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UK PubMed Central (UKPMC) is a full-text article database that extends the functionality of the original PubMed Central (PMC) repository. The UKPMC project was launched as the first 'mirror' site to PMC, which in analogy to the International Nucleotide Sequence Database Collaboration, aims to provide international preservation of the open and free-access biomedical literature. UKPMC (http:// ukpmc.ac.uk) has undergone considerable development since its inception in 2007 and now includes both a UKPMC and PubMed search, as well as access to other records such as Agricola, Patents and recent biomedical theses. UKPMC also differs from PubMed/PMC in that the full text and abstract information can be searched in an integrated manner from one input box. Furthermore, UKPMC contains 'Cited By' information as an alternative way to navigate the literature and has incorporated text-mining approaches to semantically enrich content and integrate it with related database resources. Finally, UKPMC also offers added-value services (UKPMC+) that enable grantees to deposit manuscripts, link papers to grants, publish online portfolios and view citation information on their papers. Here we describe UKPMC and clarify the relationship between PMC and UKPMC, providing historical context and future directions, 10 years on from when PMC was first launched. © The Author(s) 2010.

SOAP (Simple Object Access Protocol) (http://www.w3.org/TR/soap) based Web Services technology (http://www.w3.org/ws) has gained much attention as an open standard enabling interoperability among applications across heterogeneous architectures and different networks. The European Bioinformatics Institute (EBI) is using this technology to provide robust data retrieval and data analysis mechanisms to the scientific community and to enhance utilization of the biological resources it already provides [N. Harte, V. Silventoinen, E. Quevillon, S. Robinson, K. Kallio, X. Fustero, P. Patel, P. Jokinen and R. Lopez (2004) Nucleic Acids Res., 32, 3-9]. These services are available free to all users from http://www.ebi.ac.uk/Tools/webservices.

The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors; IPD-MHC, a database of sequences of the Major Histocompatibility Complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC share the same database structure. The sharing of a common database structure makes it easier to implement common tools for data submission and retrieval. The data are currently available online from the website and ftp directory; files will also be made available in different formats to download from the website and ftp server. The data will also be included in SRS, BLAST and FASTA search engines at the European Bioinformatics Institute.

As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics Institute (EBI) hosts six core databases, which store information on DNA sequences (EMBL-Bank), protein sequences (SWISS-PROT and TrEMBL), protein structure (MSD), whole genomes (Ensembl) and gene expression (ArrayExpress). But just as a cell would be useless if it couldn't transcribe DNA or translate RNA, our resources would be compromised if each existed in isolation. We have therefore developed a range of tools that not only facilitate the deposition and retrieval of biological information, but also allow users to carry out searches that reflect the interconnectedness of biological information. The EBI's databases and tools are all available on our website at www.ebi.ac.uk.

TheEMBLNucleotideSequenceDatabase(http://www.ebi.ac.uk/embl/)incorporates,organizesanddistributesnucleotidesequencesfromallavailablepublicsources.Thedatabaseislocatedandmain-tainedattheEuropeanBioinformaticsInstitute(EBI)nearCambridge,UK.Inaninternationalcollabora-tionwithDDBJ(Japan)andGenBank(USA),dataareexchangedamongstthecollaboratingdatabasesonadailybasistoachieveoptimalsynchronization.Webin is the preferred web-based submissionsystemforindividualsubmitters,whileautomaticproceduresallowincorporationofsequencedatafromlarge-scalegenomesequencingcentresandfromtheEuropeanPatentOffice(EPO).Databasereleasesareproducedquarterly.Networkservicesallow free access to the most up-to-date datacollection viaFTP, Emailand WorldWide Webinterfaces.EBI’sSequenceRetrievalSystem(SRS)integratesandlinksthemainnucleotideandproteindatabasesplusmanyotherspecializedmolecularbiologydatabases.Forsequencesimilaritysearch-ing, a variety of tools (e.g. Fasta, BLAST) areavailablewhichallowexternaluserstocomparetheirownsequencesagainstthelatestdataintheEMBLNucleotideSequenceDatabaseandSWISS-PROT.AllresourcescanbeaccessedviatheEBIhomepageathttp://www.ebi.ac.uk.INTRODUCTIONThe European Bioinformatics Institute (EBI), an Outstation ofthe European Molecular Biology Laboratory (EMBL) inHeidelberg (Germany), is located on the Wellcome TrustGenome Campus near Cambridge (UK), together with theSanger Institute and the Human Genome Mapping ResourceCentre (HGMP-RC). Building, maintaining and providingbiological databases and information services to support datadeposition and data exploitation are the main missions of theService Programme of the EBI (1). Databases operated at theEBI include the EMBL Nucleotide Sequence Database (aka asEMBL-Bank), protein databases SWISS-PROT & TrEMBL(2), InterPro (3), the Macromolecular Structure Database(E-MSD) (4), ArrayExpress for gene expression data (5),ENSEMBL (6) for automatic genome annotation plus severalother databases many of which are produced in collaborationwith external groups.In Europe, the vast majority of all nucleotide sequence datagenerated and published are collected, organized and dis-tributed by the EMBL Nucleotide Sequence Database, theEuropean member of the tri-partide International NucleotideSequence Database Collaboration DDBJ/EMBL/GenBank,managing sequence data worldwide since 1982. Main sourcesof data are large-scale genome sequencing projects, directsubmissions by individual scientists plus sequence dataextracted from BIOTECH patent applications to theEuropean Patent Office. To achieve optimal synchronization,all new and updated database records are exchanged on adialy basis between EMBL, DDBJ (Japan) (7) and GenBank(USA) (8).Within a 12 month period the database size has increasedfrom about 12.9 million entries comprising 13.8 Gigabases(Release 68, September 2001) to 18.3 million entries and over23 Gigabases (Release 72, September 2002). The databasegrowth has been a direct consequence of ongoing collabora-tions with sequencing projects like the Mouse GenomeSequencing Consortium (MGSC), the InternationalAnopheles Genome Project and a growing number of othergenome sequencing groups producing large quantities of newsequence data. During the same period the number oforganisms represented in the database has risen by 25% toover 100000 species.Major new developments during 2002 (described in detailbelow) include the creation of the CON(struct) or CON(tig)

The European Bioinformatics Institute (EBI) maintains and distributes the EMBL Nucleotide Sequence database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the SWISS-PROT Protein Sequence database, in collaboration with Amos Bairoch of the University of Geneva. Over fifty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists are available. The EBI network services include database searching and sequence similarity searching facilities.

Nuclear DNA binding protein p92 is a sequence specific octamer binding protein with identical molecular weight as the ubiquitous octamer binding protein Oct-1. It binds to octamer related sequences from the enhancer of human papillomavirus type 18. The activity and intracellular distribution of p92 is regulated by extracellular signals. In serum starved Hela-fibroblast hybrid cells p92 is localized to the cytosol. Serum stimulation leads to nuclear import of p92. In fractions of asynchronously growing cells, which were separated according to cell cycle phases into G1, S, and G2 populations by centrifugal elutriation, p92 DNA binding is confined to S phase. In binding site blots however, p92 DNA binding activity is also present in G1 and G2. In G1 and G2 DNA binding activity of p92 is masked by a novel nuclear inhibitor I-92. The cyclic association of p92 with its inhibitor I-92 provides a new mechanism of regulating S phase dependent activity of a sequence specific DNA binding protein.

The IMGT/HLA database (http://www.ebi.ac.uk/imgt/hla) has provided a centralized repository for the sequences of the alleles named by the WHO Nomenclature Committee for Factors of the HLA System for the past four years. Since its initial release the database has grown and is the primary source of information for the study of sequences of the human major histocompatibilty complex. The initial release of the database contained a limited number of tools. As a result of feedback from our users and developments in HLA we have been able to provide new tools and facilities. The HLA sequences have also been extended to include intron sequences and the 3' and 5' untranslated regions in the alignments and also the inclusion of new genes such as MICA. The IMGT/MHC database (http://www.ebi.ac.uk/imgt/mhc) was released in March 2002 to provide a similar resource for other species. The first release of IMGT/MHC contains the sequences of non-human primates (apes, new and old world monkeys), canines and feline sequences. Further species will be added shortly and the database aims to become the primary source of MHC data for non-human sequences.

The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences directly submitted from researchers and genome sequencing groups and collected from the scientific literature and patent applications. In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute (EBI) and constitutes Europe's primary nucleotide sequence resource. Database releases are produced quarterly and are distributed on CD-ROM. EBI's network services allow access to the most up-to-date data collection via Internet and World Wide Web interface, providing database searching and sequence similarity facilities plus access to a large number of additional databases.

A Fortran program has been written to permit comparative analysis of Grunstein-Hogness hybridisation data from small plasmid or cosmid banks. This program is particularly useful for restriction mapping using genome walking techniques and will facilitate the analysis of genomes in the 200 kb to 5000 kb size range.