BioFSharp.INSDC.ArcIR 0.3.0

.NET Standard 2.0 This package targets .NET Standard 2.0. The package is compatible with this framework or higher. 
dotnet add package BioFSharp.INSDC.ArcIR --version 0.3.0
                    


                    

                
NuGet\Install-Package BioFSharp.INSDC.ArcIR -Version 0.3.0
This command is intended to be used within the Package Manager Console in Visual Studio, as it uses the NuGet module's version of Install-Package. 
<PackageReference Include="BioFSharp.INSDC.ArcIR" Version="0.3.0" />
For projects that support PackageReference, copy this XML node into the project file to reference the package. 
<PackageVersion Include="BioFSharp.INSDC.ArcIR" Version="0.3.0" />
                    


                            Directory.Packages.props
                        

                    

                
<PackageReference Include="BioFSharp.INSDC.ArcIR" />
                    


                            Project file
For projects that support Central Package Management (CPM), copy this XML node into the solution Directory.Packages.props file to version the package. 
paket add BioFSharp.INSDC.ArcIR --version 0.3.0
                    


                    

                
#r "nuget: BioFSharp.INSDC.ArcIR, 0.3.0"
#r directive can be used in F# Interactive and Polyglot Notebooks. Copy this into the interactive tool or source code of the script to reference the package. 
#:package BioFSharp.INSDC.ArcIR@0.3.0
#:package directive can be used in C# file-based apps starting in .NET 10 preview 4. Copy this into a .cs file before any lines of code to reference the package. 
#addin nuget:?package=BioFSharp.INSDC.ArcIR&version=0.3.0
                    


                            Install as a Cake Addin
                        

                    

                
#tool nuget:?package=BioFSharp.INSDC.ArcIR&version=0.3.0
                    


                            Install as a Cake Tool

BioFSharp.INSDC.ArcIR

Maps INSDC records into the target-neutral BioFSharp.ArcIR property graph.

Parsed records become typed, related objects - projects, studies, samples, experiments, runs, organisms, instruments, protocols, data files, and organizations. Explicit per-entity converters create graph properties and annotations; they do not consume the IO package's structural decompilation. Shared entities are combined through explicit conflict-reporting merge semantics and labeled relations connect them. Bare accessions and aliases are converted to absolute adapter URNs; F1 assertions and relations receive deterministic IDs that do not depend on their current values.

All objects, type assertions, properties, annotations, and relations are stored in identity-keyed maps. Their predicates and values reference one shared graph- level term registry. The adapter covers BioProject, Study, BioSample, Experiment, Run, Analysis, Submission, and Receipt, plus supplementary papers and count data.

The graph can be rendered as text, GraphML, or a self-contained HTML page. These are derived inspection tools; the embedded HTML page is not the intended final workbench architecture. *WithAccounting F1 functions bind exact source occurrences to typed locations in the resulting graph: INSDC and JATS XML use XPointer, while count-header cells use W3C byte-position selectors. The source artifact bytes are digest-checked, and emitted locations can be qualified against the canonical persisted ArcIR state with FieldAccounting.qualifyEmitted.

Built on BioFSharp.IO.INSDC.

Part of BioFSharp.INSDC. Released under the MIT license.

Product Compatible and additional computed target framework versions.
.NET net5.0 was computed.  net5.0-windows was computed.  net6.0 was computed.  net6.0-android was computed.  net6.0-ios was computed.  net6.0-maccatalyst was computed.  net6.0-macos was computed.  net6.0-tvos was computed.  net6.0-windows was computed.  net7.0 was computed.  net7.0-android was computed.  net7.0-ios was computed.  net7.0-maccatalyst was computed.  net7.0-macos was computed.  net7.0-tvos was computed.  net7.0-windows was computed.  net8.0 was computed.  net8.0-android was computed.  net8.0-browser was computed.  net8.0-ios was computed.  net8.0-maccatalyst was computed.  net8.0-macos was computed.  net8.0-tvos was computed.  net8.0-windows was computed.  net9.0 was computed.  net9.0-android was computed.  net9.0-browser was computed.  net9.0-ios was computed.  net9.0-maccatalyst was computed.  net9.0-macos was computed.  net9.0-tvos was computed.  net9.0-windows was computed.  net10.0 was computed.  net10.0-android was computed.  net10.0-browser was computed.  net10.0-ios was computed.  net10.0-maccatalyst was computed.  net10.0-macos was computed.  net10.0-tvos was computed.  net10.0-windows was computed. 
.NET Core netcoreapp2.0 was computed.  netcoreapp2.1 was computed.  netcoreapp2.2 was computed.  netcoreapp3.0 was computed.  netcoreapp3.1 was computed. 
.NET Standard netstandard2.0 is compatible.  netstandard2.1 was computed. 
.NET Framework net461 was computed.  net462 was computed.  net463 was computed.  net47 was computed.  net471 was computed.  net472 was computed.  net48 was computed.  net481 was computed. 
MonoAndroid monoandroid was computed. 
MonoMac monomac was computed. 
MonoTouch monotouch was computed. 
Tizen tizen40 was computed.  tizen60 was computed. 
Xamarin.iOS xamarinios was computed. 
Xamarin.Mac xamarinmac was computed. 
Xamarin.TVOS xamarintvos was computed. 
Xamarin.WatchOS xamarinwatchos was computed. 
Compatible target framework(s)
Included target framework(s) (in package)
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NuGet packages

This package is not used by any NuGet packages.

GitHub repositories

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Version Downloads Last Updated
0.3.0 100 8/28/2026
0.2.1 134 7/9/2026
0.2.0 118 7/9/2026

Repository stabilization, target-neutral ArcIR extraction, immutable ArcIR state persistence, additive semantic enrichment, complete F1 accounting, and the selected-literal curation primitive.
- Added the packable, target-neutral `BioFSharp.ArcIR` `netstandard2.0` package with validated absolute IRI identities, normalized identity-keyed graph collections, shared term definitions, explicit add/upsert/merge operations, validation, and persistence contracts.
- Added canonical `.arcir.json` 1.0 persistence with a packaged JSON Schema, deterministic UTF-8/LF output, strict versioned decoding, invariant tagged values, authoritative identity keys, atomic create-new state publication, and SHA-256 artifact revisions.
- Added typed RFC 6901 fragment locations for every addressable graph entity and atomic value occurrence, including relation-property annotations, plus digest-verified resolution that keeps scalar values ID-less and provenance outside the graph state.
- Added strict inverse parsing for supported ArcIR JSON selectors and the immutable `LiteralMapping.apply` transformation for mapping one exact string occurrence to an already registered term while preserving the source literal.
- Added format-neutral additive semantic mapping and a `PolyglotSSSOM` adapter that preserves complete candidate claims, resolves only declared CURIEs, and leaves mapping selection and provenance to the integrating application.
- Added deterministic occurrence-level F1 accounting and resolvable source/output designations for all eight supported INSDC entities plus supplementary paper and count metadata.
- Removed the unused `BioFSharp` umbrella-package dependency and replaced the remaining preview dependency with stable `PolyglotSSSOM` `0.1.0`.
- Converted `BioFSharp.INSDC.ArcIR` into an INSDC-specific F1 adapter. All eight entity converters and supplementary paper/count ingestion now mint deterministic assertion/relation identities and consume the neutral core without retaining the proof-of-concept model shapes.
- Added a core-only test project and adapter regression coverage for conflict reporting, reference validation, deterministic identities, complete term resolution, and deterministic eight-entity fixture conversion.
- Limited the nested FAKE solution build to one MSBuild node, preventing runaway worker fan-out and silent process-limit failures in captured Windows builds.
- Made package creation reuse the already verified Release build outputs instead of rebuilding projects and risking locked output assemblies.
- Added dependency-vulnerability and generated-artifact drift gates to the full FAKE test path; generators now produce deterministic committed output.
- Added a versioned, forward-migrated SQLite schema with explicit foreign-key modes, transactional public writes, and exact fixture round-trip coverage for all five stored entities.
- Hardened crawler cancellation, bounded retries, strict partial-failure handling, upstream parsing, atomic writes, validation, and resume behavior while preserving injectable offline fetch seams.
- Split the test suite into focused IO, ArcIR, SQLite, crawler, and crawler-hardening modules; refreshed package-boundary and ArcIR terminology documentation; removed the stale local fsdocs publication path.
- Removed the unused structural-decompilation overlay from the proof-of-concept ArcIR package; its explicit converters remain the current mapping surface.