Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.
The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata stan...
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2014
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oai:doaj.org-article:fe650213a15044938075f67f4d601b752021-11-18T08:30:01ZSemantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.1932-620310.1371/journal.pone.0089606https://doaj.org/article/fe650213a15044938075f67f4d601b752014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24595056/?tool=EBIhttps://doaj.org/toc/1932-6203The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.Ramona L WallsJohn DeckRobert GuralnickSteve BaskaufReed BeamanStanley BlumShawn BowersPier Luigi ButtigiegNeil DaviesDag EndresenMaria Alejandra GandolfoRobert HannerAlyssa JanningLeonard KrishtalkaAndréa MatsunagaPeter MidfordNorman MorrisonÉamonn Ó TuamaMark SchildhauerBarry SmithBrian J StuckyAndrea ThomerJohn WieczorekJamie WhitacreJohn WooleyPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 3, p e89606 (2014) |
| institution |
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DOAJ |
| language |
EN |
| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Ramona L Walls John Deck Robert Guralnick Steve Baskauf Reed Beaman Stanley Blum Shawn Bowers Pier Luigi Buttigieg Neil Davies Dag Endresen Maria Alejandra Gandolfo Robert Hanner Alyssa Janning Leonard Krishtalka Andréa Matsunaga Peter Midford Norman Morrison Éamonn Ó Tuama Mark Schildhauer Barry Smith Brian J Stucky Andrea Thomer John Wieczorek Jamie Whitacre John Wooley Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. |
| description |
The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. |
| format |
article |
| author |
Ramona L Walls John Deck Robert Guralnick Steve Baskauf Reed Beaman Stanley Blum Shawn Bowers Pier Luigi Buttigieg Neil Davies Dag Endresen Maria Alejandra Gandolfo Robert Hanner Alyssa Janning Leonard Krishtalka Andréa Matsunaga Peter Midford Norman Morrison Éamonn Ó Tuama Mark Schildhauer Barry Smith Brian J Stucky Andrea Thomer John Wieczorek Jamie Whitacre John Wooley |
| author_facet |
Ramona L Walls John Deck Robert Guralnick Steve Baskauf Reed Beaman Stanley Blum Shawn Bowers Pier Luigi Buttigieg Neil Davies Dag Endresen Maria Alejandra Gandolfo Robert Hanner Alyssa Janning Leonard Krishtalka Andréa Matsunaga Peter Midford Norman Morrison Éamonn Ó Tuama Mark Schildhauer Barry Smith Brian J Stucky Andrea Thomer John Wieczorek Jamie Whitacre John Wooley |
| author_sort |
Ramona L Walls |
| title |
Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. |
| title_short |
Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. |
| title_full |
Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. |
| title_fullStr |
Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. |
| title_full_unstemmed |
Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. |
| title_sort |
semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2014 |
| url |
https://doaj.org/article/fe650213a15044938075f67f4d601b75 |
| work_keys_str_mv |
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