Linking data with Identifiers.org

点击翻译按钮获取中文摘要

Annotating data, life science datasets with cross-references to other sources of knowledge has always be very important. These metadata are often what separate valuable information from heaps of unusable data. With the advent of systems biology, the size and complexity of datasets shifted the balance from direct human interaction to automated computer processing. Such operations are greatly facilitated if the metadata is encoded following standard procedures and using controlled vocabularies. If those procedures and vocabularies are shared between different types of data, it becomes possible to align, compare and integrate different datasets. A key part of any cross-reference is the identifier of the resource it points to. This identifier must be unique, perennial, resolvable and free. Most data providers create identifiers for their own records; for example '9606' identifies 'Homo sapiens' in the Taxonomy, and '22140103' identifies the latest publication about Identifiers.org in PubMed. However, those identifiers are only unique within a given dataset so their usefulness is limited when considering records in a wider context.Identifiers.org provides such global identifiers, and resolves them to the relevant dataset. In order to achieve this purpose, it uses the information recorded in the MIRIAM Registry (http://www.ebi.ac.uk/miriam/). Therefore both projects provide a distinct part of the final technical solution. Identifiers generated with the Registry make use of the accession numbers supplied by data providers, but also contain information about the collection they come from. All identifiers are unique, resolvable and robust. They allow persons or software tools to directly access the identified pieces of data on the web, via alternative providers. Although a prototype, Identifiers.org has been adopted by a number of communities and projects, as it fulfils their need for perennial cross-references and removes their previous need for maintaining and keeping up to date long lists of ever changing web links (or URLs).As more and more communities realise the benefits of using Identifiers.org URIs, new needs and use cases have appeared. This proposal seeks to strengthen and extend the services provided by the resource in order to respond to those new user requests. We will make the resource easier to use in automated procedures, specially for semantic web applications. This involves providing the content of the Registry in Resource Description Framework (RDF) format and supply a SPARQL endpoint for query purposes. Users will be able to fine-tuned the way identifiers are resolved, via the creation of 'profiles', that will record their preferences. The resource will allow the communities (more specially the data providers themselves) to get involved in the maintenance of the Registry. This will take place via a system of "ownership" by data providers of their record in the Registry. Although we currently have automatic systems in place to detect obsolete information, having the actual data providers contributing to the maintenance would ensure better quality of the recorded information, meaning a better quality of the services provided. Finally we will improve and extend the underlying computing infrastructure. By deploying it in more more data centres, we will provide more reliable services to an ever growing number of users.The resulting resource will provide a way to seamlessly link all data annotated with the same URI to represent the same concept, a key step towards data integration. By providing a semantic glue between those datasets, Identifiers.org will facilitate data retrieval, comparison, integration, locally or through the semantic web. It will also facilitate the reasoning on the integrated datasets and lead to new, possibly automated discovery in the biomedical domain.