Standards In Genomic Sciences Research Articles

Objective: biochemical function.

DNA sequencing enables the discovery of new genes in high-throughput, low-cost experiments. Conversely, gene function is determined by low-throughput, high-cost experiments. This inverse relationship for these two types of data is a major impediment in meeting one of the major scientific challenges of our time—the understanding of genomes. This mismatch in throughput is illustrated by considering the progress made for one of the earliest sequenced genomes, that of Mycobacterium tuberculosis H37Rv (Mtb). When its genome was published in 1998, more than a quarter of its genes had no known function (Cole et al., 1998). Our lack of knowledge about these approximately 1000 “conserved hypothetical” genes in Mtb represents a serious deficiency in our understanding of its biology. Now, after more than a decade of progress, our knowledge of those proteins' functions is essentially unchanged—there are still greater than 900 genes with no known function (Lew et al., 2011). In contrast, during this same period, the scientific community has sequenced approximately 18,000 new genomes (Pagani et al., 2012), containing millions of new hypothetical proteins. Apparently, the vector of our progress has tipped decisively away from data interpretation and comprehension, and toward mere data collection. To address the issue of gene function testing and annotation for all microbes, we founded COMBREX (COMputational BRidge to EXperiments), an endeavor aimed at accelerating the rate of gene function validation (Anton et al., 2013). Two of COMBREX's more prominent initiatives were the creation of a comprehensive database for protein function data (http://combrex.bu.edu), and the deployment of a crowdsourcing platform to catalyze protein function experimentation. In the course of these two efforts, it became apparent that fundamental changes in approaches to the problem of protein function determination were needed if there was any hope of keeping pace with DNA sequencing. We suggest that the community work together to (1) re-establish the connection between existing gene annotation and the foundational experimental data that supports all annotation, (2) develop experiment design principles to help guide the identification of maximally informative targets for function validation, (3) invest in the development of higher-throughput approaches for the testing of protein function, and (4) provide an expedited publication pathway for reporting experimental results of gene function, analogous to the reporting of newly sequenced genomes in the journal “Standards in Genomic Sciences.”

Standards in Genomic Sciences: New beginnings to reflect the association between the journal and BMC.

Standards in Genomic Sciences: New beginnings to reflect the association between the journal and BMC.

Genome sequences published outside of Standards in Genomic Sciences, July - October 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Genome sequences published outside of Standards in Genomic Sciences, October–November 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Genome sequences published outside of Standards in Genomic Sciences, May-June 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Genome sequences published outside of Standards in Genomic Sciences, March-April 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Genome sequences published outside of Standards in Genomic Sciences, January-March 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Genome sequences published outside of Standards in Genomic Sciences, January-March 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

The State of Standards in Genomic Sciences

On July 20, 2009, we began the public phase of an experiment in open access publishing with the first issue of Standards in Genomic Sciences (SIGS) [1]. The rational for the journal was to fulfill a perceived need in the community for the continued publication of “genome papers”, the once familiar companion articles that accompanied the public release of genome sequencing projects. Those papers served not only as a formal record of the accomplishment of the individuals involved in the sequencing and annotation efforts, but also provided the initial (and often the only) description of the sequence itself [2]. However, by 2007, Liolios et al. [3] had already pointed out that the publication of such papers significantly lagged behind the release of new genome sequences, leaving a gap in the public research record. Beyond genome reports, there was also a growing demand for other types of articles to meet the needs of a growing ‘omics community including detailed standard operating procedures that provide sufficient detail to not only understand the methods by which sequences were generated and annotated, but to also reproduce those results. Also needed was a reliable venue for publication of white papers and the proceedings of meetings of standards-setting bodies, such as the Genomic Standards Consortium (GSC) [4]. SIGS was conceived to fill these needs. As 2011 draws to an end and we close out the final issue of Volume 5 of SIGS, we thought it appropriate to provide our authors, reviewers and readers with a brief update on the “state of the journal”, to examine the evidence that supports our original idea for the need for a journal such as SIGS, and to briefly outline key plans for the future.

Genome sequences published outside of Standards in Genomic Sciences, December 2011

Genome sequences published outside of Standards in Genomic Sciences, December 2011

Genome sequences published outside of Standards in Genomic Sciences, December 2011

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Genome sequences published outside of Standards in Genomic Sciences, October – November 2011

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Genome sequences published outside of Standards in Genomic Sciences, October – November 2011

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

A second special issue of Standards In Genomic Sciences from the Genomic Standards Consortium

Face-to-face meetings play a central role in the birth and maturation of communities. Intensive workshops filled with presentations, discussions and working group meetings have always been at the heart of the activities of the Genomic Standards Consortium (GSC). Such work-driven meetings are a key way in which the GSC fulfils its mission. Similarly, meeting reports provide a key mechanism for preserving and disseminating the consensus built at such meetings as they describe the range of speakers and participants present, topics covered and key outcomes and priorities agreed upon by the community. This issue contains a total of nine meeting reports, all from workshops held between April and December 2010. The first four describe GSC sponsored events. The first overviews the GSC 9 workshop at the J. Craig Venter Institute (JCVI) in April 2010 [1]. This pivotal meeting in the history of the GSC was the first attempt to organize an open registration meeting (with registration fees) and drew over 90 participants, the largest GSC meeting to date. The second report overviews the GSC 10 workshop held at Argonne National Labs in October of 2010 that focused on the M5 project [2]. The next two reports describe “Metagenomics, Metadata and MetaAnalysis” (M3) workshops held at the Intelligent Systems in Molecular Biology [3] and the International Society for Microbial Ecology meetings [4], respectively in 2010. Such satellite meetings allow the GSC to introduce the consensus-products of the GSC to a wider audience and also to collect essential feedback on what the community needs. As of the GSC 8 workshop, all GSC presentations have also been recorded and uploaded to the SCIVEE site. The GSC is planning its next two workshops at the Wellcome Trust Genome Campus in Hinxton, UK in April 2011 and at the Max-Plank Institute for Marine Microbiology in Bremen, Germany in September 2011. This issue also contains the first five meeting reports in SIGS contributed by external communities. The first describes a workshop held by the wider genomic annotation community as a step towards organizing a “Critical Assessment of Functional Annotation Experiment” (CAFAE) competition [5]. The next two describe the birth and early efforts to co-ordinate a megasequencing project called the Earth Microbiome Project (EMP) [6,7]. The fourth is the inaugural meeting of the BioSharing community [8]. The fifth describes the second workshop of the “Minimum Information about a Biological or Biomedical” (MIBBI) initiative [9]. The GSC is pleased to be an active member of all of these projects. We sincerely hope this special issue of meeting reports will pave the way for meeting report contributions from a wider range of related communities dedicated to creating and maintaining consensus-driven science.

A second special issue of Standards In Genomic Sciences from the Genomic Standards Consortium

A second special issue of Standards In Genomic Sciences from the Genomic Standards Consortium

Genome sequences of Bacteria and Archaea published outside of Standards in Genomic Sciences, June – September 2011

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to this subsequent versions of this list are invited to provide the bibliometric data for such references to the SIGS editorial office.

Genome sequences of Bacteria and Archaea published outside of Standards in Genomic Sciences, June – September 2011

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to this subsequent versions of this list are invited to provide the bibliometric data for such references to the SIGS editorial office.

Genome sequences published outside of Standards in Genomic Sciences, January – June 2011

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to this subsequent versions of this list are invited to provide the bibliometric data for such references to the SIGS editorial office.

Genome sequences published outside of Standards in Genomic Sciences, January – June 2011

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to this subsequent versions of this list are invited to provide the bibliometric data for such references to the SIGS editorial office.

A Call for Papers for the second special issue of SIGS from the Genomic Standards Consortium

Early issues of the Standards in Genomic Sciences (SIGS) journal have focused heavily on building a strong collection of genome notes compliant with the Minimum Information about a Genome Sequence (MIGS) checklist [1], in particular from the Genomic Encyclopedia for Bacteria and Archaea project (GEBA) [2]. This has resulted in SIGS quickly becoming the 3rdth ranked journal of all time in terms of total number of newly published genome sequences. SIGS is now branching out to also include descriptions of metagenomes and pan-genomes. As SIGS evolves it is now becoming a unique forum for publishing standards-compliant literature. Joint publication is a key step in the defining the shared interests and goals of communities. The November/December 2010 issue was a special issue containing meeting reports from five communities, including four from the Genomic Standards Consortium (GSC) [3]. In this issue, we present two types of articles new to SIGS that we believe will pave the way for similar submissions. Duhaime et al. review our current knowledge of a collection of marine phage genomes through the lens of MIGS-compliant fields, including habitat, geographic location, and host [4]. These authors contribute the first curation-based review paper to show that adherence to the GSC MIGS checklist enables a rich set of contextual data to be captured for marine phage. Likewise, SIGS now offers a forum for publishing multi-author, consensus-building papers that help define the work of the GSC and, hopefully in the future, related communities. Morrison et al. provide such a roadmap for the use of ontologies to mark up and interpret related data sources in new ways and introduce the Ontogrator software and website [5]. In a separate article, Castoe et al. present arguments from a consortium of zoologists advocating the sequencing of the garter-snake genome (Thamnophis sirtalis) [6].