BioFSharp.INSDC.Crawler 0.2.0

There is a newer version of this package available.
See the version list below for details.

dotnet add package BioFSharp.INSDC.Crawler --version 0.2.0

NuGet\Install-Package BioFSharp.INSDC.Crawler -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.INSDC.Crawler" Version="0.2.0" />

For projects that support PackageReference, copy this XML node into the project file to reference the package.

<PackageVersion Include="BioFSharp.INSDC.Crawler" Version="0.2.0" />
                    

                            Directory.Packages.props

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

                            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.Crawler --version 0.2.0

The NuGet Team does not provide support for this client. Please contact its maintainers for support.

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

                            Install as a Cake Addin

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

                            Install as a Cake Tool

The NuGet Team does not provide support for this client. Please contact its maintainers for support.

BioFSharp.INSDC.Crawler

Collects INSDC (International Nucleotide Sequence Database Collaboration) records from the ENA public archive, as part of the BioFSharp.INSDC suite.

Given a single project accession, the crawler discovers every run, experiment, sample, and study connected to it, fetches the corresponding records from ENA, and persists them — together with the cross-reference graph that links them — through the BioFSharp.INSDC.SQLite store. The result is a local, queryable snapshot of a complete study assembled from one starting accession.

Because it performs live HTTP, this package targets .NET 6+ (net8.0) rather than the netstandard2.0 baseline of the rest of the suite.

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

Product	Compatible and additional computed target framework versions.
.NET	net8.0 is compatible. 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.

Product

.NET

Compatible target framework(s)

Included target framework(s) (in package)

Learn more about Target Frameworks and .NET Standard.

net8.0
- BioFSharp.FileFormats.INSDC (>= 0.2.0)
- BioFSharp.INSDC.SQLite (>= 0.2.0)
- BioFSharp.IO.INSDC (>= 0.2.0)
- FSharp.Core (>= 10.1.300)
- FsHttp (>= 15.0.3)
- Microsoft.Data.Sqlite (>= 8.0.10)

NuGet packages

This package is not used by any NuGet packages.

GitHub repositories

This package is not used by any popular GitHub repositories.

Version	Downloads	Last Updated
0.3.0	102	8/28/2026
0.2.1	133	7/9/2026
0.2.0	120	7/9/2026

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.