Meeting report: Identifying practical applications of ontologies for biodiversity informatics

Standards in Genomic Sciences

Volumn 10, Issue MAY2015, 2015, Pages

  Deck, John ^a   Guralnick, Robert ^b   Walls, Ramona ^c   Blum, Stanley ^d   Haendel, Melissa ^e   Matsunaga, Andréa ^f   Wieczorek, John ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

^c UNIVERSITY OF ARIZONA   (United States)

^d CALIFORNIA ACADEMY OF SCIENCES   (United States)

^e OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^f UNIVERSITY OF FLORIDA   (United States)

Author keywords

Biodiversity; Community; Darwin core; Microbial ecology; Ontology; OWL; Population; RDF; Sequencing

Indexed keywords

ARTICLE; BIODIVERSITY; BIOLOGICAL ONTOLOGY; CONTROLLED VOCABULARY; ECOLOGY; GENE SEQUENCE; TAXONOMY;

EID: 84940568529     PISSN: None     EISSN: 19443277     Source Type: Journal    
DOI: 10.1186/s40793-015-0014-0     Document Type: Article

References (31)

1. A web resource describing the Basic Formal Ontology. http://ifomis.uni-saarland.de/bfo/
2. Wieczorek J, Bloom D, Guralnick R, Blum W, Döring M, De Giovanni R, et al. Darwin Core: an evolving community-developed biodiversity data standard. PLoS One. 2012;7(1), e29715.
3. Walls R, Deck J, Guralnick R, et al. Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. PLoS One. 2014;9(3):e89606.
4. Walls R, Guralnick R, Deck J, Parnell J, Rocca-Serra P, Wieczorek J, et al. Advancing practical applications of biodiversity ontologies. Standards in Genomic Science. 2014;9(1):17.
5. MIxS as RDF specification. https://code.google.com/p/mixs-as-rdf/
6. Constable H, Guralnick R, Wieczorek J, Spencer C, Peterson AT. VertNet: a new model for biodiversity data sharing. PLoS Biol. 2010;8(2), e1000309.
7. iDigBio website. http://idigbio.org/
8. Basis of Record definition. http://rs.tdwg.org/dwc/terms/basisOfRecord
9. Dublin Core type definition. http://purl.org/dc/terms/type
10. Darwin Core namespace policy. http://rs.tdwg.org/dwc/terms/namespace/index.htm
11. Dublin Core definition of Location. http://dublincore.org/documents/dcmi-terms/#terms-Location
12. Basic Formal Ontology definition of site. http://purl.obolibrary.org/obo/BFO_0000029
13. Dublin Core definition of Event class. http://purl.org/dc/dcmitype/Event
14. Darwin Core class definition of Taxon. http://rs.tdwg.org/dwc/terms/Taxon
15. Darwin Core class definition of Identification. http://rs.tdwg.org/dwc/terms/Identification
16. Darwin Core class definition of Geological Context. http://rs.tdwg.org/dwc/terms/#GeologicalContext
17. Robertson T, Döring M, Guranick R, Bloom D, Braak K, Otegui J, et al. The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the Internet. PLoS One. 2014;9(8):e102623.
18. Ocean Sampling Day. http://www.microb3.eu/osd
19. Stucky B, Deck J, Conlin T, Ziemba L, Cellinese N, Guralnick R. The BiSciCol Triplifier: bringing biodiversity data to the semantic web. BMC Bioinformatics. 2014;15:257.
20. Monarch Initiative. http://monarchinitiative.org/page/team
21. Karma data integration tool. http://www.isi.edu/integration/karma/
22. Rightfield. http://www.rightfield.org.uk/
23. Force11 Resource Identification Initiative. https://www.force11.org/Resource:identification_initiative
24. EZID. http://ezid.cdlib.org/
25. Biocode Commons Identifiers code. https://code.google.com/p/bcid/
26. BiSciCol project. http://biscicol.org/
27. iPlant. http://www.iplantcollaborative.org/
28. EAGER: An Interoperable Information Infrastructure for Biodiversity Research. http://www.nsf.gov/awardsearch/showAward?AWD_ID=1255035
29. National Ecological Observatory Network. http://www.neoninc.org/
30. Minimum Information about any sequence standard. http://wiki.gensc.org/images/3/31/MIxS_v4.xls
31. Google spreadsheet outlining the process of creating a MIxS-like version of Darwin Core. http://goo.gl/mn7593