.microscopeData.acquisition.acquisitionDateTime_start,DateTime_start,"Acquisition.AcquisitionStartDatetime, General",scan_generator.start_time,_em_imaging.date,string,, -Instrument,Exposure_time,,,MicroscopeImage.microscopeData.acquisition.camera.ExposureTime,ExposureTime,Detector-[x].ExposureTime,camera.exposure_time,_em_image_recording.average_exposure_time,float,, -,,,,,,,,,,, -Instrument,Tilt_angle,Minimal,,,TiltAngle_min_min,"Stage.AlphaTilt, Stage.BetaTilt",,_em_imaging.tilt_angle_min ,float,, -Instrument,Tilt_angle,Maximal,,,TiltAngle_max_max,,,_em_imaging.tilt_angle_max,float,, -Instrument,Tilt_angle,Increment,,,Tilt_increment_max,,,_em_imaging.tilt_angle_increment,float,, -Instrument,Cryogen,,,,,,,_em_imaging.cryogen,string,, -Instrument,Frames_per_movie,,,,NumSubFrames,,,_em_image_scans.frames_per_image,int,, -Instrument,Grids_imaged,,,,,,,_em_image_recording.num_grids_imaged,int,, -Instrument,Images_generated,,,NumberOfMovies,,,camera.simplon_parameters.nimages,_em_image_recording.num_real_images,int,, -Instrument,Binning,,,MicroscopeImage.microscopeData.acquisition.camera.Binning.x,Binning,,camera.binning,,float,, -Instrument,Pixel_size,,,MicroscopeImage.SpatialScale.pixelSize.x.numericValue,PixelSpacing,"BinaryResult.PixelSize, BinaryResult.PixelUnitX, BinaryResult.PixelUnitY",camera.pixel_size,,float,,"while there are map related pixelsizes - none of them refer to the original images, all to the reconstruction - see i.e. _em_3d_reconstruction.nominal_pixel_size" -Instrument,Specialist_Optics,,,,,,,,,, -,,,,,,,,,,, -Instrument,Specialist_Optics,Phaseplate,Used,PhasePlateUsed,,,,_em_imaging_optics.phase_plate,boolean,, -Instrument,Specialist_Optics,Phaseplate,Type,,,,,,string,, -,,,,,,,,,,, -Instrument,Specialist_Optics,Spherical_Aberration_Corrector,Used,,,,,_em_imaging_optics.sph_aberration_corrector,boolean,, -Instrument,Specialist_Optics,Spherical_Aberration_Corrector,Type,,,,,,string,, -,,,,,,,,,,, -Instrument,Specialist_Optics,Chromatic_Aberration_Corrector,Used,,,,,_em_imaging_optics.chr_aberration_corrector,boolean,, -Instrument,Specialist_Optics,Chromatic_Aberration_Corrector,Type,,,,,,string,, -,,,,,,,,,,, -Instrument,Beamshift,x,,MicroscopeImage.microscopeData.optics.BeamShift._x_max,Beamshift_x_max_max,,,,float,, -Instrument,Beamshift,y,,MicroscopeImage.microscopeData.optics.BeamShift._y_max,Beamshift_y_max_max,,,,float,, -,,,,,,,,,,, -Instrument,Beamtilt,x,,MicroscopeImage.microscopeData.optics.BeamTilt._x,TBI,,,,float,, -Instrument,Beamtilt,,,MicroscopeImage.microscopeData.optics.BeamTilt._y,TBI,,,,float,, -,,,,,,,,,,, -Instrument,Image_shift,x,,MicroscopeImage.microscopeData.optics.ImageShift._x,ImageShift_x_max_max,,,,float,, -Instrument,Image_shift,y,,MicroscopeImage.microscopeData.optics.ImageShift._y,ImageShift_y_max_max,,,,float,, -Instrument,Tilt_axis_angle,,,,TiltAxisAngle,,,,float,, -Instrument,Beamtiltgroups,,,,,,,,int,, -Instrument,GainRef_FlipRotate,,,,,,,,string,, -,,,,,,,,,,, -,,,,,,,,,string,https://schema.org/Grant, -Grant,Grant_ID,,,,,,,_pdbx_audit_support.grant_number ,string,https://schema.org/fundedItem, -Grant,Funding_agency,,,,,,,_pdbx_audit_support.funding_organization,string,https://schema.org/funder, -,,,,,,,,,,, -,,,,,,,,,string,http://purl.obolibrary.org/obo/NCIT_C42781, -Author,Name,,,,,,,,string,, -Author,FirstName,,,,,,,_pdbx_contact_author.name_first,string,https://schema.org/name, -Author,LastName,,,,,,,_pdbx_contact_author.name_last,string,https://schema.org/familyName, -Author,Email,,,,,,,_pdbx_contact_author.email,string,https://schema.org/email, -Author,Phone,,,,,,,_pdbx_contact_author.phone,string,http://semanticscience.org/resource/SIO_001324, -Author,ORCID,,,,,,,_pdbx_contact_author.identifier_ORCID,string,http://purl.obolibrary.org/obo/IAO_0000708, -Author,Role,,,,,,,_pdbx_contact_author.role,string,https://schema.org/jobTitle, -,,,,,,,,,,, -Author,Organization,Name_org,,,,,,,string,, -Author,Organization,Type_org,,,,,,_pdbx_contact_author.organization_type,string,, -Author,Organization,Country,,,,,,_pdbx_contact_author.country,string,https://schema.org/Country, -,,,,,,,,,,, -,,,,,,,,,,, -,,,,,,,,,,, -Sample,Overall_Molecule,Type,,,,,,_entity.type ,string,, -Sample,Overall_Molecule,Name,,,,,,_em_entity_assembly.name,string,, -Sample,Overall_Molecule,Source,,,,,,_entity.src_method,string,, -Sample,Overall_Molecule,Molecular_weight,,,,,,_entity.formula_weight,float,, -,,,,,,,,,,, -Sample,Molecules,Name,,,,,,_pdbx_entity_branch_descriptor.descriptor,string,,maybe better this? _pdbx_entity_branch_descriptor.type -Sample,Molecules,Type,,,,,,_entity_poly.type,string,, -Sample,Molecules,Class,,,,,,_em_entity_assembly.type,string,, -Sample,Molecules,Sequence,,,,,,_entity_poly.pdbx_seq_one_letter_code,string,, -Sample,Molecules,Natural_source,,,,,,_em_entity_assembly_naturalsource.organism,string,, -Sample,Molecules,Taxonomy_ID_source,,,,,,_em_entity_assembly_naturalsource.ncbi_tax_id ,string,, -Sample,Molecules,Expression_system,,,,,,_em_entity_assembly_recombinant.organism,string,,might also use this _entity_src_gen.pdbx_host_org_scientific_name -Sample,Molecules,Taxonomy_ID_expression,,,,,,_em_entity_assembly_recombinant.ncbi_tax_id,string,,might also use this : _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id -Sample,Molecules,Gene_name,,,,,,_entity_src_gen.pdbx_gene_src_gene,string,, -,,,,,,,,,,, -Sample,Ligands,present,,,,,,_pdbx_entry_details.has_ligand_of_interest,boolean,, -Sample,Ligands,SMILE,,,,,,_pdbx_chem_comp_depositor_info.descriptor,string,, -Sample,Ligands,Reference,,,,,,,string,,I know the onedep system knows this but cant find the pdbx entry -,,,,,,,,,,, -Sample,Specimen,Buffer,,,,,,_em_buffer.details,string,, -Sample,Specimen,Concentration,,,,,,_em_specimen.concentration,float,, -Sample,Specimen,pH,,,,,,_em_buffer.pH,float,, -Sample,Specimen,Vitrification,,,,,,_em_specimen.vitrification_applied,boolean,, -Sample,Specimen,Vitrification_cryogen,,,,,,_em_vitrification.cryogen_name,string,, -Sample,Specimen,Humidity,,,,,,_em_vitrification.humidity ,float,, -Sample,Specimen,Temperature,,,,,,_em_vitrification.chamber_temperature,float,, -Sample,Specimen,Staining,,,,,,_em_specimen.staining_applied,boolean,, -Sample,Specimen,Embedding,,,,,,_em_specimen.embedding_applied ,boolean,, -Sample,Specimen,Shadowing,,,,,,_em_specimen.shadowing_applied,boolean,, -,,,,,,,,,,, -Sample,Grid,Manufacturer,,,,,,_em_sample_support.grid_type,string,, -Sample,Grid,Material,,,,,,_em_sample_support.grid_material,string,, -Sample,Grid,Mesh,,,,,,_em_sample_support.grid_mesh_size,int,, -Sample,Grid,Film_support,,,,,,,boolean,, -Sample,Grid,Film_material,,,,,,_em_support_film.material,string,, -Sample,Grid,Film_topology,,,,,,_em_support_film.topology ,string,, -Sample,Grid,Film_thickness,,,,,,_em_support_film.thickness ,string,, -Sample,Grid,Pretreatment_type,,,,,,_em_grid_pretreatment.type,string,, -Sample,Grid,Pretreatment_time,,,,,,_em_grid_pretreatment.time,float,, -Sample,Grid,Pretreatment_pressure,,,,,,_em_grid_pretreatment.pressure,float,, -Sample,Grid,Pretreatment_atmosphere,,,,,,_em_grid_pretreatment.atmosphere ,string,, -,,,,,,,,,,, -,,,,,,,,,,, -Sample_Wild,CollectionLocation,,,,,,,,string,, -Sample_Wild,CollectionDetails,,,,,,,,string,, -Sample_Wild,SamplePreparation,,,,,,,,string,,