{ "ok": true, "resource": { "id": "RES_A0ED38D64199", "resource_type": "skill", "canonical_url": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/pathogen-variant-surveillance", "name": "pathogen-variant-surveillance", "summary_en": "Query live pathogen genomic surveillance data through the GenSpectrum LAPIS API to find which viral lineages are circulating now, how fast they are growing, and what mutations they carry. Use whenever a question depends on the current state of a pathogen population rather than on remembered facts - which SARS-CoV-2 variant is dominant, whether a Pango lineage is still designated or has been withdrawn, what clade or genotype of H5N1 is in a host or region, whether a PCR primer or assay target still matches circulating sequence, or how a lineage's prevalence has moved week to week. Triggers include \"variant surveillance\", \"genomic surveillance\", \"what variant is circulating\", \"dominant variant\", \"Pango lineage\", \"lineage prevalence\", \"growth advantage\", \"SARS-CoV-2 variant\", \"XFG\", \"clade 2.3.4.4b\", \"H5N1 genotype\", \"influenza clade\", \"RSV/mpox/measles/dengue lineage\", \"CoV-Spectrum\", \"LAPIS\", \"Nextclade\", \"pango-designation\", and any request to report what a pathogen population looks like today.", "summary_zh": "通过GenSpectrum LAPIS API查询实时病原体基因组监测数据，以了解当前流行的病毒谱系、其增长速度及携带的突变。当问题依赖于病原体种群的当前状态而非记忆中的事实时使用——例如哪种SARS-CoV-2变异株占主导、某个Pango谱系是否仍被指定或已被撤销、H5N1在宿主或地区中的进化枝或基因型、PCR引物或检测靶标是否仍与流行序列匹配、或谱系流行率逐周变化。触发词包括“variant surveillance”、“genomic surveillance”、“what variant is circulating”、“dominant variant”、“Pango lineage”、“lineage prevalence”、“growth advantage”、“SARS-CoV-2 variant”、“XFG”、“clade 2.3.4.4b”、“H5N1 genotype”、“influenza clade”、“RSV/mpox/measles/dengue lineage”、“CoV-Spectrum”、“LAPIS”、“Nextclade”、“pango-designation”，以及任何要求报告当前病原体种群状况的请求。", "description_en": "This skill provides scripts to query live pathogen genomic surveillance data via the GenSpectrum LAPIS API. It resolves lineage names against the current Pango designation, computes lineage prevalence and growth from sequence counts, compares mutation profiles between lineages, and estimates reporting lag to determine trustworthy time windows. It emphasizes using live data over memory, handles per-instance schema differences, and warns against common pitfalls that lead to silently wrong answers. The skill is intended for research use and does not provide clinical or public-health guidance.", "description_zh": "该技能提供脚本，通过GenSpectrum LAPIS API查询实时病原体基因组监测数据。它根据当前Pango命名解析谱系名称，从序列计数计算谱系流行率和增长，比较谱系间的突变谱，并估计报告延迟以确定可信的时间窗口。它强调使用实时数据而非记忆，处理不同实例的架构差异，并警告可能导致静默错误的常见陷阱。该技能用于研究目的，不提供临床或公共卫生指导。", "provider_name": "K-Dense-AI", "homepage_url": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/pathogen-variant-surveillance", "endpoint_url": null, "source_url": "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/pathogen-variant-surveillance/SKILL.md", "icon_url": null, "cover_image_url": null, "capabilities": [ "data.analyze", "data.retrieve", "data.transform", "research.analyze" ], "categories": [ "research", "data" ], "industries": [ "health", "general" ], "protocols": [ "agent-skills" ], "auth": { "type": "none", "required": false }, "pricing": { "model": "free" }, "input_schema": {}, "output_schema": {}, "metadata": { "content_language": "en", "translation_status": "original-only", "license": { "spdx_id": "MIT", "source": "https://github.com/K-Dense-AI/scientific-agent-skills/blob/1e5eeffbdad3749125afe7ab48a39694e27f181c/LICENSE" }, "github": { "repository": "K-Dense-AI/scientific-agent-skills", "owner": "K-Dense-AI", "path": "skills/pathogen-variant-surveillance/SKILL.md", "commit": "1e5eeffbdad3749125afe7ab48a39694e27f181c", "stars": 42124, "forks": 3870, "updated_at": "2026-09-03T02:47:03Z" }, "skill": { "compatibility": "Requires Python 3.11+. Scripts use only the standard library - no third-party packages. Needs network access to the public GenSpectrum LAPIS instances (lapis.cov-spectrum.org, lapis.genspectrum.org, lapis.pathoplexus.org) and to raw.githubusercontent.com for pango-designation. No API key.", "allowed_tools": "Read Write Edit Bash", "content_hash": "9db864de6bf1c29922a959b979fd50cc3533e8f0f421559653db82992918b911", "line_count": 226 }, "review_gate": { "passed": true, "reasons": [], "policy_version": "review-gate-v1", "evaluated_at": "2026-09-03T06:04:38.182Z" } }, "latest_version": "1e5eeffbdad3", "status": "listed", "health_status": "unknown", "source_kind": "imported", "source_agent": "aiworkshub-skill-reviewer", "trust": { "signal": "none", "reason": "No suspicious or malicious evidence.", "signals": { "yellow": 0, "red": 0 } }, "review_summary": { "method_version": "capability-evidence-v2", "capability_definition": "strong", "contract_completeness": "strong", "access_friction": "low", "operational_transparency": "strong", "evidence_strength": "source_inspected", "use_readiness": "guided_use", "reviewed_at": "2026-09-03T06:04:39.039Z" }, "experience_count": 0, "verified_experience_count": 0, "usage_count": 0, "success_rate": null, "first_seen_at": "2026-09-03T02:50:47.001Z", "last_seen_at": "2026-09-03T06:04:38.418Z", "published_at": "2026-09-03T06:04:38.418Z", "created_at": "2026-09-03T02:50:47.001Z", "updated_at": "2026-09-03T06:04:39.039Z", "api_url": "https://aiworkshub.io/api/v1/resources/RES_A0ED38D64199", "reviews_url": "https://aiworkshub.io/api/v1/resources/RES_A0ED38D64199/reviews", "public_url": "https://aiworkshub.io/resources/RES_A0ED38D64199", "distribution": { "canonical_identity": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/pathogen-variant-surveillance", "syndicatable": true, "origins": [ { "registry_url": "https://github.com/", "upstream_resource_id": "K-Dense-AI/scientific-agent-skills:skills/pathogen-variant-surveillance/SKILL.md", "upstream_record_url": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/pathogen-variant-surveillance", "relation": "syndicated", "metadata": { "source": 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"source-inspection" ] }, { "id": "research.analyze", "weight": 80, "confidence": 80, "evidence_ids": [ "source-record", "source-inspection" ] } ], "domains": [ { "id": "health", "weight": 90, "confidence": 90, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "research", "weight": 80, "confidence": 80, "evidence_ids": [ "source-record", "source-inspection" ] } ], "workflow_roles": [ "retrieve", "analyze" ] }, "capability_units": [ { "id": "skill:pathogen-variant-surveillance", "kind": "skill_action", "capability_id": "data.analyze", "effect": "unknown", "open_world": false, "idempotency": "idempotent", "confirmation": "explicit policy", "input_contract": "natural_language", "output_contract": "natural_language", "accepts": [ "task context" ], "produces": [ "task result" ], "runtime_auth": {}, "pricing": {}, "evidence_ids": [ "source-inspection" ], "metadata": {} } ], "access": { "distribution_license": { "spdx_id": "MIT", "source": "https://github.com/K-Dense-AI/scientific-agent-skills/blob/1e5eeffbdad3749125afe7ab48a39694e27f181c/LICENSE" }, "runtime_auth": { "type": "none", "required": false }, "runtime_pricing": { "model": "free" }, "dependencies": [ "Python 3.11+", "network access to lapis.cov-spectrum.org, lapis.genspectrum.org, lapis.pathoplexus.org, raw.githubusercontent.com" ] }, "operational_flags": [], "trust": { "signal": "none", "evidence_ids": [ "source-record", "source-inspection" ], "reason": "No suspicious or malicious evidence." }, "fit": { "good_for": [ "Answering questions about current pathogen lineage circulation, prevalence, and growth using live genomic surveillance data.", "Resolving Pango lineage names against the current designation list, including recombinants and withdrawn names.", "Comparing mutation profiles between lineages to assess assay target matches.", "Estimating reporting lag to determine reliable time windows for prevalence estimates." ], "not_for": [ "Clinical interpretation or public-health guidance.", "Outbreak response recommendations.", "Case counts (sequence counts are not case counts).", "Fitness or transmissibility estimation (growth is descriptive only)." ] }, "evidence": [ { "id": "source-record", "type": "source_record", "source": "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/pathogen-variant-surveillance/SKILL.md", "observation": "Submitted Skill record for pathogen-variant-surveillance; declared license MIT.", "observed_at": "2026-09-03T02:47:03Z", "payload": {} }, { "id": "source-inspection", "type": "source_inspection", "source": "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/pathogen-variant-surveillance/SKILL.md", "observation": "The Skill source was fetched and inspected (12312 bytes; SHA-256 9db864de6bf1c29922a959b979fd50cc3533e8f0f421559653db82992918b911).", "observed_at": "2026-09-03T06:04:27.814Z", "payload": {} } ], "unknowns": [ "Connectivity to the LAPIS instances has not been verified from this environment.", "Real-world usage of the skill has not been observed.", "The skill's scripts have not been executed or tested in this environment." ], "id": "REV_E4F87B8BEB40", "resource_id": "RES_A0ED38D64199", "evaluator_type": "platform_ai", "provider": "deepseek", "model": "deepseek-v4-flash", "review_scope": "source-inspected-skill", "created_at": "2026-09-03T06:04:39.039Z" } } }