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Standards in Genomic Sciences (2010) 2:357-360 DOI:10.4056/sigs.802738
The Genomic Standards Consortium
Meeting Report: “Metagenomics, Metadata and Meta-analysis”
(M3) Workshop at the Pacific Symposium on Biocomputing 2010
Lynette Hirschman1, Peter Sterk2,3, Dawn Field2, John Wooley4, Guy Cochrane5, Jack
Gilbert6, Eugene Kolker7, Nikos Kyrpides8, Folker Meyer9, Ilene Mizrachi10, Yasukazu
Nakamura11, Susanna-Assunta Sansone5, Lynn Schriml12, Tatiana Tatusova10, Owen White12
and Pelin Yilmaz13
1 Information Technology Center, The MITRE Corporation, Bedford, MA, USA
2 NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, UK
3 Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
4 University of California San Diego, La Jolla, CA, USA
5 European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI),
Hinxton, Cambridge, UK
6 Plymouth Marine Laboratory (PML), Plymouth, UK
7 Seattle Children’s Hospital, Seattle, WA, USA
8 Genome Biology Program, DOE Joint Genome Institute, Walnut Creek, California, USA
9 Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
10 National Center for Biotechnology Information, National Library of Medicine, National
Institutes of Health, Bethesda, MD, USA
11 DNA Data Bank of Japan, National Institute of Genetics, Yata, Mishima, Japan
12 University of Maryland School of Medicine, Baltimore, MD, USA
13 Microbial Genomics Group, Max Planck Institute for Marine Microbiology & Jacobs
University Bremen, Bremen, Germany
This report summarizes the M3 Workshop held at the January 2010 Pacific Symposium on
Biocomputing. The workshop, organized by Genomic Standards Consortium members, in-
cluded five contributed talks, a series of short presentations from stakeholders in the genom-
ics standards community, a poster session, and, in the evening, an open discussion session to
review current projects and examine future directions for the GSC and its stakeholders.
Introduction
The M3 Workshop at the Pacific Symposium on
Biocomputing (PSB) 2010 was organized by
members of the Genomic Standards Consortium to
continue the outreach by the GSC to the broader
multi-omics community and to the computational
biology community. The workshop was a follow-
on to two successful workshops held during the
second half of 2009: the International Conference
on Intelligent Systems for Molecular Biology
(ISMB) Metagenomics, Metadata and MetaAnalysis
(M3) Special Interest Group (SIG) [1], and the M5
(Metagenomics, Metadata, MetaAnalysis, Models,
and Metainfrastructure) workshop held in
conjunction with the Supercomputing ’09 (SC09)
conference, Portland, OR, United States.
PSB serves as a meeting ground to explore topical
issues of interest to a cross section of the compu-
tational biology community. In addition to the M3
Workshop, this 2010 PSB meeting included six
sessions and two other workshops:
• Computational Challenges in Comparative
Genomics
• Computational studies of non-coding RNAs
• Dynamics of Biological Networks
• Multi-resolution Modeling of Biological
Macromolecules
• Personal Genomics
• Reverse Engineering and Synthesis of
Biomolecular Systems
• In silico Biology Workshop
• GPD-Rxn Workshop: Genotype-Phenotype-
Drug Relationship Extraction from Text
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Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3)
358 Standards in Genomic Sciences
Background
The Genomic Standards Consortium (GSC) orga-
nized this workshop as part of its goal to create
richer descriptions for the collection of genomes
and metagenomes through the development of
standards and tools for supporting compliance
and exchange of contextual information [2]. Estab-
lished in September 2005, this international
community includes representatives from the In-
ternational Nucleotide Sequence Database Colla-
boration (INSDC), major genome sequencing cen-
ters, bioinformatics centers and a range of re-
search institutions.
The rapid pace of genomic and metagenomic se-
quencing projects [3], which now include studies
of microbiomes, will only increase as the use of
ultra-high-throughput sequencing methods be-
comes more commonplace. It is clear that we need
new standards to capture additional contextual
data as well as tools to support its use in down-
stream computational analyses. It is also clear that
these standards will be vital to exploring the com-
plex interactions that take place in communities –
both microbial communities, such as those sam-
pled in marine environments, and host-microbial
communities, such as those now being sampled in
the Human Microbiome Project.
The GSC has been responsible for promulgating
the MIGS/MIMS standard (Minimal Information
about Genomic/Metagenomics Sequences) [3],
and, at the 8th GSC workshop in September 2009, a
new standard MIENS (Minimal Information about
an ENvironmental Sequence) [4]. These standards
are being incorporated into the INSDC (Interna-
tional Nucleotide Sequence Database Collabora-
tion) as part of a new “structured comment field”.
This development was explored in a panel session
that was part of the workshop, involving repre-
sentatives from DDBJ, EMBL and GenBank.
As one of its activities, the GSC has launched a new
electronic journal SIGS (Standards in Genomic
Sciences)in order to provide an open-access pub-
lication for the rapid dissemination of both ge-
nome and metagenome reports compliant with
the MIGS/MIMS standards; the first three issues
have included “Short Genome Reports” on 32 se-
quenced bacterial genomes.
The M3 Workshop at PSB 2010 built directly on
the past GSC workshops and the ISMB SIG [1]. Its
focus was on comparative studies of (me-
ta)genomes that bring these sequences into “con-
text” (i.e., by geolocation, habitat, organism pheno-
type, etc). A recent paper published in PNAS illu-
strates the power of this approach [5]. It reports a
study aimed at elucidating the relationships be-
tween metabolic pathways and environmental
parameters in microbial communities using the
data and metadata from the Global Ocean Survey
(GOS), an earlier landmark paper in the history of
the field of metagenomics [6]. The kick-off of the
Human Microbiome Project and the resulting data
sets will open enormous new possibilities for the
coordinated integration of contextualized meta-
genomes.
M3 Workshop Structure
The workshop goal was to attract experimental-
ists and computational researchers making “next-
generation” use of contextual metadata. The
workshop was divided into two parts – a set of
contributed talks to highlight specific research
activities, and a panel of leaders in the metage-
nomics community who discussed the broad is-
sues related to generation of metagenomics data,
metadata standards and tools to support the me-
ta-analysis. In addition, the workshop included a
poster session to highlight recent advances re-
lated to the M3 goals and GSC activities.
Contributed Talks
The contributed talks covered the three “M”s:
Metagenomics
• Using 100 years of data to contextualize meta-
genomics in the Western English Channel. Jack
Gilbert, Plymouth Marine Laboratory, UK
• Metagenomics reveals functional shifts in the
bovine rumen microbiota composition with
propionate intake. Michael E. Sparks, Animal
and Natural Resources Institute, USDA, Agri-
cultural Research Service, Beltsville, USA
Metadata
• Gemina: Ontology and metadata standards de-
velopment provide core of infectious pathogen
surveillance and geospatial tool. Lynn Schriml,
University of Maryland School of Medicine,
Baltimore, USA
Meta-analysis
• Comparative Microbial genomics of resistance
genes in Staphylococcus aureus. Anja Staus-
gaard, The Technical University of Denmark,
2800 Kgs. Lyngby, Denmark
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Hirschman et al.
http://standardsingenomics.org 359
• Accurate taxonomic assignment of short pyro-
sequencing reads. Jose Clemente, Center for
Information Biology and DNA Databank of Ja-
pan, National Institute of Genetics, Mishima,
Japan.
The first two talks (Gilbert, Sparks) described
comparative metagenomic studies that demon-
strated the power provided by data measured (e.g.
geographic location, salinity, temperature, or pH)
and curated (e.g., habitat or host) using appropri-
ate metadata standards. The third talk by Schriml
described a new set of curated metadata stan-
dards that aided in the integration and inter-
operability of disparate datasets, drawing on GSC
sponsored work on the Environmental Ontology
EnvO. The final two talks demonstrated the power
of meta-analysis: Stausgaard used a comparative
genomics approach to identify and analyze resis-
tance genes in Staphylococcus aureus); Clemente
looked at taxonomic assignment of sequences of
short read-length, a significant hurdle for metage-
nome annotation from ultra-high-throughput se-
quencing platforms such as Illumina and SOLiD
The contributed talks were followed by flash
presentations for posters, which were available
during the break as well as later, during the main
conference.
Panel Discussion
The panel began with a set of reports from the
INSDC members: Cochrane for EBI, Nakamura for
DDBJ, Mizrachi for NCBI. Cochrane reported on
the inclusion of structured comments and support
for the new MIENS standard. This triggered some
discussion about validation of entries for the
structured comments fields, and the feasibility of
using ontologies or controlled vocabularies in
these fields.
The second part of the panel included reports
from RefSeq [7] (Tatusova), the ISA Infrastructure
[8] (Sansone), GEBA [9] and GOLD [10] (Kyr-
pides), CAMERA [11] (Grethe), the recent M5
workshop, a new approach to consensus annota-
tion (White), and computational infrastructure
needs (Meyer).
Evening Open Discussion
The evening session drew over 20 people for a
lively discussion. One topic was how to identify
other venues that might be productive, in terms of
“getting out the word” and attracting new partici-
pants. Suggestions included the International
Symposium for Microbial Ecology (ISME) meeting
in August 22-27th in Seattle. This had now led to
the inclusion of a GSC round table discussion at
this meeting on Monday the 23rd August 2010.
There was discussion of both previous meetings in
which the GSC was invited to participate, including
the 109th General Meeting of the American Society
for Microbiology (ASM), the Argonne Soils Work-
shop and SC09, as well as upcoming GSC spon-
sored events including the M3 and BioSharing SIG
at ISMB 2010, July 9-10 in Boston, and the GSC9
meeting at JCVI April 28-30th 2010 in Rockville. In
addition, Nikos Kyrpides made a plea for the GSC
to reach beyond the microbial community to in-
clude the plant genome community as well as
many of the model organism groups.
There was discussion about a different meaning of
“standards” that might serve as a kind of “Con-
sumer Reports” model for comparing and con-
trasting different tools that could be used for vari-
ous parts of the annotation pipeline. There was
discussion about whether GSC might provide or
encourage clear descriptions of current annota-
tion pipelines, building on a meeting before SC09
that discussed capture and exchange of
workflows. Another idea was to identify bottle-
necks where current methods do not scale; these
could perhaps be posed as “challenges” for the
computational biology community. There was dis-
cussion about whether GSC might put together
some gold standard data sets in order to support
some kind of CASP-like (Critical Assessment of
protein Structure Prediction [12]) or BioCreative-
like (Critical Assessment of Information Extraction
for Biology [13]) competition.
There was discussion about how the GSC could
interact with industry. Several people commented
that many of the sequencing companies are hop-
ing that the research community will develop al-
gorithms to handle the flood of data coming out of
the next generation sequencers. This might
present an opportunity to interact with the com-
mercial sector in a cooperative mode. Jack Gilbert
reported that he was already raising money from
industry for GSC9 (this resulted in an inclusion of
an industry panel at the GSC9 meeting – success-
fully integrating industrial partners in to the GSC
vision); also Folker Meyer reported that Amazon
has offered up a computing environment for large
scale experiments.
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Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3)
360 Standards in Genomic Sciences
There was a brief discussion of places where con-
trolled vocabularies and text mining might be use-
ful - this was a continuation of discussion from the
panel session, related to the use of structured
comments and validation of the content of a field.
There was discussion about the trade-offs of using
of a controlled vocabulary - the pluses are that the
values can be validated and may be more readily
“computable” (if using an ontology); the cons are
that this requires community buy in - and must
not be allowed to create any additional obstacles
to data entry. Apparently there is still quite li-
mited buy-in for researchers to deposit richly an-
notated data.
Conclusions
The organizers felt that this had been a successful
workshop. It was well-attended (around 40 partic-
ipants during the main session, and about half that
number in the evening session). The GSC presence
at PSB enabled a number of informal side-
discussions and exchanges that would not have
happened otherwise.
Acknowledgements
The organizers gratefully acknowledge the support
from the National Science Foundation grant RCN4GSC,
grant DBI-0840989. LH has also been supported in part
by NSF IIS 0844419: SGER for Utility and Usability of
Text Mining for Biological Curation. PS is supported by
NERC grant (NE/E007325/1) to DF.
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