PolyglotSSSOM 0.1.0

PolyglotSSSOM

PolyglotSSSOM is a cross-runtime YAML-metadata-plus-TSV implementation of the Simple Standard for Sharing Ontological Mappings (SSSOM). It is written once in F# and built for .NET, JavaScript, and Python.

The current 0.1.0-alpha.1 line is an implementation prerelease. Its portable domain model and strict, version-aware TSV/YAML codec are available across all three target runtimes. The exact stable-v1.0 and pinned-v1.1 specification sources are documented in spec/UPSTREAM.md.

Requirements

• .NET SDK 10.0.300 feature band
• Node.js 22 or newer
• Python 3.12 or newer
• uv

The shipped NuGet library targets netstandard2.0; .NET 10 is required only by the Fable build toolchain.

Build and test

On Windows use build.cmd; on macOS/Linux use ./build.sh.

build.cmd                  run the shared suite on .NET, Node, and Python
build.cmd BuildAll         build/transpile all three libraries
build.cmd Pack             create NuGet, npm, and wheel artifacts
build.cmd TestPackages     pack and run isolated package-consumer smokes

Generated output is written below artifacts/ and is never committed.

Package identities

• NuGet: PolyglotSSSOM
• npm: @nfdi4plants/polyglot-sssom
• PyPI: polyglot-sssom (import polyglot_sssom)

All three packages expose the portable mapping-set, mapping, lexical-value, extension, descriptor, CURIE, diagnostic, and SssomCodec APIs. Optional scalars remain absent and multivalued slots use empty arrays for zero values. The codec reads embedded or external metadata, validates v1.0 and the pinned v1.1 draft, and writes deterministic canonical embedded SSSOM/TSV.

Authoring mappings

The lexical factories cover the common entity-to-entity path without exposing the complete positional constructors. AddMapping preserves an optional record ID for general v1.0/v1.1 authoring. AddMappingWithRecordId assigns a caller-owned native v1.1 ID atomically; PolyglotSSSOM never invents one.

F#:

let document =
    SssomDocument.Create(
        "https://example.org/mappings",
        "https://example.org/license"
    )

document.Metadata.EnsurePrefix("ex", "https://example.org/")
document.Metadata.EnsurePrefix("uuid", "urn:uuid:")

let mapping =
    Mapping.CreateEntityMapping(
        "ex:source",
        "skos:exactMatch",
        "ex:target",
        "semapv:ManualMappingCuration"
    )

document.AddMappingWithRecordId("urn:uuid:example", mapping)
let content = SssomCodec.EncodeCanonical document

JavaScript:

const document = SssomDocument.Create(
  "https://example.org/mappings",
  "https://example.org/license"
);
document.Metadata.EnsurePrefix("ex", "https://example.org/");
document.Metadata.EnsurePrefix("uuid", "urn:uuid:");

const mapping = Mapping.CreateEntityMapping(
  "ex:source",
  "skos:exactMatch",
  "ex:target",
  "semapv:ManualMappingCuration"
);
document.AddMappingWithRecordId("urn:uuid:example", mapping);
const content = SssomCodec.EncodeCanonical(document);

Python:

document = sssom.SssomDocument.Create(
    "https://example.org/mappings",
    "https://example.org/license",
)
document.Metadata.EnsurePrefix("ex", "https://example.org/")
document.Metadata.EnsurePrefix("uuid", "urn:uuid:")

mapping = sssom.Mapping.CreateEntityMapping(
    "ex:source",
    "skos:exactMatch",
    "ex:target",
    "semapv:ManualMappingCuration",
)
document.AddMappingWithRecordId("urn:uuid:example", mapping)
content = sssom.SssomCodec.EncodeCanonical(document)

Call Clone() before editing when the imported document must remain available unchanged for its original round trip. Find, replace, and remove operations use the stable record_id; full document correctness remains explicit through SssomCodec.Validate or canonical encoding.