eduKateSG · Why Science?
Give mass-spectrometry methods a shared, computable language—while preserving definitions, accessions, releases, provenance and evidence limits
Choose the closest route, then return to the full index whenever you need the wider evidence chain.
Science learning becomes powerful when students can tell a measured pattern from a model, a statistical decision from a mechanism, and a useful lead from a finished conclusion. PSI-MS is the main controlled vocabulary used by HUPO-PSI mass-spectrometry standards. The official repository says it covers the complete MS analysis pipeline, including sample labelling, digestion enzymes, instrumentation, identification and quantification software, and significance parameters. It is maintained from source components and released as OBO and OWL artefacts. A valid PSI-MS accession gives a concept a shared definition; it does not prove that an instrument setting was used correctly, a score is calibrated or a biological conclusion is true. This guide supports Primary Science, PSLE Science, Secondary Science, O-Level Science and STEM education as a longform evidence-reading route; it is not medical advice, a laboratory protocol, an admission promise or a career guarantee.
Related eduKate reading: mzML and open mass-spectrometry data; mzIdentML and proteomics identification results; mzQC and mass-spectrometry quality metrics; PSI-MOD and protein modification vocabulary; Science Learning Hub; Education Hub; STEM Education; Careers by Subject Capability.
Primary and official sources checked on 12 October 2026: HUPO-PSI official PSI-MS controlled vocabulary repository and release artefacts, checked 12 October 2026; OBO Foundry Mass Spectrometry Ontology record and persistent artefacts, checked 12 October 2026; HUPO-PSI Mass Spectrometry Standards working group, checked 12 October 2026; 2026 Singapore–Cambridge O-Level Biology syllabus; MOE G2/G3 Lower Secondary Science teaching and learning syllabus; 2026 MOE G2 Computing syllabus. Specifications, vocabularies, repository services and recommendations can change, so preserve dated documentation, exact source data and software versions.
A deeper reading route
Mass-spectrometry files contain thousands of concepts that ordinary free text handles badly. The same instrument or score can be abbreviated in several ways, and the same short label can mean different things across laboratories. PSI-MS assigns stable MS accessions, definitions and relationships so software can validate and compare meaning rather than guessing from spelling.
The official repository describes coverage across an entire analysis pipeline: labels and enzymes, instrument components and acquisition, software, identification and quantification, and parameters for deciding significance. That breadth is why the vocabulary appears inside mzML, mzIdentML, mzQuantML, mzQC, mzSpecLib and related standards. One vocabulary can connect stages without collapsing their distinct evidence roles.
A controlled vocabulary term is more than a label. The accession is the durable computational key; the preferred name helps readers; the definition sets scope; synonyms help discovery; parent relationships support broader searches; and properties or cross-references add machine-readable detail. Interfaces should display helpful names while storing the accession and release used.
The repository explains that hand-edited source material and generated release artefacts have different roles. The core OBO source and a generated chromatographic-column fragment are assembled into released OBO, with OWL generated from that release. Users should archive the release artefact they actually loaded, not reconstruct it later from whatever happens to be on the main branch.
Terms evolve because technology evolves. New instruments, fragmentation methods, software and scores need community-reviewed representation; definitions are refined; obsolete terms may point toward replacements. Reproducibility therefore needs a date, data-version or file hash. A stable accession is valuable, but the vocabulary snapshot supplies the full context.
Controlled terms do not remove the need for domain reasoning. A file may cite an ionisation method that conflicts with the instrument configuration, use a score term in the wrong position or report a unit that cannot describe the value. Syntactic validity, ontology validity and scientific plausibility are three separate checks.
Term requests are part of scientific infrastructure. The official repository accepts issues and pull requests, with review by the PSI CV group. A laboratory should not mint an unofficial MS accession merely to make a pipeline pass. Local placeholders should be clearly namespaced, documented and migrated transparently when an official term becomes available.
Cross-ontology links can connect PSI-MS with units, modifications, chemical entities or other domains. These mappings are useful but require exact scope. Similar names are not automatic equivalence. A mapping receipt should preserve both accessions, the relationship type, the vocabulary releases and the curator’s reason.
A practical audit starts with one recorded method. Resolve its MS accession in the pinned ontology, read the definition and parent, inspect the value and unit, then compare the instrument log or software output. This exercise often reveals whether a term merely sounds right or accurately describes the evidence.
The optimistic value of PSI-MS is collective precision. A student, instrument vendor, repository and analysis program can use the same identifiers while still explaining concepts in accessible language. Shared terminology does not finish the science; it lets people disagree about evidence without first disagreeing about what the words mean.
A release-aware pipeline loads a named PSI-MS artefact, records its hash and rejects unknown accessions clearly. Quietly downloading the latest ontology during a run makes identical inputs time-dependent. An intentional upgrade should produce a vocabulary diff and a list of affected records so scientific changes can be reviewed separately from software maintenance.
Hierarchy queries require care. Retrieving all descendants of an instrument or technique term can be powerful, but inferred and asserted relationships may differ by ontology tool. State the reasoning method and release. The accession still identifies a concept; the query plan explains how a group of concepts was assembled for analysis.
User interfaces should never force a choice based only on a short label. Display the accession, definition, parent context and, where useful, synonyms or examples. Search can remain friendly while the stored result stays precise. If no term fits, capture the gap and submit a reviewed request rather than selecting the nearest-looking concept.
A cross-format audit can follow one MS term from an mzML acquisition record to an mzIdentML result, an mzQC metric and an mzSpecLib entry. The same accession should retain its definition, while each format supplies different structural context. This exercise teaches why shared vocabulary enables interoperability without making the formats interchangeable.
Long-term citation should point to both the project and the exact ontology used. A general repository URL helps readers find current work, while an archived OBO or OWL hash reproduces the original analysis. Together they honour the living community standard and the fixed evidence state behind a published result.
Term-level testing can use a small fixture that contains one instrument, one acquisition method, one score, one unit-bearing parameter and one obsolete accession. A pipeline should resolve the current terms, reject incompatible values and report the obsolete case without erasing it. Keeping this fixture with the workflow turns ontology maintenance into a repeatable engineering check rather than a last-minute manual inspection.
| Stage | Question | Evidence | Responsible output |
|---|---|---|---|
| Name | Which concept is intended? | MS accession, preferred label and definition | A stable shared meaning |
| Relate | How does the concept fit the domain? | Parents, properties, synonyms and cross-references | A computable vocabulary graph |
| Apply | Where is the term used? | Format rules, values, units and evidence | A machine-readable annotation |
| Preserve | Can meaning be reproduced later? | Release artefact, status, validation and migration log | A traceable terminology record |
Inside this guide
1–12 · Foundations and design
- 1. Start with the ambiguity
- 2. Use the maintained vocabulary
- 3. Store the accession
- 4. Read the definition
- 5. Use synonyms for discovery
- 6. Read parent relationships
- 7. Inspect properties
- 8. Pin the data version
- 9. Distinguish source and release artefacts
- 10. Understand OBO
- 11. Understand OWL
- 12. Cover sample preparation
13–24 · Models and estimation
- 13. Cover instrumentation
- 14. Cover acquisition
- 15. Cover software
- 16. Cover scores
- 17. Cover quantification
- 18. Apply terms in mzML
- 19. Apply terms in result formats
- 20. Apply terms in spectral libraries
- 21. Request terms transparently
- 22. Handle obsolete terms
- 23. Validate existence
- 24. Validate placement
25–36 · Diagnostics and interpretation
- 25. Validate scientific plausibility
- 26. Separate words from evidence
- 27. Separate terminology from conclusion
- 28. Connect to Primary Science
- 29. Connect to Secondary Science
- 30. Connect to mathematics
- 31. Connect to computing
- 32. Connect to pathways
- 33. Did you know?
- 34. Write a reader-ready methods note
- 35. Build a validation ladder
- 36. Finish with a reproducible bundle
Section 1 of 36
1. Start with the ambiguity
List the instrument, method, software, score or parameter that needs a shared meaning. Free text may be readable yet impossible to validate reliably.
Working checkpoint — PSI-MS: Write the concept and the evidence that uses it. Keep accession, definition, release, placement, value and experimental receipt together.
For a classroom model, reconcile fictional synonyms through stable IDs.
Section 2 of 36
2. Use the maintained vocabulary
The official repository identifies PSI-MS as the main PSI ontology for MS-based proteomics experiments.
Working checkpoint — controlled vocabulary: Pin the repository release or ontology file hash. Read every label beside its formal scope, parent relationships and status.
For future study, connect science to information systems while checking official pathways separately.
Section 3 of 36
3. Store the accession
An MS accession is a more durable key than a label that can be reworded, translated or duplicated.
Working checkpoint — ontology accession: Keep namespace, numeric identifier and displayed label together. Preserve obsolete and local history; a friendly display name is not the whole vocabulary record.
For scientific writing, cite accession, ontology release, value context, evidence and validator.
Section 4 of 36
4. Read the definition
The definition states what a term is intended to represent and often prevents an attractive but incorrect match.
Working checkpoint — mass spectrometry: Compare every annotation with the full definition. Separate terminology validity from instrument validity, statistical calibration and biological meaning.
For students, ask what the accession formally means and where it is used.
Section 5 of 36
5. Use synonyms for discovery
Synonyms help users search familiar names, but they should resolve to the governed accession.
Working checkpoint — term definition: Never store a synonym as the only identifier. Treat identifiers and units as scientific inputs: one silent substitution can change interpretation.
For parents, ask whether shared words make assumptions easier to inspect.
Section 6 of 36
6. Read parent relationships
Broader and narrower relationships support grouping and search, but they do not make every child interchangeable.
Working checkpoint — vocabulary release: Record whether queries use asserted or inferred parents. Keep accession, definition, release, placement, value and experimental receipt together.
For a classroom model, reconcile fictional synonyms through stable IDs.
Section 7 of 36
7. Inspect properties
Units, value types or other properties can constrain how a term should be used inside a format.
Working checkpoint — PSI-MS: Validate the value as well as the accession. Read every label beside its formal scope, parent relationships and status.
For future study, connect science to information systems while checking official pathways separately.
Section 8 of 36
8. Pin the data version
Terms and relationships evolve. A retrieval date is helpful, while the ontology version or exact checksum is stronger.
Working checkpoint — controlled vocabulary: Archive the OBO or OWL bytes used. Preserve obsolete and local history; a friendly display name is not the whole vocabulary record.
For scientific writing, cite accession, ontology release, value context, evidence and validator.
Section 9 of 36
9. Distinguish source and release artefacts
The repository maintains editable source components and generated release files for users and tools.
Working checkpoint — ontology accession: Do not edit generated OBO or OWL artefacts by hand. Separate terminology validity from instrument validity, statistical calibration and biological meaning.
For students, ask what the accession formally means and where it is used.
Section 10 of 36
10. Understand OBO
The OBO release is a portable text representation of terms, definitions and relationships.
Working checkpoint — mass spectrometry: Parse it with ontology-aware tools and preserve headers. Treat identifiers and units as scientific inputs: one silent substitution can change interpretation.
For parents, ask whether shared words make assumptions easier to inspect.
Section 11 of 36
11. Understand OWL
OWL is generated for semantic-web and ontology tooling. Conversion should preserve the intended vocabulary content.
Working checkpoint — term definition: Record converter and compare representative terms. Keep accession, definition, release, placement, value and experimental receipt together.
For a classroom model, reconcile fictional synonyms through stable IDs.
Section 12 of 36
12. Cover sample preparation
Terms can describe labels, enzymes and other steps before spectra are acquired.
Working checkpoint — vocabulary release: Check that method terms agree with laboratory records. Read every label beside its formal scope, parent relationships and status.
For future study, connect science to information systems while checking official pathways separately.
Section 13 of 36
13. Cover instrumentation
Instrument models, components and configurations need precise identifiers because they shape measurements.
Working checkpoint — PSI-MS: Match accessions to the actual acquisition log. Preserve obsolete and local history; a friendly display name is not the whole vocabulary record.
For scientific writing, cite accession, ontology release, value context, evidence and validator.
Section 14 of 36
14. Cover acquisition
Scan, isolation, activation and dissociation concepts affect what a spectrum can support.
Working checkpoint — controlled vocabulary: Keep settings and units with the method term. Separate terminology validity from instrument validity, statistical calibration and biological meaning.
For students, ask what the accession formally means and where it is used.
Section 15 of 36
15. Cover software
Software names and versions identify computational tools, not automatically the algorithms or parameters used.
Working checkpoint — ontology accession: Record both software term and exact version. Treat identifiers and units as scientific inputs: one silent substitution can change interpretation.
For parents, ask whether shared words make assumptions easier to inspect.
Section 16 of 36
16. Cover scores
Identification and quality scores need terms, value direction and threshold context.
Working checkpoint — mass spectrometry: Do not compare differently defined scores by number alone. Keep accession, definition, release, placement, value and experimental receipt together.
For a classroom model, reconcile fictional synonyms through stable IDs.
Section 17 of 36
17. Cover quantification
Quantitative techniques and data types distinguish intensity, ratio, concentration and other measures.
Working checkpoint — term definition: Name the value level, unit and denominator. Read every label beside its formal scope, parent relationships and status.
For future study, connect science to information systems while checking official pathways separately.
Section 18 of 36
18. Apply terms in mzML
mzML uses controlled terms to describe runs, instruments, spectra and arrays.
Working checkpoint — vocabulary release: Validate terms in their allowed structural context. Preserve obsolete and local history; a friendly display name is not the whole vocabulary record.
For scientific writing, cite accession, ontology release, value context, evidence and validator.
Section 19 of 36
19. Apply terms in result formats
mzIdentML, mzQuantML, mzTab and mzQC reuse terms for methods, scores, values and metrics.
Working checkpoint — PSI-MS: Do not assume a term belongs in every format position. Separate terminology validity from instrument validity, statistical calibration and biological meaning.
For students, ask what the accession formally means and where it is used.
Section 20 of 36
20. Apply terms in spectral libraries
mzSpecLib uses vocabulary-based metadata to make library meaning portable.
Working checkpoint — controlled vocabulary: Resolve all terms under the same pinned release. Treat identifiers and units as scientific inputs: one silent substitution can change interpretation.
For parents, ask whether shared words make assumptions easier to inspect.
Section 21 of 36
21. Request terms transparently
The official project invites issues and reviewed contributions for new concepts.
Working checkpoint — ontology accession: Provide definition, evidence and relationships instead of inventing IDs. Keep accession, definition, release, placement, value and experimental receipt together.
For a classroom model, reconcile fictional synonyms through stable IDs.
Section 22 of 36
22. Handle obsolete terms
An obsolete accession may remain in historic data and may have a replacement or migration note.
Working checkpoint — mass spectrometry: Preserve the original and document any mapping. Read every label beside its formal scope, parent relationships and status.
For future study, connect science to information systems while checking official pathways separately.
Section 23 of 36
23. Validate existence
A well-formed accession still needs to resolve in the chosen release.
Working checkpoint — term definition: Fail clearly on unknown identifiers. Preserve obsolete and local history; a friendly display name is not the whole vocabulary record.
For scientific writing, cite accession, ontology release, value context, evidence and validator.
Section 24 of 36
24. Validate placement
A real term can be invalid in a particular element or field under a format mapping rule.
Working checkpoint — vocabulary release: Run format-aware semantic checks. Separate terminology validity from instrument validity, statistical calibration and biological meaning.
For students, ask what the accession formally means and where it is used.
Section 25 of 36
25. Validate scientific plausibility
A valid term in a valid location can still contradict the instrument, units or experiment.
Working checkpoint — PSI-MS: Add independent domain review. Treat identifiers and units as scientific inputs: one silent substitution can change interpretation.
For parents, ask whether shared words make assumptions easier to inspect.
Section 26 of 36
26. Separate words from evidence
A controlled term states what an annotation means; it does not establish that the annotated event occurred.
Working checkpoint — controlled vocabulary: Link measurements, logs and analysis receipts. Keep accession, definition, release, placement, value and experimental receipt together.
For a classroom model, reconcile fictional synonyms through stable IDs.
Section 27 of 36
27. Separate terminology from conclusion
A precise score or technique name does not prove identification, mechanism or clinical meaning.
Working checkpoint — ontology accession: Keep conclusions proportional to evidence. Read every label beside its formal scope, parent relationships and status.
For future study, connect science to information systems while checking official pathways separately.
Section 28 of 36
28. Connect to Primary Science
A fictional shared vocabulary card lets younger learners separate an observation from the label attached to it. The goal is careful comparison, not memorising specialist jargon.
Working checkpoint — mass spectrometry: Use invented records, define every column and ask what remains unknown. Preserve obsolete and local history; a friendly display name is not the whole vocabulary record.
For scientific writing, cite accession, ontology release, value context, evidence and validator.
Section 29 of 36
29. Connect to Secondary Science
controlled-vocabulary term supports lessons about molecules, measurement, controls and the difference between evidence and explanation.
Working checkpoint — term definition: Trace one claim to its supporting record and state one limitation. Separate terminology validity from instrument validity, statistical calibration and biological meaning.
For students, ask what the accession formally means and where it is used.
Section 30 of 36
30. Connect to mathematics
Counts, coordinates, scores, ratios and uncertainty show why scientific data need units, definitions and compatible denominators.
Working checkpoint — vocabulary release: Recalculate one simple example and explain every symbol. Treat identifiers and units as scientific inputs: one silent substitution can change interpretation.
For parents, ask whether shared words make assumptions easier to inspect.
Section 31 of 36
31. Connect to computing
Ontology graphs, stable accessions and release validation show how computers share scientific meaning.
Working checkpoint — PSI-MS: Break one reference or field, run a check and repair it transparently. Keep accession, definition, release, placement, value and experimental receipt together.
For a classroom model, reconcile fictional synonyms through stable IDs.
Section 32 of 36
32. Connect to pathways
Scientific vocabulary work connects chemistry, instrumentation, information science and software and can illuminate STEM education and career pathways.
Working checkpoint — controlled vocabulary: Check current official education and qualification routes separately before making decisions. Read every label beside its formal scope, parent relationships and status.
For future study, connect science to information systems while checking official pathways separately.
Section 33 of 36
33. Did you know?
A short, readable controlled-vocabulary term record can depend on a much longer chain of source data, identifiers, versions and validation receipts.
Working checkpoint — ontology accession: Follow one record backwards until every dependency is named. Preserve obsolete and local history; a friendly display name is not the whole vocabulary record.
For scientific writing, cite accession, ontology release, value context, evidence and validator.
Section 34 of 36
34. Write a reader-ready methods note
State the specification or service, release, inputs, software, validation, uncertainty and the narrow claim the evidence supports.
Working checkpoint — mass spectrometry: Place the note beside the machine-readable material. Separate terminology validity from instrument validity, statistical calibration and biological meaning.
For students, ask what the accession formally means and where it is used.
Section 35 of 36
35. Build a validation ladder
Check bytes, structure, identifiers, controlled meanings, cross-references, scientific plausibility and a small known fixture in that order.
Working checkpoint — term definition: Stop at the first unresolved layer instead of polishing a later result. Treat identifiers and units as scientific inputs: one silent substitution can change interpretation.
For parents, ask whether shared words make assumptions easier to inspect.
Section 36 of 36
36. Finish with a reproducible bundle
Deliver source data or stable identifiers, metadata, software versions, configuration, validator output, checksums and a plain-language limitations note.
Working checkpoint — vocabulary release: Make the published conclusion traceable and reviewable. Keep accession, definition, release, placement, value and experimental receipt together.
For a classroom model, reconcile fictional synonyms through stable IDs.
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