oscem-converter-extracted/csv/pdb_conversions.csv at main · osc-em/oscem-converter-extracted · GitHub

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OSCEM,in PDBx/mmCIF,Ontology suggestions
,,
instrument.microscope.model,_em_imaging.microscope_model,
instrument.microscope.manufacturer,,
instrument.illumination,_em_imaging.illumination_mode,
instrument.imaging,_em_imaging.mode,
instrument.electron_source,_em_imaging.electron_source,https://purls.helmholtz-metadaten.de/emg/EMG_00000045
instrument.acceleration_voltage,_em_imaging.accelerating_voltage,https://purls.helmholtz-metadaten.de/emg/EMG_00000004
instrument.c2_aperture,_em_imaging.c2_aperture_diameter,
instrument.cs,_em_imaging.nominal_cs,
instrument.beam_convergence,,
instrument.operating_mode,,
,,
acquisition.nominal_defocus.minimal,_em_imaging.nominal_defocus_max,
acquisition.nominal_defocus.maximal,_em_imaging.nominal_defocus_min,
,,
acquisition.calibrated_defocus.minimal,_em_imaging.calibrated_defocus_max,
acquisition.calibrated_defocus.maximal,_em_imaging.calibrated_defocus_min,
acquisition.nominal_magnification,_em_imaging.nominal_magnification,
acquisition.calibrated_magnification,_em_imaging.calibrated_magnification,
acquisition.holder,_em_imaging.specimen_holder_model,
acquisition.holder_cryogen,,
,,
acquisition.temperature.minimal,_em_imaging.recording_temperature_minimum,
acquisition.temperature.maximal,_em_imaging.recording_temperature_maximum,
acquisition.alignment_procedure,_em_imaging.alignment_procedure,
acquisition.microscope_software,_em_software.name,
acquisition.detectors[N].name,_em_image_recording.film_or_detector_model,
acquisition.detectors[N].mode,_em_image_recording.detector_mode,
acquisition.detectors[N].dispersion,,
acquisition.detectors[N].collection_angle.minimal,,
acquisition.detectors[N].collection_angle.maximal,,
acquisition.dose_per_movie,_em_image_recording.avg_electron_dose_per_image,
,,
acquisition.energy_filter.used,,
acquisition.energy_filter.model,_em_imaging_optics.energyfilter_name,
acquisition.energy_filter.width_energy_filter,_em_imaging_optics.energyfilter_slit_width,
,,
acquisition.image_size.height,_em_image_scans.dimension_height,
acquisition.image_size.width,_em_image_scans.dimension_width,
acquisition.date_time,_em_imaging.date,
acquisition.exposure_time,_em_image_recording.average_exposure_time,
acquisition.screen_current,,
,,
acquisition.tilt_angle.minimal,_em_imaging.tilt_angle_min,
acquisition.tilt_angle.maximal,_em_imaging.tilt_angle_max,
acquisition.tilt_angle.increment,_em_imaging.tilt_angle_increment,
acquisition.cryogen,_em_imaging.cryogen,
acquisition.frames_per_movie,_em_image_scans.frames_per_image,
acquisition.grids_imaged,_em_image_recording.num_grids_imaged,
acquisition.images_generated,_em_image_recording.num_real_images,
acquisition.binning_camera.height,,
acquisition.binning_camera.width,,
acquisition.pixel_size,,
,,
acquisition.specialist_optics.phaseplate.used,,
acquisition.specialist_optics.phaseplate.instrument_type,_em_imaging_optics.phase_plate,
,,
acquisition.specialist_optics.spherical_aberration_corrector.used,,
acquisition.specialist_optics.spherical_aberration_corrector.instrument_type,_em_imaging_optics.sph_aberration_corrector,
,,
acquisition.specialist_optics.chromatic_aberration_corrector.used,,
acquisition.specialist_optics.chromatic_aberration_corrector.instrument_type,_em_imaging_optics.chr_aberration_corrector,
,,
acquisition.beamshift.x_max,,
acquisition.beamshift.x_min,,
acquisition.beamshift.y_max,,
acquisition.beamshift.y_min,,
,,
acquisition.beamtilt.x_max,,
acquisition.beamtilt.y_max,,
,,
acquisition.imageshift.x_max,,
acquisition.imageshift.x_min,,
acquisition.imageshift.y_max,,
acquisition.imageshift.y_min,,
acquisition.tilt_axis_angle,,
acquisition.beamtiltgroups,,
acquisition.gainref_flip_rotate,,
,,
,,https://schema.org/Grant
organizational.grants.project_id,_pdbx_audit_support.grant_number,https://schema.org/fundedItem
organizational.funder.funder_name,_pdbx_audit_support.funding_organization,https://schema.org/funder
organizational.grants.grant_name,,
organizational.grants.country,_pdbx_audit_support.country,
organizational.authors.given_name,_pdbx_contact_author.name_first,
organizational.authors.family_name,_pdbx_contact_author.name_last,
organizational.authors.email,_pdbx_contact_author.email,https://schema.org/email
organizational.authors.telephone,_pdbx_contact_author.phone,http://semanticscience.org/resource/SIO_001324
organizational.authors.orcid,_pdbx_contact_author.identifier_ORCID,http://purl.obolibrary.org/obo/IAO_0000708
organizational.authors.job_title,_pdbx_contact_author.role,https://schema.org/jobTitle
organizational.authors.country,_pdbx_contact_author.country,https://schema.org/Country
organizational.authors.work_status,,
,,
organizational.authors.name_org,,
organizational.authors.type_org,_pdbx_contact_author.organization_type,
organizational.funder.type_org,,
organizational.funder.country,,
,,
sample.name,,
sample.description,,
,,
sample.overall_molecule.molecular_type,_em_entity_assembly.type,
sample.overall_molecule.name_sample,_em_entity_assembly.name,
sample.overall_molecule.source,_entity.src_method,
sample.overall_molecule.molecular_weight,_entity.formula_weight,
sample.overall_molecule.assembly,_em_experiment.aggregation_state,
,,
sample.molecule.name_mol,_pdbx_entity_branch_descriptor.descriptor,
sample.molecule.molecular_type,_entity_poly.type,
sample.molecule.molecular_class,,
sample.molecule.sequence,_entity_poly.pdbx_seq_one_letter_code,
sample.molecule.natural_source,_em_entity_assembly_naturalsource.organism,
sample.molecule.taxonomy_id_source,_em_entity_assembly_naturalsource.ncbi_tax_id,
sample.molecule.expression_system,_em_entity_assembly_recombinant.organism,
sample.molecule.taxonomy_id_expression,_em_entity_assembly_recombinant.ncbi_tax_id,
sample.molecule.gene_name,_entity_src_gen.pdbx_gene_src_gene,
,,
sample.ligands.present,_pdbx_entry_details.has_ligand_of_interest,
sample.ligands.smiles,_pdbx_chem_comp_depositor_info.descriptor,
sample.ligands.reference,,
,,
sample.specimen.buffer,_em_buffer.details,
sample.specimen.concentration,_em_specimen.concentration,
sample.specimen.ph,_em_buffer.pH,
sample.specimen.vitrification,_em_specimen.vitrification_applied,
sample.specimen.vitrification_cryogen,_em_vitrification.cryogen_name,
sample.specimen.humidity,_em_vitrification.humidity,
sample.specimen.temperature,_em_vitrification.chamber_temperature,
sample.specimen.staining,_em_specimen.staining_applied,
sample.specimen.embedding,_em_specimen.embedding_applied,
sample.specimen.shadowing,_em_specimen.shadowing_applied,
,,
sample.grid.manufacturer,_em_sample_support.grid_type,
sample.grid.material,_em_sample_support.grid_material,
sample.grid.mesh,_em_sample_support.grid_mesh_size,
sample.grid.film_support,,
sample.grid.film_material,_em_support_film.material,
sample.grid.film_topology,_em_support_film.topology,
sample.grid.film_thickness,_em_support_film.thickness,
sample.grid.pretreatment_type,_em_grid_pretreatment.type,
sample.grid.pretreatment_time,_em_grid_pretreatment.time,
sample.grid.pretreatment_pressure,_em_grid_pretreatment.pressure,
sample.grid.pretreatment_atmosphere,_em_grid_pretreatment.atmosphere,
processing.movies.dose_per_image,_em_image_recording.avg_electron_dose_per_image
processing.micrographs.number_micrographs,_em_image_recording.num_real_images
processing.volumes.vol_resolution,_em_3d_reconstruction.resolution