hypothesis-entry
Skill53 starsChanged 55 days agoApache-2.0View on GitHub
Hypothesis entry: how hypotheses enter an OASE science program. Four strategies exist, each producing a Layer 0 artifact under raw/hypotheses/ with its own schema and threshold set. Use this skill when planning or executing hypothesis entry — deciding which strategy to use, running the adopt command, or interpreting the assessment output. Hypothesis entry feeds into Stage 0 bounded portfolio triage (see science-program-lead template §5a). Do not use this skill for downstream analysis of hypotheses (stage 1+), for reading co-scientist tournament details (use tournament-corpus), or for running a hypex tournament (use the hypex work-order path).
We split this skill into the rules it gives an agent
1 rule. About 0 are common, 0 are distinctive, and 1 is very specific to this project.
≈0
Common · estimate
Many files like this have a rule of this kind.
≈0
Distinctive · estimate
This author's own choices. Worth a look.
1
Very specific
Tied to their project's names, files or tools. Probably skip.
- Common
- Distinctive
- Very specific
- Very specific: line 96
Every strategy's analyze emits the shared oase.hypothesis-assessment.v1 core:
≈ “Common” is an estimate: at least 1 in 5 of the 308,232 skill files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.
Files
1. The four strategies
| Strategy | Command | Layer 0 schema | Availability |
| Sponsor | oase hypothesis adopt --origin sponsor | oase.hypothesis-set.v1 | Always available |
| Charter | oase hypothesis adopt --origin charter | oase.hypothesis-set.v1 | Always available |
| Co-Scientist | oase coscientist ingest | oase.coscientist.v1 | Requires a Co-Scientist export file |
| Hypex | hypex-supervisor work order, then oase hypex ingest | oase.hypex.v1 | Requires OASE-provisioned Hypex tools, templates, and supervisor lease |
Each strategy writes its own vendor-native Layer 0 artifact. The shared
contract is oase.hypothesis-assessment.v1, emitted by each strategy's
analyze command. There is no single score comparable across
strategies. score is an object carrying {value, basis} or null;
cross-strategy comparison is a judgement the program lead makes in prose.
2. When to prefer each strategy
| If the starting material is... | Use | Why |
| A sponsor-supplied list of hypotheses | oase hypothesis adopt --origin sponsor | Honest provenance; attestation recorded |
| Hypotheses authored in the program charter | oase hypothesis adopt --origin charter | Same mechanism, charter-specific infix |
| A Co-Scientist tournament export | oase coscientist ingest | Existing validated pipeline with ELO ranking |
| A need for adversarial hypothesis exploration | hypex-supervisor work order | Multi-epoch tournament with review panel, proximity, and evolution |
| A published hypothesis set (paper, prior program) | oase hypothesis adopt --origin publication or --origin prior-program | Requires --cite for the source reference |
3. Tool invocations
Adoption (sponsor, charter, prior-program, publication)
# Phase 1: adopt the hypothesis set
oase hypothesis adopt hypotheses.json \
--origin sponsor \
--attest "Provided by Dr. Smith on 2026-09-01 as starting material for the CDK4 program" \
[--cite DOI:10.1234/example]
# Phase 2: assess the adopted set
oase hypothesis analyze raw/hypotheses/<slug>.adopted.jsonCo-Scientist (unchanged)
oase coscientist ingest export.json [--top N]
oase coscientist analyze raw/hypotheses/cs-<session>.tournament.json4. Mandatory relays
| Relay code | Kind | Fires when | Obligation |
hypothesis.adopted_not_generated | Qualifier | Every adoption | Quote the attestation verbatim in any finding that rests on this artifact. Do not describe the set as OASE-derived. |
hypothesis.unranked_set | Qualifier | Every adopted set analysis | Array position is input order, not preference. Do not present as a leaderboard. |
5. The no-silent-substitution rule
If the sponsor named a strategy and oase doctor reports it unavailable,
the lead reports blocked. It does NOT silently substitute another.
A substituted strategy produces a differently-shaped artifact with a different score basis. A silent substitution is a provenance error that surfaces much later, when a finding cites an artifact whose shape does not match what the sponsor expected.
Check availability:
oase doctor --json | jq '.checks[] | select(.name | startswith("hypothesis strategy"))'6. Threshold sets
| Strategy | Threshold set | Quality thresholds? |
| Adopted (sponsor, charter, prior-program, publication) | hypothesis-set@1.0 | No — structural only (min_candidates) |
| Co-Scientist | coscientist@1.1 | Yes — ELO gap, win rate, contradiction count |
| Hypex | hypex@1.0 | Yes — but three values ship UNRESOLVED |
7. Assessment output
Every strategy's analyze emits the shared oase.hypothesis-assessment.v1
core:
{
"schema": "oase.hypothesis-assessment.v1",
"strategy": "adopted | coscientist | hypex",
"source_artifact": "raw/hypotheses/...",
"source_sha256": "...",
"candidates": [
{
"candidate_id": "...",
"statement": "...",
"rank": null,
"score": null,
"origin": "adopted | generated"
}
]
}For adopted sets: rank is always null, score is always null.
For ranked strategies: score is {value: <number>, basis: "<set>"} —
never a bare number.
Other versions1 project uses a version of this.
Word for word · 0
None found.
Edited · 1
- terravic/pde-agent-plugin★ 082% same
Wrote their own version · 0
None found.
How matches are found. Word for word: the exact same text. Edited: shares passages with this file (“99% same” means 99% of its five-word phrases also appear here; 10% or more counts). Their own version: similar meaning, or, weakest, the same name. We can’t tell which project had it first. Projects are counted among the 200 most-starred candidates, and mentions are links to the repository we found, up to 50 per site, so both counts are a floor.
In this repository82 other files it gives its agents.
- applications/open-agentic-science-engine/templates/admet-dmpk-scientist/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/bootstrapper/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/computational-biologist/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/computational-chemist/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/experimental-biologist/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/finding-validator/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/head-of-discovery/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/hypex-evolution/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/hypex-generation/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/hypex-meta-review/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/hypex-proximity/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/hypex-reflection/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/hypex-supervisor/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/hypex-tournament/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/medicinal-chemist/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/preclinical-toxicologist/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/project-curator/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/regulatory-scientist/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/research-operations-controller/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/science-program-lead/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/scientific-reviewer/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/structural-biologist/agents.mdAGENTS.md
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- The first 60 shown.
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