Microbial Experiment Schema
a data model for microbial strain experimental metadata.
The Microbial Experiment Schema is a data model (expressed in LinkML) used by microbial strain researchers in the Biosystems and Biomaterials Division at NIST.
The top-level representation of an experiment is contained in the abstract Experiment class. The expected specific metadata for each type of experiment are contained in sub-classes of Experiment, which correspond to experimental templates in the ELabFTW Electronic Lab Notebook software. Researchers enter metadata using an ELabFTW template, which is validated against this schema to ensure data integrity.
For a graphical overview of the schema structure, please see the following interactive visualization.
Classes
| Class | Description |
|---|---|
| ArrayValue | A class to hold an array of values |
| CFUMethodValue | An override of ArrayValue allowing only values from the CFUMethodEnum enum |
| FixationMethodValue | An override of ArrayValue allowing only values from the FixationMethodEnum enum |
| FluorescentProbeValue | An override of ArrayValue allowing only ELabItem values |
| |
(Deprecated) A named sub-class of ArrayValue to hold a list of microbial material links |
| MicrobialMaterialIDValue | A named sub-class of ArrayValue to hold a list of microbial material links |
| ModalitiesValue | A named sub-class of ArrayValue to hold a list of modality types |
| ObjectivesValue | An override of ArrayValue allowing only values from the ObjectivesEnum enum |
| SamplePurposeCodesValue | An override of ArrayValue allowing only values from the SamplePurposeCodeEnum enum |
| SeriesImageTypesValue | An override of ArrayValue allowing only values from the ImageTypeEnum enum |
| |
(Deprecated) An override of ArrayValue allowing only values from the TransmissionModeEnum enum |
| BooleanValue | A class to hold a boolean value |
| DateValue | A class to hold a date value |
| ELabItemValue | A class to hold a reference to an item record in ELabFTW |
| InstrumentIDValue | A named sub-class of ELabItemValue to hold an instrument identifier value |
| |
(Deprecated) A named sub-class of ELabItemValue to hold the instrument identifier |
| |
(Deprecated) A named sub-class of ELabItemValue to hold the operator identifier |
| |
(Deprecated) A named sub-class of ELabItemValue to hold the project identifier |
| OperatorIDValue | A named sub-class of ELabItemValue to hold an operator identifier value |
| ProjectIDValue | A named sub-class of ELabItemValue to hold a project identifier value |
| ELabRecord | An abstract data type representing a link to an record (experiment or resource/item) in an eLabFTW instance. Use one of the ELabItem or ELabRecord classes that implement this one rather than using it directly. |
| ELabExperiment | A class to hold metadata sufficient to reference an experiment record in an ELabFTW instance. |
| ELabItem | A class to hold metadata sufficient to reference a resource (database item) record in an ELabFTW instance. |
| ELabUser | A data type representing a link to a user in an eLabFTW instance |
| Experiment | Holds information about a specific type of Microbial Strain experiment. The specific metadata for each type of experiment is controlled by "template data classes" |
| CellCultureInBroth | Metadata describing a cell culture experiment |
| DifcoAmendedSporulationAgarProtocol | Metadata describing the preparation process for amended sporulation agar |
| ExperimentWithData | Holds information about a specific type of Microbial Strain experiment that results in the collection of data. The specific metadata for each type of experiment is controlled by "template data classes" |
| CFU | Metadata describing a colony forming unit counting experiment |
| ExperimentWithInstrument | Holds information about a specific type of Microbial Strain experiment that uses an instrument. The specific metadata for each type of experiment is controlled by "template data classes" |
| BactoBoxAcquisition | Metadata describing a data acquisition experiment using the BactoBox |
| CoulterAcquisition | Metadata describing a Coulter counter acquisition experiment |
| CytoFLEXAcquisition | Metadata describing a data acquisition using the CytoFLEX instrument |
| GenericTemplate | A generic experiment template used to help create more specific experiment templates. This template should not be used directly. |
| |
(Deprecated) A retired version of a generic experiment template used to create other templates |
| MicroscopyAcquisition | Metadata describing a microscopy acquisition experiment |
| NucleicAcidExtraction | Metadata describing a nucleic acid extraction experiment |
| ExperimentWithInstrumentNoData | Holds information about a specific type of Microbial Strain experiment that uses an instrument but does not collect data. The specific metadata for each type of experiment is controlled by "template data classes" |
| CytoFLEXVolumeCalibration | Metadata describing a volume calibration using the CytoFLEX instrument |
| FormaldehydeFixation | Metadata describing a formaldehyde fixation experiment |
| InitiateGrowthOfBSpizizenii | Metadata describing an initiate growth experiment of B. spizizenii |
| LogCOMETSamplePrep | Metadata describing a sample preparation process for a LOGComet experiment |
| SlideCleaning | Metadata describing an experiment preparing microscopy slides for microbial work |
| NumberValue | A class to hold a numerical value with a free-text string as a unit |
| AgitationValue | A class to hold a numerical value representing an agitation speed |
| CountValue | A class to hold a numerical value representing a counting measurement |
| DurationValue | A class to hold a numerical value representing a time duration measurement |
| FlowRateValue | A class to hold a numerical value representing a flow rate measurement |
| LengthValue | A class to hold a numerical value representing a linear measurement |
| TemperatureValue | A class to hold a numerical value representing a temperature measurement |
| UnitlessValue | A class to hold an explicitly unitless numerical value |
| VolumeValue | A class to hold a numerical value representing a volumetric measurement |
| StringValue | A class to hold a string value |
| BactoBoxAcquisitionTemplateNameValue | An override of StringValue specified an allowed value for the template_name for a BactoBox_Acquisition experiment |
| CellCultureInBrothTemplateNameValue | An override of StringValue specified an allowed value for the template_name for a Cell Culture in Broth experiment |
| CFUTemplateNameValue | An override of StringValue specified an allowed value for the template_name for a CFU experiment |
| CoulterAcquisitionTemplateNameValue | An override of StringValue specified an allowed value for the template_name for a Coulter_Acquisition experiment |
| CytoFLEXAcquisitionTemplateNameValue | An override of StringValue specified an allowed value for the template_name for a CytoFLEX_Acquisition experiment |
| CytoFLEXVolumeCalibrationTemplateNameValue | An override of StringValue specified an allowed value for the template_name for a CytoFLEX_VolumeCalibration experiment |
| DifcoAmendedSporulationAgarProtocolTemplateNameValue | An override of StringValue specified an allowed value for the template_name for a Difco Amended Sporulation Agar Protocol experiment |
| FCInjectionModeValue | An override of StringValue allowing only values from the FCInjectionModeEnum enum |
| FormaldehydeFixationTemplateNameValue | An override of StringValue specified an allowed value for the template_name for a FormaldehydeFixation experiment |
| IncubationAtmosphereValue | An override of StringValue allowing only values from the IncubationAtmosphereEnum enum |
| InitiateGrowthOfBSpizizeniiTemplateNameValue | An override of StringValue specified an allowed value for the template_name for a Initiate Growth of B spizizenii experiment |
| LogCOMETSamplePrepTemplateNameValue | An override of StringValue specified an allowed value for the template_name for a LogCOMET_SamplePrep experiment |
| MicroscopyAcquisitionTemplateNameValue | An override of StringValue specified an allowed value for the template_name for a Microscopy_Acquisition experiment |
| NucleicAcidExtractionTemplateNameValue | An override of StringValue specified an allowed value for the template_name for a Nucleic Acid Extraction experiment |
| NucleicAcidTypeValue | An override of StringValue allowing only a value from the NucleicAcidTypeEnum enum |
| SlideCleaningTemplateNameValue | An override of StringValue specified an allowed value for the template_name for a SlideCleaning experiment |
| UriValue | A class to hold a string value that is a URI |
Slots
| Slot | Description |
|---|---|
| (Deprecated) Data acquisition time as set by instrument | |
| (Deprecated) Data acquisition volume as set by instrument | |
| api_url | A URL for accessing this item via the eLabFTW API |
| base_url | The URL of the ELabFTW instance in which the user is registered |
| (Deprecated) Lot number of beads used for quality control of concentration measurements | |
| (Deprecated) Lot number of beads used for quality control of size measurements | |
| category_title | The name of the category for this item (called an "item type") in eLabFTW |
| (Deprecated) Volume of cell stock added to acquisition vessel | |
| cfu_method | Describes deposition format of cells on agar plate |
| core_data_path | Portion of the data pathway that will not change as the template is used to g... |
| (Deprecated) Aperture installed on Coulter counter during measurement | |
| data_acquisition_date | Date on which data were acquired according to eLabFTW record |
| (Deprecated) Which diluent was used to suspend cells for acquisition (linked item) | |
| (Deprecated) Volume of diluent added to acquisition vessel | |
| elab_experiment | A self-reference to this experiment record |
| elabid | The unique "eLabID" for this item |
| The user's email address | |
| (Deprecated) Indicates if a known error appears in the dataset | |
| (Deprecated) Set number of events to acquire in a particular gate on flow cytometer | |
| fc_acquisition_threshold_channel | Which channel as named by the manufacturer was used to threshold the data acq... |
| fc_acquisition_threshold_value | Threshold value in arbitrary units that defines the lower limit of data acqui... |
| fc_flow_rate_setting | Set flow rate of data acquisition on flow cytometer |
| (Deprecated) List of fluorescent channels acquired during a flow cytometry experiment as n... | |
| fc_injection_mode | Sample acquisition format in flow cytometer |
| first_name | The user's first (given) name |
| fixation_method | Specific treatment applied to cells to prevent future changes |
| fluorescent_probe | Fluorescent probe(s) used in the experiment, as linked item(s) from ELabFTW |
| (Deprecated) Time that cells were incubated to encourage growth | |
| growth_media_name | Name of media used to culture cells (linked item from ELabFTW) |
| id | The integer identifier for this item used by this eLabFTW instance |
| incubation_agitation | Speed of agitation that cells were incubated during an experiment |
| incubation_atmosphere | Atmosphere that cells were incubated in to encourage growth |
| incubation_duration | Length of time that cells were incubated during an experiment |
| incubation_temperature | Temperature at which cells were incubated during an experiment or culture |
| instrument_id | The instrument used to acquire the data in an experiment (linked item from EL... |
| kit_lot_number | The lot number of any relevant kits (linked item from ELabFTW) |
| (Deprecated) Date on which data were acquired according to eLabFTW record | |
| (Deprecated) Date on which data were acquired according to eLabFTW record | |
| (Deprecated) Cell material(s) used in experiment as named in the eLabFTW database (linked ... | |
| (Deprecated) Instrument operator during an experiment (a linked item from ELabFTW) | |
| (Deprecated) The project that an experiment supports (link to an ELabFTW item) | |
| last_name | The user's last name (surname) |
| library_prep | The name of a specific kit used for sequencing preparation steps |
| microbial_material_id | Cell material(s) used in experiment as named in the eLabFTW database (linked ... |
| modalities | The type (modality) of a microscopy acquisition experiment |
| nucleic_acid_type | The type of nucleic acid used in an extraction experiment |
| objective | The microscope objectives used in a microscopy acquisition experiment |
| operator_id | Instrument operator during an experiment (a linked item from ELabFTW) |
| orcid | The user's ORCID (if defined) |
| passed_volume_calibration | (?) The volume that is passed during a volume calibration |
| percent_volume_deviation | The volume deviation (measured volume divided by target volume) from a calibr... |
| project_id | The project that an experiment supports (link to an ELabFTW item) |
| (Deprecated) The lot number for a QC reagent (link to an ELabFTW item) | |
| sample_purpose_codes | The types of samples acquired in an experiment (from a controlled list) |
| series_image_types | The types of series images acquired in an experiment |
| series_images | Whether series images were acquired in an experiment |
| single_images | Whether single images were acquired in an experiment |
| specific_data_path | Portion of the data pathway specific to data from a given experimental record... |
| status_title | The status title of an ELabFTW resource |
| template_name | The name of the template used to collect metadata for an experiment in ELabFT... |
| title | A short description of this item |
| (Deprecated) The type (modality) of a microscopy acquisition experiment | |
| type | Whether this item is a resource (database item) or an experiment |
| unit | The unit corresponding to a metadata value |
| url | A (resolvable) URL for accessing this item via a web browser |
| userid | The "local" identifier number for this user in the eLabFTW instance |
| value | The actual metadata value for an attribute |
Enumerations
| Enumeration | Description |
|---|---|
| AgitationEnum | Allowed agitation speed unit type values |
| CFUMethodEnum | Allowed colony forming unit count method values |
| CountUnitEnum | Allowed count unit type values |
| DurationUnitEnum | Allowed time duration unit type values |
| ELabExperimentType | Allowed record type value for an ELabFTW experiment |
| ELabItemType | Allowed record type value for an ELabFTW item/resource |
| FCInjectionModeEnum | Allowed flow cytometry injection mode values |
| FixationMethodEnum | Allowed fixation method values |
| FlowRateUnitEnum | Allowed flow rate unit type values |
| ImageTypeEnum | Allowed microscopy image type values |
| IncubationAtmosphereEnum | Allowed cell incubation atmosphere values |
| LengthUnitEnum | Allowed linear length unit type values |
| MicroscopyModalitiesEnum | Allowed microscopy modality values |
| NucleicAcidTypeEnum | Allowed nucleic acid type values |
| ObjectivesEnum | Allowed microscopy objective values |
| SamplePurposeCodeEnum | Allowed sample purpose code values |
| TemperatureUnitEnum | Allowed temperature unit type values |
| (Deprecated) Allowed microscopy transmission mode values | |
| UnitlessEnum | Allowed value for "unitless" numerical values |
| VolumeUnitEnum | Allowed volume unit type values |
Types
| Type | Description |
|---|---|
| Boolean | A binary (true or false) value |
| 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... |
| Double | A real number that conforms to the xsd:double specification |
| 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 |
| 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... |
| Uri | a complete URI |
| Uriorcurie | a URI or a CURIE |
Subsets
| Subset | Description |
|---|---|