Analyses and research objects¶

Formats that record a scientific analysis or package research outputs. In each case ASB Schema supplies the paper-grounded content: tasks, evidence, decisions and files.

ASTRA¶

ASTRA (Agentic Schema for Transparent Research Analysis), published by Lightcone Research, records one scientific analysis while it is designed and run: inputs, outputs, decisions with named options, universes and insights backed by evidence¹. It is written in LinkML and ships a JSON Schema and a JSON-LD context².

ASB Schema produces ASTRA documents and is upstream of them for published research. The exporter of the reference pipeline writes two documents per run:

astra/astra.yaml, the science view, from the paper, its cards and its exploration trace;
astra/run_trace.yaml, the build view: one decision per resolved build flag, one per agent model, one sub-analysis per pipeline unit.

ASB source	ASTRA element
Paper processed in the run	Root analysis
Task card	Sub-analysis
Trace `decision` node	Decision with options; untested `alternatives` stay ordinary options
Trace `pivot` node	Decision whose new approach is the default and former approach an excluded option, with `trigger` as the reason
Trace `dead_end` under a decision	Excluded option, with `failure_mode` as the exclusion reason
Trace `dead_end` with no enclosing decision	Finding of the root analysis
Claim-ledger claims	Findings with quoted evidence
Build flags and agent models	Decisions of `run_trace.yaml`

Trace question and experiment nodes are reported as unmapped.

ASB Schema to ASTRA

existing

The exporter targets ASTRA 0.0.12; the current release is 0.0.14³. Moving to it means writing a root id in astra.yaml and setting Output.format on outputs that do not alias another output.

Further bridge	What it needs	Status
`EvidenceSnippet` to ASTRA `Evidence`	`snippet_id` to `id`, `text` to `quote.exact`, the card's `crossref_doi` to `doi`; `reason` to the notes of the enclosing insight	feasible
ASTRA analysis to task cards	A reader and a rule for task boundaries, since one analysis can yield several cards	feasible
`astra:` mappings in the LinkML files	`close_mappings`, for example from `ASBTaskCard` to `astra:Analysis`	feasible
Evaluation records in ASTRA	An evaluation extension, proposed in issue #74⁴	needs new code

RO-Crate¶

RO-Crate packages research data with their metadata in one JSON-LD file, ro-crate-metadata.json, based on schema.org⁵. The Workflow Run RO-Crate profiles describe executions: Process Run Crate for tool executions recorded as CreateAction entities, Workflow Run Crate for one workflow execution and Provenance Run Crate for per-step detail⁶.

Every capsule carries an RO-Crate 1.1 metadata file whose CreateAction links the tool (instrument), the inputs (object) and the outputs (result); see Capsule.

Bridge	What it needs	Status
RO-Crate 1.1	Written for every capsule; a root `datePublished` and a license entity complete it	existing
Process Run Crate	The profile IRI in the root `conformsTo` (`https://w3id.org/ro/wfrun/process/0.5` for RO-Crate 1.1), and `agent` and `endTime` on the action⁷	feasible
RO-Crate 1.2 and 1.3	New context and descriptor IRIs and `Profile` entities; `ro_crate_version` is a free string⁸	feasible
Workflow RO-Crate	A class for `workflow.yaml` and one crate per workflow with a `ComputationalWorkflow` main entity⁹	needs new code

rocrate-validator checks a crate against RO-Crate and its profiles¹⁰.

ARA¶

ARA (Agent-Native Research Artifact) defines one artifact per paper or project, a directory with PAPER.md, logic/, src/, trace/ and evidence/ layers¹¹. Its trace/ layer holds an exploration tree with the same five node types and the same two support levels as the exploration trace.

ASB Schema to ARA

existing

asb ara-export writes an ARA package for each finished run under ara_export/, builds each layer from the run's records and copies the exploration trace. ARA names the top-level list tree where the trace uses nodes, and asks for a description on question nodes¹²; the converter renames the key and fills the description.

Workflow languages¶

asb export-workflow converts the run's workflow.yaml into CWL, Nextflow and Snakemake files under exports/¹³¹⁴. Command bodies come from each card's runtime executable command; a card without one yields a structural stub. The optional card slots executable (ExecutableSpec), execution_environment (ExecutionEnvironment) and data_in, data_out (TypedArtifact) carry that command, its software stack and its typed files on the card itself.

existing

Analyses and research objects¶

ASTRA¶

RO-Crate¶

ARA¶

Workflow languages¶

See also¶