2025 marks the twenty-fifth anniversary of the completion of a working draft of the 3-Gb human genome sequence and its availability in public databases to promote research into human health and disease for the benefit of all. The sequence was produced by the International Human Genome Sequencing Consortium, which comprised sequencing centers from six countries who together undertook the largest collaborative biological project to date. Under the leadership of Sir John Sulston, the United Kingdom played a significant role in the project through the Sanger Centre (now the Wellcome Sanger Institute), which was founded in 1992 with support from the Wellcome Trust, a charitable foundation funding medical research. The Sanger Centre contributed approximately one-third of the final human genome sequence generated by the Human Genome Project and, along with the European Bioinformatics Institute, developed Ensembl, one of the major databases providing free access to genomic data and annotation for biomedical research. As a result of a chance meeting, I came to work at the Sanger Centre (and later the Wellcome Sanger Institute) from 1992 to 2007, initially as a scientific administrator and later as the Human Genome Project manager and head of sequencing. Over that period, the Sanger Centre became one of the largest genome sequencing centers in the world and began its transition to become a world-leading center in genomics research to advance biology and health.

Supplementary Table 3 from Insertional Mutagenesis in Mice Deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 Reveals Cancer Gene Interactions and Correlations with Tumor Phenotypes

Supplementary Figure Legends 1-3 from Insertional Mutagenesis in Mice Deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 Reveals Cancer Gene Interactions and Correlations with Tumor Phenotypes

Supplementary Figure Legends 1-3 from Insertional Mutagenesis in Mice Deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 Reveals Cancer Gene Interactions and Correlations with Tumor Phenotypes

SummaryUntil recently, achieving a reference‐quality genome sequence for bread wheat was long thought beyond the limits of genome sequencing and assembly technology, primarily due to the large genome size and > 80% repetitive sequence content. The release of the chromosome scale 14.5‐Gb IWGSC RefSeq v1.0 genome sequence of bread wheat cv. Chinese Spring (CS) was, therefore, a milestone. Here, we used a direct label and stain (DLS) optical map of the CS genome together with a prior nick, label, repair and stain (NLRS) optical map, and sequence contigs assembled with Pacific Biosciences long reads, to refine the v1.0 assembly. Inconsistencies between the sequence and maps were reconciled and gaps were closed. Gap filling and anchoring of 279 unplaced scaffolds increased the total length of pseudomolecules by 168 Mb (excluding Ns). Positions and orientations were corrected for 233 and 354 scaffolds, respectively, representing 10% of the genome sequence. The accuracy of the remaining 90% of the assembly was validated. As a result of the increased contiguity, the numbers of transposable elements (TEs) and intact TEs have increased in IWGSC RefSeq v2.1 compared with v1.0. In total, 98% of the gene models identified in v1.0 were mapped onto this new assembly through development of a dedicated approach implemented in the MAGAAT pipeline. The numbers of high‐confidence genes on pseudomolecules have increased from 105 319 to 105 534. The reconciled assembly enhances the utility of the sequence for genetic mapping, comparative genomics, gene annotation and isolation, and more general studies on the biology of wheat.

In this Review, the year of publication of reference 54 should be 2005, not 2015. In Box 2, “1982: GenBank ( https://www.ncbi.nlm.nih.gov/genbank/statistics/ )” should read “1982: Genbank/ENA/DDBJ” and “2007: NCBI Short Read Archive” should read “2007: NCBI and ENA Short Read Archives”; this is because the launches of these American, European and Japanese databases were coordinated. These errors have not been corrected.

Agronomy/agriculture and biodiversity (ag & biodiv) communities face several major societal, economic, and environmental challenges that data science approaches will help address. To achieve their goals, researchers of these communities must be able to rapidly discover, aggregate, integrate, and analyse different types of data and information sources. Semantic technologies, combined to open, FAIR data and services, is one of the answers to fully knowledge-driven, and transparent science and innovation. The D2KAB project (www.d2kab.org) aims to create a framework to turn agronomy and biodiversity data into knowledge – semantically described, interoperable, actionable, open – and investigate the scientific methods and tools to exploit this knowledge for applications in agriculture and biodiversity sciences. This project, funded by French ANR (2019-2023), will provide the means –ontologies and linked open data– for ag & biodiv to embrace semantic Web technologies in order to produce and exploit FAIR data and services. To do so, D2KAB will develop new original methods and algorithms in the following areas: data integration, text mining, semantic annotation, ontology alignment and linked data exploitation and visualization. D2KAB project brings together a unique multidisciplinary consortium of 12 partners to achieve this objective: 2 informatics research units (LIRMM, I3S); 6 INRA/IRSTEA/IRD research units at the interface of computer science and ag & biodiv (URGI, MaIAGE, IATE, DIST, TSCF, DIADE) specialized in agronomy or agriculture; 2 labs in biodiversity and ecosystem research (CEFE, URFM); 1 association of agriculture stakeholders (ACTA); and 1 partnership with Stanford BMIR department. Three main goals drive D2KAB’s roadmap: 1. To develop state-of-the-art methods and technologies for ontology lifecycle and alignment. 2. To build the agronomy, agriculture and biodiversity Linked Open Data cloud. 3. To enable new semantically driven agronomy and biodiversity science. The work is starting from the recommendations of several RDA WG and IG already published or in progress (e.g. Agrisemantic WG, Vocabulary Services IG, Wheat and Rice Data Interoperability WGs, Agricultural Data IG, SHARC IG). Some of the key technological building blocks of D2KAB are AgroPortal, a reference repository for ontologies and vocabularies in agronomy; AgroLD, a semantic Web knowledge base that integrates agronomic data from public databases including GO associations, Gramene, UniprotKB, and OryGenesDB ; Corese, a semantic Web factory that implements the W3C standards RDF, RDFS, OWL-RL and SPARQL, and LDScript, a Linked Data Script Language, and STTL, the SPARQL Template Transformation Language for RDF; and Alvis, a text mining for semantic normalisation of free text by ontologies. D2KAB will allow the valorization of ag & biodiv data into real world applications leading to economic impact, smart agriculture and ecological preservation. Five driving scenarios are planned: development of an ontology-based expert system to select food packaging solutions; creation of an augmented semantic reader for Plant Health Bulletins; advanced integration of textual and experimental data on wheat phenotypes; development of new ontologies on plant root traits and extension of the Thesaurus Of Plant Characteristics; integration of plant functional biogeography data related to the Mediterranean Basin. Each of the project scenarios will have a significant impact and produce concrete outcomes for ag & biodiv scientific communities and socio-economic stakeholders in agriculture.

화학공학소재연구정보센터 홈 로그인 로그아웃 연락처 사이트맵. 센터: 센터소개; 회원가입/정보수정. 뉴스: 공지사항; 연구동향; 취업정보. 연구정보: 문헌DB; KDB; Compound Search; 전문연구정보; 동영상; 심포지움 자료; 연구성과보고서; 저널정보; 논문 작성법; 참고문헌DB; 분석기기DB; 화학공정DB; PSPDB; 연구자지식지도; 상태도정보. 교육정보: 사이버강의-학부; 사이버강의-대학원; 실무강좌; 강의자료 링크; 교육자료 링크; 사이버실험실; 물성측정실험 매뉴얼. 커뮤니티: 공학포럼; 카페; 신진연구자인터뷰. 리소스: 특허정보; 술어DB; 관련법령; 자격증정보; 성과소개서; 연구보고서. 문헌DB: 학술지 검색; 학술대회 발표논문집; 최신 국내 저널; 최신 리뷰페이퍼. KDB: Periodic Table of Elements; Unit Conversion; Universal Constants; Pure Component Properties; Binary Vapor-Liquid Equil …

Plant Phenotyping data management following the FAIR (Findable, Accessible, Interoperable, Resusable) is highly challenging because of its heterogenity. Thus, simply integrating and consolidating data within a single dataset like a phenotyping network is already a complicated task which is even more complex when trying to link different datasets together. To adress this problem, the Minimal Information About Plant Phenotyping Experiment standard construction has been initiated four years ago, with the help of experts from European infrastructures and institutes like Elixir, Emphasis, INRA, WUR, iBet, IPK, EBI and IPG PAS. It adresses the need of data publication and reuse through a checklist that formalize and document the minimal metadata necessary to ensure long term FAIRness of field or greenhouse datasets, including high througputs phenotyping ones. This list has been implemented in several databases like GnpIS or eDale, in a file format, ISA Tab, in a web service, the Breeding API and an RDF implementation is under construction. We will review those implementations, show its current adoption state and detail the plans for the future evolutions of the standard. (Resume d'auteur)

The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.

This paper appeared in An et al. (2013); Mol Microbiol 88(6): 1058–1069. doi: 10.1111/mmi.12229 The authors have been made aware of issues with Fig. 3A of this paper which illustrates the different classes of virulence as determined by lesion length. In constructing this figure, leaf images reported in two other publications (An et al., 2013; EMBO J 32(18): 2430–2438 and O'Connell et al. 2013; Mol Plant Microbe Interact 26(10): 1131–1137) were used to represent Class 0 and Class IV symptoms, respectively. To address this duplication, we have replaced these panels in Fig. 3A. Professor J. L. Tang takes full responsibility for the original error. Together he and the corresponding author take accountability for the authenticity of the correction. All authors sincerely apologize for the error and emphasize that the quantitative data that is presented is correct and fully supports the conclusions drawn. References An, S.-Q., Chin, K.-H., Febrer, M., McCarthy, Y., Yang, J.-G., Liu, C.-L., et al. (2013) A cyclic GMP-dependent signalling pathway regulates bacterial phytopathogenesis. EMBO J 32: 2430– 2438. doi:10.1038/emboj.2013.165 An, S.-Q., Febrer, M., McCarthy, Y., Tang, D.-J., Clissold, L., Kaithakottil, G., et al. (2013) High-resolution transcriptional analysis of the regulatory influence of cell-to-cell signalling reveals novel genes that contribute to Xanthomonas phytopathogenesis. Mol Microbiol 88: 1058– 1069. doi:10.1111/mmi.12229 O'Connell, A., An, S.-Q., McCarthy, Y., Schulte, F., Niehaus, K., He, Y.-Q., et al. (2013) Proteomics analysis of the regulatory role of Rpf/DSF cell-to-cell signaling system in the virulence of Xanthomonas campestris. Mol Plant Microbe Interact 26: 1131– 1137. doi:10.1094/MPMI-05-13-0155-R

The objectives of the INRA plant BRCs are to gather, conserve, characterize and provide high quality plant materials to their collaborators and users, mainly researchers and breeders. For that purpose, they are ensuring a high degree of quality in their management systems and give access to their catalogs through an information system organized in two layers, (i) local information systems that allows the BRCs to manage their collection and (ii) a central system, the INRA Plant Genetic Resource Information System (GnpIS-Siregal https://urgi.versailles.inra.fr/siregal), integrated with the GnpIS information system of the URGI platform (ISO 9001). GnpIS allows linking information on plant genetic resources with genetic, genomic or phenotypic data. In the last six years, INRA has focused its efforts on the development and implementation in GnpIS of strategies and tools aiming at facilitating the access to data and at making them interoperable and re-usable. This was achieved through several international projects (e.g. FP7 TransPLANT, ARCAD FEDER, H2020 ELIXIR Excelerate) or initiatives (Wheat Initiative, Research Data Alliance, Breeding API) contributing to the development (i) of community recommendations for data standardisation (e.g. wheatis.org), (ii) of a data standard for phenotyping experiment (www.miappe.org), (iii) of several crop specific ontologies in the frame of the CropOntology (http://www.cropontology.org/), (iv) of portals giving access to data in distributed information systems and (v) of a standard Application Programming Interface for plant genetics and breeding that will facilitate the development of such portals. In addition, an effort has recently been made in curating and diffusing the data: the assignment of Digital Object Identifier (DOI) to accessions and to data sets allows to identify them more easily. Moreover, the French national collections hosted by INRA are now integrated in both Eurisco and GBIF international biodiversity portals in order to improve their accessibility.

This review commemorates the 40th anniversary of DNA sequencing, a period in which we have already witnessed multiple technological revolutions and a growth in scale from a few kilobases to the first human genome, and now to millions of human and a myriad of other genomes. DNA sequencing has been extensively and creatively repurposed, including as a 'counter' for a vast range of molecular phenomena. We predict that in the long view of history, the impact of DNA sequencing will be on a par with that of the microscope.

URGI is a genomics and bioinformatics research unit at INRA (French National institute for Agricultural Research), dedicated to plants and crop parasites. We develop and maintain a genomic and genetic Information System called GnpIS that manages multiple types of wheat data. Under the umbrella of the IWGSC (International Wheat Genome Sequencing Consortium), we have set up a Sequence Repository on the Wheat@URGI website to store, browse and BLAST the data being generated by the wheat genome project: http://wheat-urgi.versailles.inra.fr/Seq-Repository. The repository holds the wheat physical maps, the chromosome survey sequence data for the individual chromosomes of breadwheat, draft sequences for diploid and tetraploid wheats and provides browsable access to the BAC-based reference sequence for chromosome 3B, the first of the chromosomes to be completed by the consortium. I will highlight the new features and data available in the Sequence Repository (e.g., new BLAST functionalities) and, in particular, present what we have done to address needs and concerns raised during the IWGSC S&P workshop last year. In addition, I will open the discussion about the future needs for tools to facilitate the integration of data to produce the reference sequence.