Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research.

Simple item page
dc.citation.issue6
dc.citation.volume20
dc.contributor.authorRiginos C
dc.contributor.authorCrandall ED
dc.contributor.authorLiggins L
dc.contributor.authorGaither MR
dc.contributor.authorEwing RB
dc.contributor.authorMeyer C
dc.contributor.authorAndrews KR
dc.contributor.authorEuclide PT
dc.contributor.authorTitus BM
dc.contributor.authorTherkildsen NO
dc.contributor.authorSalces-Castellano A
dc.contributor.authorStewart LC
dc.contributor.authorToonen RJ
dc.contributor.authorDeck J
dc.date.available2020-11
dc.date.available2020-09-09
dc.date.issued2020-11
dc.descriptionCAUL read and publish agreement
dc.description.abstractGenetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA-based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic Observatories Metadatabase (GEOME: geome-db.org) provides an intuitive solution for maintaining links between genetic data sets stored by the International Nucleotide Sequence Database Collaboration (INSDC) and their associated ecological metadata. GEOME facilitates the deposition of raw genetic data to INSDCs sequence read archive (SRA) while maintaining persistent links to standards-compliant ecological metadata held in the GEOME database. This approach facilitates findable, accessible, interoperable and reusable data archival practices. Moreover, GEOME enables data management solutions for large collaborative groups and expedites batch retrieval of genetic data from the SRA. The article that follows describes how GEOME can enable genuinely open data workflows for researchers in the field of molecular ecology.
dc.description.publication-statusPublished
dc.format.extent1458 - 1469
dc.identifierhttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000584362200001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=c5bb3b2499afac691c2e3c1a83ef6fef
dc.identifier.citationMOLECULAR ECOLOGY RESOURCES, 2020, 20 (6), pp. 1458 - 1469
dc.identifier.doi10.1111/1755-0998.13269
dc.identifier.eissn1755-0998
dc.identifier.elements-id435377
dc.identifier.harvestedMassey_Dark
dc.identifier.issn1755-098X
dc.identifier.urihttps://hdl.handle.net/10179/17377
dc.relation.isPartOfMOLECULAR ECOLOGY RESOURCES
dc.subjectbioinformatics
dc.subjectecoinformatics
dc.subjectFAIR principles
dc.subjectgenomic
dc.subjectopen data
dc.subjectreproducible research
dc.subject.anzsrc06 Biological Sciences
dc.titleBuilding a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research.
dc.typeJournal article
pubs.notesNot known
pubs.organisational-group/Massey University
pubs.organisational-group/Massey University/College of Sciences
pubs.organisational-group/Massey University/College of Sciences/School of Natural Sciences
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Riginos_et al_2020.pdf
Size:
1.4 MB
Format:
Adobe Portable Document Format
Description:
Download
Collections
Journal Articles