Towards a standards-compliant genomic and metagenomic publication record

PDF Version Also Available for Download.

Description

Increasingly we are aware as a community of the growing need to manage the avalanche of genomic and metagenomic data, in addition to related data types like ribosomal RNA and barcode sequences, in a way that tightly integrates contextual data with traditional literature in a machine-readable way. It is for this reason that the Genomic Standards Consortium (GSC) formed in 2005. Here we suggest that we move beyond the development of standards and tackle standards-compliance and improved data capture at the level of the scientific publication. We are supported in this goal by the fact that the scientific community is ... continued below

Creation Information

Fenner, Marsha W; Garrity, George M.; Field, Dawn; Kyrpides, Nikos; Hirschman, Lynette; San-sone, Susanna-Assunta et al. April 1, 2008.

Context

This article is part of the collection entitled: Office of Scientific & Technical Information Technical Reports and was provided by UNT Libraries Government Documents Department to Digital Library, a digital repository hosted by the UNT Libraries. More information about this article can be viewed below.

Who

People and organizations associated with either the creation of this article or its content.

Provided By

UNT Libraries Government Documents Department

Serving as both a federal and a state depository library, the UNT Libraries Government Documents Department maintains millions of items in a variety of formats. The department is a member of the FDLP Content Partnerships Program and an Affiliated Archive of the National Archives.

Contact Us

What

Descriptive information to help identify this article. Follow the links below to find similar items on the Digital Library.

Description

Increasingly we are aware as a community of the growing need to manage the avalanche of genomic and metagenomic data, in addition to related data types like ribosomal RNA and barcode sequences, in a way that tightly integrates contextual data with traditional literature in a machine-readable way. It is for this reason that the Genomic Standards Consortium (GSC) formed in 2005. Here we suggest that we move beyond the development of standards and tackle standards-compliance and improved data capture at the level of the scientific publication. We are supported in this goal by the fact that the scientific community is in the midst of a publishing revolution. This revolution is marked by a growing shift away from a traditional dichotomy between 'journal articles' and 'database entries' and an increasing adoption of hybrid models of collecting and disseminating scientific information. With respect to genomes and metagenomes and related data types, we feel the scientific community would be best served by the immediate launch of a central repository of short, highly structured 'Genome Notes' that must be standards-compliant. This could be done in the context of an existing journal, but we also suggest the more radical solution of launching a new journal. Such a journal could be designed to cater to a wide range of standards-related content types that are not currently centralized in the published literature. It could also support the demand for centralizing aspects of the 'gray literature' (documents developed by institutions or communities) such as the call by the GSCl for a central repository of Standard Operating Procedures describing the genomic annotation pipelines of the major sequencing centers. We argue that such an 'eJournal', published under the Open Access paradigm by the GSC, could be an attractive publishing forum for a broader range of standardization initiatives within, and beyond, the GSC and thereby fill an unoccupied yet increasingly important niche within the current research landscape.

Subjects

Source

  • Journal Name: OMICS Journal

Language

Item Type

Identifier

Unique identifying numbers for this article in the Digital Library or other systems.

  • Report No.: LBNL-283E
  • Grant Number: DE-AC02-05CH11231
  • Office of Scientific & Technical Information Report Number: 928960
  • Archival Resource Key: ark:/67531/metadc901273

Collections

This article is part of the following collection of related materials.

Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

Office of Scientific and Technical Information (OSTI) is the Department of Energy (DOE) office that collects, preserves, and disseminates DOE-sponsored research and development (R&D) results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions.

What responsibilities do I have when using this article?

When

Dates and time periods associated with this article.

Creation Date

  • April 1, 2008

Added to The UNT Digital Library

  • Sept. 27, 2016, 1:39 a.m.

Description Last Updated

  • Oct. 3, 2016, 4:24 p.m.

Usage Statistics

When was this article last used?

Congratulations! It looks like you are the first person to view this item online.

Interact With This Article

Here are some suggestions for what to do next.

Start Reading

PDF Version Also Available for Download.

International Image Interoperability Framework

IIF Logo

We support the IIIF Presentation API

Fenner, Marsha W; Garrity, George M.; Field, Dawn; Kyrpides, Nikos; Hirschman, Lynette; San-sone, Susanna-Assunta et al. Towards a standards-compliant genomic and metagenomic publication record, article, April 1, 2008; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc901273/: accessed December 9, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.