Annotation Jamboree Research Articles

Initiating the Mollusk Genomics Annotation Community: Toward Creating the Complete Curated Gene-Set of the Japanese Pearl Oyster,Pinctada fucata

The genome sequence of the Japanese pearl oyster, the first draft genome from a mollusk, was published in February 2012. In order to curate the draft genome assemblies and annotate the predicted gene models, two annotation Jamborees were held in Okinawa and Tokyo. To date, 761 genes have been surveyed and curated. A preparatory meeting and a debriefing were held at the Misaki Marine Biological Station before and after the Jamborees. These four events, in conjunction with the sequence-decoding project, have facilitated the first series of gene annotations. Genome annotators among the Jamboree participants added 22 functional categories to the annotation system to date. Of these, 17 are included in Generic Gene Ontology. The other five categories are specific to molluskan biology, such as "Byssus Formation" and "Shell Formation", including Biomineralization and Acidic Proteins. A total of 731 genes from our latest version of gene models are annotated and classified into these 22 categories. The resulting data will serve as a useful reference for future genomic analyses of this species as well as comparative analyses among mollusks.

Database resources for the tuberculosis community

Access to online repositories for genomic and associated "-omics" datasets is now an essential part of everyday research activity. It is important therefore that the Tuberculosis community is aware of the databases and tools available to them online, as well as for the database hosts to know what the needs of the research community are. One of the goals of the Tuberculosis Annotation Jamboree, held in Washington DC on March 7th-8th 2012, was therefore to provide an overview of the current status of three key Tuberculosis resources, TubercuList (tuberculist.epfl.ch), TB Database (www.tbdb.org), and Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org). Here we summarize some key updates and upcoming features in TubercuList, and provide an overview of the PATRIC site and its online tools for pathogen RNA-Seq analysis.

Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees

Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome.

SOBA: sequence ontology bioinformatics analysis

The advent of cheaper, faster sequencing technologies has pushed the task of sequence annotation from the exclusive domain of large-scale multi-national sequencing projects to that of research laboratories and small consortia. The bioinformatics burden placed on these laboratories, some with very little programming experience can be daunting. Fortunately, there exist software libraries and pipelines designed with these groups in mind, to ease the transition from an assembled genome to an annotated and accessible genome resource. We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers for rapid feedback during annotation software development and testing. SOBA also provides annotation consistency feedback to ensure correct use of terminology within annotations, and guides users to add new terms to the Sequence Ontology when required. SOBA is available at http://www.sequenceontology.org/cgi-bin/soba.cgi.

Reconstruction annotation jamborees: a community approach to systems biology

Mol Syst Biol. 6: 361 Genome‐scale metabolic network reconstructions represent biochemical, genetic, and genomic (BiGG) knowledge bases for a target organism (Reed et al , 2006). Thus, they correspond to two‐dimensional genome annotations: that is, they contain all nodes and links that comprise a biochemical reaction network defined by the genome (Palsson, 2004). These reconstructions allow the conversion of biological knowledge into a mathematical format and subsequent computation of physiological properties. They therefore enable the formulation of a mechanistic genotype–phenotype relationship for metabolic functions in the target organism. The metabolic network reconstruction process is now well established (Thiele and Palsson, 2010) and its workflows have recently been reviewed (Reed et al , 2006; Feist et al , 2009). The development of a consensus network reconstruction that is accepted and used by the research community necessitates a collective effort to formalize such networks that are specific to a target organism. This need has led to the concept of a 2D annotation (or a reconstruction) jamboree (Mo and Palsson, 2009), in analogy to the 1D genome annotation jamborees that lead to a community‐driven genome annotation process. You may be interested in organizing a jamboree for your favorite target organism. What do you need to do? The goal of a network reconstruction jamboree is to reconcile and refine currently available BiGG knowledge about the target organism. If available, multiple existing metabolic network reconstructions made by individual research groups provide a great starting point. A jamboree should update, re‐evaluate, refine and, later on, expand the network content. These goals are most efficiently achieved through a community approach that assembles experts from different areas. Jamborees assist in fostering collaborations as well as informing the community about the properties, content, and capabilities of the consensus reconstruction to ensure its broad use for biological, biomedical, …

DDBJ Activities: Contribution to the Research in Information Biology

AbstractDDBJ (DNA Data Bank of Japan; "http://www.ddbj.nig.ac.jp/":http://www.ddbj.nig.ac.jp/)started its database activities in 1986. From the beginning, DDBJ has been one of INSDC (International Nucleotide Sequence Database Collaboration; "http://www.insdc.org/":http://www.insdc.org/) that is a tripartite collaboration with EMBL-Bank/EBI and GenBank/NCBI.The total base number of the primary nucleotide sequence data collected and distributed by INSDC exceeded 100 Gbases in August 2005. Since then it took only three years for the total base number to be doubled (200 Gbases). Now, the collaboration is being expanded to Traces (DNA sequence chromatograms) and Short Reads (raw reads data from 454, Solexa, SOLiD etc). DDBJ is also collecting and releasing gene expression data at CIBEX (Center for Information Biology gene EXpression database; "http://cibex.nig.ac.jp/":http://cibex.nig.ac.jp/). Furthermore, DDBJ contributed to international annotation jamborees such as FANTOM (mouse), H-Inv (human), RAP (rice) and E. coli K12. DDBJ provides many services to the research in information biology or bioinformatics. They include Web-API for Biology (WABI) "http://www.xml.nig.ac.jp/":http://www.xml.nig.ac.jp/ and All-round Retrieval of Sequence and Annotation (ARSA) "http://arsa.ddbj.nig.ac.jp/":http://arsa.ddbj.nig.ac.jp/. These activities are presented with the perspective of DDBJ in the coming years.

Expert Assertions Through Community Annotation Jamborees

Although there is significant optimism that community involvement can drive genome curation, results to date are disappointing. The Human Genome and Saccharomyces Genome Databases both tried community annotation experiments and few community contributions were obtained. JCVI’s own early experiences with community curation were also largely unsuccessful. Although community curation tools were publicly available on JCVI web resources and much effort was made by JCVI personnel to advertise these resources, little curation was actually submitted. Starting in late 2007, JCVI’s model for community curation changed. Instead of simply providing curation tools on websites and advertising their utility at meetings and conferences, JCVI instituted a community curation jamboree model. Annotation jamborees are an excellent form of outreach to the community. JCVI’s experience conducting jamborees is highly successful, demonstrating that jamborees are effective tools for incorporating expert annotation data into existing genome submissions, updating existing annotation, tagging annotation with updated experimental references and providing the community with opportunities to become familiar with JCVI’s annotation procedures and curation tools. Jamborees provide a means to directly interact with the community and integrate their research expertise into genomic data sets. Jamboree participants are encouraged to provide their expert input by focusing on their genes and gene families of interest, particularly those with supporting experimental evidence. Through JCVI’s NIAID Bioinformatics Resource Center, Pathema ("http://pathema.jcvi.org":http://pathema.jcvi.org), JCVI hosted two annotation jamborees incorporating expert annotation into Entamoeba and Burkholderia genome projects. These jamborees resulted in curation of 1,565 functional assignments, 3,499 Gene Ontology terms, 129 gene structures, and 296 experimental references for 11 genome projects representative of the Pathema data set. Researchers who contributed to annotation at these jamborees are being submitted as contributing authors on annotation update submissions made to GenBank for those organisms. Additionally, the annotation associated with the submission is recognized as part of community curation efforts and collaboration, and all updates and contributions are reflected on the Pathema web resource.The networking and personal communication that occurs throughout a jamboree facilitates a forum for research and data exchange, solicitation of user feedback and the establishment of new community collaborations. Although integrating and updating annotation data is important, it is our experience that the interactions that occur and collaborations that are formed are the most beneficial long-term results of jamboree efforts. Collaborations we established as a direct result of jamboree activity include continued community annotation, custom data analyses and general informatics support not otherwise solicited by the researcher. For the jamborees JCVI recently hosted, we established successful collaborations with four researchers who continued to provide curation from their own institute.

Expert Assertions Through Community Annotation Jamborees

AbstractAlthough there is significant optimism that community involvement can drive genome curation, results to date are disappointing. The Human Genome and Saccharomyces Genome Databases both tried community annotation experiments and few community contributions were obtained. JCVI’s own early experiences with community curation were also largely unsuccessful. Although community curation tools were publicly available on JCVI web resources and much effort was made by JCVI personnel to advertise these resources, little curation was actually submitted. Starting in late 2007, JCVI’s model for community curation changed. Instead of simply providing curation tools on websites and advertising their utility at meetings and conferences, JCVI instituted a community curation jamboree model. Annotation jamborees are an excellent form of outreach to the community. JCVI’s experience conducting jamborees is highly successful, demonstrating that jamborees are effective tools for incorporating expert annotation data into existing genome submissions, updating existing annotation, tagging annotation with updated experimental references and providing the community with opportunities to become familiar with JCVI’s annotation procedures and curation tools. Jamborees provide a means to directly interact with the community and integrate their research expertise into genomic data sets. Jamboree participants are encouraged to provide their expert input by focusing on their genes and gene families of interest, particularly those with supporting experimental evidence. Through JCVI’s NIAID Bioinformatics Resource Center, Pathema ("http://pathema.jcvi.org":http://pathema.jcvi.org), JCVI hosted two annotation jamborees incorporating expert annotation into Entamoeba and Burkholderia genome projects. These jamborees resulted in curation of 1,565 functional assignments, 3,499 Gene Ontology terms, 129 gene structures, and 296 experimental references for 11 genome projects representative of the Pathema data set. Researchers who contributed to annotation at these jamborees are being submitted as contributing authors on annotation update submissions made to GenBank for those organisms. Additionally, the annotation associated with the submission is recognized as part of community curation efforts and collaboration, and all updates and contributions are reflected on the Pathema web resource.The networking and personal communication that occurs throughout a jamboree facilitates a forum for research and data exchange, solicitation of user feedback and the establishment of new community collaborations. Although integrating and updating annotation data is important, it is our experience that the interactions that occur and collaborations that are formed are the most beneficial long-term results of jamboree efforts. Collaborations we established as a direct result of jamboree activity include continued community annotation, custom data analyses and general informatics support not otherwise solicited by the researcher. For the jamborees JCVI recently hosted, we established successful collaborations with four researchers who continued to provide curation from their own institute.

The role of Havana and communities in the manual curation of unfinished vertebrate genomes

AbstractManual annotation‭ (‬the‭ "‬museum‭" ‬model of annotation‭) ‬relies on a small group of specialized curators to catalogue and classify genes according to their functional roles.‭ This‬ is both costly and time consuming and therefore is used only for model organisms with sufficient funding.‭ ‬Smaller research communities often have to rely on other models of annotation,‭ ‬mainly automated annotation‭ (‬the‭ "‬factory‭" ‬model,‭ ‬e.g.‭ ‬Ensembl‭)‬,‭ ‬and the‭ "‬jamboree‭" ‬model‭ (‬in which a group of leading biologists from the community and bioinformaticians come together for a short intensive annotation workshop‭)‬.‭ ‬At the Wellcome Trust Sanger Institute‭ (‬WTSI‭)‬,‭ ‬the Havana team provides high quality manual annotation of finished vertebrate genome sequences,‭ ‬namely human,‭ ‬mouse and zebrafish.‭ ‬We also perform the curation of specific finished regions such as the MHC in dog,‭ ‬cow and pig,‭ ‬whose whole genomes have been‭ ‬assembled from unfinished BACs or from whole genome shotgun sequences.‭ ‬In addition,‭ ‬we at Havana have also hosted annotation jamborees for the cow‭ (‬Bos taurus‭) ‬and pig‭ (‬Sus scrofa‭) ‬genomes.‭ ‬During those sessions,‭ ‬the research community had the opportunity to annotate their genes of interest under expert guidance using the custom written publicly available Otterlace annotation system,‭ ‬and the unified manual annotation guidelines.‭ ‬By making use of the tools and skills acquired during the cow and pig jamborees,‭ ‬the delegates can continue annotating their genomes remotely.‭ ‬For the pig genome,‭ ‬a highly contiguous physical map has been generated by an international effort of four laboratories (available in Pre!Ensembl) and‭ ‬is being used as a substrate for the swine genome sequencing project.‭ ‬Upcoming vertebrate genomes will be sequenced to a high depth coverage with the next generation sequencing technologies‭ (‬e.g.‭ ‬Illumina,‭ ‬454,‭ ‬SOLiD‭) ‬but will have the drawback of not being manually finished.‭ ‬Manual annotation will be more accurate than the automated predictions at coping with any assembly problems derived from these high coverage but unfinished‭ (‬or automatic pre-finished‭) ‬genomes.‭ ‬Once these inherent assembly errors are corrected and the gene structures are accurately identified with manual annotation,‭ ‬the curated genes will be incorporated and merged with the predicted gene models in Ensembl to provide a unified view of the landscape of vertebrate genomes.‭ ‬I will present an introduction to our manual annotation system and our experience using it for annotation jamborees at the WTSI.

Phytophthora Genomics: The Plant Destroyers' Genome Decoded

The year 2004 was an exciting one for the Phytophthora research community. The United States Department of Energy Joint Genome Institute (JGI) completed the draft genome sequence of two Phytophthora species, Phytophthora sojae and Phytophthora ramorum. In August of that year over 50 people gathered at JGI in Walnut Creek, California, for an annotation jamboree and searched for the secrets and surprises that the two genomes have in petto. This culminated in a paper in Science in September of this year describing the highlights of the sequencing project and emphasizing the power of having the genome sequences of two closely related organisms. This MPMI Focus issue on Phytophthora genomics contains a number of more specialized manuscripts centered on gene annotation and genome organization, and complemented with manuscripts that rely on genomics resources.

Fly's time

The struggle between public and private efforts to sequence the fly genome is the subject of Michael Ashburner's new book, Won for All: How the Drosophila Genome Was Sequenced

The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information

With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was held in Japan with the aim of annotating and manually curating all the genes in the rice genome. Here we present the Rice Annotation Project Database (RAP-DB), which has been developed to provide access to the annotation data. The RAP-DB has two different types of annotation viewers, BLAST and BLAT search, and other useful features. By connecting the annotations to other rice genomics data, such as full-length cDNAs and Tos17 mutant lines, the RAP-DB serves as a hub for rice genomics. All of the resources can be accessed through .

A Human Protein Atlas for Normal and Cancer Tissues Based on Antibody Proteomics

Antibody-based proteomics provides a powerful approach for the functional study of the human proteome involving the systematic generation of protein-specific affinity reagents. We used this strategy to construct a comprehensive, antibody-based protein atlas for expression and localization profiles in 48 normal human tissues and 20 different cancers. Here we report a new publicly available database containing, in the first version, approximately 400,000 high resolution images corresponding to more than 700 antibodies toward human proteins. Each image has been annotated by a certified pathologist to provide a knowledge base for functional studies and to allow queries about protein profiles in normal and disease tissues. Our results suggest it should be possible to extend this analysis to the majority of all human proteins thus providing a valuable tool for medical and biological research.