BioFSharp.FileFormats.INSDC 0.2.0

.NET Standard 2.0 This package targets .NET Standard 2.0. The package is compatible with this framework or higher.
There is a newer version of this package available.
See the version list below for details. 
dotnet add package BioFSharp.FileFormats.INSDC --version 0.2.0
                    


                    

                
NuGet\Install-Package BioFSharp.FileFormats.INSDC -Version 0.2.0
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.FileFormats.INSDC" Version="0.2.0" />
For projects that support PackageReference, copy this XML node into the project file to reference the package. 
<PackageVersion Include="BioFSharp.FileFormats.INSDC" Version="0.2.0" />
                    


                            Directory.Packages.props
                        

                    

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


                            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.FileFormats.INSDC --version 0.2.0
                    


                    

                
#r "nuget: BioFSharp.FileFormats.INSDC, 0.2.0"
#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.FileFormats.INSDC@0.2.0
#: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.FileFormats.INSDC&version=0.2.0
                    


                            Install as a Cake Addin
                        

                    

                
#tool nuget:?package=BioFSharp.FileFormats.INSDC&version=0.2.0
                    


                            Install as a Cake Tool

BioFSharp.FileFormats.INSDC

The C# type model for INSDC (International Nucleotide Sequence Database Collaboration) sequence-database records, and the foundation of the BioFSharp.INSDC suite.

The types are generated directly from the official ENA/SRA XML schemas, so the model stays faithful to the upstream standard and covers the full record set — BioProject, Study, Sample, Experiment, Run, Analysis, Submission, and Receipt. Generation is mechanical and repeatable, so the model is regenerated rather than hand-maintained when the schemas change.

The package also carries the generated fragment selectors: for every field of every record it records the exact XPath/XPointer location that field occupies in the source XML, derived from the same serialization metadata the parser uses. Higher layers of the suite build on this to address, track, and semantically annotate individual values without ever drifting from the type model.

This package is consumed by BioFSharp.IO.INSDC and the rest of the suite; most users depend on those higher-level packages rather than referencing the type model directly.

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)
Learn more about Target Frameworks and .NET Standard.

NuGet packages (4)

Showing the top 4 NuGet packages that depend on BioFSharp.FileFormats.INSDC:

Package Downloads
BioFSharp.IO.INSDC

F# read/write support for INSDC (International Nucleotide Sequence Database Collaboration) XML records — BioProject, Study, Sample, Experiment, Run, Analysis, Submission, Receipt.
BioFSharp.INSDC.SQLite

SQLite-backed store for INSDC (International Nucleotide Sequence Database Collaboration) records — deconstructs BioProject, Study, BioSample, Experiment, and Run values into a normalized schema and reconstructs them on read.
BioFSharp.INSDC.Crawler

Crawls INSDC (International Nucleotide Sequence Database Collaboration) records from ENA — enumerates every run, experiment, sample, and study connected to a project accession and persists them via the BioFSharp.INSDC.SQLite store.
BioFSharp.INSDC.ArcIR

INSDC-specific F1 adapter that maps BioProject, Study, Sample, Experiment, Run, Analysis, Submission, and Receipt records into the target-neutral BioFSharp.ArcIR graph.

GitHub repositories

This package is not used by any popular GitHub repositories.

Version Downloads Last Updated
0.3.0 203 8/28/2026
0.2.1 231 7/9/2026
0.2.0 232 7/9/2026
0.1.0 127 5/21/2026

Expands the suite from two packages to five: `BioFSharp.FileFormats.INSDC` and
`BioFSharp.IO.INSDC` gain new capabilities, while `BioFSharp.INSDC.SQLite`,
`BioFSharp.INSDC.ArcIR`, and `BioFSharp.INSDC.Crawler` ship for the first time.
- **BioFSharp.FileFormats.INSDC** — generated per-type XPointer/XPath fragment selectors (`FragmentSelectors.cs`) so individual elements of a record can be addressed by fragment identifier.
- **BioFSharp.IO.INSDC** — structural ontology that decompiles records into ontology term/value pairs whose term names mirror the XML structure; fragment-selector tracking via per-instance `xpathOf` (bare XPath) and `xpointerOf` (`#xpointer`) lookups plus an `xpathEntries` DTO.
- **BioFSharp.INSDC.SQLite** *(new)* — SQLite-backed store that deconstructs BioProject, Study, BioSample, Experiment, and Run records into a normalized schema and reconstructs them on read, with per-entity modules and an `accession_relations` table capturing the cross-record connectivity graph.
- **BioFSharp.INSDC.ArcIR** *(new)* — maps INSDC records into ArcIR, an ARC-oriented intermediate representation (a property graph of typed, annotations-first objects and relations) with sample references resolved to their BioSample node; renders the graph to GraphML, interactive HTML, and text; ingests supplementary papers and count data.
- **BioFSharp.INSDC.Crawler** *(new)* — crawls a project accession from ENA (Portal `filereport` discovery to Browser API fetch) and persists every connected run, experiment, sample, and study via the SQLite store plus its connectivity table; exposes `crawl` / `crawlToSqlite` (with `*Async` / `*WithAsync` variants); targets net8.0 because FsHttp requires .NET 6+, published to NuGet like the rest.