[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill:01M6DAJ75ND0EC5XAVTJ819JJM":3,"skill-same:01M6DAJ75ND0EC5XAVTJ819JJM":68},{"skillNo":4,"name":5,"nameZh":6,"description":7,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":16,"categories":17,"keywords":23,"publishedAt":37,"linkOnly":38,"markdownContent":39,"markdownBody":40,"frontMatter":41,"refName":42,"commitSha":43,"skillDirectory":44,"forksCount":14,"repositoryHtmlUrl":45,"repositoryHomepageUrl":6,"ownerHtmlUrl":46,"ownerBlogUrl":6,"ownerDescription":6,"updatedAt":47,"install":48,"resources":61},"01M6DAJ75ND0EC5XAVTJ819JJM","pubmed-database",null,"Direct PubMed and NCBI E-utilities search workflows for biomedical literature, MeSH queries, PMID lookup, citation retrieval, and API-backed literature monitoring.","Prekzursil\u002Fagent-skills-toolchain","Prekzursil","https:\u002F\u002Favatars.githubusercontent.com\u002Fu\u002F54636077?v=4","01M6DACZ1PCQHD99SCR1YXG28B","Andrei Mihai Visalon","01M6DACZ670WZF535V3WYYSS4Z",0,"MIT","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002F.agents\u002Flibrary\u002Fskills\u002Fscientific-db-pubmed-database\u002FSKILL.md",[18],{"categoryNo":19,"categoryName":20,"taxonomyType":21,"taxonomyTypeDesc":22},"01JBSEEDCAT000000000000010","后端与接口","SCENARIO","使用场景",[24,25,26,27,28,29,30,31,32,33,34,35,36],"database","pubmed database","mesh","workflows","search","monitoring","lookup","api","direct","queries","community","Citation","biomedical","2026-11-10 10:12:30",false,"---\nname: pubmed-database\ndescription: Direct PubMed and NCBI E-utilities search workflows for biomedical literature, MeSH queries, PMID lookup, citation retrieval, and API-backed literature monitoring.\norigin: community\n---\n\n# PubMed Database\n\nUse this skill when a task needs biomedical literature from PubMed rather than\ngeneral web search.\n\n## When to Use\n\n- Searching MEDLINE or life-sciences literature.\n- Building PubMed queries with MeSH terms, field tags, dates, or article types.\n- Looking up PMIDs, abstracts, publication metadata, or related citations.\n- Running systematic-review search passes that need repeatable search strings.\n- Using NCBI E-utilities directly from Python, shell, or another HTTP client.\n\n## Query Construction\n\nStart with the research question, split it into concepts, then combine concepts\nwith Boolean operators.\n\n```text\nconcept_1 AND concept_2 AND filter\nsynonym_a OR synonym_b\nNOT exclusion_term\n```\n\nUseful PubMed field tags:\n\n- `[ti]`: title\n- `[ab]`: abstract\n- `[tiab]`: title or abstract\n- `[au]`: author\n- `[ta]`: journal title abbreviation\n- `[mh]`: MeSH term\n- `[majr]`: major MeSH topic\n- `[pt]`: publication type\n- `[dp]`: date of publication\n- `[la]`: language\n\nExamples:\n\n```text\ndiabetes mellitus[mh] AND treatment[tiab] AND systematic review[pt] AND 2023:2026[dp]\n(metformin[nm] OR insulin[nm]) AND diabetes mellitus, type 2[mh] AND randomized controlled trial[pt]\nsmith ja[au] AND cancer[tiab] AND 2026[dp] AND english[la]\n```\n\n## MeSH and Subheadings\n\nPrefer MeSH when the concept has a stable controlled-vocabulary term. Combine\nMeSH with title\u002Fabstract terms when the topic is new or terminology varies.\n\nCorrect subheading syntax puts the subheading before the field tag:\n\n```text\ndiabetes mellitus, type 2\u002Fdrug therapy[mh]\ncardiovascular diseases\u002Fprevention & control[mh]\n```\n\nUse `[majr]` only when the topic must be central to the paper. It can improve\nprecision but may miss relevant work.\n\n## Filters\n\nPublication types:\n\n- `clinical trial[pt]`\n- `meta-analysis[pt]`\n- `randomized controlled trial[pt]`\n- `review[pt]`\n- `systematic review[pt]`\n- `guideline[pt]`\n\nDate filters:\n\n```text\n2026[dp]\n2020:2026[dp]\n2026\u002F03\u002F15[dp]\n```\n\nAvailability filters:\n\n```text\nfree full text[sb]\nhasabstract[text]\n```\n\n## E-utilities Workflow\n\nNCBI E-utilities supports repeatable API workflows:\n\n1. `esearch.fcgi`: search and return PMIDs.\n2. `esummary.fcgi`: return lightweight article metadata.\n3. `efetch.fcgi`: fetch abstracts or full records in XML, MEDLINE, or text.\n4. `elink.fcgi`: find related articles and linked resources.\n\nUse an email and API key for production scripts. Store API keys in environment\nvariables, never in committed files or command history.\n\n```python\nimport os\nimport time\nimport requests\n\nBASE = \"https:\u002F\u002Feutils.ncbi.nlm.nih.gov\u002Fentrez\u002Feutils\"\n\n\ndef esearch(query: str, retmax: int = 20) -> list[str]:\n    params = {\n        \"db\": \"pubmed\",\n        \"term\": query,\n        \"retmode\": \"json\",\n        \"retmax\": retmax,\n        \"tool\": \"ecc-pubmed-search\",\n        \"email\": os.environ.get(\"NCBI_EMAIL\", \"\"),\n    }\n    api_key = os.environ.get(\"NCBI_API_KEY\")\n    if api_key:\n        params[\"api_key\"] = api_key\n\n    response = requests.get(f\"{BASE}\u002Fesearch.fcgi\", params=params, timeout=30)\n    response.raise_for_status()\n    time.sleep(0.35)\n    return response.json()[\"esearchresult\"][\"idlist\"]\n\n\npmids = esearch(\"hypertension[mh] AND randomized controlled trial[pt] AND 2024:2026[dp]\")\nprint(pmids)\n```\n\nFor batches, prefer NCBI history server parameters (`usehistory=y`,\n`WebEnv`, `query_key`) instead of passing very long PMID lists through URLs.\n\n## Output Discipline\n\nFor each search pass, record:\n\n- exact search string\n- database searched\n- date searched\n- filters used\n- result count\n- export format\n- any manual exclusions\n\nExample:\n\n```markdown\n| Database | Date searched | Query | Filters | Results |\n| --- | --- | --- | --- | ---: |\n| PubMed | 2026-05-11 | `sickle cell disease[mh] AND CRISPR[tiab]` | 2020:2026[dp], English | 42 |\n```\n\n## Review Checklist\n\n- Are field tags valid PubMed tags?\n- Are MeSH terms paired with free-text synonyms for newer topics?\n- Is the date range explicit and appropriate?\n- Does the search log include enough detail to reproduce the query?\n- Are API keys loaded from the environment?\n- Does HTTP code call `raise_for_status()` or otherwise handle non-200\n  responses before parsing?\n- Are rate limits respected?\n\n## References\n\n- [PubMed help](https:\u002F\u002Fpubmed.ncbi.nlm.nih.gov\u002Fhelp\u002F)\n- [NCBI E-utilities documentation](https:\u002F\u002Fwww.ncbi.nlm.nih.gov\u002Fbooks\u002FNBK25501\u002F)\n- [NCBI API key guidance](https:\u002F\u002Fsupport.nlm.nih.gov\u002FkbArticle\u002F?pn=KA-05317)\n- NCBI support: \u003Ceutilities@ncbi.nlm.nih.gov>\n","# PubMed Database\n\nUse this skill when a task needs biomedical literature from PubMed rather than\ngeneral web search.\n\n## When to Use\n\n- Searching MEDLINE or life-sciences literature.\n- Building PubMed queries with MeSH terms, field tags, dates, or article types.\n- Looking up PMIDs, abstracts, publication metadata, or related citations.\n- Running systematic-review search passes that need repeatable search strings.\n- Using NCBI E-utilities directly from Python, shell, or another HTTP client.\n\n## Query Construction\n\nStart with the research question, split it into concepts, then combine concepts\nwith Boolean operators.\n\n```text\nconcept_1 AND concept_2 AND filter\nsynonym_a OR synonym_b\nNOT exclusion_term\n```\n\nUseful PubMed field tags:\n\n- `[ti]`: title\n- `[ab]`: abstract\n- `[tiab]`: title or abstract\n- `[au]`: author\n- `[ta]`: journal title abbreviation\n- `[mh]`: MeSH term\n- `[majr]`: major MeSH topic\n- `[pt]`: publication type\n- `[dp]`: date of publication\n- `[la]`: language\n\nExamples:\n\n```text\ndiabetes mellitus[mh] AND treatment[tiab] AND systematic review[pt] AND 2023:2026[dp]\n(metformin[nm] OR insulin[nm]) AND diabetes mellitus, type 2[mh] AND randomized controlled trial[pt]\nsmith ja[au] AND cancer[tiab] AND 2026[dp] AND english[la]\n```\n\n## MeSH and Subheadings\n\nPrefer MeSH when the concept has a stable controlled-vocabulary term. Combine\nMeSH with title\u002Fabstract terms when the topic is new or terminology varies.\n\nCorrect subheading syntax puts the subheading before the field tag:\n\n```text\ndiabetes mellitus, type 2\u002Fdrug therapy[mh]\ncardiovascular diseases\u002Fprevention & control[mh]\n```\n\nUse `[majr]` only when the topic must be central to the paper. It can improve\nprecision but may miss relevant work.\n\n## Filters\n\nPublication types:\n\n- `clinical trial[pt]`\n- `meta-analysis[pt]`\n- `randomized controlled trial[pt]`\n- `review[pt]`\n- `systematic review[pt]`\n- `guideline[pt]`\n\nDate filters:\n\n```text\n2026[dp]\n2020:2026[dp]\n2026\u002F03\u002F15[dp]\n```\n\nAvailability filters:\n\n```text\nfree full text[sb]\nhasabstract[text]\n```\n\n## E-utilities Workflow\n\nNCBI E-utilities supports repeatable API workflows:\n\n1. `esearch.fcgi`: search and return PMIDs.\n2. `esummary.fcgi`: return lightweight article metadata.\n3. `efetch.fcgi`: fetch abstracts or full records in XML, MEDLINE, or text.\n4. `elink.fcgi`: find related articles and linked resources.\n\nUse an email and API key for production scripts. Store API keys in environment\nvariables, never in committed files or command history.\n\n```python\nimport os\nimport time\nimport requests\n\nBASE = \"https:\u002F\u002Feutils.ncbi.nlm.nih.gov\u002Fentrez\u002Feutils\"\n\n\ndef esearch(query: str, retmax: int = 20) -> list[str]:\n    params = {\n        \"db\": \"pubmed\",\n        \"term\": query,\n        \"retmode\": \"json\",\n        \"retmax\": retmax,\n        \"tool\": \"ecc-pubmed-search\",\n        \"email\": os.environ.get(\"NCBI_EMAIL\", \"\"),\n    }\n    api_key = os.environ.get(\"NCBI_API_KEY\")\n    if api_key:\n        params[\"api_key\"] = api_key\n\n    response = requests.get(f\"{BASE}\u002Fesearch.fcgi\", params=params, timeout=30)\n    response.raise_for_status()\n    time.sleep(0.35)\n    return response.json()[\"esearchresult\"][\"idlist\"]\n\n\npmids = esearch(\"hypertension[mh] AND randomized controlled trial[pt] AND 2024:2026[dp]\")\nprint(pmids)\n```\n\nFor batches, prefer NCBI history server parameters (`usehistory=y`,\n`WebEnv`, `query_key`) instead of passing very long PMID lists through URLs.\n\n## Output Discipline\n\nFor each search pass, record:\n\n- exact search string\n- database searched\n- date searched\n- filters used\n- result count\n- export format\n- any manual exclusions\n\nExample:\n\n```markdown\n| Database | Date searched | Query | Filters | Results |\n| --- | --- | --- | --- | ---: |\n| PubMed | 2026-05-11 | `sickle cell disease[mh] AND CRISPR[tiab]` | 2020:2026[dp], English | 42 |\n```\n\n## Review Checklist\n\n- Are field tags valid PubMed tags?\n- Are MeSH terms paired with free-text synonyms for newer topics?\n- Is the date range explicit and appropriate?\n- Does the search log include enough detail to reproduce the query?\n- Are API keys loaded from the environment?\n- Does HTTP code call `raise_for_status()` or otherwise handle non-200\n  responses before parsing?\n- Are rate limits respected?\n\n## References\n\n- [PubMed help](https:\u002F\u002Fpubmed.ncbi.nlm.nih.gov\u002Fhelp\u002F)\n- [NCBI E-utilities documentation](https:\u002F\u002Fwww.ncbi.nlm.nih.gov\u002Fbooks\u002FNBK25501\u002F)\n- [NCBI API key guidance](https:\u002F\u002Fsupport.nlm.nih.gov\u002FkbArticle\u002F?pn=KA-05317)\n- NCBI support: \u003Ceutilities@ncbi.nlm.nih.gov>\n",{"name":5,"origin":34,"description":7},"main","a298c929b6cbd662e1fce54302ce520d5ceea1a5",".agents\u002Flibrary\u002Fskills\u002Fscientific-db-pubmed-database","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain","https:\u002F\u002Fgithub.com\u002FPrekzursil","2026-11-02 14:30:57",{"source":8,"skillName":5,"commands":49,"prompt":59,"zipAvailable":60},[50,53,56],{"tool":51,"command":52},"npx","npx skills add Prekzursil\u002Fagent-skills-toolchain --skill pubmed-database",{"tool":54,"command":55},"bunx","bunx skills add Prekzursil\u002Fagent-skills-toolchain --skill pubmed-database",{"tool":57,"command":58},"pnpm","pnpm dlx skills add Prekzursil\u002Fagent-skills-toolchain --skill pubmed-database","安装技能，技能地址：https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002F.agents\u002Flibrary\u002Fskills\u002Fscientific-db-pubmed-database\u002FSKILL.md",true,[62],{"path":63,"resourceType":64,"resourceTypeDesc":65,"sizeBytes":66,"sourceHtmlUrl":67},"agents\u002Fopenai.yaml","REFERENCE","参考文档",82,"https:\u002F\u002Fgithub.com\u002Fnexuslinkproductions\u002Fyuri-os\u002Fblob\u002Fmain\u002F.agents\u002Fskills\u002Fhatch-pet\u002Fagents\u002Fopenai.yaml",[69,91,120,147,161,177],{"skillNo":70,"name":71,"nameZh":6,"description":72,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":73,"categories":74,"keywords":75,"publishedAt":37},"01M6DF7D7478R55P46REYH4QAC","clarify-requirements","Resolve genuine pre-execution ambiguity by scanning repo context, generating 1-6 grounded options, and asking 1-3 focused questions via AskUserQuestion. NOT for mid-task use (injection risk); NOT when the goal is already unambiguous; use to disambiguate vague prompts before any file edits.","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Fworkspace-hooks\u002Fskills\u002Fclarify-requirements\u002FSKILL.md",[],[76,77,78,79,80,81,82,83,84,85,86,87,88,89,90],"clarify requirements","clarify","requirements","risk","options","task","prompts","goal","scanning","use","context","repo","injection","execution","file",{"skillNo":92,"name":93,"nameZh":6,"description":94,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":95,"categories":96,"keywords":100,"publishedAt":37},"01M6DF79CA4BHJS66J8EZDBPWJ","openmm-md","Run FREE, open-source, Windows-native GPU molecular dynamics via the openmm-md MCP (OpenMM + CUDA on the local NVIDIA GPU). Use for protein \u002F protein-ligand MD when you want a free stack or are on Windows without a Schrodinger license. Covers the full workflow (prepare, solvate, minimize, equilibrate, production, analyze, mmgbsa) AND an honest decision guide vs Schrodinger Desmond, including how to run Desmond legitimately on Linux or a cloud GPU with a real license. This is a deliberately LESSER free alternative and does NOT replace the schrodinger MCP tools. Do NOT use it to pick a free tool when a validated FEP+, WaterMap, IFD-MD, or Prime MM-GBSA result is actually required.","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Fmcp\u002Fopenmm-md-mcp\u002Fskill\u002Fopenmm-md\u002FSKILL.md",[97],{"categoryNo":98,"categoryName":99,"taxonomyType":21,"taxonomyTypeDesc":22},"01JBSEEDCAT000000000000023","Skill与智能体开发",[101,102,103,104,105,106,107,108,109,110,111,112,113,114,85,115,116,117,118,119],"openmm md","how","decision","pick","linux","analyze","tool","stack","open","NVIDIA","gpu","license","workflow","windows","free","molecular dynamics","local","do","MCP",{"skillNo":121,"name":122,"nameZh":6,"description":123,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":124,"categories":125,"keywords":132,"publishedAt":37},"01M6DF76C1MG85VEWP8VZCBNMN","visual-review","Take screenshots of web pages and UI using Playwright for visual review and iteration","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Feditor\u002Fmetaswarm\u002Fskills\u002Fvisual-review\u002FSKILL.md",[126,129],{"categoryNo":127,"categoryName":128,"taxonomyType":21,"taxonomyTypeDesc":22},"01JBSEEDCAT000000000000003","演示文稿",{"categoryNo":130,"categoryName":131,"taxonomyType":21,"taxonomyTypeDesc":22},"01JBSEEDCAT000000000000008","测试与质量",[133,134,135,136,137,138,139,140,141,142,102,143,144,145,146],"review","visual","visual review","pages","web","false","iteration","take","check","slides","ui","screenshot","playwright","screenshots",{"skillNo":148,"name":149,"nameZh":6,"description":150,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":151,"categories":152,"keywords":153,"publishedAt":37},"01M6DF73AQVCBZKEN0YXEX9FXP","status","Diagnostic status report — shows metaswarm installation state, project setup, and potential issues","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Feditor\u002Fmetaswarm\u002Fskills\u002Fstatus\u002FSKILL.md",[],[149,154,155,156,157,158,159,160],"setup","report","project","installation","project setup","issues","state",{"skillNo":162,"name":163,"nameZh":6,"description":164,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":165,"categories":166,"keywords":168,"publishedAt":37},"01M6DF6X6C2XB0P6GX76P7TTYV","start","Use when starting work on any task, when the user mentions metaswarm, or when the user wants to begin tracked development work","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Feditor\u002Fmetaswarm\u002Fskills\u002Fstart\u002FSKILL.md",[167],{"categoryNo":98,"categoryName":99,"taxonomyType":21,"taxonomyTypeDesc":22},[163,169,81,170,171,172,85,173,174,175,176],"start issue","issue","ready","work on issue","user","work","work on","development",{"skillNo":178,"name":154,"nameZh":6,"description":179,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":180,"categories":181,"keywords":182,"publishedAt":37},"01M6DF6QMJ9AJKFKHHKRT005PQ","Interactive project setup — detects your project, configures metaswarm, writes project-local files","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Feditor\u002Fmetaswarm\u002Fskills\u002Fsetup\u002FSKILL.md",[],[154,156,117,183,158,184],"files","interactive"]