Limits...
Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens.

Kilian N, Henning T, Plitzner P, Müller A, Güntsch A, Stöver BC, Müller KF, Berendsohn WG, Borsch T - Database (Oxford) (2015)

Bottom Line: Structured character data are therefore not only needed for the knowledge generation process but also for easily adapting characterizations of taxa.We aim to facilitate the construction and reproducibility of taxon characterizations from structured character data of changing sample sets by establishing a stable and unambiguous association between each sampled individual and the data processed from it.Our workflow implementation uses the European Distributed Institute of Taxonomy Platform, a comprehensive taxonomic data management and publication environment to: (i) establish a reproducible connection between sampled individuals and all samples derived from them; (ii) stably link sample-based character data with the metadata of the respective samples; (iii) record and store structured specimen-based character data in formats allowing data exchange; (iv) reversibly assign sample metadata and character datasets to taxa in an editable classification and display them and (v) organize data exchange via standard exchange formats and enable the link between the character datasets and samples in research collections, ensuring high visibility and instant re-usability of the data.

View Article: PubMed Central - PubMed

Affiliation: Botanic Garden and Botanical Museum Berlin-Dahlem, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany and n.kilian@bgbm.org.

No MeSH data available.


Generalized scheme of the steps in systematics from the investigation of organism individuals to the characterization of taxa. The first column lists the processes (lower case letters + italics) and products (upper case letters + normal style), the diagram illustrates the data flow and the last column numbers the steps as explained in the following: (1) samples of individuals are examined, providing different types of character data (green, blue, yellow), not all of them necessarily available for all samples. (2) Analysis of relationships (e.g. phylogenetic or tokogenetic), using e.g. available molecular character data (blue), reveals evolutionary relationships among the sampled individuals, grouping them into unclassified entities such as clades. In a phenetic approach, the evolutionary analysis in this step is replaced by an evaluation of morphological similarities and discontinuities. (3) In order to translate inferred (from whatever analysis) relationships into classification, the unclassified entities with the included samples and character data are assigned to taxa, also employing further character data types (yellow, green). (4) Naming of taxa and aggregating (summing up) of the character data from the individuals included results in named and characterized taxa. Further sampled individuals not included in the evolutionary analysis but matching the taxon characterization can be included, their data adding to the characterization.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4589695&req=5

bav094-F1: Generalized scheme of the steps in systematics from the investigation of organism individuals to the characterization of taxa. The first column lists the processes (lower case letters + italics) and products (upper case letters + normal style), the diagram illustrates the data flow and the last column numbers the steps as explained in the following: (1) samples of individuals are examined, providing different types of character data (green, blue, yellow), not all of them necessarily available for all samples. (2) Analysis of relationships (e.g. phylogenetic or tokogenetic), using e.g. available molecular character data (blue), reveals evolutionary relationships among the sampled individuals, grouping them into unclassified entities such as clades. In a phenetic approach, the evolutionary analysis in this step is replaced by an evaluation of morphological similarities and discontinuities. (3) In order to translate inferred (from whatever analysis) relationships into classification, the unclassified entities with the included samples and character data are assigned to taxa, also employing further character data types (yellow, green). (4) Naming of taxa and aggregating (summing up) of the character data from the individuals included results in named and characterized taxa. Further sampled individuals not included in the evolutionary analysis but matching the taxon characterization can be included, their data adding to the characterization.

Mentions: Biological systematics, referred to as systematics in this study, aims to assess organismic diversity by attempting to identify natural biological entities above the individual level (taxa), to uncover their relationships and to characterize, classify and name them (1). All analyses in systematics (Figure 1) are based on ‘samples’, a term used in this study in the unspecified sense of a probe or examination object taken from an individual organism. Examination of these samples produces ‘character data’—often named ‘descriptive data’ (2, 3) and sometimes ‘comparative data’ (1)—a class of data referring to ‘taxonomic characters’ (4), which each have two or more states and can cover all data suitable to characterize a taxon in comparison with related or similar taxa. Character data that are suitable for use in evolutionary analyses are processed in order to group sampled individuals into natural biological entities. Evolutionary analyses may include to study tokogenetic relationships within a species, or to study sampled individuals as representatives of species in a phylogenetic context. The character data may be analysed also using a phenetic or other approach. The results in each case are initially unclassified entities, which in subsequent steps can be assigned to taxa and then be named (Figure 1) (5, 6). The taxon assignment of unclassified entities revealed from evolutionary analyses translates evolutionary relationships into a classification. This translation essentially employs decisions on appropriate circumscriptions and ranks of taxa, guided by certain sets of criteria, which may be subject to debate. Additional individuals that match these taxa can also be assigned to them. Taxon assignment of individuals, i.e. the process of matching sampled individuals with taxa, thus of their identification, uses a subset of character data as indicators that are considered diagnostic for a taxon and for its distinction from similar or related taxa. The available character data obtained from all sampled individuals of a taxon are finally ‘aggregated’, thus summed up, into a comprehensive ‘taxon characterization’ (7) (frequently but less appropriately referred to as ‘description’, see section two of this study). Taxon characterizations are thus the product of the taxon delimitation (5) and may vary in so far as different taxon delimitations are applied (‘taxon concepts’) (5, 8–10) or different geographic scopes may be considered. The characterizations of higher taxa (taxa that include subordinate taxa) are in the same way the product of taxon delimitation and are the sum of their included subordinate taxa. The taxon characterizations of all subordinate taxa making up a higher taxon are thus to be aggregated into the characterization of the corresponding higher taxon.Fig. 1.


Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens.

Kilian N, Henning T, Plitzner P, Müller A, Güntsch A, Stöver BC, Müller KF, Berendsohn WG, Borsch T - Database (Oxford) (2015)

Generalized scheme of the steps in systematics from the investigation of organism individuals to the characterization of taxa. The first column lists the processes (lower case letters + italics) and products (upper case letters + normal style), the diagram illustrates the data flow and the last column numbers the steps as explained in the following: (1) samples of individuals are examined, providing different types of character data (green, blue, yellow), not all of them necessarily available for all samples. (2) Analysis of relationships (e.g. phylogenetic or tokogenetic), using e.g. available molecular character data (blue), reveals evolutionary relationships among the sampled individuals, grouping them into unclassified entities such as clades. In a phenetic approach, the evolutionary analysis in this step is replaced by an evaluation of morphological similarities and discontinuities. (3) In order to translate inferred (from whatever analysis) relationships into classification, the unclassified entities with the included samples and character data are assigned to taxa, also employing further character data types (yellow, green). (4) Naming of taxa and aggregating (summing up) of the character data from the individuals included results in named and characterized taxa. Further sampled individuals not included in the evolutionary analysis but matching the taxon characterization can be included, their data adding to the characterization.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4589695&req=5

bav094-F1: Generalized scheme of the steps in systematics from the investigation of organism individuals to the characterization of taxa. The first column lists the processes (lower case letters + italics) and products (upper case letters + normal style), the diagram illustrates the data flow and the last column numbers the steps as explained in the following: (1) samples of individuals are examined, providing different types of character data (green, blue, yellow), not all of them necessarily available for all samples. (2) Analysis of relationships (e.g. phylogenetic or tokogenetic), using e.g. available molecular character data (blue), reveals evolutionary relationships among the sampled individuals, grouping them into unclassified entities such as clades. In a phenetic approach, the evolutionary analysis in this step is replaced by an evaluation of morphological similarities and discontinuities. (3) In order to translate inferred (from whatever analysis) relationships into classification, the unclassified entities with the included samples and character data are assigned to taxa, also employing further character data types (yellow, green). (4) Naming of taxa and aggregating (summing up) of the character data from the individuals included results in named and characterized taxa. Further sampled individuals not included in the evolutionary analysis but matching the taxon characterization can be included, their data adding to the characterization.
Mentions: Biological systematics, referred to as systematics in this study, aims to assess organismic diversity by attempting to identify natural biological entities above the individual level (taxa), to uncover their relationships and to characterize, classify and name them (1). All analyses in systematics (Figure 1) are based on ‘samples’, a term used in this study in the unspecified sense of a probe or examination object taken from an individual organism. Examination of these samples produces ‘character data’—often named ‘descriptive data’ (2, 3) and sometimes ‘comparative data’ (1)—a class of data referring to ‘taxonomic characters’ (4), which each have two or more states and can cover all data suitable to characterize a taxon in comparison with related or similar taxa. Character data that are suitable for use in evolutionary analyses are processed in order to group sampled individuals into natural biological entities. Evolutionary analyses may include to study tokogenetic relationships within a species, or to study sampled individuals as representatives of species in a phylogenetic context. The character data may be analysed also using a phenetic or other approach. The results in each case are initially unclassified entities, which in subsequent steps can be assigned to taxa and then be named (Figure 1) (5, 6). The taxon assignment of unclassified entities revealed from evolutionary analyses translates evolutionary relationships into a classification. This translation essentially employs decisions on appropriate circumscriptions and ranks of taxa, guided by certain sets of criteria, which may be subject to debate. Additional individuals that match these taxa can also be assigned to them. Taxon assignment of individuals, i.e. the process of matching sampled individuals with taxa, thus of their identification, uses a subset of character data as indicators that are considered diagnostic for a taxon and for its distinction from similar or related taxa. The available character data obtained from all sampled individuals of a taxon are finally ‘aggregated’, thus summed up, into a comprehensive ‘taxon characterization’ (7) (frequently but less appropriately referred to as ‘description’, see section two of this study). Taxon characterizations are thus the product of the taxon delimitation (5) and may vary in so far as different taxon delimitations are applied (‘taxon concepts’) (5, 8–10) or different geographic scopes may be considered. The characterizations of higher taxa (taxa that include subordinate taxa) are in the same way the product of taxon delimitation and are the sum of their included subordinate taxa. The taxon characterizations of all subordinate taxa making up a higher taxon are thus to be aggregated into the characterization of the corresponding higher taxon.Fig. 1.

Bottom Line: Structured character data are therefore not only needed for the knowledge generation process but also for easily adapting characterizations of taxa.We aim to facilitate the construction and reproducibility of taxon characterizations from structured character data of changing sample sets by establishing a stable and unambiguous association between each sampled individual and the data processed from it.Our workflow implementation uses the European Distributed Institute of Taxonomy Platform, a comprehensive taxonomic data management and publication environment to: (i) establish a reproducible connection between sampled individuals and all samples derived from them; (ii) stably link sample-based character data with the metadata of the respective samples; (iii) record and store structured specimen-based character data in formats allowing data exchange; (iv) reversibly assign sample metadata and character datasets to taxa in an editable classification and display them and (v) organize data exchange via standard exchange formats and enable the link between the character datasets and samples in research collections, ensuring high visibility and instant re-usability of the data.

View Article: PubMed Central - PubMed

Affiliation: Botanic Garden and Botanical Museum Berlin-Dahlem, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany and n.kilian@bgbm.org.

No MeSH data available.