science

LSID

LSID is a science topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand LSID rather than just read about it. In short: 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).

Key takeaways

LSID belongs to science; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect LSID to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of LSID from memory before moving on to harder problems.

Reference excerpt

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 DOIs used by many publishers. An LSID is represented as a uniform resource name (URN) with the following format:

urn:lsid:⟨Authority⟩:⟨Namespace⟩:⟨ObjectID⟩[:⟨Version⟩] The lsid: namespace, however, is not registered with the Internet Assigned Numbers Authority (IANA), and so these are not strictly URNs or URIs. LSIDs may be resolved in URLs, e.g. http://zoobank.org/urn:lsid:zoobank.org:pub:CDC8D258-8F57-41DC-B560-247E17D3DC8C

Controversy over the use of LSIDs There has been a lot of interest in LSIDs in both the bioinformatics and the biodiversity communities, with the latter continuing to use them 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.

Alternative identifiers for organisms Alternative identifiers have been proposed for organisms, e.g. the DOI system. NamesforLife (N4L), a private company, set up a system to apply DOIs to organisms. For example, doi:10.1601/nm.3093 is the DOI for Escherichia coli, and doi:10.1601/tx.3093 is the corresponding taxon.

See also Resource Description Framework MicroArray and Gene Expression ZooBank MycoBank MIRIAM URIs International Geo Sample Number SciCrunch

Notes

External links LSID Resolution Project LSID Assigning and Resolution Authority from The University of Texas at Austin A Position on LSIDs - Reflections from someone involved in implementation and roll out of LSIDs

Worked examples

Example 1 — a first encounter with LSID

Start with the simplest possible case. Write down what LSID claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In science, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to LSID before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about LSID ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of LSID

In research: LSID appears in science research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses LSID in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: LSID is common in secondary-school and first-year university syllabi. It links to neighbouring topics Bioinformatics, Identifiers, Index (publishing), so understanding it makes those chapters shorter.
In everyday life: Look for LSID outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study LSID in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what LSID means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain LSID out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is LSID in simple terms?

Why does LSID matter?

Because it connects several science ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study LSID?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on LSID.