LSID
Encyclopedia
Life Science Identifiers are a way to name and locate pieces of information on the web. Essentially, an LSID is a unique identifier for some data, and the LSID protocol specifies a standard way to locate the data (as well as a standard way of describing that data). They are a little like DOI
s used by many publishers.
An LSID is represented as a Uniform Resource Name
(URN) with the following format.
and the biodiversity
communities, with the latter continuing to use them intensively as a way of identifying species in global catalogues . However, more recently, as understanding has increased of how HTTP
URIs can perform a similar naming task, the use of LSIDs as identifiers has been criticized as violating the Web Architecture good practice of reusing existing URI schemes. Nevertheless, the explicit separation of data from metadata; specification of a method for discovering multiple locations for data-retrieval; and the ability to discover multiple independent sources of metadata for any identified thing were crucial parts of the LSID and its resolution specification that have not successfully been mimicked by an HTTP-only approach.
The World Wide Web
provides a globally distributed communication framework that is essential for almost all scientific collaboration, including bioinformatics. However, several limits and inadequacies were thought to exist, one of which was the inability to programmatically identify locally named objects that may be widely distributed over the network. This perceived shortcoming would have limited our ability to integrate multiple knowledgebases, each of which gives partial information of a shared domain, as is commonly seen in bioinformatics. The Life Science Identifier (LSID) and LSID Resolution System (LSRS) were designed to provide simple and elegant solutions to this problem, consistent with next-generation semantic web
and semantic grid
, based on the extension of existing internet technologies. However, it has more recently been pointed out that some of these perceived shortcomings are not intrinsic to HTTP URIs, and much (though not all) of the functionality that LSIDs provide can be obtained using properly crafted HTTP URIs.
Digital object identifier
A digital object identifier is a character string used to uniquely identify an object such as an electronic document. Metadata about the object is stored in association with the DOI name and this metadata may include a location, such as a URL, where the object can be found...
s used by many publishers.
An LSID is represented as a Uniform Resource Name
Uniform Resource Name
A uniform resource name is a uniform resource identifier that uses the urn scheme and does not imply availability of the identified resource. Both URNs and URLs are URIs, and a particular URI may be a name and a locator at the same time.The functional requirements for uniform resource names are...
(URN) with the following format.
- URN:LSID:
: : [: ]
Controversy over the use of LSIDs
There has been a lot of interest in LSIDs in both the bioinformaticsBioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
and the biodiversity
Biodiversity
Biodiversity is the degree of variation of life forms within a given ecosystem, biome, or an entire planet. Biodiversity is a measure of the health of ecosystems. Biodiversity is in part a function of climate. In terrestrial habitats, tropical regions are typically rich whereas polar regions...
communities, with the latter continuing to use them intensively as a way of identifying species in global catalogues . However, more recently, as understanding has increased of how HTTP
Hypertext Transfer Protocol
The Hypertext Transfer Protocol is a networking protocol for distributed, collaborative, hypermedia information systems. HTTP is the foundation of data communication for the World Wide Web....
URIs can perform a similar naming task, the use of LSIDs as identifiers has been criticized as violating the Web Architecture good practice of reusing existing URI schemes. Nevertheless, the explicit separation of data from metadata; specification of a method for discovering multiple locations for data-retrieval; and the ability to discover multiple independent sources of metadata for any identified thing were crucial parts of the LSID and its resolution specification that have not successfully been mimicked by an HTTP-only approach.
The World Wide Web
World Wide Web
The World Wide Web is a system of interlinked hypertext documents accessed via the Internet...
provides a globally distributed communication framework that is essential for almost all scientific collaboration, including bioinformatics. However, several limits and inadequacies were thought to exist, one of which was the inability to programmatically identify locally named objects that may be widely distributed over the network. This perceived shortcoming would have limited our ability to integrate multiple knowledgebases, each of which gives partial information of a shared domain, as is commonly seen in bioinformatics. The Life Science Identifier (LSID) and LSID Resolution System (LSRS) were designed to provide simple and elegant solutions to this problem, consistent with next-generation semantic web
Semantic Web
The Semantic Web is a collaborative movement led by the World Wide Web Consortium that promotes common formats for data on the World Wide Web. By encouraging the inclusion of semantic content in web pages, the Semantic Web aims at converting the current web of unstructured documents into a "web of...
and semantic grid
Semantic Grid
The Semantic Grid refers to an approach to Grid computing in which information, computing resources and services are described using the semantic data model. In this model the data and metadata are expressed through facts . Therefore it becomes directly understandable for humans...
, based on the extension of existing internet technologies. However, it has more recently been pointed out that some of these perceived shortcomings are not intrinsic to HTTP URIs, and much (though not all) of the functionality that LSIDs provide can be obtained using properly crafted HTTP URIs.
See also
- Resource Description FrameworkResource Description FrameworkThe Resource Description Framework is a family of World Wide Web Consortium specifications originally designed as a metadata data model...
- MicroArray and Gene ExpressionMicroArray and Gene ExpressionThe MicroArray and Gene Expression group is a project of the FGED Society to develop a standard for the representation of gene expression data from microarrays to facilitate the exchange of information between different data systems...
- ZooBankZooBankZooBank is an open access website intended to be the official International Commission on Zoological Nomenclature registry of zoological nomenclature. It was officially proposed in 2005 by the executive secretary of ICZN...
- MIRIAM URIs
- International Geo Sample NumberInternational Geo Sample NumberThe International Geo Sample Number or IGSN is a 9 character sample identification code generated by the System for Earth Sample Registration . The IGSN preserves the identity of a sample even as it is moved from lab to lab and as data appear in different publications, thus eliminating ambiguity...
External links
- Life Sciences Identifiers: OMG Final Available Specification
- LSID Resolution Project
- LSID best practices from IBM
- LSID Assigning and Resolution Authority from The University of Texas at Austin
- Life Science Identifier from BioPathways Consortium
- LSID Tester
- A Position on LSIDs - Reflections from some one involved in implementation and roll out of LSIDs