Related Experiment Video
Updated: Apr 13, 2026
10:23
A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
Published on: July 11, 2025
766
Making species checklists understandable to machines - a shift from relational databases to ontologies
Nina Laurenne1, Jouni Tuominen1, Hannu Saarenmaa2
1Semantic Computing Research Group (SeCo), Department of Media Technology, Aalto University, P.O. Box 15500, 00076 Aalto, Espoo, Finland.
Journal of Biomedical Semantics
|May 5, 2015
Summary
Scientific names are ambiguous and change over time. Using HTTP URIs instead of Life Science Identifiers (LSIDs) for species checklists improves data integration and enables intelligent biological applications.
Area of Science:
- Life Sciences
- Bioinformatics
- Taxonomy
Background:
- Scientific names are crucial for indexing and searching biological information.
- Ambiguity and changes in scientific names create challenges for data integration.
- Persistent identifiers are needed to overcome these issues.
Purpose of the Study:
- To present taxonomic information using two models: relational databases with LSIDs and Semantic Web ontologies with HTTP URIs.
- To explore methods for managing changes in scientific names over time.
- To compare the effectiveness of LSIDs and HTTP URIs for representing taxonomic data.
Main Methods:
- Developed a model for species checklists in relational databases using Life Science Identifiers (LSIDs).
- Introduced the TaxMeOn meta-ontology for modeling species checklists as Semantic Web ontologies using HTTP URIs.
- Investigated the management of evolving scientific names.
Main Results:
- Demonstrated species checklist representation using LSIDs in relational databases.
- Presented a Semantic Web ontology model (TaxMeOn) using HTTP URIs for detailed taxonomic representation.
- Explored methods for handling scientific name changes.
Conclusions:
- HTTP URIs are preferable to LSIDs for representing species checklist data.
- HTTP URIs facilitate data integration via Linked Data principles, preventing information silos.
- Semantic Web technologies and HTTP URIs enable intelligent biological applications by representing data semantics.
Keywords:
HTTP URILSIDLinked dataOntologyScientific nameSemantic webSpecies checklistTaxonomic conceptMore Related Videos
Related Concept Videos
02:40The Tree of Life - Bacteria, Archaea, Eukaryotes
42.2K
The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...
42.2K
02:51Multi-species Conserved Sequences
5.0K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
5.0K
02:54Evolutionary Relationships through Genome Comparisons
7.3K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
7.3K
02:56The Fossil Record
28.6K
The fossil record documents only a small fraction of all organisms that have ever inhabited Earth. Fossilization is a rare process, and most organisms never become fossils. Moreover, the fossil record only exhibits fossils that have been discovered. Nevertheless, sedimentary rock fossils of long-lived, abundant, hard-bodied organisms dominate the fossil record. These fossils offer valuable information, such as an organism's physical form, behavior, and age. Studying the fossil record helps...
28.6K
01:31Formation of Species
47.0K
Speciation describes the formation of one or more new species from one or sometimes multiple original species. The resulting species are discrete from the parent species, and barriers to reproduction will typically exist. There are two primary mechanisms, speciation with and without geographic isolation—allopatric and sympatric speciation, respectively.
47.0K
01:17What is a Species?
52.2K
Overview
52.2K