Using EMBL-EBI resources to explore stem cell data

Editor's Notes

• #6: We’re the second largest of the five EMBL sites; there is the main lab and administrative centre in Heidelberg; structural biology labs in Hamburg and Grenoble; mouse biology in Monterotondo, near Rome, and bioinformatics in Hinxton. There are around 1,400 staff within EMBL and about 330 of those work at the EBI.
• #7: EBI shares its central four mission objectives with EMBL, although focussed on bioinformatics rather than molecular biology. The EBI is at the centre of Europe’s efforts to collect, organise and make all types biological data available and we do this by providing services so researchers can access and make sense of the information, by being active in bioinformatics research, by providing training and by working closely with industry.
• #8: The research groups map roughly onto many of the areas that we provide services in; collaboration between services and research is widespread. For example, collaborations between Wolfgang Huber’s group and the ArrayExpress developers are leading to new methods for microarray data analysis; Dietrich Rebholz-Schuhmann is working closely with our literature services team (Peter Stoehr) to develop innovative literature mining methods, some of which will be used in the new UK PubMedCentral service. Some of the services groups (Brazma, Birney and Apweiler) also have research components.
• #9: To train researchers in using the EBI’s resources, we have a tripartite training programme, encompassing training courses in-house at the EBI, the Bioinformatics Roadshow where EBI trainers travel out to host organisations to provide hands-on training on resources requested by the host, and most recently, we are launched an elearning programme for anyone to use so they can undertake some training in their own time.
• #11: The training programme aims to cover all the core EBI resources, both at introductory and an advanced level. For example, the two day dip course shown here, gives an overview of different resources and acts as a way to orientate yourself and become familiar with the range of resources, whereas a more specific course, such as one on transcriptomics will link the use of several different resources together.
• #12: As an alternative of coming to us, you can now access EBI training from anywhere in the world via our Moodle-based elearning which has just been launched. We currently offer three courses which have been developed with an external consultancy company; and then we are going to use the same format to develop additional courses covering the use of other EBI resources. The elearning is free to use and you just need to register to get a username and password.
• #13: Each course is modular and the different parts allow people to use a combination of learning methods – computer based elements such as the video tutorial and quiz, and computer independent parts such as the print version of the tutorial so you can learn on the go, and a guided reflective task so you can learn by doing.
• #16: The slide shows the core resources at the EBI mapped on to the same arrow to show the range of data you can access through the EBI. The EBI is the European centre for the collection and dissemination of biological data; we do this in collaboration with other global centres such as NCBI, the Institute of Genetics in Japan, the Swiss Institute of Bioinformatics and Cold Spring Harbor.
• #17: We launched a new website and search engine just over a year ago. Our website gets over 2 million hits a day and it’s the gateway for accessing the information you want. The search engine, the EB-eye, allows integrated searching of all our core data resources from a single search box – it’s like a google for all the information held at the EBI.
• #18: Ensembl provides a framework for working with the genomes of higher animals (metazoans). It presents, via an interactive website, the human genome together with other genomes that are important for addressing questions in medical research and molecular biology. It uses automated methods for gene prediction and annotation to provide a consistent view of completely sequenced genomes. Users can view the data at many levels, from entire chromosomes down to single nucleotide polymorphisms. As well as accessing a wealth of data for each species, users can also perform cross-species comparisons.
• #19: Ensembl Genomes is the combined repository for non-vertebrate genome data, consisting of five resources: Ensembl Bacteria, Ensembl Fungi, Ensembl Metazoa, Ensembl Plants, and Ensembl Protists, bringing the power of the Ensembl system to all branches of life. Ensembl Genomes re-uses and extends software developed for vertebrate genomes in the context of the Ensembl project, and replaces several pre-existing resources (Integr8, Genome Reviews and ASTD) thereby unifying services and simplifying data access for users.
• #20: EMBL-Bank is Europe's primary nucleotide sequence resource. The database is produced in an international collaboration (the International Sequence Database Collaboration, INSDC) with GenBank (USA) and the DNA Database of Japan (DDBJ). Main sources of DNA and RNA sequences are direct submissions from individual researchers, genome sequencing  projects and patent applications. Users can search the data using either keyword-based searches or using sequence homology tools such as BLAST and FASTA to compare their own sequence with the contents of EMBL-Bank. There’s also a map-based search (EMBLWorld) for exploring sequences derived from environmental genome sequencing projects. The data belong to the submitter and can only be updated by the submitter, but other researchers can submit ‘third party annotations’ to EMBL-Bank if they’re associated with a peer-reviewed publication.
• #21: ArrayExpress is the world’s first and largest MIAME-compliant repository for microarray-based data (mostly gene expression data, but it also takes CGH and chip-chIP data). You can search the repository to view and download experiments; a subset of the data in the repository is hand-picked for the Data Warehouse, which can be searched on the basis of gene names and allows you to view gene expression data for different time points or experimental conditions.
• #22: UniProt is the gold-standard resource for information on proteins. It comprises three different databases, but I haven’t shown all three here for the sake of simplicity. UniProtKB is the central database of protein sequences with accurate, consistent, and rich sequence and functional annotation. It comprises the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section. The UniProt archive is an archive of all the protein sequences in the public domain, and the UniRef databases are a series of three databases that store sequences of 100%, 90% and 50% identity in the same records to speed up searching without losing information. UniProtKB contains more than 29 million cross references to over 100 other data resources; a few key ones are shown here.
• #23: InterPro amalgamates several different databases of protein signatures, which use different methods, into a single resource, providing a powerful tool for protein classification.
• #24: The proteomics services team produces a range of resources for the proteomics research community; they are also heavily involved in the development of standards for proteomics research, and their resources adhere to these standards. IntAct provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. PRIDE is an open-source public repository of protein identifications, peptide identifications, post-translational modifications and mass spectra. The Integrated relational Enzyme database provides a complete, freely available database storing the most up-to-date version of the Enzyme Nomenclature approved by the NC-IUBMB. Chemical Entities of Biological Interest (ChEBI) aims to provide standardised descriptions of molecular entities that enable other databases at the EMBL-EBI and worldwide to annotate their entries in a consistent fashion.
• #26: The Macromolecular Structure Database (MSD) is the European resource for the collection, organisation and dissemination of data about biological macromolecular structures. The MSD is one of three partners in the worldwide Protein Data Bank (wwPDB), the consortium entrusted with the collation, maintenance and distribution of the global repository of macromolecular structure data. The MSD team has developed a wide range of resources for the analysis of data in the PDB.
• #27: Reactome aims to develop a curated resource of core pathways and reactions in human biology, although other species are also covered. It treats both metabolic and signalling pathways in the same way, providing both a human- and a computer-readable account of all the processes in a pathway. It makes extensive use of crosslinks to other data resources; the data in Reactome can also be exported to a number of different types of modelling software so that they can be incorporated into computer models of living systems.
• #36: As well as providing services, the EBI does research…
• #37: An integration platform for biological data a way of bringing together data from different providers federation unifies data sources that are different to each other
• #42: As well as providing services, the EBI does research…
• #45: As well as providing services, the EBI does research…
• #53: As well as providing services, the EBI does research…
• #61: As well as providing services, the EBI does research…
• #66: As well as providing services, the EBI does research…
• #71: As well as providing services, the EBI does research…
• #95: As well as providing services, the EBI does research…
• #96: If you need help using any of our databases it’s available; if our online support pages can’t answer your question we offer e-mail support and promise to get back to you within 2 working days.