NucLexNuclear Medicine Lexicon and Theranostics Ontology
Stage W0: private living prototype12 of 30 manuscripts drafted, 0 reviewed; 50 lexicon entries in draftWhat each later stage would need to show

Mathematical and computational foundations

Semantic web standards

An identifier names a thing. A triple says something about it. A query finds what was said. None of these steps checks whether it is true.

MonographBriefNX-M08Proposed length 2,500 to 5,000 words

Writing brief. This monograph has been assigned but the manuscript is not yet written or approved. What follows is the commissioning brief: its question, outline, evidence instructions, and review requirements.

Central question

How do identifiers and representations work together?

Reader promise

The reader will be able to take one example through the stack (identify, state, define, store, query) and say at each step what has been established.

Required development

  1. Explain IRIs, RDF triples, vocabularies, and OWL as layers. An IRI (RFC 3987) identifies; an RDF triple states; a vocabulary such as RDF Schema or SKOS gives shared predicates; OWL adds formal definitions with a specified semantics. Show one synthetic statement at each layer, with example.org for every local IRI.
  2. Distinguish syntax, semantics, storage, and query. Syntax is Turtle, JSON-LD, or RDF/XML; the same triples can be written in any. Semantics is what RDF 1.1 Semantics and OWL 2 Direct Semantics say the triples entail. Storage is a triple store, whose choice affects performance, not meaning. Query is SPARQL, whose results depend on the store's contents and, if enabled, the entailment regime.
  3. Provide reproducible examples: a Turtle file of at most twenty triples and three SPARQL queries with expected results, so that a reader can load the file into any conforming store and obtain the same answers. Record the store and version used.
  4. Show a query that returns a false answer because a triple is false, and one that returns nothing because a triple is missing.

Evidence and review

Evidence to obtain: the W3C Recommendations for RDF 1.1 Concepts and Semantics, Turtle, JSON-LD 1.1, SPARQL 1.1 Query and Entailment Regimes, and OWL 2 Overview and Direct Semantics, each cited by date; RFC 3987 for IRIs; and the status of RDF 1.2 and SPARQL 1.2 at source check. Every example must have been executed and the results recorded.

Review concern: a reader may take a SPARQL result as a finding about biology. The manuscript must state that a result reports what the store contains under the chosen entailment regime, that the truth of the contents is a separate question with its own provenance, and that NucLex operates no live endpoint.

RDF, OWL, Identifier, Knowledge graphs for the graph the standards encode, Description logics for the semantics behind OWL, and Provenance and evidence for the question of truth. Link at the point of use.

Review requirements

Source check against the dated Recommendations. Technical review by someone who has run the examples in a conforming store. Editorial check that no IRI implies a live service.

Review gate for this monograph

A query result is not proof of biological truth.

The assignment exists. The manuscript has not been written or approved.