National Microbiome Data Collaborative Schema Documentation
The NMDC Schema is a foundational framework designed to standardize metadata for the National Microbiome Data Collaborative (NMDC) and collaborating data providors. By establishing a structured approach to metadata, the NMDC Schema enables researchers to organize, share, and interpret complex datasets with consistency and clarity. The NMDC Schema is critical substrate used to facilitate interoperability and collaboration, as it provide a common language for data exchange across systems and disciplines. In the context of the NMDC, this schema supports the integration of microbiome data from medicine, agriculture, bioenergy, and environmental science into a cohesive platform.
This schema is organized into two modules:
-
A core set of elements for representing data values represented in LinkML format (https://w3id.org/linkml/) consisting of a set classes, slots, types, and enumerations that are used to define the structure of the NMDC schema.
-
A subset of the MIxS schema developed by the Genomic Standards Consortium, that is used to describe the environmental context of samples.
URI: https://w3id.org/nmdc/nmdc
Classes
| Class | Description |
|---|---|
| AttributeValue | The value for any value of a attribute for a sample |
| ControlledTermValue | A controlled term or class from an ontology |
| ControlledIdentifiedTermValue | A controlled term or class from an ontology, requiring the presence of term w... |
| GeolocationValue | A normalized value for a location on the earth's surface |
| ImageValue | An attribute value representing an image |
| PersonValue | An attribute value representing a person |
| QuantityValue | A simple quantity, e |
| TextValue | A basic string value |
| TimestampValue | A value that is a timestamp |
| CreditAssociation | This class supports binding associated researchers to studies |
| Database | An abstract holder for any set of metadata and data |
| Doi | A centrally registered identifier symbol used to uniquely identify objects gi... |
| EukEval | This class contains information pertaining to evaluating if a Metagenome-Asse... |
| FailureCategorization | |
| FunctionalAnnotation | An assignment of a function term (e |
| FunctionalAnnotationAggMember | |
| GenomeFeature | A feature localized to an interval along a genome |
| MagBin | |
| MetaboliteIdentification | This is used to link a metabolomics analysis workflow to a specific metabolit... |
| MobilePhaseSegment | A fluid mixture of substances that flow though a chromatographic stationary p... |
| NamedThing | a databased entity or concept/class |
| GeneProduct | A molecule encoded by a gene that has an evolved function |
| InformationObject | Any data or knowledge that reduces uncertainty or enhances understanding abou... |
| CalibrationInformation | A calibration object that is associated with a process |
| Configuration | A set of parameters that define the actions of a process and is shared among ... |
| ChromatographyConfiguration | A set of parameters that define and control the actions of a chromatography p... |
| MassSpectrometryConfiguration | A set of parameters that define and control the actions of a mass spectrometr... |
| DataObject | An object that primarily consists of symbols that represent information |
| Manifest | A qualified collection of DataObjects that can be analyzed together in the sa... |
| MaterialEntity | |
| Instrument | A material entity that is designed to perform a function in a scientific inve... |
| Sample | A sample is a material entity that can be characterized by an experiment |
| Biosample | Biological source material which can be characterized by an experiment |
| ProcessedSample | |
| Site | |
| FieldResearchSite | A site, outside of a laboratory, from which biosamples may be collected |
| OntologyClass | A representation of class defined in an external ontology |
| ChemicalEntity | An atom or molecule that can be represented with a chemical formula |
| EnvironmentalMaterialTerm | |
| FunctionalAnnotationTerm | Abstract grouping class for any term/descriptor that can be applied to a func... |
| OrthologyGroup | A set of genes or gene products in which all members are orthologous |
| Pathway | A pathway is a sequence of steps/reactions carried out by an organism or comm... |
| PlannedProcess | |
| CollectingBiosamplesFromSite | |
| DataGeneration | The methods and processes used to generate omics data from a biosample or org... |
| MassSpectrometry | Spectrometry where the sample is converted into gaseous ions which are charac... |
| NucleotideSequencing | A DataGeneration in which the sequence of DNA or RNA molecules is generated |
| MaterialProcessing | A process that takes one or more samples as inputs and generates one or more ... |
| ChemicalConversionProcess | A process that results in the interconversion of chemical species by a reacti... |
| ChromatographicSeparationProcess | The process of using a selective partitioning of the analyte or interferent b... |
| DissolvingProcess | A mixing step where a soluble component is mixed with a liquid component |
| Extraction | A material separation in which a desired component of an input material is se... |
| FiltrationProcess | The process of segregation of phases; e |
| LibraryPreparation | |
| MixingProcess | The combining of components, particles or layers into a more homogeneous stat... |
| Pooling | physical combination of several instances of like material |
| SubSamplingProcess | Separating a sample aliquot from the starting material for downstream activit... |
| ProtocolExecution | A PlannedProces that has PlannedProcess parts |
| StorageProcess | A planned process with the objective to preserve and protect material entitie... |
| WorkflowExecution | Represents an instance of an execution of a particular workflow |
| MagsAnalysis | A workflow execution activity that uses computational binning tools to group ... |
| MetabolomicsAnalysis | |
| MetagenomeAnnotation | A workflow execution activity that provides functional and structural annotat... |
| MetagenomeAssembly | A workflow execution activity that converts sequencing reads into an assemble... |
| MetagenomeSequencing | Initial sequencing activity that precedes any analysis |
| MetaproteomicsAnalysis | |
| MetatranscriptomeAnnotation | |
| MetatranscriptomeAssembly | |
| MetatranscriptomeExpressionAnalysis | A workflow process that provides expression values and read counts for gene f... |
| NomAnalysis | |
| ReadBasedTaxonomyAnalysis | A workflow execution activity that performs taxonomy classification using seq... |
| ReadQcAnalysis | A workflow execution activity that performs quality control on raw Illumina r... |
| Study | A study summarizes the overall goal of a research initiative and outlines the... |
| OntologyRelation | A relationship between two ontology classes as specified either directly in t... |
| PeptideQuantification | This is used to link a metaproteomics analysis workflow to a specific peptide... |
| PortionOfSubstance | A portion of any matter of defined composition that has discrete existence, w... |
| ProteinQuantification | This is used to link a metaproteomics analysis workflow to a specific protein |
| Protocol |
Slots
| Slot | Description |
|---|---|
| abs_air_humidity | Actual mass of water vapor - mh20 - present in the air water vapor mixture |
| add_date | The date on which the information was added to the database |
| add_recov_method | Additional (i |
| additional_info | Information that doesn't fit anywhere else |
| address | The street name and building number where the sampling occurred |
| adj_room | List of rooms (room number, room name) immediately adjacent to the sampling r... |
| aero_struc | Aerospace structures typically consist of thin plates with stiffeners for the... |
| agrochem_addition | Addition of fertilizers, pesticides, etc |
| air_PM_concen | Concentration of substances that remain suspended in the air, and comprise mi... |
| air_temp | Temperature of the air at the time of sampling |
| air_temp_regm | Information about treatment involving an exposure to varying temperatures; sh... |
| al_sat | Aluminum saturation (esp |
| al_sat_meth | Reference or method used in determining Al saturation |
| alkalinity | Alkalinity, the ability of a solution to neutralize acids to the equivalence ... |
| alkalinity_method | Method used for alkalinity measurement |
| alkyl_diethers | Concentration of alkyl diethers |
| all_proteins | the list of protein identifiers that are associated with the peptide sequence |
| alt | Altitude is a term used to identify heights of objects such as airplanes, spa... |
| alternative_descriptions | A list of alternative descriptions for the entity |
| alternative_identifiers | A list of alternative identifiers for the entity |
| alternative_names | A list of alternative names used to refer to the entity |
| alternative_titles | A list of alternative titles for the entity |
| aminopept_act | Measurement of aminopeptidase activity |
| ammonium | Concentration of ammonium in the sample |
| ammonium_nitrogen | Concentration of ammonium nitrogen in the sample |
| amount_light | The unit of illuminance and luminous emittance, measuring luminous flux per u... |
| analysis_identifiers | |
| analysis_type | Select all the data types associated or available for this biosample |
| analyte_category | The type of analyte(s) that were measured in the data generation process and ... |
| ances_data | Information about either pedigree or other ancestral information description ... |
| annual_precpt | The average of all annual precipitation values known, or an estimated equival... |
| annual_temp | Mean annual temperature |
| antibiotic_regm | Information about treatment involving antibiotic administration; should inclu... |
| api | API gravity is a measure of how heavy or light a petroleum liquid is compared... |
| applied_roles | |
| applies_to_person | |
| arch_struc | An architectural structure is a human-made, free-standing, immobile outdoor c... |
| aromatics_pc | Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that d... |
| asm_score | A score for comparing metagenomic assembly quality from same sample |
| asphaltenes_pc | Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that d... |
| assembly_identifiers | |
| associated_dois | A list of DOIs associated with a resource, such as a list of DOIS associated ... |
| associated_studies | The study associated with a resource |
| atmospheric_data | Measurement of atmospheric data; can include multiple data |
| avg_dew_point | The average of dew point measures taken at the beginning of every hour over a... |
| avg_occup | Daily average occupancy of room |
| avg_temp | The average of temperatures taken at the beginning of every hour over a 24 ho... |
| bac_prod | Bacterial production in the water column measured by isotope uptake |
| bac_resp | Measurement of bacterial respiration in the water column |
| bacteria_carb_prod | Measurement of bacterial carbon production |
| barometric_press | Force per unit area exerted against a surface by the weight of air above that... |
| basin | Name of the basin (e |
| bathroom_count | The number of bathrooms in the building |
| bedroom_count | The number of bedrooms in the building |
| benzene | Concentration of benzene in the sample |
| best_protein | the specific protein identifier most correctly associated with the peptide se... |
| bin_name | Name of the metagenome-assembled genome |
| bin_quality | The quality of the metagenome-assembled genome based on MIMAG standards (http... |
| binned_contig_num | Number of contigs that ended up in a medium or high quality bin |
| biochem_oxygen_dem | Amount of dissolved oxygen needed by aerobic biological organisms in a body o... |
| biocide | List of biocides (commercial name of product and supplier) and date of admini... |
| biocide_admin_method | Method of biocide administration (dose, frequency, duration, time elapsed bet... |
| biogas_retention_time | |
| biogas_temperature | |
| biol_stat | The level of genome modification |
| biomass | Amount of biomass; should include the name for the part of biomass measured, ... |
| biomaterial_purity | |
| biosample_categories | |
| biosample_identifiers | |
| biosample_set | This property links a database object to the set of samples within it |
| biotic_regm | Information about treatment(s) involving use of biotic factors, such as bacte... |
| biotic_relationship | Description of relationship(s) between the subject organism and other organis... |
| bishomohopanol | Concentration of bishomohopanol |
| blood_press_diast | Resting diastolic blood pressure, measured as mm mercury |
| blood_press_syst | Resting systolic blood pressure, measured as mm mercury |
| bromide | Concentration of bromide |
| build_docs | The building design, construction and operation documents |
| build_occup_type | The primary function for which a building or discrete part of a building is i... |
| building_setting | A location (geography) where a building is set |
| built_struc_age | The age of the built structure since construction |
| built_struc_set | The characterization of the location of the built structure as high or low hu... |
| built_struc_type | A physical structure that is a body or assemblage of bodies in space to form ... |
| bulk_elect_conductivity | Electrical conductivity is a measure of the ability to carry electric current... |
| calcium | Concentration of calcium in the sample |
| calibration_object | the file containing calibration data object |
| calibration_set | This property links a database object to the set of calibrations within it |
| calibration_standard | the reference standard(s) used for calibration |
| calibration_target | the target measurement of the calibration |
| carb_dioxide | Carbon dioxide (gas) amount or concentration at the time of sampling |
| carb_monoxide | Carbon monoxide (gas) amount or concentration at the time of sampling |
| carb_nitro_ratio | Ratio of amount or concentrations of carbon to nitrogen |
| ceil_area | The area of the ceiling space within the room |
| ceil_cond | The physical condition of the ceiling at the time of sampling; photos or vide... |
| ceil_finish_mat | The type of material used to finish a ceiling |
| ceil_struc | The construction format of the ceiling |
| ceil_texture | The feel, appearance, or consistency of a ceiling surface |
| ceil_thermal_mass | The ability of the ceiling to provide inertia against temperature fluctuation... |
| ceil_type | The type of ceiling according to the ceiling's appearance or construction |
| ceil_water_mold | Signs of the presence of mold or mildew on the ceiling |
| chem_administration | List of chemical compounds administered to the host or site where sampling oc... |
| chem_mutagen | Treatment involving use of mutagens; should include the name of mutagen, amou... |
| chem_oxygen_dem | A measure of the capacity of water to consume oxygen during the decomposition... |
| chem_treat_method | Method of chemical administration(dose, frequency, duration, time elapsed bet... |
| chem_treatment | List of chemical compounds administered upstream the sampling location where ... |
| chemical_conversion_category | The type of chemical conversion process |
| chemical_entity_set | This property links a database object to the set of chemical entities within ... |
| chemical_formula | A generic grouping for molecular formulae and empirical formulae |
| chimera_check | Tool(s) used for chimera checking, including version number and parameters, t... |
| chloride | Concentration of chloride in the sample |
| chlorophyll | Concentration of chlorophyll |
| chromatographic_category | The type of chromatography used in a process |
| climate_environment | Treatment involving an exposure to a particular climate; treatment regimen in... |
| collected_from | The Site from which a Biosample was collected |
| collecting_biosamples_from_site_set | |
| collection_date | The time of sampling, either as an instance (single point in time) or interva... |
| collection_date_inc | Date the incubation was harvested/collected/ended |
| collection_time | The time of sampling, either as an instance (single point) or interval |
| collection_time_inc | Time the incubation was harvested/collected/ended |
| community | |
| completeness | Estimate of the completeness of the metagenome-assembled genome, estimated by... |
| completion_date | |
| compression_type | If provided, specifies the compression type |
| concentration | The concentration of a substance used in a process |
| conditionings | Preliminary treatment of either phase with a suitable solution of the other p... |
| conduc | Electrical conductivity of water |
| configuration_set | This property links a database object to the set of configurations within it |
| contained_in | A type of container |
| container_size | The volume of the container an analyte is stored in or an activity takes plac... |
| contamination | Estimate of the completeness of the metagenome-assembled genome, estimated by... |
| contig_bp | Total size in bp of all contigs |
| contigs | The sum of the (length*log(length)) of all contigs, times some constant |
| cool_syst_id | The cooling system identifier |
| core_field | basic fields |
| count | |
| crop_rotation | Whether or not crop is rotated, and if yes, rotation schedule |
| ctg_l50 | Given a set of contigs, the L50 is defined as the sequence length of the shor... |
| ctg_l90 | The L90 statistic is less than or equal to the L50 statistic; it is the lengt... |
| ctg_logsum | Maximum contig length |
| ctg_max | Maximum contig length |
| ctg_n50 | Given a set of contigs, each with its own length, the N50 count is defined as... |
| ctg_n90 | Given a set of contigs, each with its own length, the N90 count is defined as... |
| ctg_powsum | Powersum of all contigs is the same as logsum except that it uses the sum of ... |
| cult_root_med | Name or reference for the hydroponic or in vitro culture rooting medium; can ... |
| cur_land_use | Present state of sample site |
| cur_vegetation | Vegetation classification from one or more standard classification systems, o... |
| cur_vegetation_meth | Reference or method used in vegetation classification |
| data_category | The category of the file, such as instrument data from data generation or pro... |
| data_generation_set | This property links a database object to the set of data generations within i... |
| data_object_set | This property links a database object to the set of data objects within it |
| data_object_type | The type of file represented by the data object |
| date_created | from database class |
| date_last_rain | The date of the last time it rained |
| definition | The definition of the ontology term as provided by the ontology |
| density | Density of the sample, which is its mass per unit volume (aka volumetric mass... |
| depos_env | Main depositional environment (https://en |
| depth | The vertical distance below local surface, e |
| description | a human-readable description of a thing |
| dew_point | The temperature to which a given parcel of humid air must be cooled, at const... |
| diether_lipids | Concentration of diether lipids; can include multiple types of diether lipids |
| display_order | When rendering information, this attribute to specify the order in which the ... |
| diss_carb_dioxide | Concentration of dissolved carbon dioxide in the sample or liquid portion of ... |
| diss_hydrogen | Concentration of dissolved hydrogen |
| diss_inorg_carb | Dissolved inorganic carbon concentration in the sample, typically measured af... |
| diss_inorg_nitro | Concentration of dissolved inorganic nitrogen |
| diss_inorg_phosp | Concentration of dissolved inorganic phosphorus in the sample |
| diss_iron | Concentration of dissolved iron in the sample |
| diss_org_carb | Concentration of dissolved organic carbon in the sample, liquid portion of th... |
| diss_org_nitro | Dissolved organic nitrogen concentration measured as; total dissolved nitroge... |
| diss_oxygen | Concentration of dissolved oxygen |
| diss_oxygen_fluid | Concentration of dissolved oxygen in the oil field produced fluids as it cont... |
| dna_absorb1 | 260/280 measurement of DNA sample purity |
| dna_absorb2 | 260/230 measurement of DNA sample purity |
| dna_collect_site | Provide information on the site your DNA sample was collected from |
| dna_concentration | |
| dna_cont_type | Tube or plate (96-well) |
| dna_cont_well | |
| dna_container_id | |
| dna_dnase | |
| dna_isolate_meth | Describe the method/protocol/kit used to extract DNA/RNA |
| dna_organisms | List any organisms known or suspected to grow in co-culture, as well as estim... |
| dna_project_contact | |
| dna_samp_id | |
| dna_sample_format | Solution in which the DNA sample has been suspended |
| dna_sample_name | Give the DNA sample a name that is meaningful to you |
| dna_seq_project | |
| dna_seq_project_name | |
| dna_seq_project_pi | |
| dna_volume | |
| dnase_rna | |
| doi_category | The resource type the corresponding doi resolves to |
| doi_provider | The authority, or organization, the DOI is associated with |
| doi_value | A digital object identifier, which is intended to persistantly identify some ... |
| door_comp_type | The composite type of the door |
| door_cond | The phsical condition of the door |
| door_direct | The direction the door opens |
| door_loc | The relative location of the door in the room |
| door_mat | The material the door is composed of |
| door_move | The type of movement of the door |
| door_size | The size of the door |
| door_type | The type of door material |
| door_type_metal | The type of metal door |
| door_type_wood | The type of wood door |
| door_water_mold | Signs of the presence of mold or mildew on a door |
| down_par | Visible waveband radiance and irradiance measurements in the water column |
| drainage_class | Drainage classification from a standard system such as the USDA system |
| drawings | The buildings architectural drawings; if design is chosen, indicate phase-con... |
| duration | The elapsed time of an activity |
| ecosystem | An ecosystem is a combination of a physical environment (abiotic factors) and... |
| ecosystem_category | Ecosystem categories represent divisions within the ecosystem based on specif... |
| ecosystem_path_id | A unique id representing the GOLD classifiers associated with a sample |
| ecosystem_subtype | Ecosystem subtypes represent further subdivision of Ecosystem types into more... |
| ecosystem_type | Ecosystem types represent things having common characteristics within the Eco... |
| efficiency_percent | Percentage of volatile solids removed from the anaerobic digestor |
| elev | Elevation of the sampling site is its height above a fixed reference point, m... |
| elevator | The number of elevators within the built structure |
| eluent_introduction_category | A high-level categorization for how the processed sample is introduced into a... |
| An email address for an entity such as a person | |
| embargoed | If true, the data are embargoed and not available for public access |
| emsl_biosample_identifiers | A list of identifiers for the biosample from the EMSL database |
| emsl_identifiers | |
| emsl_project_identifiers | Identifiers that link a NMDC study to the EMSL user facility website hosting ... |
| emsl_store_temp | The temperature at which the sample should be stored upon delivery to EMSL |
| emulsions | Amount or concentration of substances such as paints, adhesives, mayonnaise, ... |
| encodes | The gene product encoded by this feature |
| end | The end of the feature in positive 1-based integer coordinates |
| end_date | The date on which any process or activity was ended |
| ended_at_time | |
| env_broad_scale | Report the major environmental system the sample or specimen came from |
| env_local_scale | Report the entity or entities which are in the sample or specimen’s local vic... |
| env_medium | Report the environmental material(s) immediately surrounding the sample or sp... |
| env_package | MIxS extension for reporting of measurements and observations obtained from o... |
| environment_field | field describing environmental aspect of a sample |
| escalator | The number of escalators within the built structure |
| ethylbenzene | Concentration of ethylbenzene in the sample |
| etl_software_version | from database class |
| eukaryotic_evaluation | Contains results from evaluating if a Metagenome-Assembled Genome is of eukar... |
| execution_resource | The computing resource or facility where the workflow was executed |
| exp_duct | The amount of exposed ductwork in the room |
| exp_pipe | The number of exposed pipes in the room |
| experimental_factor | Experimental factors are essentially the variable aspects of an experiment de... |
| experimental_factor_other | Other details about your sample that you feel can't be accurately represented... |
| ext_door | The number of exterior doors in the built structure |
| ext_wall_orient | The orientation of the exterior wall |
| ext_window_orient | The compass direction the exterior window of the room is facing |
| external_database_identifiers | Link to corresponding identifier in external database |
| extraction_targets | Provides the target biomolecule that has been separated from a sample during ... |
| extreme_event | Unusual physical events that may have affected microbial populations |
| fao_class | Soil classification from the FAO World Reference Database for Soil Resources |
| feature_category | A Sequence Ontology term that describes the category of a feature |
| feature_type | TODO: Yuri to write |
| fertilizer_regm | Information about treatment involving the use of fertilizers; should include ... |
| field | Name of the hydrocarbon field (e |
| field_research_site_set | |
| file_size_bytes | Size of the file in bytes |
| filter_material | A porous material on which solid particles present in air or other fluid whic... |
| filter_method | Type of filter used or how the sample was filtered |
| filter_pore_size | A quantitative or qualitative measurement of the physical dimensions of the p... |
| filter_type | A device which removes solid particulates or airborne molecular contaminants |
| filtration_category | The type of conditioning applied to a filter, device, etc |
| final_concentration | When solutions A (containing substance X) and B are combined together, this s... |
| fire | Historical and/or physical evidence of fire |
| fireplace_type | A firebox with chimney |
| flooding | Historical and/or physical evidence of flooding |
| floor_age | The time period since installment of the carpet or flooring |
| floor_area | The area of the floor space within the room |
| floor_cond | The physical condition of the floor at the time of sampling; photos or video ... |
| floor_count | The number of floors in the building, including basements and mechanical pent... |
| floor_finish_mat | The floor covering type; the finished surface that is walked on |
| floor_struc | Refers to the structural elements and subfloor upon which the finish flooring... |
| floor_thermal_mass | The ability of the floor to provide inertia against temperature fluctuations |
| floor_water_mold | Signs of the presence of mold or mildew in a room |
| fluor | Raw or converted fluorescence of water |
| freq_clean | The number of times the sample location is cleaned |
| freq_cook | The number of times a meal is cooked per week |
| functional_annotation_agg | |
| functional_annotation_set | This property links a database object to the set of all functional annotation... |
| funding_sources | A list of organizations, along with the award numbers, that underwrite financ... |
| fungicide_regm | Information about treatment involving use of fungicides; should include the n... |
| furniture | The types of furniture present in the sampled room |
| gap_pct | The gap size percentage of all scaffolds |
| gaseous_environment | Use of conditions with differing gaseous environments; should include the nam... |
| gaseous_substances | Amount or concentration of substances such as hydrogen sulfide, carbon dioxid... |
| gc_avg | Average of GC content of all contigs |
| gc_std | Standard deviation of GC content of all contigs |
| gender_restroom | The gender type of the restroom |
| gene_count | Number of genes |
| gene_function_id | The identifier for the gene function |
| generates_calibration | calibration information is generated a process |
| genetic_mod | Genetic modifications of the genome of an organism, which may occur naturally... |
| genome_feature_set | This property links a database object to the set of all features |
| geo_loc_name | The geographical origin of the sample as defined by the country or sea name f... |
| gff_coordinate | A positive 1-based integer coordinate indicating start or end |
| git_url | The url that points to the exact github location of a workflow |
| glucosidase_act | Measurement of glucosidase activity |
| gnps_identifiers | |
| gnps_task_identifiers | identifiers that link a NMDC study to a web-based report about metabolomics a... |
| gold_analysis_project_identifiers | identifiers for corresponding analysis projects in GOLD |
| gold_biosample_identifiers | identifiers for corresponding sample in GOLD |
| gold_identifiers | |
| gold_path_field | This is a grouping for any of the gold path fields |
| gold_sequencing_project_identifiers | identifiers for corresponding sequencing project in GOLD |
| gold_study_identifiers | identifiers for corresponding project(s) in GOLD |
| gravidity | Whether or not subject is gravid, and if yes date due or date post-conception... |
| gravity | Information about treatment involving use of gravity factor to study various ... |
| growth_facil | Type of facility where the sampled plant was grown; controlled vocabulary: gr... |
| growth_habit | Characteristic shape, appearance or growth form of a plant species |
| growth_hormone_regm | Information about treatment involving use of growth hormones; should include ... |
| gtdbtk_class | Taxonomic class assigned by GTDB-Tk |
| gtdbtk_domain | Taxonomic domain assigned by GTDB-Tk |
| gtdbtk_family | Taxonomic family assigned by GTDB-Tk |
| gtdbtk_genus | Taxonomic genus assigned by GTDB-Tk |
| gtdbtk_order | Taxonomic order assigned by GTDB-Tk |
| gtdbtk_phylum | Taxonomic phylum assigned by GTDB-Tk |
| gtdbtk_species | Taxonomic genus assigned by GTDB-Tk |
| habitat | |
| hall_count | The total count of hallways and cooridors in the built structure |
| handidness | The handidness of the individual sampled |
| has_boolean_value | Links a quantity value to a boolean |
| has_chromatography_configuration | The identifier of the associated ChromatographyConfiguration, providing infor... |
| has_credit_associations | This slot links a study to a credit association |
| has_failure_categorization | |
| has_function | |
| has_input | An input to a process |
| has_mass_spectrometry_configuration | The identifier of the associated MassSpectrometryConfiguration |
| has_maximum_numeric_value | The maximum value part, expressed as number, of the quantity value when the v... |
| has_metabolite_identifications | |
| has_minimum_numeric_value | The minimum value part, expressed as number, of the quantity value when the v... |
| has_numeric_value | Links a quantity value to a number |
| has_output | An output from a process |
| has_peptide_quantifications | |
| has_process_parts | A list of process parts that make up a protocol |
| has_raw_value | The value that was specified for an annotation in raw form, i |
| has_unit | Links a QuantityValue to a unit |
| hc_produced | Main hydrocarbon type produced from resource (i |
| hcr | Main Hydrocarbon Resource type |
| hcr_fw_salinity | Original formation water salinity (prior to secondary recovery e |
| hcr_geol_age | Geological age of hydrocarbon resource (Additional info: https://en |
| hcr_pressure | Original pressure of the hydrocarbon resource |
| hcr_temp | Original temperature of the hydrocarbon resource |
| heat_cool_type | Methods of conditioning or heating a room or building |
| heat_deliv_loc | The location of heat delivery within the room |
| heat_sys_deliv_meth | The method by which the heat is delivered through the system |
| heat_system_id | The heating system identifier |
| heavy_metals | Heavy metals present in the sequenced sample and their concentrations |
| heavy_metals_meth | Reference or method used in determining heavy metals |
| height_carper_fiber | The average carpet fiber height in the indoor environment |
| herbicide_regm | Information about treatment involving use of herbicides; information about tr... |
| highest_similarity_score | |
| homepage_website | The website address (URL) of an entity's homepage |
| horizon_meth | Reference or method used in determining the horizon |
| host_age | Age of host at the time of sampling; relevant scale depends on species and st... |
| host_body_habitat | Original body habitat where the sample was obtained from |
| host_body_product | Substance produced by the body, e |
| host_body_site | Name of body site where the sample was obtained from, such as a specific orga... |
| host_body_temp | Core body temperature of the host when sample was collected |
| host_color | The color of host |
| host_common_name | Common name of the host |
| host_diet | Type of diet depending on the host, for animals omnivore, herbivore etc |
| host_disease_stat | List of diseases with which the host has been diagnosed; can include multiple... |
| host_dry_mass | Measurement of dry mass |
| host_family_relation | Familial relationships to other hosts in the same study; can include multiple... |
| host_genotype | Observed genotype |
| host_growth_cond | Literature reference giving growth conditions of the host |
| host_height | The height of subject |
| host_last_meal | Content of last meal and time since feeding; can include multiple values |
| host_length | The length of subject |
| host_life_stage | Description of life stage of host |
| host_name | |
| host_phenotype | Phenotype of human or other host |
| host_sex | Gender or physical sex of the host |
| host_shape | Morphological shape of host |
| host_subject_id | A unique identifier by which each subject can be referred to, de-identified |
| host_subspecf_genlin | Information about the genetic distinctness of the host organism below the sub... |
| host_substrate | The growth substrate of the host |
| host_symbiont | The taxonomic name of the organism(s) found living in mutualistic, commensali... |
| host_taxid | NCBI taxon id of the host, e |
| host_tot_mass | Total mass of the host at collection, the unit depends on host |
| host_wet_mass | Measurement of wet mass |
| humidity | Amount of water vapour in the air, at the time of sampling |
| humidity_regm | Information about treatment involving an exposure to varying degree of humidi... |
| id | A unique identifier for a thing |
| igsn_biosample_identifiers | A list of identifiers for the biosample from the IGSN database |
| igsn_identifiers | |
| img_identifiers | A list of identifiers that relate the biosample to records in the IMG databas... |
| in_manifest | one or more combinations of other DataObjects that can be analyzed together |
| inchi | |
| inchi_key | |
| indoor_space | A distinguishable space within a structure, the purpose for which discrete ar... |
| indoor_surf | Type of indoor surface |
| indust_eff_percent | Percentage of industrial effluents received by wastewater treatment plant |
| infiltrations | The amount of time it takes to complete each infiltration activity |
| inorg_particles | Concentration of particles such as sand, grit, metal particles, ceramics, etc |
| input_base_count | The nucleotide base count number of input reads for QC analysis |
| input_contig_num | Total number of input contigs |
| input_mass | Total mass of sample used in activity |
| input_read_bases | TODO |
| input_read_count | The sequence count number of input reads for QC analysis |
| input_volume | The volume of the input sample |
| insdc_analysis_identifiers | |
| insdc_assembly_identifiers | |
| insdc_bioproject_identifiers | identifiers for corresponding project in INSDC Bioproject |
| insdc_biosample_identifiers | identifiers for corresponding sample in INSDC |
| insdc_experiment_identifiers | |
| insdc_identifiers | Any identifier covered by the International Nucleotide Sequence Database Coll... |
| insdc_secondary_sample_identifiers | secondary identifiers for corresponding sample in INSDC |
| insdc_sra_ena_study_identifiers | identifiers for corresponding project in INSDC SRA / ENA |
| inside_lux | The recorded value at sampling time (power density) |
| instrument_set | This property links a database object to the set of instruments within it |
| instrument_used | What instrument was used during DataGeneration or MaterialProcessing |
| int_wall_cond | The physical condition of the wall at the time of sampling; photos or video p... |
| internal_calibration | whether internal calibration was used, if false, external calibration was use... |
| investigation_field | field describing aspect of the investigation/study to which the sample belong... |
| ionization_source | The ionization source used to introduce processed samples into a mass spectro... |
| is_pressurized | Whether or not pressure was applied to a thing or process |
| is_stranded | Is the (RNA) library stranded or non-stranded (unstranded) |
| isotope_exposure | List isotope exposure or addition applied to your sample |
| iw_bt_date_well | Injection water breakthrough date per well following a secondary and/or terti... |
| iwf | Proportion of the produced fluids derived from injected water at the time of ... |
| jgi_portal_analysis_project_identifiers | identifiers for corresponding analysis projects in JGI Portal |
| jgi_portal_identifiers | identifiers for entities according to JGI Portal |
| jgi_portal_study_identifiers | Identifiers that link a NMDC study to a website hosting raw and analyzed data... |
| known_as | The substance from which a portion was taken |
| language | Should use ISO 639-1 code e |
| last_clean | The last time the floor was cleaned (swept, mopped, vacuumed) |
| lat_lon | The geographical origin of the sample as defined by latitude and longitude |
| latitude | latitude |
| lbc_thirty | lime buffer capacity, determined after 30 minute incubation |
| lbceq | lime buffer capacity, determined at equilibrium after 5 day incubation |
| library_preparation_kit | |
| library_type | |
| light_intensity | Measurement of light intensity |
| light_regm | Information about treatment(s) involving exposure to light, including both li... |
| light_type | Application of light to achieve some practical or aesthetic effect |
| link_addit_analys | Link to additional analysis results performed on the sample |
| link_class_info | Link to digitized soil maps or other soil classification information |
| link_climate_info | Link to climate resource |
| lithology | Hydrocarbon resource main lithology (Additional information: http://petrowiki |
| local_class | Soil classification based on local soil classification system |
| local_class_meth | Reference or method used in determining the local soil classification |
| location | |
| longitude | longitude |
| low_depth_contig_num | Number of contigs which were excluded from binning for depth of coverage |
| magnesium | Concentration of magnesium in the sample |
| mags_list | Contains detailed information about each metagenome-assembled genome |
| manganese | Concentration of manganese in the sample |
| manifest_category | The type of context in which the constituent DataObjects can be analyzed toge... |
| manifest_set | This property links a database object to the set of manifests within it |
| mass | A physical quality that inheres in a bearer by virtue of the proportion of th... |
| mass_analyzers | The kind of mass analyzer(s) used during the spectra collection |
| mass_spectrometry_acquisition_strategy | Mode of running a mass spectrometer method by which m/z ranges are selected a... |
| mass_spectrum_collection_modes | Indicates whether mass spectra were collected in full profile, reduced profil... |
| material_component_separation | A material processing in which components of an input material become segrega... |
| material_processing_set | This property links a database object to the set of material processing withi... |
| max_occup | The maximum amount of people allowed in the indoor environment |
| md5_checksum | MD5 checksum of file (pre-compressed) |
| mean_frict_vel | Measurement of mean friction velocity |
| mean_peak_frict_vel | Measurement of mean peak friction velocity |
| mech_struc | mechanical structure: a moving structure |
| mechanical_damage | Information about any mechanical damage exerted on the plant; can include mul... |
| members_id | Names of the contigs that make up a metagenome-assembled genome |
| metabolite_identified | the specific metabolite identifier |
| metabolomics_analysis_category | The category of metabolomics analysis being performed |
| metagenome_annotation_id | The identifier for the analysis activity that generated the functional annota... |
| metagenome_assembly_parameter | |
| metaproteomics_analysis_category | The category of metaproteomics analysis being performed |
| methane | Methane (gas) amount or concentration at the time of sampling |
| mgnify_analysis_identifiers | |
| mgnify_identifiers | |
| mgnify_project_identifiers | identifiers for corresponding project in MGnify |
| micro_biomass_c_meth | Reference or method used in determining microbial biomass carbon |
| micro_biomass_meth | Reference or method used in determining microbial biomass |
| micro_biomass_n_meth | Reference or method used in determining microbial biomass nitrogen |
| microbial_biomass | The part of the organic matter in the soil that constitutes living microorgan... |
| microbial_biomass_c | The part of the organic matter in the soil that constitutes living microorgan... |
| microbial_biomass_n | The part of the organic matter in the soil that constitutes living microorgan... |
| min_q_value | smallest Q-Value associated with the peptide sequence as provided by MSGFPlus... |
| mineral_nutr_regm | Information about treatment involving the use of mineral supplements; should ... |
| misc_param | Any other measurement performed or parameter collected, that is not listed he... |
| mod_date | The last date on which the database information was modified |
| model | |
| modifier_substance | The type of modification being done |
| n_alkanes | Concentration of n-alkanes; can include multiple n-alkanes |
| name | A human readable label for an entity |
| ncbi_lineage | Comma delimited ordered list of NCBI taxonomy names |
| ncbi_lineage_tax_ids | Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId) |
| ncbi_project_name | |
| ncbi_taxonomy_name | |
| neon_biosample_identifiers | |
| neon_identifiers | identifiers for entities according to NEON |
| neon_study_identifiers | |
| nitrate | Concentration of nitrate in the sample |
| nitrate_nitrogen | Concentration of nitrate nitrogen in the sample |
| nitrite | Concentration of nitrite in the sample |
| nitrite_nitrogen | Concentration of nitrite nitrogen in the sample |
| nitro | Concentration of nitrogen (total) |
| non_microb_biomass | Amount of biomass; should include the name for the part of biomass measured, ... |
| non_microb_biomass_method | Reference or method used in determining biomass |
| non_min_nutr_regm | Information about treatment involving the exposure of plant to non-mineral nu... |
| notes | |
| nucl_acid_amp | A link to a literature reference, electronic resource or a standard operating... |
| nucl_acid_ext | A link to a literature reference, electronic resource or a standard operating... |
| nucleic_acid_sequence_source_field | |
| num_16s | Number of 16s sequences detected, a subunit of prokaryotic ribosomes |
| num_23s | Number of 23 seqeuences detected, a subunit of ribosomes |
| num_5s | Number of 5s seqeuences detected, a subunit of ribosomes |
| num_aligned_reads | The sequence count number of input reads aligned to assembled contigs |
| num_input_reads | The sequence count number of input reads for assembly |
| num_t_rna | Number of transfer transfer RNAs |
| number_of_contig | Number of contigs |
| number_pets | The number of pets residing in the sampled space |
| number_plants | The number of plant(s) in the sampling space |
| number_resident | The number of individuals currently occupying in the sampling location |
| object | |
| object_set | Applies to a property that links a database object to a set of objects |
| objective | The scientific objectives associated with the entity |
| occup_density_samp | Average number of occupants at time of sampling per square footage |
| occup_document | The type of documentation of occupancy |
| occup_samp | Number of occupants present at time of sample within the given space |
| omics_processing_identifiers | |
| omics_type | The type of omics data |
| ontology_class_set | This property links a database object to the set of ontology classes within i... |
| orcid | The ORCID of a person |
| ordered_mobile_phases | The solution(s) that moves through a chromatography column |
| org_carb | Concentration of organic carbon |
| org_count_qpcr_info | If qpcr was used for the cell count, the target gene name, the primer sequenc... |
| org_matter | Concentration of organic matter |
| org_nitro | Concentration of organic nitrogen |
| org_nitro_method | Method used for obtaining organic nitrogen |
| org_particles | Concentration of particles such as faeces, hairs, food, vomit, paper fibers, ... |
| organism_count | Total cell count of any organism (or group of organisms) per gram, volume or ... |
| other_treatment | Other treatments applied to your samples that are not applicable to the provi... |
| output_base_count | After QC analysis nucleotide base count number |
| output_read_bases | TODO |
| output_read_count | After QC analysis sequence count number |
| owc_tvdss | Depth of the original oil water contact (OWC) zone (average) (m TVDSS) |
| oxy_stat_samp | Oxygenation status of sample |
| oxygen | Oxygen (gas) amount or concentration at the time of sampling |
| part_of | Links a resource to another resource that either logically or physically incl... |
| part_org_carb | Concentration of particulate organic carbon |
| part_org_nitro | Concentration of particulate organic nitrogen |
| particle_class | Particles are classified, based on their size, into six general categories:cl... |
| pcr_cond | Description of reaction conditions and components of PCR in the form of 'init... |
| pcr_cycles | |
| pcr_primers | PCR primers that were used to amplify the sequence of the targeted gene, locu... |
| peptide_sequence | |
| peptide_sequence_count | count of peptide sequences grouped to the best_protein |
| peptide_spectral_count | sum of filter passing MS2 spectra associated with the peptide sequence within... |
| peptide_sum_masic_abundance | combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... |
| permeability | Measure of the ability of a hydrocarbon resource to allow fluids to pass thro... |
| perturbation | Type of perturbation, e |
| pesticide_regm | Information about treatment involving use of insecticides; should include the... |
| petroleum_hydrocarb | Concentration of petroleum hydrocarbon |
| ph | Ph measurement of the sample, or liquid portion of sample, or aqueous phase o... |
| ph_meth | Reference or method used in determining ph |
| ph_regm | Information about treatment involving exposure of plants to varying levels of... |
| phaeopigments | Concentration of phaeopigments; can include multiple phaeopigments |
| phase | The phase for a coding sequence entity |
| phosphate | Concentration of phosphate |
| phosplipid_fatt_acid | Concentration of phospholipid fatty acids; can include multiple values |
| photon_flux | Measurement of photon flux |
| plant_growth_med | Specification of the media for growing the plants or tissue cultured samples,... |
| plant_product | Substance produced by the plant, where the sample was obtained from |
| plant_sex | Sex of the reproductive parts on the whole plant, e |
| plant_struc | Name of plant structure the sample was obtained from; for Plant Ontology (PO)... |
| polarity_mode | the polarity of which ions are generated and detected |
| pollutants | Pollutant types and, amount or concentrations measured at the time of samplin... |
| pool_dna_extracts | Indicate whether multiple DNA extractions were mixed |
| porosity | Porosity of deposited sediment is volume of voids divided by the total volume... |
| potassium | Concentration of potassium in the sample |
| pour_point | Temperature at which a liquid becomes semi solid and loses its flow character... |
| pre_treatment | The process of pre-treatment removes materials that can be easily collected f... |
| predicate | |
| pres_animal_insect | The type and number of animals or insects present in the sampling space |
| pressure | Pressure to which the sample is subject to, in atmospheres |
| prev_land_use_meth | Reference or method used in determining previous land use and dates |
| previous_land_use | Previous land use and dates |
| primary_prod | Measurement of primary production, generally measured as isotope uptake |
| primary_treatment | The process to produce both a generally homogeneous liquid capable of being t... |
| principal_investigator | Principal Investigator who led the study and/or generated the dataset |
| processed_sample_set | This property links a database object to the set of processed samples within ... |
| processing_institution | The organization that processed the sample |
| prod_rate | Oil and/or gas production rates per well (e |
| prod_start_date | Date of field's first production |
| profile_image_url | A url that points to an image of a person |
| profile_position | Cross-sectional position in the hillslope where sample was collected |
| project_id | Proposal IDs or names associated with dataset |
| proport_woa_temperature | |
| proposal_dna | |
| proposal_rna | |
| protein_spectral_count | sum of filter passing MS2 spectra associated with the best protein within a g... |
| protein_sum_masic_abundance | combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... |
| protocol_execution_category | |
| protocol_execution_set | This property links a database object to the set of protocol executions withi... |
| protocol_link | |
| qc_comment | Slot to store additional comments about laboratory or workflow output |
| qc_failure_what | Provides a summary about what caused a lab or workflow process to fail |
| qc_failure_where | Describes the nmdc schema class that corresonds to where the failure occurred |
| qc_status | Stores information about the result of a process (ie the process of sequencin... |
| quad_pos | The quadrant position of the sampling room within the building |
| radiation_regm | Information about treatment involving exposure of plant or a plant part to a ... |
| rainfall_regm | Information about treatment involving an exposure to a given amount of rainfa... |
| reactor_type | Anaerobic digesters can be designed and engineered to operate using a number ... |
| read_qc_analysis_statistic | |
| redox_potential | Redox potential, measured relative to a hydrogen cell, indicating oxidation o... |
| rel_air_humidity | Partial vapor and air pressure, density of the vapor and air, or by the actua... |
| rel_humidity_out | The recorded outside relative humidity value at the time of sampling |
| rel_samp_loc | The sampling location within the train car |
| related_identifiers | Identifiers assigned to a thing that is similar to that which is represented ... |
| relations | |
| replicate_number | If sending biological replicates, indicate the rep number here |
| reservoir | Name of the reservoir (e |
| resins_pc | Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that d... |
| resolution_categories | The relative resolution at which spectra were collected |
| rna_absorb1 | 260/280 measurement of RNA sample purity |
| rna_absorb2 | 260/230 measurement of RNA sample purity |
| rna_collect_site | Provide information on the site your RNA sample was collected from |
| rna_concentration | |
| rna_cont_type | Tube or plate (96-well) |
| rna_cont_well | |
| rna_container_id | |
| rna_isolate_meth | Describe the method/protocol/kit used to extract DNA/RNA |
| rna_organisms | List any organisms known or suspected to grow in co-culture, as well as estim... |
| rna_project_contact | |
| rna_samp_id | |
| rna_sample_format | Solution in which the RNA sample has been suspended |
| rna_sample_name | Give the RNA sample a name that is meaningful to you |
| rna_seq_project | |
| rna_seq_project_name | |
| rna_seq_project_pi | |
| rna_volume | |
| room_air_exch_rate | The rate at which outside air replaces indoor air in a given space |
| room_architec_elem | The unique details and component parts that, together, form the architecture ... |
| room_condt | The condition of the room at the time of sampling |
| room_connected | List of rooms connected to the sampling room by a doorway |
| room_count | The total count of rooms in the built structure including all room types |
| room_dim | The length, width and height of sampling room |
| room_door_dist | Distance between doors (meters) in the hallway between the sampling room and ... |
| room_door_share | List of room(s) (room number, room name) sharing a door with the sampling roo... |
| room_hallway | List of room(s) (room number, room name) located in the same hallway as sampl... |
| room_loc | The position of the room within the building |
| room_moist_dam_hist | The history of moisture damage or mold in the past 12 months |
| room_net_area | The net floor area of sampling room |
| room_occup | Count of room occupancy at time of sampling |
| room_samp_pos | The horizontal sampling position in the room relative to architectural elemen... |
| room_type | The main purpose or activity of the sampling room |
| room_vol | Volume of sampling room |
| room_wall_share | List of room(s) (room number, room name) sharing a wall with the sampling roo... |
| room_window_count | Number of windows in the room |
| root_cond | Relevant rooting conditions such as field plot size, sowing density, containe... |
| root_med_carbon | Source of organic carbon in the culture rooting medium; e |
| root_med_macronutr | Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S);... |
| root_med_micronutr | Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, ... |
| root_med_ph | pH measurement of the culture rooting medium; e |
| root_med_regl | Growth regulators in the culture rooting medium such as cytokinins, auxins, g... |
| root_med_solid | Specification of the solidifying agent in the culture rooting medium; e |
| root_med_suppl | Organic supplements of the culture rooting medium, such as vitamins, amino ac... |
| salinity | The total concentration of all dissolved salts in a liquid or solid sample |
| salinity_category | Categorical description of the sample's salinity |
| salinity_meth | Reference or method used in determining salinity |
| salt_regm | Information about treatment involving use of salts as supplement to liquid an... |
| samp_capt_status | Reason for the sample |
| samp_collec_device | The device used to collect an environmental sample |
| samp_collec_method | The method employed for collecting the sample |
| samp_collect_point | Sampling point on the asset were sample was collected (e |
| samp_dis_stage | Stage of the disease at the time of sample collection, e |
| samp_floor | The floor of the building, where the sampling room is located |
| samp_loc_corr_rate | Metal corrosion rate is the speed of metal deterioration due to environmental... |
| samp_mat_process | A brief description of any processing applied to the sample during or after r... |
| samp_md | In non deviated well, measured depth is equal to the true vertical depth, TVD... |
| samp_name | A local identifier or name that for the material sample used for extracting n... |
| samp_preserv | Preservative added to the sample (e |
| samp_room_id | Sampling room number |
| samp_size | The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... |
| samp_sort_meth | Method by which samples are sorted; open face filter collecting total suspend... |
| samp_store_dur | Duration for which the sample was stored |
| samp_store_loc | Location at which sample was stored, usually name of a specific freezer/room |
| samp_store_temp | Temperature at which sample was stored, e |
| samp_subtype | Name of sample sub-type |
| samp_taxon_id | NCBI taxon id of the sample |
| samp_time_out | The recent and long term history of outside sampling |
| samp_transport_cond | Sample transport duration (in days or hrs) and temperature the sample was exp... |
| samp_tvdss | Depth of the sample i |
| samp_type | The type of material from which the sample was obtained |
| samp_vol_we_dna_ext | Volume (ml) or mass (g) of total collected sample processed for DNA extractio... |
| samp_weather | The weather on the sampling day |
| samp_well_name | Name of the well (e |
| sample_collection_day | |
| sample_collection_hour | |
| sample_collection_minute | |
| sample_collection_month | |
| sample_collection_site | |
| sample_collection_year | |
| sample_link | A unique identifier to assign parent-child, subsample, or sibling samples |
| sample_shipped | The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent... |
| sample_state_information | The chemical phase of a pure sample, or the state of a mixed sample |
| sample_type | Type of sample being submitted |
| sampled_portion | The portion of the sample that is taken for downstream activity |
| saturates_pc | Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that d... |
| scaf_bp | Total size in bp of all scaffolds |
| scaf_l50 | Given a set of scaffolds, the L50 is defined as the sequence length of the sh... |
| scaf_l90 | The L90 statistic is less than or equal to the L50 statistic; it is the lengt... |
| scaf_l_gt50k | Total size in bp of all scaffolds greater than 50 KB |
| scaf_logsum | The sum of the (length*log(length)) of all scaffolds, times some constant |
| scaf_max | Maximum scaffold length |
| scaf_n50 | Given a set of scaffolds, each with its own length, the N50 count is defined ... |
| scaf_n90 | Given a set of scaffolds, each with its own length, the N90 count is defined ... |
| scaf_n_gt50k | Total sequence count of scaffolds greater than 50 KB |
| scaf_pct_gt50k | Total sequence size percentage of scaffolds greater than 50 KB |
| scaf_powsum | Powersum of all scaffolds is the same as logsum except that it uses the sum o... |
| scaffolds | Total sequence count of all scaffolds |
| season | The season when sampling occurred |
| season_environment | Treatment involving an exposure to a particular season (e |
| season_precpt | The average of all seasonal precipitation values known, or an estimated equiv... |
| season_temp | Mean seasonal temperature |
| season_use | The seasons the space is occupied |
| secondary_treatment | The process for substantially degrading the biological content of the sewage |
| sediment_type | Information about the sediment type based on major constituents |
| separation_method | The method that was used to separate a substance from a solution or mixture |
| seq_meth | Sequencing machine used |
| seq_quality_check | Indicate if the sequence has been called by automatic systems (none) or under... |
| seqid | The ID of the landmark used to establish the coordinate system for the curren... |
| sequencing_field | |
| sewage_type | Type of wastewater treatment plant as municipial or industrial |
| shad_dev_water_mold | Signs of the presence of mold or mildew on the shading device |
| shading_device_cond | The physical condition of the shading device at the time of sampling |
| shading_device_loc | The location of the shading device in relation to the built structure |
| shading_device_mat | The material the shading device is composed of |
| shading_device_type | The type of shading device |
| sieving | Collection design of pooled samples and/or sieve size and amount of sample si... |
| silicate | Concentration of silicate |
| size_frac | Filtering pore size used in sample preparation |
| size_frac_low | Refers to the mesh/pore size used to pre-filter/pre-sort the sample |
| size_frac_up | Refers to the mesh/pore size used to retain the sample |
| slope_aspect | The direction a slope faces |
| slope_gradient | Commonly called 'slope' |
| sludge_retent_time | The time activated sludge remains in reactor |
| smiles | A string encoding of a molecular graph, no chiral or isotopic information |
| sodium | Sodium concentration in the sample |
| soil_annual_season_temp | |
| soil_horizon | Specific layer in the land area which measures parallel to the soil surface a... |
| soil_text_measure | The relative proportion of different grain sizes of mineral particles in a so... |
| soil_texture_meth | Reference or method used in determining soil texture |
| soil_type | Description of the soil type or classification |
| soil_type_meth | Reference or method used in determining soil series name or other lower-level... |
| solar_irradiance | The amount of solar energy that arrives at a specific area of a surface durin... |
| soluble_inorg_mat | Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hy... |
| soluble_iron_micromol | |
| soluble_org_mat | Concentration of substances such as urea, fruit sugars, soluble proteins, dru... |
| soluble_react_phosp | Concentration of soluble reactive phosphorus |
| source_concentration | When solutions A (containing substance X) and B are combined together, this s... |
| source_mat_id | A unique identifier assigned to a material sample (as defined by http://rs |
| space_typ_state | Customary or normal state of the space |
| specific | The building specifications |
| specific_ecosystem | Specific ecosystems represent specific features of the environment like aphot... |
| specific_humidity | The mass of water vapour in a unit mass of moist air, usually expressed as gr... |
| sr_dep_env | Source rock depositional environment (https://en |
| sr_geol_age | Geological age of source rock (Additional info: https://en |
| sr_kerog_type | Origin of kerogen |
| sr_lithology | Lithology of source rock (https://en |
| standing_water_regm | Treatment involving an exposure to standing water during a plant's life span,... |
| start | The start of the feature in positive 1-based integer coordinates |
| start_date | The date on which any process or activity was started |
| start_date_inc | Date the incubation was started |
| start_time_inc | Time the incubation was started |
| started_at_time | |
| stationary_phase | The material the stationary phase is comprised of used in chromatography |
| storage_process_set | This property links a database object to the set of storage processes within ... |
| store_cond | Explain how and for how long the soil sample was stored before DNA extraction... |
| strand | The strand on which a feature is located |
| stranded_orientation | Lists the strand orientiation for a stranded RNA library preparation |
| study_category | The type of research initiative |
| study_identifiers | |
| study_image | Links a study to one or more images |
| study_set | This property links a database object to the set of studies within it |
| subject | |
| substance_role | The role of a substance in a process |
| substances_used | The substances that are combined to enable a ChemicalConversionProcess |
| substances_volume | The volume of the combined substances that was included in a ChemicalConversi... |
| substructure_type | The substructure or under building is that largely hidden section of the buil... |
| subsurface_depth | |
| sulfate | Concentration of sulfate in the sample |
| sulfate_fw | Original sulfate concentration in the hydrocarbon resource |
| sulfide | Concentration of sulfide in the sample |
| surf_air_cont | Contaminant identified on surface |
| surf_humidity | Surfaces: water activity as a function of air and material moisture |
| surf_material | Surface materials at the point of sampling |
| surf_moisture | Water held on a surface |
| surf_moisture_ph | ph measurement of surface |
| surf_temp | Temperature of the surface at the time of sampling |
| suspend_part_matter | Concentration of suspended particulate matter |
| suspend_solids | Concentration of substances including a wide variety of material, such as sil... |
| tan | Total Acid Number (TAN) is a measurement of acidity that is determined by th... |
| target_gene | Targeted gene or locus name for marker gene studies |
| target_subfragment | Name of subfragment of a gene or locus |
| technical_reps | If sending technical replicates of the same sample, indicate the replicate co... |
| temp | Temperature of the sample at the time of sampling |
| temp_out | The recorded temperature value at sampling time outside |
| temperature | The value of a temperature measurement or temperature used in a process |
| term | pointer to an ontology class |
| tertiary_treatment | The process providing a final treatment stage to raise the effluent quality b... |
| tidal_stage | Stage of tide |
| tillage | Note method(s) used for tilling |
| tiss_cult_growth_med | Description of plant tissue culture growth media used |
| title | A name given to the entity that differs from the name/label programmatically ... |
| toluene | Concentration of toluene in the sample |
| too_short_contig_num | Number of contigs which were excluded from binning for length |
| tot_carb | Total carbon content |
| tot_depth_water_col | Measurement of total depth of water column |
| tot_diss_nitro | Total dissolved nitrogen concentration, reported as nitrogen, measured by: to... |
| tot_inorg_nitro | Total inorganic nitrogen content |
| tot_iron | Concentration of total iron in the sample |
| tot_nitro | Total nitrogen concentration of water samples, calculated by: total nitrogen ... |
| tot_nitro_cont_meth | Reference or method used in determining the total nitrogen |
| tot_nitro_content | Total nitrogen content of the sample |
| tot_org_c_meth | Reference or method used in determining total organic carbon |
| tot_org_carb | Definition for soil: total organic carbon content of the soil, definition oth... |
| tot_part_carb | Total particulate carbon content |
| tot_phosp | Total phosphorus concentration in the sample, calculated by: total phosphorus... |
| tot_phosphate | Total amount or concentration of phosphate |
| tot_sulfur | Concentration of total sulfur in the sample |
| total_bases | Total number of basepairs |
| train_line | The subway line name |
| train_stat_loc | The train station collection location |
| train_stop_loc | The train stop collection location |
| turbidity | Measure of the amount of cloudiness or haziness in water caused by individual... |
| tvdss_of_hcr_press | True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... |
| tvdss_of_hcr_temp | True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... |
| typ_occup_density | Customary or normal density of occupants |
| type | the class_uri of the class that has been instantiated |
| unbinned_contig_num | Number of contigs which did not end up in a medium or high quality bin |
| url | |
| uses_calibration | calibration information is used by a process |
| value | |
| vendor | |
| ventilation_rate | Ventilation rate of the system in the sampled premises |
| ventilation_type | Ventilation system used in the sampled premises |
| version | |
| vfa | Concentration of Volatile Fatty Acids in the sample |
| vfa_fw | Original volatile fatty acid concentration in the hydrocarbon resource |
| vis_media | The building visual media |
| viscosity | A measure of oil's resistance to gradual deformation by shear stress or t... |
| volatile_org_comp | Concentration of carbon-based chemicals that easily evaporate at room tempera... |
| volume | The volume of a substance |
| wall_area | The total area of the sampled room's walls |
| wall_const_type | The building class of the wall defined by the composition of the building ele... |
| wall_finish_mat | The material utilized to finish the outer most layer of the wall |
| wall_height | The average height of the walls in the sampled room |
| wall_loc | The relative location of the wall within the room |
| wall_surf_treatment | The surface treatment of interior wall |
| wall_texture | The feel, appearance, or consistency of a wall surface |
| wall_thermal_mass | The ability of the wall to provide inertia against temperature fluctuations |
| wall_water_mold | Signs of the presence of mold or mildew on a wall |
| was_generated_by | |
| was_informed_by | |
| wastewater_type | The origin of wastewater such as human waste, rainfall, storm drains, etc |
| water_cont_soil_meth | Reference or method used in determining the water content of soil |
| water_content | Water content measurement |
| water_current | Measurement of magnitude and direction of flow within a fluid |
| water_cut | Current amount of water (%) in a produced fluid stream; or the average of the... |
| water_feat_size | The size of the water feature |
| water_feat_type | The type of water feature present within the building being sampled |
| water_prod_rate | Water production rates per well (e |
| water_temp_regm | Information about treatment involving an exposure to water with varying degre... |
| watering_regm | Information about treatment involving an exposure to watering frequencies, tr... |
| websites | A list of websites that are associated with the entity |
| weekday | The day of the week when sampling occurred |
| win | A unique identifier of a well or wellbore |
| wind_direction | Wind direction is the direction from which a wind originates |
| wind_speed | Speed of wind measured at the time of sampling |
| window_cond | The physical condition of the window at the time of sampling |
| window_cover | The type of window covering |
| window_horiz_pos | The horizontal position of the window on the wall |
| window_loc | The relative location of the window within the room |
| window_mat | The type of material used to finish a window |
| window_open_freq | The number of times windows are opened per week |
| window_size | The window's length and width |
| window_status | Defines whether the windows were open or closed during environmental testing |
| window_type | The type of windows |
| window_vert_pos | The vertical position of the window on the wall |
| window_water_mold | Signs of the presence of mold or mildew on the window |
| workflow_execution_set | This property links a database object to the set of workflow executions |
| xylene | Concentration of xylene in the sample |
| zinc | Concentration of zinc in the sample |
Enumerations
Types
| Type | Description |
|---|---|
| Boolean | A binary (true or false) value |
| Bytes | An integer value that corresponds to a size in bytes |
| Curie | a compact URI |
| Date | a date (year, month and day) in an idealized calendar |
| DateOrDatetime | Either a date or a datetime |
| Datetime | The combination of a date and time |
| Decimal | A real number with arbitrary precision that conforms to the xsd:decimal speci... |
| DecimalDegree | A decimal degree expresses latitude or longitude as decimal fractions |
| Double | A real number that conforms to the xsd:double specification |
| ExternalIdentifier | A CURIE representing an external identifier |
| Float | A real number that conforms to the xsd:float specification |
| Integer | An integer |
| Jsonpath | A string encoding a JSON Path |
| Jsonpointer | A string encoding a JSON Pointer |
| LanguageCode | A language code conforming to ISO_639-1 |
| Ncname | Prefix part of CURIE |
| Nodeidentifier | A URI, CURIE or BNODE that represents a node in a model |
| Objectidentifier | A URI or CURIE that represents an object in the model |
| Sparqlpath | A string encoding a SPARQL Property Path |
| String | A character string |
| Time | A time object represents a (local) time of day, independent of any particular... |
| Unit | |
| Uri | a complete URI |
| Uriorcurie | a URI or a CURIE |
Subsets
| Subset | Description |
|---|---|