Stefen, Clara http://orcid.org/0000-0001-7986-110X
Wagner, Franziska http://orcid.org/0000-0001-6623-6700
Asztalos, Marika http://orcid.org/0000-0002-4090-1159
Giere, Peter http://orcid.org/0000-0002-5570-0085
Grobe, Peter
Hiller, Michael http://orcid.org/0000-0003-3024-1449
Hofmann, Rebecca http://orcid.org/0000-0003-4985-6099
Jähde, Maria
Lächele, Ulla
Lehmann, Thomas http://orcid.org/0000-0002-1946-7968
Ortmann, Sylvia http://orcid.org/0000-0003-2520-6251
Peters, Benjamin http://orcid.org/0000-0002-2737-7006
Ruf, Irina http://orcid.org/0000-0002-9728-1210
Schiffmann, Christian
Thier, Nadja
Unterhitzenberger, Gabriele
Vogt, Lars http://orcid.org/0000-0002-8280-0487
Rudolf, Matthias
Wehner, Peggy
Stuckas, Heiko http://orcid.org/0000-0002-5690-0994
Funding for this research was provided by:
Leibniz-Gemeinschaft (SAW-2016-SGN-2)
LOEWE-Centre for Translational Biodiversity Genomics
Senckenberg Naturhistorische Sammlungen Dresden
Article History
Received: 14 January 2021
Accepted: 22 October 2021
First Online: 7 December 2021
Declarations
:
: None known for all authors.
: Not applicable as no experiments with living animals were performed.
: All authors agreed to the work.
: All authors agree to the publication.<b>Glossary</b>Anatomy – "The demonstrable facts of animal structure, or also, by transference to the object, the structure or even the tissue of the animal itself." (SnodgrassCitationRef removed:173). In other words, anatomy is the part of the phenotype of an organism that refers to its physical and structural properties. At the same time, it refers to the science of anatomy, with anatomical data being facts about the anatomy of organisms.Data repository – A large database infrastructure that collects, manages, and stores data sets for data analysis, sharing and reporting. A data repository is also known as a data library or data archive. <i><u>NCBI GenBank</u></i><i> is an example of a data repository for a sequence database.</i>Machine actionable – Data and metadata that are structured in a formalized and consistent way so that machines (i.e., computers) can read and use them with algorithms that were programmed against this structure. Machine actionability of data and metadata includes for instance the use of persistent identifiers for data creators (e.g., ORCIDs), organizations and funding agencies, but also open accessibility of data for machines through a corresponding application programming interface (API), and basic semantics that allow algorithms to distinguish different categories of information and apply rules to them. Machine actionability in this sense goes beyond machine readability which only requires data and metadata to be readable by a machine, i.e., data and metadata must be provided in a machine readable format. Machine readability does not necessarily require data and metadata to provide basic semantics for allowing algorithms to distinguish different categories of information contained in them.Morphology – “Our philosophy or science of animal form, a mental concept derived from evidence based on anatomy and embryology, usually incapable of proof, attempting to discover structural homologies and to explain how animal organization has come to be as it is.” (SnodgrassCitationRef removed:173). In other words, morphology refers to the interpretations of anatomical facts within theories and hypotheses such as homology.NEXUS file – A file format widely used in bioinformatics. It stores information about taxa, phenotypic characters, trees, and other information relevant for phylogenetics. Several phylogenetic programs such as PAUP, MrBayes, and Mac Clade use this format.Phenome – the entirety of all observable physical or physiological traits or characteristics of an organismPhenotypic trait – A specific part of the phenotype of an organism. The phenotype of an organism refers to its observable constituents, properties, and relations that can be considered to result from the interaction of the organism’s genotype with itself and its environment. Anatomy is the part of the phenotype that refers to the physical and structural properties of the organism.Ontology – Ontologies are dictionaries that can be used for describing a certain reality. They consist of labeled classes and relations between classes, both with clear definitions that are ideally created by experts through consensus and that are formulated in a highly formalized canonical syntax and standardized format with the goal to yield a lexical or taxonomic framework for knowledge representation (SmithCitationRef removed). Each ontology class and relation (also called property) possesses its own Uniform Resource Identifier (URI*) through which it can be identified and individually referenced. Ontologies contain expert-curated domain knowledge about specific kinds of entities together with their properties and relations in the form of classes defined through universal statements (Schulz et al. 2009, Schulz and JansenCitationRef removed). Ontologies in this sense do not include statements about particular entities (i.e., empirical data) (Vogt et al.CitationRef removed).URI – A Uniform Resource Identifier (URI) is a string of characters that follows a specific structure and unambiguously identifies a particular resource. The URI can also serve as a URL (web address), and can be resolved to an IP address.