Egenomics: Cataloguing Our Complete Genome Collection III

Hindawi Publishing Corporation Comparative and Functional Genomics Volume 2007, Article ID 47304, 7 pages doi:10.1155/2007/47304

Meeting Report eGenomics: Cataloguing Our Complete Genome Collection III

Dawn Field,1 George Garrity,2 Tanya Gray,1 Jeremy Selengut,3 Peter Sterk,4 Nick Thomson,5 Tatiana Tatusova,6 Guy Cochrane,4 Frank Oliver Glockner,¨ 7 Renzo Kottmann,7 Allyson L. Lister,8 Yoshio Tateno,9 and Robert Vaughan4

1 Molecular Evolution and Bioinformatics Section, Oxford Centre for Ecology and Hydrology, Mansﬁeld Road, Oxford, Oxfordshire OX1 3SR, UK 2 Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA 3 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA 4 European Molecular Biology Laboratory Outstation–The European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK 5 The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK 6 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA 7 Microbial Genomics Group, Max Planck Institute for Marine Microbiology and International University Bremen, 28359 Bremen, Germany 8 CISBAN and School of Computing Science, Newcastle University, Newcastle upon Tyne NE1 7RU, UK 9 Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 441-8540, Japan Received 28 December 2006; Accepted 28 December 2006

Recommended by Stephen Oliver

This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS), Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The ﬁrst half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS) speciﬁcation (v1.1), consensus on a variety of features to be added to the Genome Catalogue (GCat), agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates) and working towards a single, global list of all public genomes and metagenomes.

Copyright © 2007 Dawn Field et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

1. INTRODUCTION only increase as the application of ultra-high-throughput methods becomes commonplace. The primary aim of The Genomic Standards Consortium (GSC) is an initiative developing a new genomic standard is to ensure that working towards richer descriptions of our collection of gen- those researchers generating genomes contribute to an omes and metagenomes (further information about Ge- increase in the quality and quantity of metadata, so nomic Standards Consortium can be found at http://gensc that interpretation and analyses of the genome collec- .sf.net)[1]. Established in September 2005, the goal of tion can be carried out in a comprehensive and unhin- this international community is to promote mechanisms dered manner, especially from an ecological and envi- standardizing the description of genomes and the ex- ronmental perspective [2]. More background information change and integration of genomic data. Genomic sequenc- about the GSC can be found at its website http://gensc.sf ing projects are being completed at a rapid pace that will .net. 2 Comparative and Functional Genomics

The 3rd workshop was organized by Dawn Field (Ox- rapidly. Eukaryotic microbial genomics is only now begin- ford Centre for Ecology and Hydrology) and Tatiana ning its exponential growth phase just as bacterial microbial Tatusova (National Center for Biotechnology Information) genomics did 10 years ago. Difficulties arise in the selection and took place at the National Institute for Environmental of eukaryotic genomes as some, like many protists, have ex- eScience (NIEeS) in Cambridge, England, on 11–13 Septem- traordinarily large genomes and include large quantities of ber, 2006. Participants included developers of community- repetitive DNA. based standards, computer scientists, researchers building Rob Edwards (San Diego State University) started his talk genomic databases and conducting large-scale compara- with slides of a sampling trip to Christmas Island, explain- tive genomic analyses, and biologists from various disci- ing this was the reason he missed the first GSC workshop. plines who are applying genomic data in their own set- Rob proceeded to describe a range of metagenomic data sets tings. These participants included representatives of ma- from a variety of environments that have been generated with jor sequence databases (DDBJ/EMBL/NCBI) and sequenc- 454 pyrosequencing technology. In total, Rob has collected ing centres (JGI/Sanger/TIGR), a combination which proved information from 71 libraries (12 from collaborators), 2 of essential for building the future roadmap for the GSC. The which were published, and 12 of which were in the INSDC workshop built upon the previous two workshops, the first databases at the time of the workshop. He remarked that of which [1] led to the formation of the GSC and the second while the rate of sequencing has increased tremendously, the of which [3] aided its integration with the wider “OMICS” average read length has not and is currently 103 bp. Short- standardization community. read length and massive amounts of data continue to make The workshop began with an introduction from the or- the informatics of 454 data sets challenging. However, Rob ganizers. Dawn Field (Oxford Centre for Ecology and Hy- showed several examples where such data is providing in- drology) welcomed returning and new participants and em- sights into the genes and functions of organisms from a range phasized the need to place GSC activities within the con- of habitats (see, e.g., [5]). With the growth in environmen- text of wider international standardization activities, many tal metagenomics projects, he stressed the importance of in- of which were represented by speakers at this meeting. Ta- cluding global positioning system (GPS) coordinates (lati- tiana Tatusova (NCBI Entrez Genomes) further set the con- tude and longitude) for each sample. These are critical fields, text for the event by relating her memories of the phenome- already found in the MIGS specification and supported by nal growth in the number of genomes over the past 10 years. the optional “/lat lon” qualifier in INSDC files. Submission She also underscored the need to work with the wider com- to public databases is in progress, and all datasets are avail- munity, highlighting the recent ASM/NCBI Workshop on able from http://scums.sdsu.edu/. For further reading, Rob Microbial Genome Annotation, Washington, DC, USA and has authored a white paper on random community genomics the National Academy of Sciences study of metagenomics as [6]. two examples of recent allied initiatives. George Kowalchuk (Netherlands Institute of Ecology) discussed the Dutch Ecogenomics program (http://www 2. SESSION I: OVERVIEW OF OUR CURRENT AND www.ecogenomics.nl)acooperativeeffort of institutions FUTURE GENOME COLLECTION and companies financed by natural gas tax revenues and overseen by the Netherlands Genomics Initiative (http:// As Dave Ussery (Technical University Denmark), the session www.genomics.nl). Molecular methods in microbial ecology chair, stated in his introduction, the first session was designed of soils are starting to answer the simple question of “what to “remind everyone of the problem.” Sandie Baldauf (Uni- is there?” and it is proposed that integrated (meta-)genomics versity of York) kicked off the meeting with an overview of approaches will start to provide a greater understanding of eukaryotic diversity by reviewing current understanding of the more important question of “what are they doing?” The the eukaryotic tree of life [4]. For each of the eight major major themes of the program are bioremediation, ecological lineages of eukaryotes, she described the salient features of insurance, ecotoxicology and disease suppression (health in- representative species and presented an estimate of the num- teractions), all of which are brought together via overarching ber of finished and future genomes that would be available bioinformatics and technological platforms. He stressed that for specific taxa. To date, animals and fungi remain the best there is a growing need to work on a “microbially relevant” sampled taxa by far, while the majority of eukaryotic lin- scale to pick apart the biology of complex communities and eages are represented only by an EST project, or not at all. to do so, his group is currently using targeted metagenomic Single-celled eukaryotes were highlighted as fascinating, not approaches and sequencing of key taxa within characterized only because of their unusual molecular biology (e.g., ciliates communities. Such studies will help characterize the normal have massively scrambled genes, euglenoid plastid genomes operating range of life support functions via an integrated have twintrons (introns within introns) and trypanosomes ecogenomics approach and the study of the interactions of have massive RNA editing of mitochondrial transcripts), but internal and external stress factors. also because of their intriguing biological features (e.g., di- Paul Gilna (University of California, San Diego) gave an noflagellates cause various types of toxic shellfish poisoning introductory talk about a new project to build a community and produce the most potent toxins known to science). Eu- resource for microbial ecologists who use metagenomics to karyotic diversity will remain under-sampled for the near fu- study natural diversity. The recently launched “Community ture, but numbers of known species are expected to increase Cyberinfrastructure for Advanced Marine Microbial Ecology Dawn Field et al. 3

Research and Analysis” project, or CAMERA, has a five-year Natalia Maltsev (Argonne National Laboratory) was grant of 24.5 m from the Moore Foundation to build the present at the first GSC workshop but could not attend this computational infrastructure required for large-scale analy- meeting, therefore Dawn Field presented the Maltsev lab’s ses of metagenomic data sets, with special emphasis on the new project to make genomic annotations freely available global ocean survey (GOS) samples from the Sorcerer II voy- in GFF3 format. The repository can be found at ftp://ftp age. In addition to sequences, he pointed out that each sam- .mcs.anl.gov/pub/compbio/PUMA2/gff/gff files.Areoccur- ple site could be linked to vast quantities of other data, in- ring theme throughout the workshop was the strong desire cluding terabytes of satellite data. Metadata that has been of members of the GSC to see downstream analyses held in captured for the GOS samples includes information on the various databases seamlessly integrated with INSDC files to site, sampling, and experimental parameters (i.e., filter ap- produce an integrated source of information about genomes. plied to separate different size organisms prior to sequenc- The group agreed that GFF3 was a viable approach that ing or insert size). He stressed the need to learn from his- should be supported but that a significant amount of com- tory and to remember that the growth of databases in the munity consensus-building would have to precede such ac- coming years is not linear. CAMERA intends to use next tivities as it is possible to create GFF-compliant files that are generation computational infrastructure including tiled-wall not easily integrated because, for example, they use different videoconferencing rooms, the lambda rail (10 GB network), sets of features or optional fields. and the TeraGrid (1000s of CPUs) to provide access to At the end of this session Peter Sterk (EBI), Dawn Field data for metagenomic researchers across the US and be- (CEH Oxford), and Tanya Gray (CEH Oxford) presented an yond. overview of the current status of the MIGS specification, its The clear theme to emerge from the opening session was implementation as an XML schema, and a demonstration of a sense of the vast number of genomes and metagenomes the alpha release of the Genome Catalogue (GCat) software. that will be available in the near future, the potential this This introduction was aimed at providing a background for technology offers to better understand the natural world, and discussions on Day 2. Progress since the last two workshops the wide range of technological advances that will be derived has included the following. from these efforts. There was a general feeling that the global (i) Launch of the GSC website: http://gensc.sf.net. genomics initiative was comparable to the space race of the 20th century and the overall social and economic benefits (ii) The publication of a special issue of the journal would be as great or greater. As such, it sets the stage for a OMICS: a journal of integrative biology [8], which in- further set of presentations on how the international com- cluded contributions by GSC members and the meet- munity can ensure that this data can be dealt with and used ing report from the 2nd GSC workshop [3]. at its full potential. (iii) The drafting of MIGS 1.0 checklist and implementation as an XML schema (with the initiation of suitable controlled vocabularies). 3. SESSION II: DATABASES AND METADATA CAPTURE (iv) Alpha release of the Genome Catalogue (GCat) soft- AND EXCHANGE EFFORTS ware.

George Garrity (Michigan State University) chaired the next In brief, the current version of MIGS that emerged from session on international metadata capture and exchange the first two GSC workshops has now been implemented as efforts. Tatiana Tatusova (NCBI) spoke on the sequenc- an XML schema for the purpose of discussing the informa- ing project registry and how information about genome tion to be captured. The GCat software has been developed sequencing projects will be exchanged between collabora- to provide a web interface that is generated “on-the-fly” from tors using a web services protocol. Persistent identifiers for an underlying XML schema. GCat is designed to have a low genomes and genes are part of the essential infrastructure development overhead which makes it especially useful in the for the future organization of the complete genome collec- short term while the MIGS specification is in flux. The ben- tion [7]. After presenting on the annotation of the com- efit of this early implementation is that the GSC can support plete E. coli K-12 genome and genomic resources at DDBJ, both the discussion of MIGS with case study genomes and Yoshio Tateno (DDBJ) spoke about the systematic evalua- the collection of MIGS-compliant genome reports. GCat has tion and classification of the predicted proteins in the com- been developed in collaboration with the GSC implementa- plete bacterial genomes in the INSDC. In the Gene Trek in tion working group. Prokaryote Space (GTPS) project, proteins in the bacterial genomes have first been predicted using Glimmer and RBS- 4. SESSION III: ALLIED PROJECTS AND finder, and then evaluated and classified by BLASTP and In- ONTOLOGY DEVELOPMENT terPro into six grades. The predicted proteins have then been further compared with all genes in the bacterial division of On the second day of the workshop, the focus shifted the INSDC. The results of the comparison were also used for to allied projects that are already leading the way in the the evaluation and classification. Among all predicted pro- area of the standardization and integration of biological teins (1,254,150), 556,815 were evaluated as currently reli- information. Dawn Field chaired a session on a series of able ones. The methods and results of GTPS are presented at such projects, which had all been selected for their im- http://gtps.ddbj.nig.ac.jp. mediate relevance to the GSC and its future aims. George 4 Comparative and Functional Genomics

Garrity (Michigan State University) presented the Namesfor- be taken over by the recently founded NIH-funded National Life (N4L) (http://www.names4life.com)project[9], a pro- Center for Biomedical Ontologies (NCBO). Through this totype of which is accessible via the DOI resolver (http:// funding it will be possible to add more functions and ser- dx.doi.org/10.1601/tx.0). This prototype aims to disam- vices to OBO. Within a year, compound terms like “myoblast biguate and future-proof biological nomenclature by com- fusion” should be deconvoluted by explicitly referencing or- bating the knowledge bleed that occurs when information thogonal ontologies (in this case the cell-type ontology). Fi- dispersed in the scientific literature and databases is no nally, the OBO-Foundry is an effort to propagate best prac- longer accessible because key search terms (names) and con- tices and to develop truly orthogonal ontologies. cepts (taxa) have changed over time. The N4L technology Trish Whetzel (University of Pennsylvania) presented an is based on a semantic resolution service that couples Digi- overview of the ontology for biomedical investigations (OBI, tal Object Identifiers (DOIs) with an ontology that expresses previously known as the ontology for functional genomics nomenclatural acts and taxonomic concepts as a collection investigation, or FuGO). OBI aims to provide an ontology for of XML information objects that are persistently addressable the unambiguous description of the components of biomedi- and resolve nomenclatural acts in a contemporaneous man- cal (biological) investigations including the design, protocols ner. A key benefit of using DOIs is the ease of integration and instrumentation, material, data, and types of analyses with the published literature, databases, and other electronic used. The application of this ontology to the annotation of sources of information that have already adopted this stan- a wide range of investigations would allow consistent anno- dard. tation of data across technological and biological domains, George also spoke briefly about a related initiative, lead thus enabling powerful concept-driven queries over the data. by Rick Stevens (Argonne National Laboratories) and Eddy She presented an overview of which parts of the MIGS spec- Rubin (Joint Genome Institute) to produce draft genome se- ification could be placed within OBI. quences for all of the taxonomic-type strains of prokaryotes. Additionally, phenotypic descriptions in MIGS could use The project would take approximately five years to complete, the newly established phenotype and trait ontology (PATO), provide much needed reference genomes that are essential described by Suzi Lewis (Berkeley). The development of this for correct assembly of metagenomes, fill existing phyloge- ontology has been driven by the need to help the biomedi- netic gaps, and provide a foundation to meaningful linkage cal community describe the phenotypes associated with spe- to vast amounts of data, information, and knowledge about cific genes in different taxa, but is now becoming wider in these organisms that would significantly enhance inference. scope due to interest from a variety of communities. Both The obvious benefits of the proposal were immediately seized OBI and PATO are part of the OBO Foundry, which aims to upon by participants. provide a unified set of ontologies that can explicitly describe Chris Taylor (European Bioinformatics Institute) de- organisms and their molecules, phenotypes, and traits. The scribed the new MIBBI project, an initiative aimed at bring- day when the semantic resolution espoused by OBO becomes ing the MIxxx community of “Minimum Information” possible is drawing ever nearer. checklist developers together to create a unified source of The last speaker in the session was Frank Oliver Glockner¨ “OMICS” checklists (http://mibbi.sf.net). The future goal (Max Planck Institute for Marine Microbiology) who dis- of the project is to formulate an MIBBI Foundry in which cussed the need to place sequences into their proper environ- participants will commit themselves to the integration of mental context (e.g., marine, terrestrial, symbiotic). He sug- the ever-growing list of checklists such that the commu- gested the exact location (GPS), depth (altitude), and time nity can work towards multiomic standards. MIBBI has been (x, y, z, t) of any sample be taken in any molecular field study. driven by the Protein Standards Initiative (PSI), the Report- This geospatial information can then be used as a universal ing Structures for Biological Investigations (RSBI), and the anchor to allow for sequence data in the context of prevailing GSC. It represents a valuable opportunity for the GSC to biodiversity and habitat parameters. It will also allow sup- work more closely with a wide range of standardization ac- plementing the on-site information with dynamic data lay- tivities in the “OMICS” and allied sciences. ers from global monitoring systems leading to an integrated The next three talks focused on international efforts at ecosystem assessment. ontology development. Michael Ashburner (University of He introduced the International Census of Marine Mi- Cambridge) gave the history of ontology work that has arisen crobes (ICoMM) initiative (http://icomm.mbl.edu)asanad- from the development of the Gene Ontology (GO). From ditional source of geo-referenced data for microbial diversity, the beginning, one “problem” with GO was that it contained detailed the Metafunctions project (www.metafunctions.org) many other implicit ontologies—chemical compounds, for that integrates genomic information with habitat param- example. Over time, an increasing number of ontologies eters, and described the design and use of the Megx.net appeared, and GO developers became concerned that each database [10]. Furthermore, he introduced “Minimum In- was being developed independently. The GO developers es- formation about a Metagenomic Sequence” (MIMS) as an sentially wanted a one-stop-shop, and established the Open integrated extension of MIGS (http://gensc.sf.net). In ad- Biomedical Ontologies (OBO) Library as a sourceforge site dition to the core information captured in MIGS on lati- (http://obo.sf.net), encouraging colleagues to submit their tude, longitude, depth (altitude), time, and date of sampling, ontologies to the collection. Now the number of registered MIMS would capture a more extensive list of habitat param- ontologies has increased to more than fifty and OBO will eters that provide a rich set of contextual data for the sake of Dawn Field et al. 5 hypothesis generation and testing as well as ecosystems biol- development of future content. Jeremy Selengut talked about ogy. how it would be possible, using an intelligent interface, to In the absence of Nikos Kyrpides (Joint Genome Insti- step users through the input of data far more easily. By pre- tute), Dawn Field briefly demonstrated the Genomes Online senting more general questions first, users could be guided by Database (GOLD v2.0) [11], in particular pointing out the relevant, context-dependent input forms. For example, users new search engine, the inclusion of the descriptors pheno- who selected “draft” genome would then be prompted to fill type, ecotype, disease, project relevance and availability and in information for “estimated size of genome” while those their controlled vocabularies. Nikos reports that while many who selected “complete” genome would not. Similarly, sub- authors submit data directly to GOLD, he still curates a large mitters of metagenomic data would not be burdened with amount of data and is keen to have community input. The questions only relevant to single-isolate studies and vice- group expressed interest in having these controlled vocab- versa. ularies made available to the wider community. It also un- Rob Edwards (SDSU) then presented an excellent case derscored the value of GOLD as an authoritative genomic study for the GSC by relating his experiences with metadata database with an extensive user community that should be capture for his collection of metagenomic libraries. This col- tightly integrated into any future GSC strategy. lection of data sets makes an excellent case study. His take- home message is that researchers cannot be expected to com- 5. SESSION IV: GROUP DISCUSSION OF ply with standards of annotation that are presented post hoc. THE MIGS SPECIFICATION, THE GENOME Rather, the best chance of gaining compliance is to have such CATALOGUE, AND FUTURE TERM standards at the start of experimental work. Rob also stressed CAPTURE ACTIVITIES that, as a potential adopter of such a system, he would not be willing to enter data two or more times. He emphasized the This session marked the shift in the workshop from formal need for having no redundancy in the submission procedure presentations to group discussion. All participants moved to developed for users (e.g., to INSDC and GCat), which would a computer room where each had an access to a computer for require a tight linkage between submission forms. the purpose of evaluating the GSC website and the Genome The group followed this with a discussion of the of- Catalogue. The session was led by Dawn Field and Jeremy fer made prior to the workshop by EMBL participants Guy Selengut (TIGR) and started with a discussion of the MIGS Cochrane and Bob Vaughan to enter the EMBL genomes specification. In particular, the group focused on fields which into GCat for the purpose of generating useful content which were candidates for removal from the current specification, might encourage authors to submit further information. Ta- ff which helped the group to better define the general scope of tiana Tatusova (NCBI) o ered to do the same for the NCBI the specification. As a result, the GSC agreed that all fields genome collection. It was agreed that doing so would allow must meet the following criteria: the GSC to quantify the amount of optional information (e.g., lat lon) that is already available in INSDC fields and (i) to be an appropriate extension of existing INSDC qual- make it possible to work together towards a single, global list ifiers and information collected in the INSDC Project of genomes and metagenomes in the public domain. Metadata database; Finally, the group briefly discussed the capture of terms (ii) to consist of objective facts about genomic investiga- in genome reports and agreed to continue work towards tions (information that, ideally, the generators of a the posting of controlled vocabularies already in use by the genomecanbestprovide,butthisdoesnotexcludein- community to the GSC website. All terms used to complete putbyrelevantexperts); MIGS-compliant genome reports will be submitted by de- (iii) to contain specific information about the genome se- fault to OBI [12] unless a more relevant ontology already ex- quenced, while general information (e.g., about a ists. species) should be held in authoritative databases; (iv) to include clearly defined pieces of information using 6. DAY 3: ROADMAP AND WRAP-UP DISCUSSIONS values selected from controlled vocabularies. It was clear from initial discussions that each part of the To start the day, Peter Sterk led a panel discussion with MIGS specification was of varying importance to each re- members of the INSDC. The INSDC was represented by searcher. To get a good overview of the importance of each Bob Vaughan and Guy Cochrane of EMBL, Tatiana Tatusova field in the specification, a lightning round vote was taken of the NCBI, and Yoshio Tateno of the DDBJ. The INSDC for all fields in the specification, and the number of votes has a long history of describing nucleotide sequences and recorded. It was found that a few clear cases could be made is now dedicating substantial efforts to building custom so- for dropping or compressing fields by using them as con- lutions for managing genomic data [7]. Guy Cochrane be- trolled vocabulary terms in other fields of a more general na- gan the session by giving an introduction to the INSDC ture. A complete list of modifications used to produce MIGS and outlined how the collaborators come together each May v1.1 following this workshop can be found in the GSC Wiki to hold an annual meeting in which formal proposals for under “MIGS Change Log” (http://gensc.sf.net). changes to INSDC policy can be considered. It was agreed The discussions then shifted to the issues surround- that Guy, through EMBL, would take forward an agenda item ing the use of the Genome Catalogue by the GSC and the to present the MIGS specification at the May 2007 meeting 6 Comparative and Functional Genomics

(it had already been briefly introduced in May 2006) and re- (4) Develop guidelines for the submission of genomes report back to the GSC. ports. These guidelines will emphasize that genomes should The main issue addressed in this panel session was that of be submitted first to the INSDC and that the GSC then rec- the “MIGS-to-INSDC” mapping, which provides a defined ommends that INSDC refer authors to GCat. way for information in MIGS to be formatted for inclusion (5) Actively work to generate MIGS-compliant genome re- in EMBL/DDBJ/Genbank documents. Developed by Bob ports. The first valid reports are in the catalogue and the GSC and Guy and approved by the INSDC, this mapping places will work with curators at key institutions (EBI, NCBI, JGI, each MIGS field into the official INSDC feature table (see TIGR, Sanger Institute) to curate further reports. http://www.ebi.ac.uk/embl/WebFeat/index.html). The most (6) Build a batch upload facility into GCat.Thisisre- frequently used optional qualifier in the mapping is /isola- quired to allow GCat to deal with EMBL- and NCBI- tion source. When many fields in MIGS go into a single qual- produced lists of information about their genomes for ifier, they will be written out as modifiers of feature qualifiers the sake of populating GCat with content, quantifying the (e.g., /isolation source=“altitude: 1500 M” or /note=“ploidy amount of optional information already associated with level: tetraploid”). It was further discussed that any field not these genomes (e.g., the lat lon qualifier) and working to- already mapped into an INSDC qualifier could be placed into wards producing a single, global list of genomes in the public community-regulated structured comments (using the con- domain. Likewise, it will be necessary to support the future vention of tag-value pairs) by the submitters of the origi- submission of Rob Edward’s complete set of metagenomic nal sequences. Guy Cochrane also raised the issue of some datasets and, subsequent to the meeting, the full set of Sanger MIGS fields becoming a formal part of the INSDC optional Institute genomes volunteered by Nick Thomson. source qualifiers. He suggested that EMBL would take for- (7) Develop a policy on ownership of the contents of the ward a proposal to add “health/disease status of host” to the genome reports. It was agreed that all data should be placed next INSDC Collaborators meeting in May 2007. into the public domain as soon as deposited, and that a system of curation by the GSC and social tagging by any mem- 7. THE GSC ROADMAP ber of the community should be developed. Tatiana Tatusova (NCBI) stated that all data must be completely open access The final session of the meeting was moderated by the GSC for NCBI’s participation. coordinators (George Garrity, Nick Thomson, Jeremy Se- (8) Seek funding to help support the implementation and lengut, Peter Sterk, Tatiana Tatusova, and Dawn Field). This adoption of MIGS. Critical to the future success of this initia- session was dedicated to summarizing agreed action points tive will be the capacity of the GSC to find resources for cu- and building consensus on the way forward. During the dis- ration (e.g., aid submitters, validate submissions, work with cussions on Day 2, Paul Gilna (UCSD) observed that the GSC the INSDC, make sure information content stays compati- is well placed to lead by example on the issue of adoption of ble with changes in the MIGS specification and the intro- MIGS. This fact came into focus on Day 3 when the GSC duction of new controlled vocabulary terms/ontologies). Al- ffi agreed that, as part of developing a presence in the genomics though curation-based activities are di cult to fund, they are community, members would work to develop a logo, adver- vital for the success of the project, and to the community as tise the GSC website, advertise the GSC goals and aims in a whole. The cost of data curation by individual researchers ffi relevant public presentations, talk to their home institutions is di cult to estimate, but considerably higher, both in fi- about adoption of MIGS, and request official permission to nancial and productivity terms. There is a pressing need for use the logos of participating projects and institutions on the community to work with vetted datasets. Matt Kane (Na- GSC website. Perhaps most importantly GSC participants tional Science Foundation) spoke briefly on the Research Co- ff agreed to complete MIGS-compliant genome reports. ordination Network program o ered by NSF which could be In brief, based on workshop discussions the GSC has de- an opportunity to pursue for further support of networking, veloped the following ten-point Roadmap. workshops, and related activities. The GSC agreed to explore (1) Update MIGS to version 1.1 before genome reports are this option further. accepted and post to the website for further community consul- (9) Return to NIEeS in 2007 for a 4th workshop.Ideally,all tation. Now available on the web, this version is more stream- of the above activities would be completed or well under way lined and strongly typed for the sake of future validation at the time of the 4th workshop and the GSC would be able (e.g., selection from a controlled vocabulary is now expected to extend its Roadmap accordingly. for most values). (10) Complete MIGS 2.0.WeplantocompleteMIGS2.0, (2) Implement GCat identifiers. The group agreed they a production version of MIGS complete with an appropri- should take the form NNNNNN GCAT (where N is a num- ate set of terms formalized within OBI [12] and other rele- ber from 0 to 9) to avoid any confusion with INSDC acces- vant ontologies, and a significantly improved version of the sion numbers. In taking this step, the GSC has paved the way Genome Catalogue, by October 2007. towards creation and adoption of a community infrastruc- In conclusion, this workshop has produced an improved ture for supporting MIGS compliance. version of MIGS (v1.1), an updated XML schema (v1.1), (3) Produce a production version of GCat ready to ac- consensus on a wide range of features to add to GCat, and cept published genome reports. This is available at http:// further actions within the group that support the genera- gensc.sf.net. tion and submission of MIGS-compliant genome reports to Dawn Field et al. 7

GCat. Since the workshop, GCat identifiers have been im- [10] T. Lombardot, R. Kottmann, H. Pfeffer, et al., “Megx.net— plemented and the first MIGS-compliant genome reports database resources for marine ecological genomics,” Nucleic for published and unpublished projects have been submit- Acids Research, vol. 34, Database issue, pp. D390–D393, 2006. ted [13–16]. A variety of value-added features have also been [11] K. Liolios, N. Tavernarakis, P.Hugenholtz, and N. C. Kyrpides, developed within the Genome Catalogue including the abil- “The Genomes On Line Database (GOLD) v.2: a monitor of ity to view genomes on a map based on their latitude and genome projects worldwide,” Nucleic Acids Research, vol. 34, Database issue, pp. D332–D334, 2006. longitude and the ability to access information using REST [12] P. L. Whetzel, R. R. Brinkman, H. C. Causton, et al., “Develop- style web services. If the GSC can meet its target of produc- ment of FuGO: an ontology for functional genomics investiga- ing the infrastructure required to support MIGS (specifica- tions,” OMICS: A Journal of Integrative Biology, vol. 10, no. 2, tion, a working repository, and access to appropriate terms) pp. 199–204, 2006. it should put the community in a stronger position to push [13] F. E. Angly, B. Felts, M. Breitbart, et al., “The marine viromes for enforcement of compliance. The GSC continues to make of four oceanic regions,” PLoS Biology, vol. 4, no. 11, pp. 2121– its open call for support and involvement in this initiative. 2131, 2006. The GSC welcomes new members, links to new projects, and [14] F. O. Glockner,¨ M. Kube, M. Bauer, et al., “Complete genome researchers willing to describe the genomes with the submis- sequence of the marine planctomycete Pirellula sp. strain 1,” sion of MIGS-compliant genome reports as part of the fur- Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 14, pp. 8298–8303, 2003. ther development of this project. Anyone interested in know- ff [15] R. Rabus, A. Ruepp, T. Frickey, et al., “The genome of Desul- ing more about or joining this e ort is encouraged to con- fotalea psychrophila, a sulfate-reducing bacterium from per- tact any of the coordinators or join the GSC mailing lists manently cold Arctic sediments,” Environmental Microbiology, (http://gensc.sf.net). vol. 6, no. 9, pp. 887–902, 2004. [16] M. Bauer, M. Kube, H. Teeling, et al., “Whole genome analysis ACKNOWLEDGMENTS of the marine Bacteroidetes ‘Gramella forsetii’ reveals adap- tations to degradation of polymeric organic matter,” Environ- The authors acknowledge the invaluable contributions of mental Microbiology, vol. 8, no. 12, pp. 2201–2213, 2006. all of the participants who attended the workshop. This workshop was funded and hosted by NIEeS and an NERC International Opportunities Fund Award (NE/3521773/1) to the first author.

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