isLeastSpecificTargetCategoryQuantityInclusive Guidelines

Title

isLeastSpecificTargetCategoryQuantityInclusive Guidelines

Date version issued

2024-02-28

Date created

2024-02-28

Part of TDWG Standard

http://www.tdwg.org/standards/450

This version

http://rs.tdwg.org/dwc/doc/inclusive/2024-02-28

Latest version

http://rs.tdwg.org/dwc/doc/inclusive/

Abstract

The Humboldt Extension for ecological inventories mints the term eco:isLeastSpecificTargetCategoryQuantityInclusive to describe how to treat counts of organisms when records from a single dwc:Event include multiple target categories. This document describes how to use that term.

Contributors

Yi-Ming Gan (Royal Belgian Institute of Natural Sciences), Wesley M. Hochachka (Cornell Lab of Ornithology), John Wieczorek (VertNet), Yanina V. Sica (Yale University), Peter Brenton (Atlas of Living Australia, CSIRO), Steven J. Baskauf (Vanderbilt University Libraries)

Creator

TDWG Humboldt Extension Task Group

Bibliographic citation

TDWG Humboldt Extension Task Group. 2024. isLeastSpecificTargetCategoryQuantityInclusive Guidelines. Biodiversity Information Standards (TDWG). http://rs.tdwg.org/dwc/doc/inclusive/2024-02-28

1 Introduction (non-normative)

This document elaborates upon the meaning and use of the term eco:isLeastSpecificTargetCategoryQuantityInclusive. Use of this term is necessary in order to describe how to treat counts of organisms (or any other organisms quantity) when records from a single dwc:Event (http://rs.tdwg.org/dwc/terms/Event) include multiple target categories (e.g., taxonomic ranks within a higher rank or different life stages for the same species). For example, a statement whether the least specific target category quantity is inclusive should be reported when an dwc:Event includes records reporting quantities that are associated with subcategories (e.g., subspecies) and records reporting quantities for more general categories (e.g., the species). In this example, the higher taxon rank (i.e., species) is the least specific category, because it is more general than the subspecies category nested below it. Species and subspecies are just one example of a pair of category and subcategory. Other examples of subcategories are life stages (e.g., “adult”, “larva”, “egg”), and sexes.

1.1 Status of the content of this document

Sections 3 of this document is normative. The other sections are non-normative.

1.2 RFC 2119 key words

The key words “MUST”, “MUST NOT”, “REQUIRED”, “SHALL”, “SHALL NOT”, “SHOULD”, “SHOULD NOT”, “RECOMMENDED”, “MAY”, and “OPTIONAL” in this document are to be interpreted as described in BCP 14 [RFC2119] [RFC8174] when, and only when, they are written in capitals (as shown here).

1.3 Namespaces and terminology

The namespace eco: abbreviates http://rs.tdwg.org/eco/terms/ and is used with terms minted for the Humboldt Extension for ecological inventories. dwc: abbreviates http://rs.tdwg.org/dwc/terms/, and is used with terms in the main Darwin Core vocabulary namespace. Words in code markup are term IRIs or literal values. The word “organisms” is used colloquially and is not used in the technical sense of the dwc:Organism class.

2 Rationale (non-normative)

The term eco:isLeastSpecificTargetCategoryQuantityInclusive was introduced into the Humboldt Extension for ecological inventories late in development, after testing it with real-world cases (Sica et al., 2022). Testing revealed that the quantities of organisms stored in two major biodiversity databases — OBIS (OBIS, 2023) and eBird (Sullivan et al., 2014) — need to be treated differently in order to calculate the total quantity of organisms in the least specific category. In the specific case of data in the OBIS database, the information for a single dwc:Event can contain multiple records for a species, with one record for a species listing the quantity of individual organisms for the species without specifying any subcategory of life stage, and other records for the same species in the same dwc:Event listing quantities for different life stages (e.g., one record for adults and another record for juveniles). In this example the single dwc:Event will contain 3 records: one for the species without any life stage specified, one for adults of the species, and one for juveniles of the species. For the OBIS data, the quantity in the record for which no life stage is specified is the sum of three quantities: the number of juveniles, the number of adults, and the number of individuals that were not recorded as belonging to any specific life stage. In other words, when using OBIS data, the total quantity of individuals recorded for a species, across all life stages combined, has been pre-calculated and stored in the database; unless the quantities of individuals within specific life stages are of interest, the information in the life stage subcategories can be ignored. The value of the term eco:isLeastSpecificTargetCategoryQuantityInclusive in this case would be true - the least specific category (species without any life stage specified) already includes the counts of the more specific subcategories.

eBird stores information about quantities of organisms differently. For the example of a dwc:Event that contains separate records for subspecies and their parent species, the total number of individuals of the species needs to be calculated by the end user as the sum of the quantity reported for the species plus the quantities reported for the subspecies. In other words, the total quantity of organisms of each species has not been pre-calculated and must be derived by the end user. The value of the term eco:isLeastSpecificTargetCategoryQuantityInclusive in this case would be false - the least specific category (species) does not include the counts of the more specific subcategories (subspecies).

In summary, the term eco:isLeastSpecificTargetCategoryQuantityInclusive is required to inform the end user of whether they will need to derive the total quantity of organisms for the least specific category (e.g., for a species), or whether this total quantity has already been calculated prior to the data being entered into the database. Note that, if a dataset contains only simple targets that have no subcategories, the result of the term eco:isLeastSpecificTargetCategoryQuantityInclusive being true or false is exactly the same - the count is the total in either case. Only in this circumstance does the term not strictly need to be populated. However, given that data records acquire a “life of their own” separate from their associated metadata when aggregated from multiple data sets, best practice is to include and populate the term eco:isLeastSpecificTargetCategoryQuantityInclusive.

3 Usage guidelines (normative)

The term eco:isLeastSpecificTargetCategoryQuantityInclusive is defined as “The total detected quantity of organisms for a dwc:Taxon (including subsets thereof) in a dwc:Event is given explicitly in a single record (dwc:organismQuantity value) for that dwc:Taxon.”

Values MUST be true and false. If true, the dwc:organismQuantity values for a dwc:Taxon in an dwc:Event is inclusive of all organisms of the dwc:Taxon (including more specific scopes such as different life stages or lower taxonomic ranks) and the total detected quantity of organisms for that dwc:Taxon in the dwc:Event MUST NOT be determined by summing the dwc:organismQuantity values for all records of the dwc:Taxon in the dwc:Event. Instead, the total detected quantity of organisms for the dwc:Taxon in an dwc:Event MUST be reported in a single record for the dwc:Taxon in the dwc:Event, with this record having no further specific scopes. In this case the sum of dwc:organismQuantity values for the reported subsets of the dwc:Taxon MUST NOT exceed the value of dwc:organismQuantity for the single record for the dwc:Taxon without subsets (i.e., the total). If false, the dwc:organismQuantity values for a dwc:Taxon in an dwc:Event MUST be added to get the total detected quantity of organisms for that dwc:Taxon in the dwc:Event.

4 Examples (non-normative)

4.1 Single dwc:Taxon example

As an example of the difference between true and false values for eco:isLeastSpecificTargetCategoryQuantityInclusive, suppose there are three records (see Table 1) with dwc:organismQuantity for a dwc:Taxon (taxon_01) for an dwc:Event (event_01). One record is for adults of the dwc:Taxon with dwc:organismQuantity = 1 and dwc:organismQuantityType = individuals, one record is for juveniles of the dwc:Taxon with dwc:organismQuantity = 2 and dwc:organismQuantityType = individuals, and one record is for the dwc:Taxon without specifying the life stage and with dwc:organismQuantity = 4 and dwc:organismQuantityType = individuals.

If eco:isLeastSpecificTargetCategoryQuantityInclusive is true for event_01, then the total number of individuals of taxon_01 for the dwc:Event is 4 (the least specific dwc:Taxon record — the one with no more specific scopes — includes all individuals of the dwc:Taxon). This means that there was 1 adult, 2 juveniles and 1 individual of taxon_01 whose life stage was not recorded.

If eco:isLeastSpecificTargetCategoryQuantityInclusive is false for event_01, then the total number of individuals of taxon_01 for the dwc:Event is 7 (the least specific dwc:Taxon record - the one with no more specific scopes - does not include all individuals of the dwc:Taxon, rather, it is a separate category that must also be added to get the total). This means there was 1 adult, 2 juveniles and 4 individuals of taxon_01 whose life stage was not recorded.

Table 1. Organism quantities in dwc:Occurrence records

4.2 Nested taxa example

Suppose there are three records (see Table 2) with dwc:organismQuantity for three taxa (Hirundo rustica and two subspecies) for a dwc:Event (event_01). The record for the species has dwc:organismQuantity = 3 and dwc:organismQuantityType = individuals. The record for H. r. rustica has dwc:organismQuantity = 2 and dwc:organismQuantityType = individuals. The record for H. r. gutturalis has dwc:organismQuantity = 4 and dwc:organismQuantityType = individuals.

If eco:isLeastSpecificTargetCategoryQuantityInclusive is true for event_01, then the total number of individuals of the species H. rustica for the dwc:Event is 3 (the least specific dwc:Taxon record includes all individuals of the dwc:Taxon). This means there were 2 H. r. rustica, 1 H. r. gutturalis, and no other H. rustica of any kind detected.

If eco:isLeastSpecificTargetCategoryQuantityInclusive is false for event_01, then the total number of individuals of the species H. rustica for the dwc:Event is 6 (the least specific dwc:Taxon record does not include all individuals of the dwc:Taxon). This means there were 2 H. r. rustica, 1 H. r. gutturalis, and 3 other H. rustica detected that were not identified to subspecies.

Table 2. Organism quantities in dwc:Event records

5 References

OBIS (2023) Ocean Biodiversity Information System. Intergovernmental Oceanographic Commission of UNESCO. https://www.obis.org/.

Sica Y. V., K. Ingenloff, Y-M GAN, Z. Kachian, S. J. Baskauf, J. Wieczorek, P. F. Zermoglio, R. D. Stevenson (2022). Application of Humboldt Extension to Real-world Cases. Biodiversity Information Science and Standards 6: e91502. https://doi.org/10.3897/biss.6.91502

Sullivan, B. L., J. L. Aycrigg, J. H. Barry, R. E. Bonney, N. Bruns, C. B. Cooper, T. Damoulas, A. A. Dhondt, T. Dietterich, A. Farnsworth, D. Fink, et al. (2014). The eBird enterprise: an integrated approach to development and application of citizen science. Biological Conservation 169:31-40. https://10.1016/j.biocon.2013.11.003