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name: project-context description: "Route potential-target and publication notes for the coronavirus repository while preserving scientific evidence, hypotheses, and structure provenance." metadata: disco-role: operating disable-model-invocation: true license: CC BY 4.0

Project context

Use this sub-skill when the task is about a potential target, target rationale, existing drugs, a target hypothesis, preparation notes, a publication summary, a citation, a DOI or preprint, or SARS/SARS-CoV-2 structural provenance.

This is a context-and-provenance route. It helps a future agent write or review concise Markdown notes; it does not establish medical efficacy, reproduce a paper, curate coordinates, or run molecular dynamics.

Route the request

1. Identify the note kind before editing:
   • Target note: rationale, existing drugs, hypotheses, and preparation notes.
   • Publication note: citation and DOI/preprint status, brief summary, and additional notes.
   • Cross-cutting provenance: structure IDs, virus lineage, complex or apo state, and any modeled or transformed input.
2. Use the complete bundled field lists in templates.md. Do not depend on the repository's original templates being present.
3. Preserve the status of every substantive statement. Mark it as source-backed evidence, a project hypothesis, an unresolved question, or a preparation observation. Never upgrade a hypothesis into a demonstrated effect.
4. Cite the source for scientific claims. If a DOI, preprint, or citation cannot be confirmed from supplied material, write not verified or not supplied; do not guess.
5. If a note names a structure, cross-check its PDB/structure identifier and name against the documented structural provenance before presenting it as the prepared system. Record any homology model, truncation, alignment, protonation, capping, or other transformation as a transformation—not as the experimental source structure.
6. Link a structure-referencing note to the sibling system-preparation route for preparation and simulation details. Route residue/chain/ligand edits to structure-curation.

Target-note contract

Follow the repository's target-note concepts in a compact, explicit record:

• target name and aliases;
• rationale for the target in the SARS/SARS-2 life cycle, with citation and evidence status;
• existing drugs as a neutral inventory table (Drug, Target Location, Notes), with source and status for each row;
• hypotheses about how intervention could affect the target, explicitly labeled as hypotheses;
• preparation notes describing the intended structure, assembly, complex state, and provenance, with a handoff link if a system exists;
• unresolved questions, especially when the target name, lineage, or structural input is ambiguous.

Do not infer drug efficacy, clinical benefit, or safety from an inventory entry, an in-vitro observation, a docking idea, or a molecular-dynamics plan. A note can record a reported observation and separately state what the project proposes to investigate.

Publication-note contract

Use one folder-level Markdown note per article as the repository convention describes. Include:

• the article title and proper citation;
• DOI when verified, otherwise an explicit missing/unverified marker;
• whether the item is peer-reviewed, a preprint, or unknown from the supplied evidence;
• a brief, source-faithful two- or three-point summary;
• additional notes, quotations, identifiers, or questions with their evidence status;
• any structure IDs mentioned by the article, separately cross-checked against project preparation records.

A PDF is source evidence, not a runtime dependency. Do not make note creation depend on PDF extraction or network retrieval. If the supplied material is only a title, link, or incomplete README, state the limit and leave unverified fields visible.

Structural provenance rules

Treat an identifier and a scientific interpretation as separate fields. At minimum record:

• structure identifier and exact source name;
• SARS-CoV, SARS-CoV-2, or unknown lineage;
• molecule or complex represented and relevant chains/ranges if known;
• experimental method/resolution when supplied;
• local preparation label, if any;
• transformations and their evidence (extraction, truncation, alignment, homology modeling, protonation, capping, or ligand edits);
• cross-check result and remaining uncertainty.

For example, the repository documents 2AJF as a SARS-CoV spike RBD:ACE2 source while also documenting a SARS-CoV-2 modeled derivative; those must not be collapsed into one source claim. Similar distinctions apply to 6VSB, 6M17, 6LU7, 2FE8, and other IDs recorded by system-preparation documentation. Use only the identity and facts supplied by the note or bundled references.

A structure name mismatch, missing source ID, or unexplained SARS-versus-SARS-2 substitution is a provenance block. Stop the contextual claim, report the mismatch, and route coordinate repair to structure-curation. If the structure is already validated and the question is solvation/equilibration or serialized outputs, route to system-preparation instead.

Boundaries and safe behavior

• No OpenMM, Folding@home, simulation, equilibration, or long-trajectory commands here.
• No PDB, FASTA, SDF, chain, residue, or ligand manipulation here.
• No PDF reading, DOI lookup, web retrieval, or checkout-path assumption is required at runtime.
• Notes complement structure curation and simulation validation; they never replace either one.
• Do not claim a structure was prepared, simulated, or validated merely because a publication or target note mentions it.
• Keep medical, therapeutic, and drug-effect language scoped to what the cited source actually reports.

Review checklist

Before handing off a note, verify that the correct note kind and all required fields are present, each claim has an evidence status, citation/DOI/preprint uncertainty is explicit, and the target/structure names agree. Check internal route links and use the troubleshooting guidance in troubleshooting.md for blocked cases. No executable project-context script is intentionally bundled.