TODO: * crossreferences (emdb and pdb entries) * electronCrystallographyValidation * do we want to include a keyword field? * modelling * segmentation Enumerations Enumerations are generally capitalized Exceptions include 1) Units 2) Important enumerations that are kept the same as in 1.9 for compatibility 3) Names etc that need a particular case _emd_admin Contains administrative details about the entry. At least one assembly or a component must be described. This map represent the final reconstructions. This can be the result of several imageProcessing techniques, with different symmetries. Therefore, the final map should be considered as a composite of maps. For example: EMD-1001 The XML schema version that validates the header file. This attribute should contain a default value: the current schema version. for pdbx categories with "PDB" in name, we should request duplicate categories with "EMDB" substituted _pdbx_version _pdbx_database_status Copy of the last status element in the status_history_list. _database_PDB_rev is used in coordinate files _audit is equivalent content, currently used for PDB SF files Should we have lastUpdate? Should we have headerReleaseDate? This date refers to when map, structure factors, layerlines, images, FSCs and all other related files are released publicly. This date should correspond to a Wednesday according to the current release cycle. This list contains old entries that have been replaced because of this newer entry. _pdbx_database_PDB_obs_spr List of old entries _pdbx_database_PDB_obs_spr If this element appears means that the current entry is obsoleted. The newer entry which replaces this entry is listed here. List of new entries. new pdbx category to be created for this, will link grant#/funding body with _pdbx_audit_author _pdbx_contact_author with role "responsible scientist" Private information. Do not expose to the public. It can be the same as principalInvestigator. _struct.title (type=text) Should it be string or normalizedString? _pdbx_audit_author -- atomization of address category desired, at least country. PubMed format: Taylor TJ 'author' element includes principalInvestigator and correspodingScientitst (if different from principalInvestigator). Deprecated (2014-10-21) Deprecated (2014-10-21) Deprecated (2015-11-18) _emd_admin.last_update _emd_admin.current_status These are PDB standard statuses (in order of common progression): * Not yet released PROC: to be processed WAIT: processing started, waiting for author input to continue processing AUTH: processed, waiting for author review and approval REPL: author sent new coordinates, entry to be reprocessed REFI: re-refined entry, processing pending availability of primary publication POLC: waiting for a wwPDB policy decision HPUB: processing complete, entry on hold until publication HOLD: processing complete, entry on hold until a certain date * REL: present in current archive * WDRN: never publicly released * OBS: no longer in the archive HOLD1 and HOLD2 should be converted to HOLD What format? Initials? Full names? Comments are meaningful only to track changes in released entries. Example: "Change in pixel size from: 1.3 to 2.5 angs." British would specify county here _citation _citation_author Some policy decision has to be agreed about who and in what circunstances this section can be included/modified. Example 1: Author 1 solves Component A -> submit structure Author 2 solves Component B -> submit structure related to Component A, but author 1 entry is not modified. Can author 1 (after submission) request the addition of this new relationship? That can add a lot of work for annotators. Example 2: Author 1 solves a ribosome structure. Can he link to all the tomographms that include ribosomes? Do these 'related PDB structures' refer to the initial PDB model? If we want to include a transformation matrices for rigid-body fitted models, then this section only applies to flexible fitted models or de-novo built. I think we should include Ingvar in this discussion. Links can be specified to other databases holding related image data. For example a link to a database with the raw 2D images used in the map reconstruction. You may also specify links to databases holding image data at the lightmicroscopy scale that is related to this experiment. EMDB entries related to this entry Add docked? List of related EMDB entries Maybe it can be combined with pdbReference into one datatype. PDB entries related to this entry. The chainID list can be used to specify which specific chains are related to this map. Add docked? List of related PDB entries 'id' attribute: Autogenerated unique identifier that it used internally to cross reference this external cross reference! We are assuming one method per map - is that OK? This should be an element of the spceimen preparation. However, we only want one instance of it, and the specimenPreparation is a list. _emd_specimen.macromolecules_and_complexes ADDED If this is not specified then it is assumed that the processing applies to all components. More than one imageProcessing element can be specified. This is useful when more that one symmetry was used to obtain final map. imageProcessing is an abstract element forming a substitution group. It must be substituted by a derived element. Enforcement of which substitutions are valid for which method will be done in Schematron: Substitution Method =============================================================== singleparticleProcessing singleparticle maximumliklihoodProcessing singleparticle subtomogramAveragingProcessing subtomogramAveraging tomographyProcessing tomography electronCrystallographyProcessing electronCrystallography ihrsrHelicalProcessing helicalReconstruction layerlinesHelicalProcessing helicalReconstruction Unique identifier that will allow the DA system to be refactored in terms of experiments rather than maps. Can be autogenerated unless user wants to specify a previously existing one. General term describing the sample. For example: Human papillomavirus Coarse grained representation of sample described in form of GO terms. This approach give great flexibility, allowing depositors to describe the sample at very different levels of complexity. This is useful for tomography, when depositors don't want to fully describe the map at fine detail. There are links between components and assemblies and viceversa. Problem: there is not direct mapping between the assembly and the corresponding region of the map. This can be achieved using the segmentation mechanism. Fine grained description of the sample. TODO: what should format should this field has? EMDB? TODO:format Unnecessary? -> could go into details. Provide company + model of the grids _emd_specimen_grid.material _emd_specimen_grid.mesh This is the number of squares in the grid. This can be autogenerated from the gridType Additional layers of carbon can also be specified here. How do we enforce directionality? Is it really meaningful to ask for time/pressure? _emd_specimen_grid.details _emd_specimen.grid_details _emd_structure_determination_microscopy.optics_energyfilter_name _emd_structure_determination_microscopy.optics_energyfilter_lower _emd_structure_determination_microscopy.optics_energyfilter_upper _emd_buffer.ph _emd_buffer_component category ADDED _emd_buffer_component.concentration ADDED _emd_buffer_component.concentration_units _emd_buffer_component.formula ADDED _emd_buffer_component.name ADDED _emd_buffer.details _emd_specimen_vitrification.cryogen_name _emd_specimen_vitrification.chamber_humidity _emd_specimen_vitrification.chamber_temperature _emd_specimen_vitrification.instrument _emd_specimen_vitrification.details Deprecated (2014-10-21) Deprecated (2014/11/13) _emd_specimen.concentration _emd_buffer category ADDED _emd_specimen.staining ADDED _emd_specimen.staining_type ADDED _emd_specimen.staining_material ADDED Add controlled vocabulary _emd_specimen.staining_details _emd_specimen.sugar_embedding ADDED _emd_specimen.sugar_embedding.material ADDED Add controlled vocabulary _emd_specimen.sugar_embedding.details ADDED _emd_shadowing ADDED as a category in dict _emd_shadowing.material ADDED Add controlled vocabulary _emd_shadowing.angle ADDED _emd_shadowing.thickness ADDED Check units and range. _emd_shadowing.details ADDED _emd_specimen_grid ## EMD_SPECIMEN_GRID ## _emd_specimen_vitrification ## EMD_SPECIMEN_VITRIFICATION ## _emd_specimen.details example: 'This sample was monodisperse.' 1775 'Au was deposited at a 30 degree angle to 15 nm thickness.' 1776 'Colloidal gold particles were deposited by dipping into dilute solution.' 1777 'The specimen was frozen at high pressure using the bal-tec hpm 010 instrument.' 1778 'The embedded sample was sectioned at 100 K to 50 nm final thickness.' Unique identifier. Autogenerated TODO: add limits and units. Add freeze fracture Add controlled vocabulary Add controlled vocabulary Add controlled vocabulary? TODO: add limits and units. _emd_specimen Should we include at this level helical and crystal parameters? For a given EM method the relevant derived specimenPreparation substitution element may be specified. Checking will be enforced via Schematron. For tomography only 1 microscopy element should be specified. Rules: Method Preparation element singleparticle none - specimenPreparation electronCrystallography none - specimenPreparation helicalReconstruction none - specimenPreparation tomography tomographyPreparation, max occurs = 1 subtomogramAveraging tomographyPreparation Substitution when method is tomography or subtomogramAveraging. For tomography, maxoccurs = 1. Substitution when method is tomography or subtomogramAveraging. For tomography, maxoccurs = 1. Specimen preparation techniques used on this scope. Microsocpe model Do we want to support 'spotscan'? _emd_structure_determination_microscopy.illumination_mode _emd_structure_determination_microscopy.imaging_mode in emd-DA.dic but not here: DARK FIELD DIFFRACTION _emd_structure_determination_microscopy.electron_source _emd_structure_determination_microscopy.acceleration_voltage _emd_structure_determination_microscopy.nominal_cs Positive values: underfocus Negative values: overfocus _emd_structure_determination_microscopy.nominal_defocus_min Positive values: underfocus Negative values: overfocus _emd_structure_determination_microscopy.calibrated_defocus_min Positive values: underfocus Negative values: overfocus _emd_structure_determination_microscopy.nominal_defocus_max Positive values: underfocus Negative values: overfocus _emd_structure_determination_microscopy.calibrated_defocus_max _emd_structure_determination_microscopy.nominal_magnification From a biological perspective, it it really meaningful to ask for this? As measured on image. Should take into account post-column magnification. _emd_structure_determination_microscopy.calibrated_magnification _emd_structure_determination_microscopy.specimen_holder_model in emd-DA.dic but not here: FEI TITAN KRIOS AUTOGRID HOLDER _emd_structure_determination_microscopy.cooling_holder_cryogen Temperature at which the microscope is maintained Modify!!! Average temperature that the specimen is maintained in the microscope. _emd_structure_determination_microscopy.average_temperature Modify !!! Average temperature that the specimen is maintained in the microscope. _emd_structure_determination_microscopy.average_temperature Average temperature that the specimen is maintained in the microscope. _emd_structure_determination_microscopy.average_temperature TODO: add allowed range and units Only for backward compatibility with v1.9.6. Should not be used with any new entries _emd_structure_determination_microscopy.details Deprecated (2014-10-21) We should add _em_imaging.detector_distance (in crystallographyMicroscopy) TODO: add controlled vocabulary Can be derived from detectorModel so is this meaningful? Sometimes multiple frames are added up to one image Tomography: electron dose per image. Crystallography: the dose per real/diffraction image. Deprecated (2014-10-21) Deprecated (2014-10-21) Deprecated (2014/11/12) Deprecated (2014/11/14) SHOULD NOT BE USED FOR TOMOGRAPHY - only for compatibility purposes with v1.9!! Use tomography microscopy instead. Angle is assumed in degrees Deprecated (2014/11/14) SHOULD NOT BE USED FOR TOMOGRAPHY - only for compatibility purposes with v1.9!! Use tomography microscopy instead. Angle is assumed in degrees Auto generated by application Multiple series are only relevant for subtomogram averages _emd_structure_determination_microscopy.tomography_axis1_min_angle _emd_structure_determination_microscopy.tomography_axis1_max_angle _emd_structure_determination_microscopy.tomography_axis1_angle_increment Rotation of axis relative to axis1 Differences between axis1 and axis2 in degrees. _emd_structure_determination_microscopy.crystallography_camera_length _emd_structure_determination_microscopy.crystallography_tilt_angle_list Multiple series are only relevant for subtomogram averages Does this correspond to microscope or microscopy?? For a given EM method the relevant derived microscopy substitution element may be specified. Checking will be enforced via Schematron. For tomography only 1 microscopy element should be specified. Rules: Method Substition element ========================================================== singleparticle none - use microscopy electronCrystallography crystallographyMicroscopy helicalReconstruction none - use microscopy tomography tomographyMicroscopy, max occurs = 1 subtomogramAveraging tomographyMicroscopy Derived microscopy type used for tomography and sub-tomogram averaging Derived microscopy type used for electron crystallography Images may have been recorded on different detectors Number of 2D images used in making the 3D reconstruction Only one symmetry element per processing type. Use additional processing type elements, and specify the sample components for each if more that one symmetry has been applied. Add facet: FAT... Contour, mask dilation filtering. _emd_specimen_grid.support_film_material enumeration: CARBON 'FORMVAR PLUS CARBON' 'CELLULOSE ACETATE PLUS CARBON' 'PARLODION PLUS CARBON' 'HOLEY CARBON' Lacy: Net of holes, with minimum support film between the holes. Holey: Irregularly spaced holes of varying sizes Hole array: Regularly spaced holes of constant sizes Find in paper the standard way to encode it. Assignment of Euler angles by matching to closest reference projection Angular distance between neighboring reference projections in degrees Allow portions of PDBs Number of copies in map. Should it be part of 'interpretation' section? Allow portions of PDBs It should be a controlled vocabulary: * Rigid body docking (manual or automatic) * Flexible fitting * Rigid body docking + flexible fitting Necessary? Necessary? Necessary? Final round of alignment Angular distance between neighboring reference projections in degrees Example of more that one starting model: one model used for particle picking and another used for Euler angle assignment. TODO: what should format should this field has? EMDB? TODO:format Final round of alignment Example of more that one starting model: one model used for particle picking and another used for Euler angle assignment. Phasing? Allow porions of PDBs Carsten Sachse suggested to add number of ASU. Example of more that one starting model: one model used for particle picking and another used for Euler angle assignment. Example of more that one starting model: one model used for particle picking and another used for Euler angle assignment. Add support for helical It could be combined with point symmetry if we adopt Heymman et al. The pdb model may have been built up from several actual PDB models. Only one symmetry element per processing type. Use additional processing type elements, and specify the sample components for each if more that one symmetry has been applied. Optional for tomography Optional for tomography. Optional for tomography. Deprecated (2014-10-21) Depending on the problem, one can either reference the sample on the macromolecule level or the complex level. _emd_specimen.macromolecule_id_list _emd_specimen.complex_id_list ADDED Deprecated (2014-10-21) Same content as 'name' Same content as 'name' element Same content as 'name' Same content as 'name' element Same content as 'name' Same content as 'name' For example: HeLa For example: Mitochondrion Expression system (or host system if virus) Deprecated (2014/11/14) Does not make any sense for cellular component Present for legacy compatibility with 1.9 This item is currently optional, but I propose to make it mandatory. This item is currently optional, but I propose to make it mandatory. Deprecated (2014/11/17) Placeholder for corresponding element in v1.9 Deprecated (2014/11/17) Placeholder for corresponding element in v1.9 Deprecated (2014/11/17) Placeholder for corresponding element in v1.9 Deprecated (2014/11/17) Placeholder for corresponding element in v1.9 Expression system (or host system if virus) Deprecated (2014/11/17) Added only to transfer eukaryotic (eukaryotic-ribosomes) and prokaryotic (prokaryotic-robosomes) from v1.9 Take this name from Gene Ontology. Should more than one category allowed? All the GO terms should be descendant of 'cellular_component' http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0005575 Currently we only support Gene Ontology. 'sample' supramolecule has value 0 Links to the sample macromolecule list Number of copies within parent Oligomeric state in parent, or if sample, the oligomeric state of sample UniProtKB, UniParc, interPro Deprecated 2014/12/3 Take this name from Gene Ontology. More than one category is allowed. All the GO terms should be descendant of 'cellular_component' http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0005575 Should be ICTV number be allowed for virus? Currently we only support Gene Ontology. Root complex is 0 Links to the sample macromolecule list Expression system (or host system if virus) Allowed values: 1 kDa - 10^9 MDa kDa/nm is for helices. This item is currently optional, but I propose to make it mandatory. This item is currently optional, but I propose to make it mandatory. Link to assembly or component id. Deprecated (2014-10-21) Deprecated (2014-10-21) It is true, if the current status is 'OBS' and the entry has been replaced by newer entries. This is true if the current status is 'REL' and there are older entries that have been made obsoleted because of this one. URL link to publicly available database of light microscopy images. Unique set of macromolecular chain(s) We need to have a base type and specific types for each componenetType: protein (ask uniprot id, EC, interPro, etc...), DNA sequence, etc.. Unique set of macromolecular chain(s) We need to have a base type and specific types for each componenetType: protein (ask uniprot id, EC, interPro, etc...), DNA sequence, etc.. Thesis/dissertations included Deprecated (2014-10-21) Example: London This should be substitution group so each external reference type has a proper format: example doi -> doi format; pubmed -> pubmed format, etc... PubMed abbreviation format This should be substitution group so each external reference type has a proper format: example doi -> doi format; pubmed -> pubmed format, etc... Range not suitable for electronDiffraction. TODO: add limits and units. _emd_specimen.crystal_formation_details Rosenthal PB and Henderson R, Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy, J. Mol. Biol. 333 (2003), 721–745 http://dx.doi.org/10.1016/j.jmb.2003.07.013 Mandatory for all component. For synthetic components like 'EM labels' is 'synthetic construct' Taxonomy ID: 32630 For example: HeLa Deprecated (2014-10-21) Mandatory for all component. For synthetic components like 'EM labels' is 'synthetic construct' Taxonomy ID: 32630 Deprecated (2014-10-21) For example: Epithelium For example: HeLa For example: Mitochondrion For example: Mitochondrion intermembrane space Allow portions of PDBs Number of copies in map. Should it be part of 'interpretation' section? Deprecated (2014/11/12) kDa/nm is for helices. kDa/nm is for helices. Allowed values: 1 Da - 5 MDa Deprecated 2014/12/3 Autogenerated unique identifier. Format: A1C UniProtKB, UniParc, interPro Enzyme classification. Format: "EC 3.4.11.4" Is naturalExpression and recombinantExpression suitable for this component? Format: A1C RefSeq, genbank Deprecated 2014/11/29 Only added for transfer of 1.9 Deprecated 2014/11/29 Added only for transfer of 1.9 data Is naturalExpression and recombinantExpression suitable for this component? What would be a proper format? Format: A1C RefSeq, Genbank should have their own validation Deprecated 2014/11/29 Only added for transfer of 1.9 Deprecated 2014/11/29 Added only for transfer of 1.9 data Is naturalExpression and recombinantExpression suitable for this component? CardBank Is naturalExpression and recombinantExpression suitable for this component? LMSD (Lipidomics database) Is naturalExpression and recombinantExpression suitable for this component? CAS, PubChem, DrugBank, ChEBI, ChEMBL Controlled vocabulary? Number of 2D images used in making the 3D reconstruction Only one symmetry element per processing type. Use additional processing type elements, and specify the sample components for each if more that one symmetry has been applied. Contour, mask dilation filtering. Use to cater for cyclic-pseudo-peptide, other, peptide nucleic acid and polydeoxyribonucleotide/polyribonucleotide hybrid categories. Most items are optional and there is no checking done Format: A1C RefSeq, genbank For now: cyclic-pseudo-peptide, other, peptide nucleic acid and polydeoxyribonucleotide/polyribonucleotide hybrid categories Deprecated 2015/11/16 Only added for transfer of 1.9 Deprecated 2015/11/16 Added only for transfer of 1.9 data vertical horizontal Length used to sample the reciprocal lattice lines in the c-direction. 180 >= gamma >= 90 17 groups datatype: fraction datatype: fraction Final number of classes used Average number of members (images, 3D volumes or subtomograms) per class in the final set of class averages