Part 4 – Metadata and Databasing

This section defines the metadata fields used to describe spectral reflectance measurements of herbarium specimens. This standardization supports interoperability, cross-project data aggregation, and future integration into biodiversity informatics platforms.

Projects can download the IHerbSpec Metadata Spreadsheet (available at https://iherbspec.github.io/protocol) as a foundation for organizing their metadata. This spreadsheet includes all required and optional but recommended fields defined the tables in Section 4.1. The controlled vocabularies necessary for enumerating certain fields are provided in Section 4.2. Finally, Section 4.3 provides general guidelines for data and metadata storage and dissemination.

While metadata are expected to be disseminated in a flat file format, such as the IHerbSpec Metadata Spreadsheet, fields are presented here in logical groups—project, specimen, and tissue—to support conceptual understanding and integration with local databases.

4.1 Metadata Tables

Table 4.1: Session Metadata

Session metadata are those metadata usually associated globally with a continuous digitization project. These metadata can usually be captured once per project and automatically populated for each measurement instance.

Metadata Field	Filename Code (Table 3.2)	Status	Field Description	Data Type
`projectId`	`PI`	Required	Unique identifier for the spectral measurement project. Example: `HUHERYspec1`.	TEXT
`sessionId`	`SN`	Required	Unique identifier for a measurement session, generated as `YYYYMMDDHHMM`. Example: `20240617132251`.	TEXT
`instrumentModel`	-	Required	Spectroradiometer model name. Example: `SVC HR-1024i`.	TEXT
`opticalSetupDescription`	-	Required	Description of optical probe setup. Example: `LC-RP contact probe with leaf clip removed`.	TEXT
`measurementSettings`	-	Required	Instrument settings for measurements. Example: `2 seconds, high light setting`.	TEXT
`whiteReferenceDescription`	-	Required	Material of the white reference. Example: `Spectralon SL Standard 99%`.	TEXT
`operator`	-	Optional	Name(s) of person(s) conducting measurements.	TEXT
`lightSourceType`	-	Optional	Light source for optical setup. Example: `tungsten halogen`.	TEXT
`distanceTargetToSensor`	-	Optional	Distance (mm) between target tissue and sensor face. Example: `12`.	NUMERIC
`lensFieldOfView`	-	Optional	Angle (degrees) of sensor field of view. Example: `22.5`.	NUMERIC
`angleLightToSensor`	-	Optional	Angle (degrees) of light source to sensor. Example: `10`.	NUMERIC
`measurementAreaDiameter`	-	Optional	Diameter (mm) of illuminated tissue area. Example: `6`.	NUMERIC

1: **Fig. 4.1.** Schematic of Session Metadata fields related to optical setup (see Table 4.1). `distanceTargetToSensor`, `fieldOfView`, `angleLightToSensor`, `measurementAreaDiameter`

Table 4.2: Specimen Metadata

Specimen metadata include identifiers and information about the physical specimen, with priority given to required fields needed to link spectral measurements to existing digital records (e.g., specimenId). Optional fields related to taxonomic determination and specimen storage environment are included to support integrative research, quality control, and downstream analysis.

Users should avoid duplicating metadata that are already digitized, maintained, and available in herbarium or institutional platforms, as these sources are better suited for future updates. Instead, users are encouraged to reference those records and supplement only missing required or recommended fields. Due to variation in the metadata recorded on institutional platforms, users should apply caution in the interpretation of presence or absence of determination information or any other recommended but optional fields.

Metadata Field	Filename Code (Table 3.2)	Status	Field Description	Data Type
`herbariumCode`	`HC`	Required	Acronym for herbarium or collection (Index Herbariorum code). Examples: `GH`, `P`, `US-Botany`.	TEXT
`specimenId`	`SI`	Required	Identifier for specimen or record (catalog no., barcode, GUID, or collector+number). Examples: `00238762`, `Thorne24070a`.	TEXT
`scientificName`	-	Optional	Full scientific name at lowest confident rank. Examples: Quercus bicolor, Erythroxylum coca ipadu.	TEXT
`identificationQualifier`	-	Optional	Uncertainty in taxonomic ID (Darwin Core). Examples: `cf.`, `aff.`	TEXT
`identifiedBy`	-	Optional	-	Person/group who made the identification. Example: `T. Plowman`.	TEXT
`dateIdentified`	-	Optional	Date of identification. Examples: `1999`, `2004-12-30`.	TEXT
`isTempControlled`	-	Optional	Whether storage has active temperature control.	BOOLEAN
`annualTempMin`	-	Optional	Minimum annual storage temperature (°C). Example: `18`.	TEXT
`annualTempMax`	-	Optional	Maximum annual storage temperature (°C). Example: `26`.	TEXT
`isHumidityControlled`	-	Optional	Whether storage has active humidity control.	BOOLEAN
`annualHumidityMin`	-	Optional	Minimum annual storage relative humidity (%). Example: `20`.	TEXT
`annualHumidityMax`	-	Optional	Maximum annual storage relative humidity (%). Example: `60`.	TEXT

Table 4.3: Tissue Metadata

Fields describing the type, condition, and position of the tissue measured. Includes required and recommended metadata for linking spectral measurements to individual tissue units. Note that timestamps for tissue measurement files are often captured within the file.

Metadata Field	Filename Code (Table 3.2)	Status	Field Description	Data Type
`backgroundClass`	`BG`	Required	EEnumerated abbreviated code from Background Class Codes Table 4.7 describing the type of background used behind target tissue. Both abbreviated codes and descriptive codes are accepted. Examples: `BGW`, `BGB`, `BGP`.	ENUM Table 4.7
`hasLowReflectanceBackground`	-	Required	True or False statement that the background (black or paper) has low reflectance as defined as less than 4% reflectance across the spectral range of the instrument. For a paper background, this would be scored `false`.	BOOLEAN
`backgroundDescription`	-	Cond. Req.	Description of the black or other background material, including manufacturer and product information when available. Not required for paper backgrounds. Required field when tissue has black or other type (not paper) of background. Example: `Musou IR Flock`	TEXT
`targetClass`	`TC`	Required	Free text or enumerated code from Target Class Codes (Table 4.5) describing type of tissue or background being measured. Both abbreviated codes and full codes can be used. Examples: `AD`, `perigynium`.	TEXT or ENUM (Table 4.5)
`targetTissueId`	`TN`	Optional	Character index tracking the measured tissue units when multiple tissues are measured from a single specimen (e.g., `loose1`, `1`, `2`). For compound or more complex structures, projects are encouraged to develop their own consistent naming convention. Examples: `loose1`, `leaflet1`, `petal1`.	TEXT
`tissueDevelopmentalStage`	-	Required	Tissue developmental stage as coded in Developmental Stage Class Codes Table 4.4. Examples: `Mature`, `Uncertain`.	ENUM Table 4.4
`hasBackgroundInMeasurement`	-	Required	True or false values indicating that the target tissue does not cover the full measurement area and the background is part of the measurement.	BOOLEAN
`percentBackgroundInMeasurement`	-	Optional	Numeric estimate for the percentage of the measurement area that is not covered by the target tissue and is background material (black background or herbarium paper). It is recommended to describe the estimation method in the comment field. Example: `25`.	INTEGER
`hasGlue`	-	Required	True/False/Uncertain: glue present in measurement area.	ENUM (true/false/uncertain)
`hasNonGlueContamination`	-	Required	True, false, or uncertain values indicating a contaminant other than glue is present in the measurement area. This includes foreign biotic or abiotic agents on the target tissue, such as fungus or preservatives.	ENUM (true/false/uncertain)
`measurementFlags`	-	Optional	SStandardized categorical descriptors of the condition of the tissue within the measurement area. Values are selected from the predefined Tissue Descriptor Codes Table 4.6. Multiple descriptors should be separated with a pipe character (`\|`). Example: `GoodPreservation\|PathogenPresent`.	ENUM (Table 4.6)
`tissueNotes`	-	Optional	Free-text field used to record additional observations on the condition of the specimen that may aid interpretation of spectral data. It can be used to clarify or elaborate on descriptors already included in measurementFlags, such as the conditions evidencing the quality of preservation (e.g., a MediumPreservation flag could be explained with the note, ‘measurement area discolored and wrinkled’). Notes should specify whether the information applies to the measurement area, the tissue unit, or the specimen as a whole. Examples: `mold in measurement area`, `formaldehyde preserved`.	TEXT
`tissueLocation`	-	Optional	The location of the target tissue on the herbarium sheet. For mounted tissues, record as an `X,Y` coordinate in centimeters, with `0,0` at the top-left corner of the sheet (e.g., `17,29`; see Fig. 4.2). If the sheet has non-square angles, align it flush with the left-side ruler. For unmounted tissues, provide a descriptive note indicating location. Examples: `17,29`, `envelope TCAD_TN1`.	TEXT (coordinates preferred)
`comment`	-	Optional	Free-text field for recording any additional notes relevant to the measurement, including observations about the instrument, session, specimen, tissue, or data quality that are not captured elsewhere in the metadata. Example: `Amazing specimen.`	TEXT
`measurementIndex`	`IDX`	Required	The measurement number index appended to the base filename (Part 3, Table 3.2: IDX) to properly associate each row of metadata with its single, corresponding measurement file. Example: `0001`.	TEXT

2: **Fig. 4.2**: Diagram of coordinate system for scoring `tissueLocation` in Tissue Metadata. Herbarium sheet is placed on top of the benchtop black background with centimeter rulers at top and left sides for ‘`x,y`’ notation of measurement area (white dashed circles) in centimeters with `0,0` at the top left. Black background cards are placed under unglued portions of leaves. From left to right, tissue `TCAB_TN3` has the location `10,26`, tissue `TCAD_TN2` has location `17,16` and tissue `TCAD_TN1` is stored with a label in a glassine envelope inside the packet with location `envelope TCAD_TN1`. For reference, specimen NEBC_00651639 metadata fields are proposed in Appendix II. Specimen courtesy of the New England Botanical Society.

4.2 Controlled Vocabularies

Table 4.4: Developmental Stage Class Codes

Available codes for enumerating the required tissueDevelopmentalStage metadata Table 4.3. Codes follow ‘CamelCase’ format with capitalized initial letters.

Code	Description
`Young`	Actively developing tissue that is not yet fully expanded; may appear thinner, lighter in color, or more pliable than mature tissue.
`Mature`	Fully developed and expanded tissue showing typical structural and color characteristics for the taxon; not visibly senescent.
`Old`	Senescent tissue showing visible signs of aging or decline, such as yellowing, darkening, curling, or drying.
`Uncertain`	The development stage has been assessed but cannot be confidently determined due to intermediate features, damage, or insufficient visual cues.
`NotScored`	Developmental stage was not assessed or recorded for this tissue.

Table 4.5: Target Class Codes.

Available codes for enumerating the required targetClass metadata Table 4.3. Either the abbreviated code or the full CamelCase-formatted code (with an initial capital letter) may be used.

Code	Full code	Description
`W`	`WhiteReference`	White reference.
`WC`	`WhiteCalibratedReference`	White calibrated reflectance standard (see Section 5.3).
`B`	`BlackBackground`	Black background material, recorded when used as background for other target tissue measurements.
`BC`	`BlackCalibratedReference`	Black calibrated reflectance standard (see Section 5.3).
`P`	`Paper`	Herbarium sheet paper, recorded when used as background for other target tissue measurements.
`AB`	`LeafAbaxial`	Abaxial leaf surface.
`AD`	`LeafAdaxial`	Adaxial leaf surface.
`LF`	`Leaf`	Leaf surface. Applied when the abaxial and adaxial side cannot be differentiated or when leaves are terete or otherwise not bifacial (e.g. Senecio rowleyanus).
`PT`	`Petal`	Petal.
`IF`	`Inflorescence`	Inflorescence.
`BR`	`Bract`	Bract.
`FR`	`Fruit`	Fruit. The specific tissue (e.g., exocarp, mesocarp) can be described in tissueNotes.
`PSS`	`Photosynthetic-SucculentStem`	Photosynthetic stem as in succulents like Cactus.
`OB`	`OuterBark`	Outer bark, rhytidome. Woody branch outer bark as in Hadlich et al. (2018).
`IB`	`InnerBark`	Phloem. Woody branch inner bark as in Hadlich et al. (2018).
`HS`	`HerbaceousStem`	Herbaceous stem; can be photosynthetic as in PSS.
`WD`	`Wood`	Wood.

Table 4.6: Tissue Descriptor Codes

Code	Description
`GoodPreservation`	Tissue in the measurement area appears well preserved in color, structure, and texture (including original features from disease or herbivory) and shows minimal signs of degradation or breakage from pressing, drying, or storage. Tissues that are simply discolored may still be considered well preserved if other aspects of integrity are maintained.
`MediumPreservation`	Tissue in the measurement area shows moderate degradation, such as partial discoloration, wilting, or deformation. Some structural loss may be present, though not severe. Evidence of degradation from other parts of the specimen (e.g., mold elsewhere on the tissue) may support assigning this level of preservation, but such observations should be recorded in tissueNotes if not present within the measurement area. This is expected to be the most common preservation condition for herbarium specimens used in spectral measurement.
`PoorPreservation`	Tissue in the measurement area shows clear signs of degradation, including severe discoloration, wrinkling, deformation, or breakage. Mold, insect damage, or other signs of poor preservation may also be present. As with other flags, evidence of degradation outside the measurement area (e.g., mold elsewhere on the tissue) may support the assigned flag but should be recorded in tissueNotes if not directly observed in the measurement area. Note that natural discoloration tendencies of certain taxa should be considered when applying this flag (see Appendix II).
`MidveinPresent`	Target measurement area contains midvein or similarly prominent secondary venation.
`OrganismPresent`	Indicates that a visible organism (e.g., bryophyte, lichen, fungal structure) is present on or within the measurement area. This includes epiphyllous, endophytic, or other leaf-associated organisms, regardless of their ecological role (e.g., mutualistic, parasitic, or incidental). This flag serves as a general indicator and can be used in conjunction with more specific organism flags below.
`BryophytePresent`	Indicates that a visible bryophyte (e.g., moss, liverwort, or hornwort) is present on or within the measurement area.
`LichenPresent`	Indicates that a visible lichen thallus or fragment is present on or within the measurement area.
`FungusPresent`	Indicates that fungal structures are visible in the measurement area (e.g., hyphae, mycelium, fruiting body) and are presumed to be pre-mortem associates, such as endophytes or pathogens active while the plant was alive. This flag can overlap with PathogenPresent or MoldPresent.
`PathogenPresent`	Target measurement area contains necrotic tissue or other signs of pathogenic infection. Can be used with FungusPresent when fungal pathogens are suspected or known. This flag is based on visible tissue symptoms, not molecular confirmation.
`MoldPresent`	Indicates that the measurement area shows signs of post-mortem fungal growth (e.g., surface mold, fuzz, bloom), likely resulting from poor drying or storage conditions. In practice, mold may be difficult to distinguish from other fungal growth without microscopic or culture analysis. Use judgment and note uncertainty in tissueNotes if needed.
`HerbivoryPresent`	Target measurement area contains herbivory.
`AlcoholPresent`	Target measurement area was preserved with ethanol or other alcohol.
`PreservativePresent`	Target measurement area contains chemical preservative contamination excluding alcohol preservatives (e.g., diatoms, formaldehyde).
`BurnPresent`	Target measurement area contains burned tissue.
`DebrisPresent`	Target measurement area contains non-specific material not described in other codes (e.g., dust, soil particles, insect parts, fibers, etc.) that may interfere with clean measurements. Can be elaborated in the tissueNotes field.

Table 4.7: Background and White Reference Class Codes

Available codes for enumerating the required tissueBackgroundClass metadata Table 4.3. Either the abbreviated code or the full CamelCase with initial capital letter jformatted code may be used.

Code	Full code	Description
`W`	`WhiteReference`	White reference.
`B`	`BlackBackground`	Black background (<4% reflectance).
`P`	`PaperBackground`	Herbarium sheet paper.
`O`	`OtherBackground`	Other background material (must be described in metadata).

Navigate the protocol

Proceed to Part 5

Browse additional parts and appendices:

Part 1 – Overview
Part 2 – Measurement and Metadata Workflow
Part 3 – Filename Conventions and Formats
Part 4 – Metadata and Databasing
Part 5 – Instrumentation and Materials Guidelines
Part 6 – Selecting Tissues for Spectral Measurement
References
Appendix I – Number of Measurements per Tissue
Appendix II – Tissue Metadata for Quality Control