Genomic Observatories Meta-Database

Abbreviation:GEOME

General Information

The Genomic Observatories Meta-Database (GEOME) is a web-based database that captures the who, what, where, and when of biological samples and associated genetic sequences. GEOME helps users with the following goals: ensure the metadata from your biological samples is findable, accessible, interoperable, and reusable; improve the quality of your data and comply with global data standards; and integrate with R, ease publication to NCBI's sequence read archive, and work with an associated LIMS. The initial use case for GEOME came from the Diversity of the Indo-Pacific Network (DIPnet) resource.

Homepage https://geome-db.org/

Countries that developed this resource United States

Created in 2017

Taxonomic range

All

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: GEOME; Genomic Observatories Meta-Database; DOI: https://doi.org/10.25504/FAIRsharing.wOcTaM; Last edited: March 10, 2021, 1:07 p.m.; Last accessed: Apr 16 2021 9:55 p.m.

Publication for citation The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples. Deck J,Gaither MR,Ewing R,Bird CE,Davies N,Meyer C,Riginos C,Toonen RJ,Crandall ED; PLoS Biol ; 2017; 10.1371/journal.pbio.2002925;

This record is maintained by eric_crandall

Record added: May 27, 2020, 12:07 p.m.
Record updated: Feb. 18, 2021, 4:33 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.wOcTaM' by 'The FAIRsharing Team' at 16:33, 18 Feb 2021 (approved):

	'organizations' has been modified:
		Before:
			The National Evolutionary Synthesis Center (NESCent), USA|https://www.nescent.org|Funds
			National Science Foundation (NSF), USA|https://www.nsf.gov/|Funds
			David and Lucile Packard Foundation, Los Altos, CA, USA|https://www.packard.org/|Funds
			BID: Biodiversity Information for Development|https://www.gbif.org/fr/programme/82243/bid-biodiversity-information-for-development|Funds
			Dongsha Atoll Research Station (DARS)|https://dongsha-mr.nsysu.edu.tw/p/406-1272-204375,r1755.php?Lang=zh-tw|Maintains
			California State University, Monterey Bay, Marina, CA, USA|https://csumb.edu/|Undefined
		After:
			National Science Foundation (NSF), USA|https://www.nsf.gov/|Funds
			The Gordon and Betty Moore Foundation, USA|https://www.moore.org/|Funds
			National Oceanic and Atmospheric Administration  (NOAA) MD, USA|https://www.noaa.gov|Funds
			Berkeley National History Museums, University of California, Berkeley, CA, USA|https://bnhm.berkeley.edu/|Maintains
			Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI, USA|http://www.himb.hawaii.edu/|Maintains
			Biocode, LLC, Junction City, Oregon, USA|https://biocodellc.com/|Maintains
			Smithsonian National Museum of Natural History, Washington DC, USA|https://naturalhistory.si.edu/|Maintains
			University of Queensland, Australia|http://uq.edu.au/|Maintains
			Pennsylvania State University, University Park, PA, USA|https://www.psu.edu/|Maintains
		Added:
			The Gordon and Betty Moore Foundation, USA|https://www.moore.org/|Funds
			National Oceanic and Atmospheric Administration  (NOAA) MD, USA|https://www.noaa.gov|Funds
			Berkeley National History Museums, University of California, Berkeley, CA, USA|https://bnhm.berkeley.edu/|Maintains
			Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI, USA|http://www.himb.hawaii.edu/|Maintains
			Biocode, LLC, Junction City, Oregon, USA|https://biocodellc.com/|Maintains
			Smithsonian National Museum of Natural History, Washington DC, USA|https://naturalhistory.si.edu/|Maintains
			University of Queensland, Australia|http://uq.edu.au/|Maintains
			Pennsylvania State University, University Park, PA, USA|https://www.psu.edu/|Maintains
		Removed:
			The National Evolutionary Synthesis Center (NESCent), USA|https://www.nescent.org|Funds
			David and Lucile Packard Foundation, Los Altos, CA, USA|https://www.packard.org/|Funds
			BID: Biodiversity Information for Development|https://www.gbif.org/fr/programme/82243/bid-biodiversity-information-for-development|Funds
			Dongsha Atoll Research Station (DARS)|https://dongsha-mr.nsysu.edu.tw/p/406-1272-204375,r1755.php?Lang=zh-tw|Maintains
			California State University, Monterey Bay, Marina, CA, USA|https://csumb.edu/|Undefined

	'standardsImplemented' has been modified:
		Before:
		After:
			FASTA Sequence Format
			FASTQ Sequence and Sequence Quality Format
			Minimum Information about any (x) Sequence
			Darwin Core
			Resource Description Framework
		Added:
			FASTA Sequence Format
			FASTQ Sequence and Sequence Quality Format
			Minimum Information about any (x) Sequence
			Darwin Core
			Resource Description Framework
		Removed:

	'related_databases' has been modified:
		Before:
		After:
			GenBank
			Sequence Read Archive
		Added:
			GenBank
			Sequence Read Archive
		Removed:

	'supportLinks' has been modified:
		Before:
			help|https://geome-db.org/about
			online documentation|http://diversityindopacific.net/workshops-meetings/
		After:
			FAQ|https://docs.google.com/document/d/1tEFpclCyJ6aLnypmtdfdjLVhiWQ-rYhGqu5eGhq3s5s/edit
			email|jdeck@berkeley.edu
			help|https://geome-db.org/docs/helpDocumentation.pdf
			online documentation|https://geome-db.org/about
		Added:
			FAQ|https://docs.google.com/document/d/1tEFpclCyJ6aLnypmtdfdjLVhiWQ-rYhGqu5eGhq3s5s/edit
			email|jdeck@berkeley.edu
			help|https://geome-db.org/docs/helpDocumentation.pdf
			online documentation|https://geome-db.org/about
		Removed:
			help|https://geome-db.org/about
			online documentation|http://diversityindopacific.net/workshops-meetings/

	'name' has been modified:
		Before: Diversity of the Indo-Pacific Network
		After: Genomic Observatories Meta-Database

	'licences' has been modified:
		Before:
			DIPnet Data Usage Agreement|http://diversityindopacific.net/data-usage-agreement/|Data
		After:
			GEOME Data Usage Policy|https://geome-db.org/about|Data
			Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication|https://creativecommons.org/publicdomain/zero/1.0/|Data
		Added:
			GEOME Data Usage Policy|https://geome-db.org/about|Data
			Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication|https://creativecommons.org/publicdomain/zero/1.0/|Data
		Removed:
			DIPnet Data Usage Agreement|http://diversityindopacific.net/data-usage-agreement/|Data

	'tools' has been modified:
		Before:
		After:
			GEOME R Package||https://cran.r-project.org/web/packages/geomedb/index.html
			Biocode LIMS Plugin||https://github.com/biocodellc/biocode-lims/releases
		Added:
			GEOME R Package||https://cran.r-project.org/web/packages/geomedb/index.html
			Biocode LIMS Plugin||https://github.com/biocodellc/biocode-lims/releases
		Removed:

	'onto_disciplines' has been modified:
		Before:
			Biodiversity
			Data Submission, Annotation and Curation
			Genetics
			Life Science
			Oceania Studies
			Oceanography
		After:
			Biodiversity
			Ecology
			Evolutionary Biology
			Genetics
			Oceanography
		Added:
			Ecology
			Evolutionary Biology
		Removed:
			Data Submission, Annotation and Curation
			Life Science
			Oceania Studies

	'onto_domains' has been modified:
		Before:
			Resource metadata
		After:
			Biospecimen
			Evolution
			centrally registered identifier
			None
		Added:
			Biospecimen
			Evolution
			centrally registered identifier
			None
		Removed:
			Resource metadata

	'contact' has been modified:
		Before:  Professor Cynthia Riginos
		After: Eric Crandall

	'contactEmail' has been modified:
		Before: c.riginos@uq.edu.au
		After: ecrandall@psu.edu

	'grants' has been modified:
		Before:
		After:
			DBI-0956426; Biological Science Collections Tracker
			DEB-1457848; DIPnet RCN
			EF-0905606; NESCent catalysis and working group funding
			GBMF1619 Moorea Biocode
			NMFS-PIRO-NA15NMF4270330
		Added:
			DBI-0956426; Biological Science Collections Tracker
			DEB-1457848; DIPnet RCN
			EF-0905606; NESCent catalysis and working group funding
			GBMF1619 Moorea Biocode
			NMFS-PIRO-NA15NMF4270330
		Removed:

	'publications' has been modified:
		Before:
		After:
			The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples.|Deck J,Gaither MR,Ewing R,Bird CE,Davies N,Meyer C,Riginos C,Toonen RJ,Crandall ED|PLoS Biol|2017
		Added:
			The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples.|Deck J,Gaither MR,Ewing R,Bird CE,Davies N,Meyer C,Riginos C,Toonen RJ,Crandall ED|PLoS Biol|2017
		Removed:

	'yearOfCreation' has been modified:
		Before: 2012
		After: 2017

	'dataProcesses' has been modified:
		Before:
			Search the database, data access, https://geome-db.org/query
			Upload your data, data access, https://geome-db.org/
			Propose a paper, data curation, http://diversityindopacific.net/how-to-propose-a-paper/
			GitHub repository, data access, http://dipnet.github.io/popgenDB/
			Workbench, data access, https://geome-db.org/workbench/dashboard
		After:
			Query Data (Map View), data access, https://geome-db.org/query
			Workbench (Browse Data), data access, https://geome-db.org/workbench/dashboard
		Added:
			Query Data (Map View), data access, https://geome-db.org/query
			Workbench (Browse Data), data access, https://geome-db.org/workbench/dashboard
		Removed:
			Search the database, data access, https://geome-db.org/query
			Upload your data, data access, https://geome-db.org/
			Propose a paper, data curation, http://diversityindopacific.net/how-to-propose-a-paper/
			GitHub repository, data access, http://dipnet.github.io/popgenDB/
			Workbench, data access, https://geome-db.org/workbench/dashboard

	'shortname' has been modified:
		Before: DIPnet
		After: GEOME

	'accessPoints' has been modified:
		Before:
		After:
			REST|https://api.geome-db.org/apidocs/|Swagger API documentation
		Added:
			REST|https://api.geome-db.org/apidocs/|Swagger API documentation
		Removed:

	'homepage' has been modified:
		Before: http://diversityindopacific.net/
		After: https://geome-db.org/

	'description' has been modified:
		Before: The Diversity of the Indo-Pacific Network (DIPnet) aims to advance genetic diversity research in the Indo-Pacific by aggregating population genetic metadata into a searchable database (GeOME). The primary goal is to promote collaboration and advocate best practices for conducting biodiversity research.
		After: The Genomic Observatories Meta-Database (GEOME) is a web-based database that captures the who, what, where, and when of biological samples and associated genetic sequences. GEOME helps users with the following goals: ensure the metadata from your biological samples is findable, accessible, interoperable, and reusable; improve the quality of your data and comply with global data standards; and integrate with R, ease publication to NCBI's sequence read archive, and work with an associated LIMS. The initial use case for GEOME came from the Diversity of the Indo-Pacific Network (DIPnet) resource.

Edits to 'https://fairsharing.org/FAIRsharing.wOcTaM' by 'The FAIRsharing Team' at 15:05, 15 Feb 2021 (approved):

	'contactEmail' has been modified:
		Before: ecrandall@csumb.edu
		After: c.riginos@uq.edu.au

	'contact' has been modified:
		Before: Eric D. Crandall
		After:  Professor Cynthia Riginos

	'contactORCID' has been modified:
		Before: 0000-0001-8580-3651
		After:

Edits to 'https://fairsharing.org/FAIRsharing.wOcTaM' by 'The FAIRsharing Team' at 16:55, 05 Jun 2020 (approved):

	'description' has been modified:
		Before: The Diversity of the Indo-Pacific Network (DIPnet) aims at advance genetic diversity research in the Indo-Pacific by aggregating population genetic metadata into a searchable database (GeOME). Our primary goal to promote collaboration and advocate best practices for conducting biodiversity research.
		After: The Diversity of the Indo-Pacific Network (DIPnet) aims to advance genetic diversity research in the Indo-Pacific by aggregating population genetic metadata into a searchable database (GeOME). The primary goal is to promote collaboration and advocate best practices for conducting biodiversity research.

Edits to 'https://fairsharing.org/FAIRsharing.wOcTaM' by 'The FAIRsharing Team' at 12:09, 27 May 2020 (approved):

	'organizations' has been modified:
		Before:
			The National Evolutionary Synthesis Center (NESCent), USA|https://www.nescent.org|Funds
			National Science Foundation (NSF), USA|https://www.nsf.gov/|Funds
			Dongsha Atoll Research Station (DARS) |https://dongsha-mr.nsysu.edu.tw/p/406-1272-204375,r1755.php?Lang=zh-tw|Maintains
			David and Lucile Packard Foundation, Los Altos, CA, USA|https://www.packard.org/|Funds
			BID: Biodiversity Information for Development|https://www.gbif.org/fr/programme/82243/bid-biodiversity-information-for-development|Funds
		After:
			The National Evolutionary Synthesis Center (NESCent), USA|https://www.nescent.org|Funds
			National Science Foundation (NSF), USA|https://www.nsf.gov/|Funds
			David and Lucile Packard Foundation, Los Altos, CA, USA|https://www.packard.org/|Funds
			BID: Biodiversity Information for Development|https://www.gbif.org/fr/programme/82243/bid-biodiversity-information-for-development|Funds
			Dongsha Atoll Research Station (DARS) |https://dongsha-mr.nsysu.edu.tw/p/406-1272-204375,r1755.php?Lang=zh-tw|Maintains
			California State University, Monterey Bay, Marina, CA, USA|https://csumb.edu/|Undefined
		Added:
			California State University, Monterey Bay, Marina, CA, USA|https://csumb.edu/|Undefined
		Removed:

Support

General

FAQ	FAQ
support email	John Deck
help	User Guide
online documentation	About

Additional Information

Contact

Eric Crandall

Tools

GEOME R Package	https://cran.r-project.org/web/packages/geomedb/index.html
Biocode LIMS Plugin	https://github.com/biocodellc/biocode-lims/releases

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Access

Query Data (Map View)	https://geome-db.org/query
Workbench (Browse Data)	https://geome-db.org/workbench/dashboard

REST Web Services

Swagger API documentation

https://api.geome-db.org/apidocs/

Publications

The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples.

Deck J,Gaither MR,Ewing R,Bird CE,Davies N,Meyer C,Riginos C,Toonen RJ,Crandall ED
PLoS Biol 2017

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

Minimum Information about any (x) Sequence

Terminology Artifacts

Darwin Core

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by eric_crandall

Funds

National Science Foundation (NSF), USA (Government body)
The Gordon and Betty Moore Foundation, USA (Charitable foundation)
National Oceanic and Atmospheric Administration (NOAA) MD, USA (Government body)

Maintains

Berkeley National History Museums, University of California, Berkeley, CA, USA (University)
Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI, USA (University)
Biocode, LLC, Junction City, Oregon, USA (Company)
Smithsonian National Museum of Natural History, Washington DC, USA (Government body)
University of Queensland, Australia (University)
Pennsylvania State University, University Park, PA, USA (University)

Grant Number(s)

DBI-0956426; Biological Science Collections Tracker (National Science Foundation (NSF), USA)
DEB-1457848; DIPnet RCN (National Science Foundation (NSF), USA)
EF-0905606; NESCent catalysis and working group funding (National Science Foundation (NSF), USA)
GBMF1619 Moorea Biocode (The Gordon and Betty Moore Foundation, USA)
NMFS-PIRO-NA15NMF4270330 (National Oceanic and Atmospheric Administration (NOAA) MD, USA)

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