cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies

ABSTRACT The number of samples in high-throughput comparative “omics” studies is increasing rapidly due to declining experimental costs. To keep sample data and metadata manageable and to ensure the integrity of scientific results as the scale of these projects continues to increase, it is essential...

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Autores principales:	John H. Chase, Evan Bolyen, Jai Ram Rideout, J. Gregory Caporaso
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2016
Materias:	bioinformatics microbiome metagenome metabolome transcriptome genomes Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/1a48cff42ca742b887f3818ea08abf6c
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spelling	oai:doaj.org-article:1a48cff42ca742b887f3818ea08abf6c2021-12-02T19:45:29Zcual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies10.1128/mSystems.00010-152379-5077https://doaj.org/article/1a48cff42ca742b887f3818ea08abf6c2016-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00010-15https://doaj.org/toc/2379-5077ABSTRACT The number of samples in high-throughput comparative “omics” studies is increasing rapidly due to declining experimental costs. To keep sample data and metadata manageable and to ensure the integrity of scientific results as the scale of these projects continues to increase, it is essential that we transition to better-designed sample identifiers. Ideally, sample identifiers should be globally unique across projects, project teams, and institutions; short (to facilitate manual transcription); correctable with respect to common types of transcription errors; opaque, meaning that they do not contain information about the samples; and compatible with existing standards. We present cual-id, a lightweight command line tool that creates, or mints, sample identifiers that meet these criteria without reliance on centralized infrastructure. cual-id allows users to assign universally unique identifiers, or UUIDs, that are globally unique to their samples. UUIDs are too long to be conveniently written on sampling materials, such as swabs or microcentrifuge tubes, however, so cual-id additionally generates human-friendly 4- to 12-character identifiers that map to their UUIDs and are unique within a project. By convention, we use “cual-id” to refer to the software, “CualID” to refer to the short, human-friendly identifiers, and “UUID” to refer to the globally unique identifiers. CualIDs are used by humans when they manually write or enter identifiers, while the longer UUIDs are used by computers to unambiguously reference a sample. Finally, cual-id optionally generates printable label sticker sheets containing Code 128 bar codes and CualIDs for labeling of sample collection and processing materials. IMPORTANCE The adoption of identifiers that are globally unique, correctable, and easily handwritten or manually entered into a computer will be a major step forward for sample tracking in comparative omics studies. As the fields transition to more-centralized sample management, for example, across labs within an institution, across projects funded under a common program, or in systems designed to facilitate meta- and/or integrated analysis, sample identifiers generated with cual-id will not need to change; thus, costly and error-prone updating of data and metadata identifiers will be avoided. Further, using cual-id will ensure that transcription errors in sample identifiers do not require the discarding of otherwise-useful samples that may have been expensive to obtain. Finally, cual-id is simple to install and use and is free for all use. No centralized infrastructure is required to ensure global uniqueness, so it is feasible for any lab to get started using these identifiers within their existing infrastructure.John H. ChaseEvan BolyenJai Ram RideoutJ. Gregory CaporasoAmerican Society for MicrobiologyarticlebioinformaticsmicrobiomemetagenomemetabolometranscriptomegenomesMicrobiologyQR1-502ENmSystems, Vol 1, Iss 1 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	bioinformatics microbiome metagenome metabolome transcriptome genomes Microbiology QR1-502
spellingShingle	bioinformatics microbiome metagenome metabolome transcriptome genomes Microbiology QR1-502 John H. Chase Evan Bolyen Jai Ram Rideout J. Gregory Caporaso cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies
description	ABSTRACT The number of samples in high-throughput comparative “omics” studies is increasing rapidly due to declining experimental costs. To keep sample data and metadata manageable and to ensure the integrity of scientific results as the scale of these projects continues to increase, it is essential that we transition to better-designed sample identifiers. Ideally, sample identifiers should be globally unique across projects, project teams, and institutions; short (to facilitate manual transcription); correctable with respect to common types of transcription errors; opaque, meaning that they do not contain information about the samples; and compatible with existing standards. We present cual-id, a lightweight command line tool that creates, or mints, sample identifiers that meet these criteria without reliance on centralized infrastructure. cual-id allows users to assign universally unique identifiers, or UUIDs, that are globally unique to their samples. UUIDs are too long to be conveniently written on sampling materials, such as swabs or microcentrifuge tubes, however, so cual-id additionally generates human-friendly 4- to 12-character identifiers that map to their UUIDs and are unique within a project. By convention, we use “cual-id” to refer to the software, “CualID” to refer to the short, human-friendly identifiers, and “UUID” to refer to the globally unique identifiers. CualIDs are used by humans when they manually write or enter identifiers, while the longer UUIDs are used by computers to unambiguously reference a sample. Finally, cual-id optionally generates printable label sticker sheets containing Code 128 bar codes and CualIDs for labeling of sample collection and processing materials. IMPORTANCE The adoption of identifiers that are globally unique, correctable, and easily handwritten or manually entered into a computer will be a major step forward for sample tracking in comparative omics studies. As the fields transition to more-centralized sample management, for example, across labs within an institution, across projects funded under a common program, or in systems designed to facilitate meta- and/or integrated analysis, sample identifiers generated with cual-id will not need to change; thus, costly and error-prone updating of data and metadata identifiers will be avoided. Further, using cual-id will ensure that transcription errors in sample identifiers do not require the discarding of otherwise-useful samples that may have been expensive to obtain. Finally, cual-id is simple to install and use and is free for all use. No centralized infrastructure is required to ensure global uniqueness, so it is feasible for any lab to get started using these identifiers within their existing infrastructure.
format	article
author	John H. Chase Evan Bolyen Jai Ram Rideout J. Gregory Caporaso
author_facet	John H. Chase Evan Bolyen Jai Ram Rideout J. Gregory Caporaso
author_sort	John H. Chase
title	cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies
title_short	cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies
title_full	cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies
title_fullStr	cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies
title_full_unstemmed	cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies
title_sort	cual-id: globally unique, correctable, and human-friendly sample identifiers for comparative omics studies
publisher	American Society for Microbiology
publishDate	2016
url	https://doaj.org/article/1a48cff42ca742b887f3818ea08abf6c
work_keys_str_mv	AT johnhchase cualidgloballyuniquecorrectableandhumanfriendlysampleidentifiersforcomparativeomicsstudies AT evanbolyen cualidgloballyuniquecorrectableandhumanfriendlysampleidentifiersforcomparativeomicsstudies AT jairamrideout cualidgloballyuniquecorrectableandhumanfriendlysampleidentifiersforcomparativeomicsstudies AT jgregorycaporaso cualidgloballyuniquecorrectableandhumanfriendlysampleidentifiersforcomparativeomicsstudies
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cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies

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