Background The UniProt consortium was formed in 2002 by groups from the Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) at Georgetown University, and soon afterwards the website www.uniprot.org was set up as a central entry point to UniProt resources. Requests to this address were redirected to one of the three organisations' websites. While these sites shared a set of static pages with general information about UniProt, their pages for searching and viewing data were different. To provide users with a consistent view and to cut the cost of maintaining three separate sites, the consortium decided to develop a common website for UniProt. Following several years of intense development and a year of public beta testing, the www.uniprot.org domain was switched to the newly developed site described in this paper in July 2008. Description The UniProt consortium is the main provider of protein sequence and annotation data for much of the life sciences community. The www.uniprot.org website is the primary access point to this data and to documentation and basic tools for the data. These tools include full text and field-based text search, similarity search, multiple sequence alignment, batch retrieval and database identifier mapping. This paper discusses the design and implementation of the new website, which was released in July 2008, and shows how it improves data access for users with different levels of experience, as well as to machines for programmatic access. http://www.uniprot.org/ is open for both academic and commercial use. The site was built with open source tools and libraries. Feedback is very welcome and should be sent to help@uniprot.org. Conclusions The new UniProt website makes accessing and understanding UniProt easier than ever. The two main lessons learned are that getting the basics right for such a data provider website has huge benefits, but is not trivial and easy to underestimate, and that there is no substitute for using empirical data throughout the development process to decide on what is and what is not working for your users.

Co-reference resolution, or the determination of ‘equivalent’ URIs referring to the same concept or entity, is a significant hurdle to overcome in the realisation of large scale Seman- tic Web applications. However, it has only recently gained the attention of research communities in the Semantic Web context, and while activities are now underway in identifying co-referent or conflated URIs, little consideration has been given to tools and techniques for storing, manipulating, and reusing co-reference information. This paper provides an overview of the specification, im- plementation, interactions and experiences in using the Co- reference Resolution Service (CRS) to facilitate rigorous man- agement of URI co-reference data, and enable interoperation between multiple Linked Open Data sources. Comparisons are made throughout the paper contrasting the differences in the way the CRS manages multiple URIs for the same resource with the emerging practice of using owl:sameAs to identify duplicate URIs. The advantages and benefits that have been gained from deploying the CRS on a site with multiple Linked Data repositories are also highlighted.

The PILIN project (Persistent Identifier and Linking Infrastructure) was identified as an important national initiative in the third quarter of 2006. It was approved as a sub project of the ARROW II (Australian Research Repositories on line to the world) suite of activities in September 2006. As various projects matured, including FRODO and MERRI, there was a growing realisation that sustainable identifier infrastructure was required to deal with the vast amount of digital assets being produced and stored within universities. This was and is a particular challenge for e-research communities where massive amounts of data are being generated without any means of managing this data over any length of time. Many organisations, including the National Library of Australia, had been experimenting with persistent identifiers for some time. However there was no consensus or consistency across the educational and cultural/collecting agencies sectors. The PILIN project was an opportunity to comprehensively test the needs and parameters of identifier infrastructure as well as to establish the foundations of a future national service. Prior to project commencement it was decided to use the Handle technology (http://www.handle.net ) as core software while at the same time approaching the project from a technology neutral stance as far as was possible. Despite its ARROW base the PILIN project was set up to have diverse stakeholders across all education and into cultural organisations/collecting agencies.

Facile and meaningful integration of data from disparate resources is the ‘holy grail’ of bioinformatics. Some resources have begun to address this problem by providing their data using Semantic Web standards, specifically the Resource Description Framework (RDF) and the Web Ontology Language (OWL). Unfortunately, adoption of Semantic Web standards has been slow overall, and even in cases where the standards are being utilized, interconnectivity between resources is rare. In response, we have seen the emergence of centralized ‘semantic warehouses’ that collect public data from third parties, integrate it, translate it into OWL/RDF and provide it to the community as a unified and queryable resource. One limitation of the warehouse approach is that queries are confined to the resources that have been selected for inclusion. A related problem, perhaps of greater concern, is that the majority of bioinformatics data exists in the ‘Deep Web’—that is, the data does not exist until an application or analytical tool is invoked, and therefore does not have a predictable Web address. The inability to utilize Uniform Resource Identifiers (URIs) to address this data is a barrier to its accessibility via URI-centric Semantic Web technologies. Here we examine ‘The State of the Union’ for the adoption of Semantic Web standards in the health care and life sciences domain by key bioinformatics resources, explore the nature and connectivity of several community-driven semantic warehousing projects, and report on our own progress with the CardioSHARE/Moby-2 project, which aims to make the resources of the Deep Web transparently accessible through SPARQL queries.

We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://bcms.bioinfo.cnio.es/). This prototype platform is a joint effort of 13 research groups and provides automatically generated annotations for PubMed/Medline abstracts. Annotation types cover gene names, gene IDs, species, and protein-protein interactions. The annotations are distributed by the meta-server in both human and machine readable formats (HTML/XML). This service is intended to be used by biomedical researchers and database annotators, and in biomedical language processing. The platform allows direct comparison, unified access, and result aggregation of the annotations.

As much as we like watching reruns of The Prisoner, we have to say it is time we were assigned a number as we attempt to quantify scientific progress both in general and for the individual in a virtual world in which scientific progress is based on more than the impact of a journal article. What do you think? Who knows—perhaps some day you will be rewarded for your time, energy, and intellect that go into a thoughtful response to this Perspective.