[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill-google-deepmind-pubchem-database":3,"mdc--817l3x-key":33,"related-repo-google-deepmind-pubchem-database":1276,"related-org-google-deepmind-pubchem-database":1383},{"slug":4,"name":4,"fn":5,"description":6,"org":7,"tags":11,"stars":22,"repoUrl":23,"updatedAt":24,"license":25,"forks":26,"topics":27,"repo":28,"sourceUrl":31,"mdContent":32},"pubchem-database","query PubChem for chemical data","Query PubChem, search by name\u002FCID\u002FSMILES, retrieve properties, similarity\u002Fsubstructure searches, bioactivity, for cheminformatics. Use when a user asks about a specific chemical, drug, or molecule.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},"google-deepmind","Google DeepMind","https:\u002F\u002Fpexgzepcugksgbtrxkhf.supabase.co\u002Fstorage\u002Fv1\u002Fobject\u002Fpublic\u002Forg-logos\u002Fgoogle-deepmind.png",[12,16,19],{"name":13,"slug":14,"type":15},"Research","research","tag",{"name":17,"slug":18,"type":15},"Bioinformatics","bioinformatics",{"name":20,"slug":21,"type":15},"Chemistry","chemistry",2333,"https:\u002F\u002Fgithub.com\u002Fgoogle-deepmind\u002Fscience-skills","2026-07-12T07:52:13.190484",null,234,[],{"repoUrl":23,"stars":22,"forks":26,"topics":29,"description":30},[],"GDM Science Skills to speed up agentic scientific workflows with better grounding and higher token efficiency. Integrate insights from AlphaGenome, AFDB, UniProt and 30+ other databases and tools.","https:\u002F\u002Fgithub.com\u002Fgoogle-deepmind\u002Fscience-skills\u002Ftree\u002FHEAD\u002Fskills\u002Fpubchem_database","---\nname: pubchem-database\ndescription: >\n  Query PubChem, search by name\u002FCID\u002FSMILES, retrieve properties,\n  similarity\u002Fsubstructure searches, bioactivity, for cheminformatics. Use when a\n  user asks about a specific chemical, drug, or molecule.\n---\n\n# PubChem Database\n\n## Prerequisites\n\n1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure\n    `uv` is installed and on PATH.\n2.  **User Notification**: If .licenses\u002Fpubchem_database_LICENSE.txt does not\n    already exist in the workspace root directory then (1) prominently notify\n    the user to check the terms at\n    https:\u002F\u002Fpubchem.ncbi.nlm.nih.gov\u002Fdocs\u002Fcitation-guidelines and\n    https:\u002F\u002Fpubchem.ncbi.nlm.nih.gov\u002Fdocs\u002Fpug-rest, then (2) create the file\n    recording the notification text and timestamp.\n\n## Quick Start\n\nPubChem queries are executed via a robust Python wrapper script to respect\nterms-of-service and handle complex JSON parsing. This script allows safe\nmulti-agent use of APIs.\n\nExample: Resolve a chemical name to its Compound ID (CID)\n\n```bash\nuv run scripts\u002Fpubchem_api.py resolve --name \"aspirin\" --output result.json\n```\n\n## Core Rules\n\n-   **Use the Wrapper**: ALWAYS execute the provided helper scripts to query the\n    database rather than accessing the database directly. The scripts\n    automatically enforce the required rate limit gracefully.\n-   Read the generated JSON output file, and process it with jq or code.\n-   **Verify Facts**: ALWAYS verify information retrieved from memory with a\n    database query if the user asks for a specific fact that can be checked in\n    PubChem. Do not rely solely on internal knowledge.\n-   **Notification**: If this skill is used, ensure this is mentioned in the\n    output.\n\n## Core Capabilities\n\n**1. Compound Resolution (Name or InChI to Identifiers)** Convert chemical\u002Ftrade\nnames or InChI strings into PubChem CIDs, SMILES, and InChIKeys.\n\n```bash\nuv run scripts\u002Fpubchem_api.py resolve --name \"ibuprofen\" --output result.json\n# OR\nuv run scripts\u002Fpubchem_api.py resolve --inchi \"InChI=1S\u002FC3\u002Fc1-3-2\u002Fi1+1\" --output result.json\n```\n\n**2. Physical & Chemical Property Retrieval** Fetch computed properties (e.g.,\nMolecularWeight, XLogP, TPSA).\n\n```bash\nuv run scripts\u002Fpubchem_api.py properties --cid 2244 --output result.json\n```\n\n**3. Synonyms and Trade Names** Find alternative names and brand names.\n\n```bash\nuv run scripts\u002Fpubchem_api.py synonyms --cid 2244 --output result.json\n```\n\n## Advanced Context\n\n**4. Safety and Hazard Information (GHS)** Retrieve Global Harmonized System\nhazard statements and handling precautions (uses PUG-View).\n\n```bash\nuv run scripts\u002Fpubchem_api.py safety --cid 2244 --output result.json\n```\n\n**5. Drug and Medication Information** Fetch FDA pharmacology data, mechanism of\naction, and therapeutic uses (uses PUG-View).\n\n```bash\nuv run scripts\u002Fpubchem_api.py pharmacology --cid 2244 --output result.json\n```\n\n**6. Custom Heading (PUG-View)** Retrieve any specific heading from the PUG-View\nsystem (e.g., 'Geometry', 'Crystal Structures').\n\n```bash\nuv run scripts\u002Fpubchem_api.py view --cid 3939 --heading \"Crystal Structures\" --output result.json\n```\n\n**7. Image Generation** Retrieve 2D chemical structure images. The script\nreturns a Markdown-formatted image link.\n\n```bash\nuv run scripts\u002Fpubchem_api.py image --cid 2244 --output result.json\n```\n\n## Complex Search & Biology\n\n**8. Structure-Based Searching (Similarity & Substructure)** Find molecules\nsimilar to a SMILES string or containing a specific substructure.\n\n```bash\nuv run scripts\u002Fpubchem_api.py similarity --smiles \"CC(=O)OC1=CC=CC=C1C(=O)O\" --output result.json\n```\n\nand\n\n```bash\nuv run scripts\u002Fpubchem_api.py substructure --smiles \"C1=CC=CC=C1\" --output result.json\n```\n\n**9. BioAssay & Target Interactions** Identify genes or proteins a chemical\ninteracts with.\n\n```bash\nuv run scripts\u002Fpubchem_api.py assays --cid 2244 --output result.json\n```\n\n## Advanced Usage & Workflows\n\n**10. Cross-references (Xrefs)** Fetch identifiers cross-referenced with a CID\n(e.g., PatentID, PubMedID).\n\n```bash\nuv run scripts\u002Fpubchem_api.py xrefs --cid 2244 --type \"PatentID\" --output result.json\n```\n\n**11. Property Range Search** Find CIDs within a specific property range.\nSupported features include: `molecular_weight`, `heavy_atom_count`, `xlogp`,\n`tpsa`, `h_bond_donor_count`, `h_bond_acceptor_count`, `rotatable_bond_count`,\n`exact_mass`, `monoisotopic_mass`, and `complexity`.\n\n```bash\nuv run scripts\u002Fpubchem_api.py range --feature molecular_weight --min 400.0 --max 400.05 --output result.json\n```\n\n**12. Custom PUG-REST Query** Execute a raw path against the PUG-REST API.\n\n```bash\nuv run scripts\u002Fpubchem_api.py query --path \"compound\u002Fcid\u002F2244\u002Fxrefs\u002FPatentID\u002FJSON\" --output result.json\n```\n\n## Fallback Search Strategies\n\nIf direct resolution by name or formula fails (e.g., for complex compounds or\nspecific ions):\n\n-   **Search for parent\u002Fneutral molecule**: If searching for an ion or salt, try\n    searching for the neutral parent compound.\n-   **Deconstruct complex formulas**: If a complex formula returns no results,\n    try searching for major components or ligands.\n-   **Use substructure or similarity search**: If you have a SMILES string or\n    can generate one for a component, use it to find related compounds.\n\n## Complex Queries and Multi-Step Tasks\n\n*   **Custom\u002FComplex Queries**: For more details, read\n    [references\u002Fendpoints.md](references\u002Fendpoints.md) to construct raw PUG-REST\n    URLs.\n*   **Multi-Step Tasks**: For complex tasks like drug discovery pipelines,\n    follow the checklists in [references\u002Fworkflows.md](references\u002Fworkflows.md).\n",{"data":34,"body":35},{"name":4,"description":6},{"type":36,"children":37},"root",[38,46,53,116,122,128,133,202,208,247,253,263,370,380,426,436,479,485,495,538,548,591,601,663,673,716,722,732,785,790,842,852,895,901,911,972,1056,1121,1131,1184,1190,1195,1228,1234,1270],{"type":39,"tag":40,"props":41,"children":42},"element","h1",{"id":4},[43],{"type":44,"value":45},"text","PubChem Database",{"type":39,"tag":47,"props":48,"children":50},"h2",{"id":49},"prerequisites",[51],{"type":44,"value":52},"Prerequisites",{"type":39,"tag":54,"props":55,"children":56},"ol",{},[57,88],{"type":39,"tag":58,"props":59,"children":60},"li",{},[61,72,74,79,81,86],{"type":39,"tag":62,"props":63,"children":64},"strong",{},[65],{"type":39,"tag":66,"props":67,"children":69},"code",{"className":68},[],[70],{"type":44,"value":71},"uv",{"type":44,"value":73},": Read the ",{"type":39,"tag":66,"props":75,"children":77},{"className":76},[],[78],{"type":44,"value":71},{"type":44,"value":80}," skill and follow its Setup instructions to ensure\n",{"type":39,"tag":66,"props":82,"children":84},{"className":83},[],[85],{"type":44,"value":71},{"type":44,"value":87}," is installed and on PATH.",{"type":39,"tag":58,"props":89,"children":90},{},[91,96,98,106,108,114],{"type":39,"tag":62,"props":92,"children":93},{},[94],{"type":44,"value":95},"User Notification",{"type":44,"value":97},": If .licenses\u002Fpubchem_database_LICENSE.txt does not\nalready exist in the workspace root directory then (1) prominently notify\nthe user to check the terms at\n",{"type":39,"tag":99,"props":100,"children":104},"a",{"href":101,"rel":102},"https:\u002F\u002Fpubchem.ncbi.nlm.nih.gov\u002Fdocs\u002Fcitation-guidelines",[103],"nofollow",[105],{"type":44,"value":101},{"type":44,"value":107}," and\n",{"type":39,"tag":99,"props":109,"children":112},{"href":110,"rel":111},"https:\u002F\u002Fpubchem.ncbi.nlm.nih.gov\u002Fdocs\u002Fpug-rest",[103],[113],{"type":44,"value":110},{"type":44,"value":115},", then (2) create the file\nrecording the notification text and timestamp.",{"type":39,"tag":47,"props":117,"children":119},{"id":118},"quick-start",[120],{"type":44,"value":121},"Quick Start",{"type":39,"tag":123,"props":124,"children":125},"p",{},[126],{"type":44,"value":127},"PubChem queries are executed via a robust Python wrapper script to respect\nterms-of-service and handle complex JSON parsing. This script allows safe\nmulti-agent use of APIs.",{"type":39,"tag":123,"props":129,"children":130},{},[131],{"type":44,"value":132},"Example: Resolve a chemical name to its Compound ID (CID)",{"type":39,"tag":134,"props":135,"children":140},"pre",{"className":136,"code":137,"language":138,"meta":139,"style":139},"language-bash shiki shiki-themes material-theme-lighter material-theme material-theme-palenight","uv run scripts\u002Fpubchem_api.py resolve --name \"aspirin\" --output result.json\n","bash","",[141],{"type":39,"tag":66,"props":142,"children":143},{"__ignoreMap":139},[144],{"type":39,"tag":145,"props":146,"children":149},"span",{"class":147,"line":148},"line",1,[150,155,161,166,171,176,182,187,192,197],{"type":39,"tag":145,"props":151,"children":153},{"style":152},"--shiki-light:#E2931D;--shiki-default:#FFCB6B;--shiki-dark:#FFCB6B",[154],{"type":44,"value":71},{"type":39,"tag":145,"props":156,"children":158},{"style":157},"--shiki-light:#91B859;--shiki-default:#C3E88D;--shiki-dark:#C3E88D",[159],{"type":44,"value":160}," run",{"type":39,"tag":145,"props":162,"children":163},{"style":157},[164],{"type":44,"value":165}," scripts\u002Fpubchem_api.py",{"type":39,"tag":145,"props":167,"children":168},{"style":157},[169],{"type":44,"value":170}," resolve",{"type":39,"tag":145,"props":172,"children":173},{"style":157},[174],{"type":44,"value":175}," --name",{"type":39,"tag":145,"props":177,"children":179},{"style":178},"--shiki-light:#39ADB5;--shiki-default:#89DDFF;--shiki-dark:#89DDFF",[180],{"type":44,"value":181}," \"",{"type":39,"tag":145,"props":183,"children":184},{"style":157},[185],{"type":44,"value":186},"aspirin",{"type":39,"tag":145,"props":188,"children":189},{"style":178},[190],{"type":44,"value":191},"\"",{"type":39,"tag":145,"props":193,"children":194},{"style":157},[195],{"type":44,"value":196}," --output",{"type":39,"tag":145,"props":198,"children":199},{"style":157},[200],{"type":44,"value":201}," result.json\n",{"type":39,"tag":47,"props":203,"children":205},{"id":204},"core-rules",[206],{"type":44,"value":207},"Core Rules",{"type":39,"tag":209,"props":210,"children":211},"ul",{},[212,222,227,237],{"type":39,"tag":58,"props":213,"children":214},{},[215,220],{"type":39,"tag":62,"props":216,"children":217},{},[218],{"type":44,"value":219},"Use the Wrapper",{"type":44,"value":221},": ALWAYS execute the provided helper scripts to query the\ndatabase rather than accessing the database directly. The scripts\nautomatically enforce the required rate limit gracefully.",{"type":39,"tag":58,"props":223,"children":224},{},[225],{"type":44,"value":226},"Read the generated JSON output file, and process it with jq or code.",{"type":39,"tag":58,"props":228,"children":229},{},[230,235],{"type":39,"tag":62,"props":231,"children":232},{},[233],{"type":44,"value":234},"Verify Facts",{"type":44,"value":236},": ALWAYS verify information retrieved from memory with a\ndatabase query if the user asks for a specific fact that can be checked in\nPubChem. Do not rely solely on internal knowledge.",{"type":39,"tag":58,"props":238,"children":239},{},[240,245],{"type":39,"tag":62,"props":241,"children":242},{},[243],{"type":44,"value":244},"Notification",{"type":44,"value":246},": If this skill is used, ensure this is mentioned in the\noutput.",{"type":39,"tag":47,"props":248,"children":250},{"id":249},"core-capabilities",[251],{"type":44,"value":252},"Core Capabilities",{"type":39,"tag":123,"props":254,"children":255},{},[256,261],{"type":39,"tag":62,"props":257,"children":258},{},[259],{"type":44,"value":260},"1. Compound Resolution (Name or InChI to Identifiers)",{"type":44,"value":262}," Convert chemical\u002Ftrade\nnames or InChI strings into PubChem CIDs, SMILES, and InChIKeys.",{"type":39,"tag":134,"props":264,"children":266},{"className":136,"code":265,"language":138,"meta":139,"style":139},"uv run scripts\u002Fpubchem_api.py resolve --name \"ibuprofen\" --output result.json\n# OR\nuv run scripts\u002Fpubchem_api.py resolve --inchi \"InChI=1S\u002FC3\u002Fc1-3-2\u002Fi1+1\" --output result.json\n",[267],{"type":39,"tag":66,"props":268,"children":269},{"__ignoreMap":139},[270,314,324],{"type":39,"tag":145,"props":271,"children":272},{"class":147,"line":148},[273,277,281,285,289,293,297,302,306,310],{"type":39,"tag":145,"props":274,"children":275},{"style":152},[276],{"type":44,"value":71},{"type":39,"tag":145,"props":278,"children":279},{"style":157},[280],{"type":44,"value":160},{"type":39,"tag":145,"props":282,"children":283},{"style":157},[284],{"type":44,"value":165},{"type":39,"tag":145,"props":286,"children":287},{"style":157},[288],{"type":44,"value":170},{"type":39,"tag":145,"props":290,"children":291},{"style":157},[292],{"type":44,"value":175},{"type":39,"tag":145,"props":294,"children":295},{"style":178},[296],{"type":44,"value":181},{"type":39,"tag":145,"props":298,"children":299},{"style":157},[300],{"type":44,"value":301},"ibuprofen",{"type":39,"tag":145,"props":303,"children":304},{"style":178},[305],{"type":44,"value":191},{"type":39,"tag":145,"props":307,"children":308},{"style":157},[309],{"type":44,"value":196},{"type":39,"tag":145,"props":311,"children":312},{"style":157},[313],{"type":44,"value":201},{"type":39,"tag":145,"props":315,"children":317},{"class":147,"line":316},2,[318],{"type":39,"tag":145,"props":319,"children":321},{"style":320},"--shiki-light:#90A4AE;--shiki-light-font-style:italic;--shiki-default:#546E7A;--shiki-default-font-style:italic;--shiki-dark:#676E95;--shiki-dark-font-style:italic",[322],{"type":44,"value":323},"# OR\n",{"type":39,"tag":145,"props":325,"children":327},{"class":147,"line":326},3,[328,332,336,340,344,349,353,358,362,366],{"type":39,"tag":145,"props":329,"children":330},{"style":152},[331],{"type":44,"value":71},{"type":39,"tag":145,"props":333,"children":334},{"style":157},[335],{"type":44,"value":160},{"type":39,"tag":145,"props":337,"children":338},{"style":157},[339],{"type":44,"value":165},{"type":39,"tag":145,"props":341,"children":342},{"style":157},[343],{"type":44,"value":170},{"type":39,"tag":145,"props":345,"children":346},{"style":157},[347],{"type":44,"value":348}," --inchi",{"type":39,"tag":145,"props":350,"children":351},{"style":178},[352],{"type":44,"value":181},{"type":39,"tag":145,"props":354,"children":355},{"style":157},[356],{"type":44,"value":357},"InChI=1S\u002FC3\u002Fc1-3-2\u002Fi1+1",{"type":39,"tag":145,"props":359,"children":360},{"style":178},[361],{"type":44,"value":191},{"type":39,"tag":145,"props":363,"children":364},{"style":157},[365],{"type":44,"value":196},{"type":39,"tag":145,"props":367,"children":368},{"style":157},[369],{"type":44,"value":201},{"type":39,"tag":123,"props":371,"children":372},{},[373,378],{"type":39,"tag":62,"props":374,"children":375},{},[376],{"type":44,"value":377},"2. Physical & Chemical Property Retrieval",{"type":44,"value":379}," Fetch computed properties (e.g.,\nMolecularWeight, XLogP, TPSA).",{"type":39,"tag":134,"props":381,"children":383},{"className":136,"code":382,"language":138,"meta":139,"style":139},"uv run scripts\u002Fpubchem_api.py properties --cid 2244 --output result.json\n",[384],{"type":39,"tag":66,"props":385,"children":386},{"__ignoreMap":139},[387],{"type":39,"tag":145,"props":388,"children":389},{"class":147,"line":148},[390,394,398,402,407,412,418,422],{"type":39,"tag":145,"props":391,"children":392},{"style":152},[393],{"type":44,"value":71},{"type":39,"tag":145,"props":395,"children":396},{"style":157},[397],{"type":44,"value":160},{"type":39,"tag":145,"props":399,"children":400},{"style":157},[401],{"type":44,"value":165},{"type":39,"tag":145,"props":403,"children":404},{"style":157},[405],{"type":44,"value":406}," properties",{"type":39,"tag":145,"props":408,"children":409},{"style":157},[410],{"type":44,"value":411}," --cid",{"type":39,"tag":145,"props":413,"children":415},{"style":414},"--shiki-light:#F76D47;--shiki-default:#F78C6C;--shiki-dark:#F78C6C",[416],{"type":44,"value":417}," 2244",{"type":39,"tag":145,"props":419,"children":420},{"style":157},[421],{"type":44,"value":196},{"type":39,"tag":145,"props":423,"children":424},{"style":157},[425],{"type":44,"value":201},{"type":39,"tag":123,"props":427,"children":428},{},[429,434],{"type":39,"tag":62,"props":430,"children":431},{},[432],{"type":44,"value":433},"3. Synonyms and Trade Names",{"type":44,"value":435}," Find alternative names and brand names.",{"type":39,"tag":134,"props":437,"children":439},{"className":136,"code":438,"language":138,"meta":139,"style":139},"uv run scripts\u002Fpubchem_api.py synonyms --cid 2244 --output result.json\n",[440],{"type":39,"tag":66,"props":441,"children":442},{"__ignoreMap":139},[443],{"type":39,"tag":145,"props":444,"children":445},{"class":147,"line":148},[446,450,454,458,463,467,471,475],{"type":39,"tag":145,"props":447,"children":448},{"style":152},[449],{"type":44,"value":71},{"type":39,"tag":145,"props":451,"children":452},{"style":157},[453],{"type":44,"value":160},{"type":39,"tag":145,"props":455,"children":456},{"style":157},[457],{"type":44,"value":165},{"type":39,"tag":145,"props":459,"children":460},{"style":157},[461],{"type":44,"value":462}," synonyms",{"type":39,"tag":145,"props":464,"children":465},{"style":157},[466],{"type":44,"value":411},{"type":39,"tag":145,"props":468,"children":469},{"style":414},[470],{"type":44,"value":417},{"type":39,"tag":145,"props":472,"children":473},{"style":157},[474],{"type":44,"value":196},{"type":39,"tag":145,"props":476,"children":477},{"style":157},[478],{"type":44,"value":201},{"type":39,"tag":47,"props":480,"children":482},{"id":481},"advanced-context",[483],{"type":44,"value":484},"Advanced Context",{"type":39,"tag":123,"props":486,"children":487},{},[488,493],{"type":39,"tag":62,"props":489,"children":490},{},[491],{"type":44,"value":492},"4. Safety and Hazard Information (GHS)",{"type":44,"value":494}," Retrieve Global Harmonized System\nhazard statements and handling precautions (uses PUG-View).",{"type":39,"tag":134,"props":496,"children":498},{"className":136,"code":497,"language":138,"meta":139,"style":139},"uv run scripts\u002Fpubchem_api.py safety --cid 2244 --output result.json\n",[499],{"type":39,"tag":66,"props":500,"children":501},{"__ignoreMap":139},[502],{"type":39,"tag":145,"props":503,"children":504},{"class":147,"line":148},[505,509,513,517,522,526,530,534],{"type":39,"tag":145,"props":506,"children":507},{"style":152},[508],{"type":44,"value":71},{"type":39,"tag":145,"props":510,"children":511},{"style":157},[512],{"type":44,"value":160},{"type":39,"tag":145,"props":514,"children":515},{"style":157},[516],{"type":44,"value":165},{"type":39,"tag":145,"props":518,"children":519},{"style":157},[520],{"type":44,"value":521}," safety",{"type":39,"tag":145,"props":523,"children":524},{"style":157},[525],{"type":44,"value":411},{"type":39,"tag":145,"props":527,"children":528},{"style":414},[529],{"type":44,"value":417},{"type":39,"tag":145,"props":531,"children":532},{"style":157},[533],{"type":44,"value":196},{"type":39,"tag":145,"props":535,"children":536},{"style":157},[537],{"type":44,"value":201},{"type":39,"tag":123,"props":539,"children":540},{},[541,546],{"type":39,"tag":62,"props":542,"children":543},{},[544],{"type":44,"value":545},"5. Drug and Medication Information",{"type":44,"value":547}," Fetch FDA pharmacology data, mechanism of\naction, and therapeutic uses (uses PUG-View).",{"type":39,"tag":134,"props":549,"children":551},{"className":136,"code":550,"language":138,"meta":139,"style":139},"uv run scripts\u002Fpubchem_api.py pharmacology --cid 2244 --output result.json\n",[552],{"type":39,"tag":66,"props":553,"children":554},{"__ignoreMap":139},[555],{"type":39,"tag":145,"props":556,"children":557},{"class":147,"line":148},[558,562,566,570,575,579,583,587],{"type":39,"tag":145,"props":559,"children":560},{"style":152},[561],{"type":44,"value":71},{"type":39,"tag":145,"props":563,"children":564},{"style":157},[565],{"type":44,"value":160},{"type":39,"tag":145,"props":567,"children":568},{"style":157},[569],{"type":44,"value":165},{"type":39,"tag":145,"props":571,"children":572},{"style":157},[573],{"type":44,"value":574}," pharmacology",{"type":39,"tag":145,"props":576,"children":577},{"style":157},[578],{"type":44,"value":411},{"type":39,"tag":145,"props":580,"children":581},{"style":414},[582],{"type":44,"value":417},{"type":39,"tag":145,"props":584,"children":585},{"style":157},[586],{"type":44,"value":196},{"type":39,"tag":145,"props":588,"children":589},{"style":157},[590],{"type":44,"value":201},{"type":39,"tag":123,"props":592,"children":593},{},[594,599],{"type":39,"tag":62,"props":595,"children":596},{},[597],{"type":44,"value":598},"6. Custom Heading (PUG-View)",{"type":44,"value":600}," Retrieve any specific heading from the PUG-View\nsystem (e.g., 'Geometry', 'Crystal Structures').",{"type":39,"tag":134,"props":602,"children":604},{"className":136,"code":603,"language":138,"meta":139,"style":139},"uv run scripts\u002Fpubchem_api.py view --cid 3939 --heading \"Crystal Structures\" --output result.json\n",[605],{"type":39,"tag":66,"props":606,"children":607},{"__ignoreMap":139},[608],{"type":39,"tag":145,"props":609,"children":610},{"class":147,"line":148},[611,615,619,623,628,632,637,642,646,651,655,659],{"type":39,"tag":145,"props":612,"children":613},{"style":152},[614],{"type":44,"value":71},{"type":39,"tag":145,"props":616,"children":617},{"style":157},[618],{"type":44,"value":160},{"type":39,"tag":145,"props":620,"children":621},{"style":157},[622],{"type":44,"value":165},{"type":39,"tag":145,"props":624,"children":625},{"style":157},[626],{"type":44,"value":627}," view",{"type":39,"tag":145,"props":629,"children":630},{"style":157},[631],{"type":44,"value":411},{"type":39,"tag":145,"props":633,"children":634},{"style":414},[635],{"type":44,"value":636}," 3939",{"type":39,"tag":145,"props":638,"children":639},{"style":157},[640],{"type":44,"value":641}," --heading",{"type":39,"tag":145,"props":643,"children":644},{"style":178},[645],{"type":44,"value":181},{"type":39,"tag":145,"props":647,"children":648},{"style":157},[649],{"type":44,"value":650},"Crystal Structures",{"type":39,"tag":145,"props":652,"children":653},{"style":178},[654],{"type":44,"value":191},{"type":39,"tag":145,"props":656,"children":657},{"style":157},[658],{"type":44,"value":196},{"type":39,"tag":145,"props":660,"children":661},{"style":157},[662],{"type":44,"value":201},{"type":39,"tag":123,"props":664,"children":665},{},[666,671],{"type":39,"tag":62,"props":667,"children":668},{},[669],{"type":44,"value":670},"7. Image Generation",{"type":44,"value":672}," Retrieve 2D chemical structure images. The script\nreturns a Markdown-formatted image link.",{"type":39,"tag":134,"props":674,"children":676},{"className":136,"code":675,"language":138,"meta":139,"style":139},"uv run scripts\u002Fpubchem_api.py image --cid 2244 --output result.json\n",[677],{"type":39,"tag":66,"props":678,"children":679},{"__ignoreMap":139},[680],{"type":39,"tag":145,"props":681,"children":682},{"class":147,"line":148},[683,687,691,695,700,704,708,712],{"type":39,"tag":145,"props":684,"children":685},{"style":152},[686],{"type":44,"value":71},{"type":39,"tag":145,"props":688,"children":689},{"style":157},[690],{"type":44,"value":160},{"type":39,"tag":145,"props":692,"children":693},{"style":157},[694],{"type":44,"value":165},{"type":39,"tag":145,"props":696,"children":697},{"style":157},[698],{"type":44,"value":699}," image",{"type":39,"tag":145,"props":701,"children":702},{"style":157},[703],{"type":44,"value":411},{"type":39,"tag":145,"props":705,"children":706},{"style":414},[707],{"type":44,"value":417},{"type":39,"tag":145,"props":709,"children":710},{"style":157},[711],{"type":44,"value":196},{"type":39,"tag":145,"props":713,"children":714},{"style":157},[715],{"type":44,"value":201},{"type":39,"tag":47,"props":717,"children":719},{"id":718},"complex-search-biology",[720],{"type":44,"value":721},"Complex Search & Biology",{"type":39,"tag":123,"props":723,"children":724},{},[725,730],{"type":39,"tag":62,"props":726,"children":727},{},[728],{"type":44,"value":729},"8. Structure-Based Searching (Similarity & Substructure)",{"type":44,"value":731}," Find molecules\nsimilar to a SMILES string or containing a specific substructure.",{"type":39,"tag":134,"props":733,"children":735},{"className":136,"code":734,"language":138,"meta":139,"style":139},"uv run scripts\u002Fpubchem_api.py similarity --smiles \"CC(=O)OC1=CC=CC=C1C(=O)O\" --output result.json\n",[736],{"type":39,"tag":66,"props":737,"children":738},{"__ignoreMap":139},[739],{"type":39,"tag":145,"props":740,"children":741},{"class":147,"line":148},[742,746,750,754,759,764,768,773,777,781],{"type":39,"tag":145,"props":743,"children":744},{"style":152},[745],{"type":44,"value":71},{"type":39,"tag":145,"props":747,"children":748},{"style":157},[749],{"type":44,"value":160},{"type":39,"tag":145,"props":751,"children":752},{"style":157},[753],{"type":44,"value":165},{"type":39,"tag":145,"props":755,"children":756},{"style":157},[757],{"type":44,"value":758}," similarity",{"type":39,"tag":145,"props":760,"children":761},{"style":157},[762],{"type":44,"value":763}," --smiles",{"type":39,"tag":145,"props":765,"children":766},{"style":178},[767],{"type":44,"value":181},{"type":39,"tag":145,"props":769,"children":770},{"style":157},[771],{"type":44,"value":772},"CC(=O)OC1=CC=CC=C1C(=O)O",{"type":39,"tag":145,"props":774,"children":775},{"style":178},[776],{"type":44,"value":191},{"type":39,"tag":145,"props":778,"children":779},{"style":157},[780],{"type":44,"value":196},{"type":39,"tag":145,"props":782,"children":783},{"style":157},[784],{"type":44,"value":201},{"type":39,"tag":123,"props":786,"children":787},{},[788],{"type":44,"value":789},"and",{"type":39,"tag":134,"props":791,"children":793},{"className":136,"code":792,"language":138,"meta":139,"style":139},"uv run scripts\u002Fpubchem_api.py substructure --smiles \"C1=CC=CC=C1\" --output result.json\n",[794],{"type":39,"tag":66,"props":795,"children":796},{"__ignoreMap":139},[797],{"type":39,"tag":145,"props":798,"children":799},{"class":147,"line":148},[800,804,808,812,817,821,825,830,834,838],{"type":39,"tag":145,"props":801,"children":802},{"style":152},[803],{"type":44,"value":71},{"type":39,"tag":145,"props":805,"children":806},{"style":157},[807],{"type":44,"value":160},{"type":39,"tag":145,"props":809,"children":810},{"style":157},[811],{"type":44,"value":165},{"type":39,"tag":145,"props":813,"children":814},{"style":157},[815],{"type":44,"value":816}," substructure",{"type":39,"tag":145,"props":818,"children":819},{"style":157},[820],{"type":44,"value":763},{"type":39,"tag":145,"props":822,"children":823},{"style":178},[824],{"type":44,"value":181},{"type":39,"tag":145,"props":826,"children":827},{"style":157},[828],{"type":44,"value":829},"C1=CC=CC=C1",{"type":39,"tag":145,"props":831,"children":832},{"style":178},[833],{"type":44,"value":191},{"type":39,"tag":145,"props":835,"children":836},{"style":157},[837],{"type":44,"value":196},{"type":39,"tag":145,"props":839,"children":840},{"style":157},[841],{"type":44,"value":201},{"type":39,"tag":123,"props":843,"children":844},{},[845,850],{"type":39,"tag":62,"props":846,"children":847},{},[848],{"type":44,"value":849},"9. BioAssay & Target Interactions",{"type":44,"value":851}," Identify genes or proteins a chemical\ninteracts with.",{"type":39,"tag":134,"props":853,"children":855},{"className":136,"code":854,"language":138,"meta":139,"style":139},"uv run scripts\u002Fpubchem_api.py assays --cid 2244 --output result.json\n",[856],{"type":39,"tag":66,"props":857,"children":858},{"__ignoreMap":139},[859],{"type":39,"tag":145,"props":860,"children":861},{"class":147,"line":148},[862,866,870,874,879,883,887,891],{"type":39,"tag":145,"props":863,"children":864},{"style":152},[865],{"type":44,"value":71},{"type":39,"tag":145,"props":867,"children":868},{"style":157},[869],{"type":44,"value":160},{"type":39,"tag":145,"props":871,"children":872},{"style":157},[873],{"type":44,"value":165},{"type":39,"tag":145,"props":875,"children":876},{"style":157},[877],{"type":44,"value":878}," assays",{"type":39,"tag":145,"props":880,"children":881},{"style":157},[882],{"type":44,"value":411},{"type":39,"tag":145,"props":884,"children":885},{"style":414},[886],{"type":44,"value":417},{"type":39,"tag":145,"props":888,"children":889},{"style":157},[890],{"type":44,"value":196},{"type":39,"tag":145,"props":892,"children":893},{"style":157},[894],{"type":44,"value":201},{"type":39,"tag":47,"props":896,"children":898},{"id":897},"advanced-usage-workflows",[899],{"type":44,"value":900},"Advanced Usage & Workflows",{"type":39,"tag":123,"props":902,"children":903},{},[904,909],{"type":39,"tag":62,"props":905,"children":906},{},[907],{"type":44,"value":908},"10. Cross-references (Xrefs)",{"type":44,"value":910}," Fetch identifiers cross-referenced with a CID\n(e.g., PatentID, PubMedID).",{"type":39,"tag":134,"props":912,"children":914},{"className":136,"code":913,"language":138,"meta":139,"style":139},"uv run scripts\u002Fpubchem_api.py xrefs --cid 2244 --type \"PatentID\" --output result.json\n",[915],{"type":39,"tag":66,"props":916,"children":917},{"__ignoreMap":139},[918],{"type":39,"tag":145,"props":919,"children":920},{"class":147,"line":148},[921,925,929,933,938,942,946,951,955,960,964,968],{"type":39,"tag":145,"props":922,"children":923},{"style":152},[924],{"type":44,"value":71},{"type":39,"tag":145,"props":926,"children":927},{"style":157},[928],{"type":44,"value":160},{"type":39,"tag":145,"props":930,"children":931},{"style":157},[932],{"type":44,"value":165},{"type":39,"tag":145,"props":934,"children":935},{"style":157},[936],{"type":44,"value":937}," xrefs",{"type":39,"tag":145,"props":939,"children":940},{"style":157},[941],{"type":44,"value":411},{"type":39,"tag":145,"props":943,"children":944},{"style":414},[945],{"type":44,"value":417},{"type":39,"tag":145,"props":947,"children":948},{"style":157},[949],{"type":44,"value":950}," --type",{"type":39,"tag":145,"props":952,"children":953},{"style":178},[954],{"type":44,"value":181},{"type":39,"tag":145,"props":956,"children":957},{"style":157},[958],{"type":44,"value":959},"PatentID",{"type":39,"tag":145,"props":961,"children":962},{"style":178},[963],{"type":44,"value":191},{"type":39,"tag":145,"props":965,"children":966},{"style":157},[967],{"type":44,"value":196},{"type":39,"tag":145,"props":969,"children":970},{"style":157},[971],{"type":44,"value":201},{"type":39,"tag":123,"props":973,"children":974},{},[975,980,982,988,990,996,997,1003,1005,1011,1012,1018,1019,1025,1026,1032,1033,1039,1040,1046,1048,1054],{"type":39,"tag":62,"props":976,"children":977},{},[978],{"type":44,"value":979},"11. Property Range Search",{"type":44,"value":981}," Find CIDs within a specific property range.\nSupported features include: ",{"type":39,"tag":66,"props":983,"children":985},{"className":984},[],[986],{"type":44,"value":987},"molecular_weight",{"type":44,"value":989},", ",{"type":39,"tag":66,"props":991,"children":993},{"className":992},[],[994],{"type":44,"value":995},"heavy_atom_count",{"type":44,"value":989},{"type":39,"tag":66,"props":998,"children":1000},{"className":999},[],[1001],{"type":44,"value":1002},"xlogp",{"type":44,"value":1004},",\n",{"type":39,"tag":66,"props":1006,"children":1008},{"className":1007},[],[1009],{"type":44,"value":1010},"tpsa",{"type":44,"value":989},{"type":39,"tag":66,"props":1013,"children":1015},{"className":1014},[],[1016],{"type":44,"value":1017},"h_bond_donor_count",{"type":44,"value":989},{"type":39,"tag":66,"props":1020,"children":1022},{"className":1021},[],[1023],{"type":44,"value":1024},"h_bond_acceptor_count",{"type":44,"value":989},{"type":39,"tag":66,"props":1027,"children":1029},{"className":1028},[],[1030],{"type":44,"value":1031},"rotatable_bond_count",{"type":44,"value":1004},{"type":39,"tag":66,"props":1034,"children":1036},{"className":1035},[],[1037],{"type":44,"value":1038},"exact_mass",{"type":44,"value":989},{"type":39,"tag":66,"props":1041,"children":1043},{"className":1042},[],[1044],{"type":44,"value":1045},"monoisotopic_mass",{"type":44,"value":1047},", and ",{"type":39,"tag":66,"props":1049,"children":1051},{"className":1050},[],[1052],{"type":44,"value":1053},"complexity",{"type":44,"value":1055},".",{"type":39,"tag":134,"props":1057,"children":1059},{"className":136,"code":1058,"language":138,"meta":139,"style":139},"uv run scripts\u002Fpubchem_api.py range --feature molecular_weight --min 400.0 --max 400.05 --output result.json\n",[1060],{"type":39,"tag":66,"props":1061,"children":1062},{"__ignoreMap":139},[1063],{"type":39,"tag":145,"props":1064,"children":1065},{"class":147,"line":148},[1066,1070,1074,1078,1083,1088,1093,1098,1103,1108,1113,1117],{"type":39,"tag":145,"props":1067,"children":1068},{"style":152},[1069],{"type":44,"value":71},{"type":39,"tag":145,"props":1071,"children":1072},{"style":157},[1073],{"type":44,"value":160},{"type":39,"tag":145,"props":1075,"children":1076},{"style":157},[1077],{"type":44,"value":165},{"type":39,"tag":145,"props":1079,"children":1080},{"style":157},[1081],{"type":44,"value":1082}," range",{"type":39,"tag":145,"props":1084,"children":1085},{"style":157},[1086],{"type":44,"value":1087}," --feature",{"type":39,"tag":145,"props":1089,"children":1090},{"style":157},[1091],{"type":44,"value":1092}," molecular_weight",{"type":39,"tag":145,"props":1094,"children":1095},{"style":157},[1096],{"type":44,"value":1097}," --min",{"type":39,"tag":145,"props":1099,"children":1100},{"style":414},[1101],{"type":44,"value":1102}," 400.0",{"type":39,"tag":145,"props":1104,"children":1105},{"style":157},[1106],{"type":44,"value":1107}," --max",{"type":39,"tag":145,"props":1109,"children":1110},{"style":414},[1111],{"type":44,"value":1112}," 400.05",{"type":39,"tag":145,"props":1114,"children":1115},{"style":157},[1116],{"type":44,"value":196},{"type":39,"tag":145,"props":1118,"children":1119},{"style":157},[1120],{"type":44,"value":201},{"type":39,"tag":123,"props":1122,"children":1123},{},[1124,1129],{"type":39,"tag":62,"props":1125,"children":1126},{},[1127],{"type":44,"value":1128},"12. Custom PUG-REST Query",{"type":44,"value":1130}," Execute a raw path against the PUG-REST API.",{"type":39,"tag":134,"props":1132,"children":1134},{"className":136,"code":1133,"language":138,"meta":139,"style":139},"uv run scripts\u002Fpubchem_api.py query --path \"compound\u002Fcid\u002F2244\u002Fxrefs\u002FPatentID\u002FJSON\" --output result.json\n",[1135],{"type":39,"tag":66,"props":1136,"children":1137},{"__ignoreMap":139},[1138],{"type":39,"tag":145,"props":1139,"children":1140},{"class":147,"line":148},[1141,1145,1149,1153,1158,1163,1167,1172,1176,1180],{"type":39,"tag":145,"props":1142,"children":1143},{"style":152},[1144],{"type":44,"value":71},{"type":39,"tag":145,"props":1146,"children":1147},{"style":157},[1148],{"type":44,"value":160},{"type":39,"tag":145,"props":1150,"children":1151},{"style":157},[1152],{"type":44,"value":165},{"type":39,"tag":145,"props":1154,"children":1155},{"style":157},[1156],{"type":44,"value":1157}," query",{"type":39,"tag":145,"props":1159,"children":1160},{"style":157},[1161],{"type":44,"value":1162}," --path",{"type":39,"tag":145,"props":1164,"children":1165},{"style":178},[1166],{"type":44,"value":181},{"type":39,"tag":145,"props":1168,"children":1169},{"style":157},[1170],{"type":44,"value":1171},"compound\u002Fcid\u002F2244\u002Fxrefs\u002FPatentID\u002FJSON",{"type":39,"tag":145,"props":1173,"children":1174},{"style":178},[1175],{"type":44,"value":191},{"type":39,"tag":145,"props":1177,"children":1178},{"style":157},[1179],{"type":44,"value":196},{"type":39,"tag":145,"props":1181,"children":1182},{"style":157},[1183],{"type":44,"value":201},{"type":39,"tag":47,"props":1185,"children":1187},{"id":1186},"fallback-search-strategies",[1188],{"type":44,"value":1189},"Fallback Search Strategies",{"type":39,"tag":123,"props":1191,"children":1192},{},[1193],{"type":44,"value":1194},"If direct resolution by name or formula fails (e.g., for complex compounds or\nspecific ions):",{"type":39,"tag":209,"props":1196,"children":1197},{},[1198,1208,1218],{"type":39,"tag":58,"props":1199,"children":1200},{},[1201,1206],{"type":39,"tag":62,"props":1202,"children":1203},{},[1204],{"type":44,"value":1205},"Search for parent\u002Fneutral molecule",{"type":44,"value":1207},": If searching for an ion or salt, try\nsearching for the neutral parent compound.",{"type":39,"tag":58,"props":1209,"children":1210},{},[1211,1216],{"type":39,"tag":62,"props":1212,"children":1213},{},[1214],{"type":44,"value":1215},"Deconstruct complex formulas",{"type":44,"value":1217},": If a complex formula returns no results,\ntry searching for major components or ligands.",{"type":39,"tag":58,"props":1219,"children":1220},{},[1221,1226],{"type":39,"tag":62,"props":1222,"children":1223},{},[1224],{"type":44,"value":1225},"Use substructure or similarity search",{"type":44,"value":1227},": If you have a SMILES string or\ncan generate one for a component, use it to find related compounds.",{"type":39,"tag":47,"props":1229,"children":1231},{"id":1230},"complex-queries-and-multi-step-tasks",[1232],{"type":44,"value":1233},"Complex Queries and Multi-Step Tasks",{"type":39,"tag":209,"props":1235,"children":1236},{},[1237,1254],{"type":39,"tag":58,"props":1238,"children":1239},{},[1240,1245,1247,1252],{"type":39,"tag":62,"props":1241,"children":1242},{},[1243],{"type":44,"value":1244},"Custom\u002FComplex Queries",{"type":44,"value":1246},": For more details, read\n",{"type":39,"tag":99,"props":1248,"children":1250},{"href":1249},"references\u002Fendpoints.md",[1251],{"type":44,"value":1249},{"type":44,"value":1253}," to construct raw PUG-REST\nURLs.",{"type":39,"tag":58,"props":1255,"children":1256},{},[1257,1262,1264,1269],{"type":39,"tag":62,"props":1258,"children":1259},{},[1260],{"type":44,"value":1261},"Multi-Step Tasks",{"type":44,"value":1263},": For complex tasks like drug discovery pipelines,\nfollow the checklists in ",{"type":39,"tag":99,"props":1265,"children":1267},{"href":1266},"references\u002Fworkflows.md",[1268],{"type":44,"value":1266},{"type":44,"value":1055},{"type":39,"tag":1271,"props":1272,"children":1273},"style",{},[1274],{"type":44,"value":1275},"html .light .shiki span {color: var(--shiki-light);background: var(--shiki-light-bg);font-style: var(--shiki-light-font-style);font-weight: var(--shiki-light-font-weight);text-decoration: var(--shiki-light-text-decoration);}html.light .shiki span {color: var(--shiki-light);background: var(--shiki-light-bg);font-style: var(--shiki-light-font-style);font-weight: var(--shiki-light-font-weight);text-decoration: var(--shiki-light-text-decoration);}html .default .shiki span {color: var(--shiki-default);background: var(--shiki-default-bg);font-style: var(--shiki-default-font-style);font-weight: var(--shiki-default-font-weight);text-decoration: var(--shiki-default-text-decoration);}html .shiki span {color: var(--shiki-default);background: var(--shiki-default-bg);font-style: var(--shiki-default-font-style);font-weight: var(--shiki-default-font-weight);text-decoration: var(--shiki-default-text-decoration);}html .dark .shiki span {color: var(--shiki-dark);background: var(--shiki-dark-bg);font-style: var(--shiki-dark-font-style);font-weight: var(--shiki-dark-font-weight);text-decoration: var(--shiki-dark-text-decoration);}html.dark .shiki span {color: var(--shiki-dark);background: var(--shiki-dark-bg);font-style: var(--shiki-dark-font-style);font-weight: var(--shiki-dark-font-weight);text-decoration: var(--shiki-dark-text-decoration);}",{"items":1277,"total":1382},[1278,1293,1308,1326,1338,1353,1369],{"slug":1279,"name":1279,"fn":1280,"description":1281,"org":1282,"tags":1283,"stars":22,"repoUrl":23,"updatedAt":1292},"alphafold-database-fetch-and-analyze","retrieve and analyze AlphaFold protein structures","Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid sequence — ask for a UniProt ID first.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1284,1285,1288,1291],{"name":17,"slug":18,"type":15},{"name":1286,"slug":1287,"type":15},"Genomics","genomics",{"name":1289,"slug":1290,"type":15},"Life Sciences","life-sciences",{"name":13,"slug":14,"type":15},"2026-07-12T07:51:51.827211",{"slug":1294,"name":1294,"fn":1295,"description":1296,"org":1297,"tags":1298,"stars":22,"repoUrl":23,"updatedAt":1307},"alphagenome-single-variant-analysis","analyze genetic variant effects with AlphaGenome","Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about non-coding variant effects, pathogenicity, clinical significance, disease associations, functional effects, gene expression changes, splicing disruption, or regulatory effects in promoters and enhancers. Also use for resolving biological terms to tissue\u002Fcell-type ontologies (UBERON\u002FCL) or analyzing variants in chr:pos:ref>alt format.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1299,1300,1303,1304],{"name":17,"slug":18,"type":15},{"name":1301,"slug":1302,"type":15},"Genetics","genetics",{"name":13,"slug":14,"type":15},{"name":1305,"slug":1306,"type":15},"RNA-seq","rna-seq","2026-07-12T07:51:39.494803",{"slug":1309,"name":1309,"fn":1310,"description":1311,"org":1312,"tags":1313,"stars":22,"repoUrl":23,"updatedAt":1325},"chembl-database","query ChEMBL database for bioactive molecules","Query the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures. Use when the user asks about compounds, targets, IC50\u002FKi values, drug mechanisms, or structure searches.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1314,1317,1318,1321,1324],{"name":1315,"slug":1316,"type":15},"ChEMBL","chembl",{"name":20,"slug":21,"type":15},{"name":1319,"slug":1320,"type":15},"Database","database",{"name":1322,"slug":1323,"type":15},"Pharmacology","pharmacology",{"name":13,"slug":14,"type":15},"2026-07-12T07:51:35.544306",{"slug":1327,"name":1327,"fn":1328,"description":1329,"org":1330,"tags":1331,"stars":22,"repoUrl":23,"updatedAt":1337},"clinical-trials-database","query clinical trial data","Query ClinicalTrials.gov via APIv2. Use when you want to search for trials by condition, drug, location, status, or phase; retrieve trial details by NCT ID; check eligibility\u002Finclusion criteria; count trials across conditions or time periods; identify a sponsor's trial portfolio; find recruiting trials for patient matching.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1332,1335,1336],{"name":1333,"slug":1334,"type":15},"Clinical Trials","clinical-trials",{"name":1289,"slug":1290,"type":15},{"name":13,"slug":14,"type":15},"2026-07-12T07:52:06.846705",{"slug":1339,"name":1339,"fn":1340,"description":1341,"org":1342,"tags":1343,"stars":22,"repoUrl":23,"updatedAt":1352},"clinvar-database","retrieve clinical significance from ClinVar database","Use when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding \"hard positive\" benchmark controls for human genomic variants.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1344,1347,1348,1351],{"name":1345,"slug":1346,"type":15},"ClinVar","clinvar",{"name":1301,"slug":1302,"type":15},{"name":1349,"slug":1350,"type":15},"Healthcare","healthcare",{"name":13,"slug":14,"type":15},"2026-07-12T07:51:36.86094",{"slug":1354,"name":1354,"fn":1355,"description":1356,"org":1357,"tags":1358,"stars":22,"repoUrl":23,"updatedAt":1368},"credentials","manage and verify API credentials safely","Instructions for handling API keys and credentials safely, verifying their presence, and prompting the user to add them if missing using a safe protocol.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1359,1362,1365],{"name":1360,"slug":1361,"type":15},"Compliance","compliance",{"name":1363,"slug":1364,"type":15},"Operations","operations",{"name":1366,"slug":1367,"type":15},"Security","security","2026-07-12T07:52:17.355491",{"slug":1370,"name":1370,"fn":1371,"description":1372,"org":1373,"tags":1374,"stars":22,"repoUrl":23,"updatedAt":1381},"dbsnp-database","search genetic variants in dbSNP database","Use when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database. Resolves between rsIDs, genomic coordinates in VCF format, and HGVS strings. For an rsID, returns variant type, gene associations, clinical significance, allele frequencies, and genomic coordinates (GRCh38).\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1375,1376,1377,1380],{"name":17,"slug":18,"type":15},{"name":1301,"slug":1302,"type":15},{"name":1378,"slug":1379,"type":15},"NCBI","ncbi",{"name":13,"slug":14,"type":15},"2026-07-12T07:51:33.054229",38,{"items":1384,"total":1382},[1385,1392,1399,1407,1413,1420,1426,1433,1445,1460,1471,1481],{"slug":1279,"name":1279,"fn":1280,"description":1281,"org":1386,"tags":1387,"stars":22,"repoUrl":23,"updatedAt":1292},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1388,1389,1390,1391],{"name":17,"slug":18,"type":15},{"name":1286,"slug":1287,"type":15},{"name":1289,"slug":1290,"type":15},{"name":13,"slug":14,"type":15},{"slug":1294,"name":1294,"fn":1295,"description":1296,"org":1393,"tags":1394,"stars":22,"repoUrl":23,"updatedAt":1307},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1395,1396,1397,1398],{"name":17,"slug":18,"type":15},{"name":1301,"slug":1302,"type":15},{"name":13,"slug":14,"type":15},{"name":1305,"slug":1306,"type":15},{"slug":1309,"name":1309,"fn":1310,"description":1311,"org":1400,"tags":1401,"stars":22,"repoUrl":23,"updatedAt":1325},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1402,1403,1404,1405,1406],{"name":1315,"slug":1316,"type":15},{"name":20,"slug":21,"type":15},{"name":1319,"slug":1320,"type":15},{"name":1322,"slug":1323,"type":15},{"name":13,"slug":14,"type":15},{"slug":1327,"name":1327,"fn":1328,"description":1329,"org":1408,"tags":1409,"stars":22,"repoUrl":23,"updatedAt":1337},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1410,1411,1412],{"name":1333,"slug":1334,"type":15},{"name":1289,"slug":1290,"type":15},{"name":13,"slug":14,"type":15},{"slug":1339,"name":1339,"fn":1340,"description":1341,"org":1414,"tags":1415,"stars":22,"repoUrl":23,"updatedAt":1352},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1416,1417,1418,1419],{"name":1345,"slug":1346,"type":15},{"name":1301,"slug":1302,"type":15},{"name":1349,"slug":1350,"type":15},{"name":13,"slug":14,"type":15},{"slug":1354,"name":1354,"fn":1355,"description":1356,"org":1421,"tags":1422,"stars":22,"repoUrl":23,"updatedAt":1368},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1423,1424,1425],{"name":1360,"slug":1361,"type":15},{"name":1363,"slug":1364,"type":15},{"name":1366,"slug":1367,"type":15},{"slug":1370,"name":1370,"fn":1371,"description":1372,"org":1427,"tags":1428,"stars":22,"repoUrl":23,"updatedAt":1381},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1429,1430,1431,1432],{"name":17,"slug":18,"type":15},{"name":1301,"slug":1302,"type":15},{"name":1378,"slug":1379,"type":15},{"name":13,"slug":14,"type":15},{"slug":1434,"name":1434,"fn":1435,"description":1436,"org":1437,"tags":1438,"stars":22,"repoUrl":23,"updatedAt":1444},"embl-ebi-ols","search biomedical ontologies in EMBL-EBI OLS","Query and search the EMBL-EBI Ontology Lookup Service (OLS) for biomedical ontology terms, definitions, and hierarchies across 250+ ontologies (e.g., GO, DOID, HP). Use when the user asks to search for terms, retrieve details, navigate hierarchies (parents, children, ancestors), look up properties and individuals, get autocomplete suggestions, or access ontology metadata and statistics.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1439,1440,1443],{"name":17,"slug":18,"type":15},{"name":1441,"slug":1442,"type":15},"Ontology","ontology",{"name":13,"slug":14,"type":15},"2026-07-12T07:51:59.368324",{"slug":1446,"name":1446,"fn":1447,"description":1448,"org":1449,"tags":1450,"stars":22,"repoUrl":23,"updatedAt":1459},"encode-ccres-database","query ENCODE regulatory and experimental data","Query the ENCODE Registry of cis-Regulatory Elements (cCREs) via the SCREEN GraphQL API, or make custom queries to the ENCODE Portal REST API for experiments and files (ChIP-seq peaks, etc.). Use when you want to query regulatory annotations or raw experimental data across human cell types.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1451,1452,1455,1456],{"name":17,"slug":18,"type":15},{"name":1453,"slug":1454,"type":15},"GraphQL","graphql",{"name":13,"slug":14,"type":15},{"name":1457,"slug":1458,"type":15},"REST API","rest-api","2026-07-12T07:52:10.597139",{"slug":1461,"name":1461,"fn":1462,"description":1463,"org":1464,"tags":1465,"stars":22,"repoUrl":23,"updatedAt":1470},"ensembl-database","query genomic and protein data from Ensembl","Query the Ensembl database to resolve gene, transcript, and protein IDs, fetch genomic or protein sequences, retrieve gene structures (exons), and get variant consequence and effect predictions (VEP). Use this skill as a primary ID translator, genomic sequence database and variant effect prediction tool.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1466,1467,1468,1469],{"name":17,"slug":18,"type":15},{"name":1301,"slug":1302,"type":15},{"name":1289,"slug":1290,"type":15},{"name":13,"slug":14,"type":15},"2026-07-12T07:51:41.645835",{"slug":1472,"name":1472,"fn":1473,"description":1474,"org":1475,"tags":1476,"stars":22,"repoUrl":23,"updatedAt":1480},"foldseek-structural-search","perform 3D protein structural searches","Performs 3D structural searches of proteins against various databases (PDB, AlphaFold, CATH, MGnify, etc.) using the Foldseek API. Use ONLY when the user provides a physical 3D coordinate file (.cif, .mmcif, or .pdb) and wants to find structurally similar proteins. Do NOT use if the user only provides a protein sequence, gene name, or UniProt ID.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1477,1478,1479],{"name":17,"slug":18,"type":15},{"name":1289,"slug":1290,"type":15},{"name":13,"slug":14,"type":15},"2026-07-12T07:52:09.354992",{"slug":1482,"name":1482,"fn":1483,"description":1484,"org":1485,"tags":1486,"stars":22,"repoUrl":23,"updatedAt":1491},"gnomad-database","query genetic variant data from gnomAD","Query the Genome Aggregation Database (gnomAD). Use when determining the rarity or allele frequency of specific genetic variants, retrieving gene constraint metrics (pLI, LOEUF) to assess loss-of-function intolerance, finding variants in a genomic region or gene, or querying structural variants. Don't use for analyzing individual patient genomes, tracking somatic mutations in cancer (use COSMIC), or requesting raw sequencing reads (use ENA).\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1487,1488,1489,1490],{"name":17,"slug":18,"type":15},{"name":1301,"slug":1302,"type":15},{"name":1289,"slug":1290,"type":15},{"name":13,"slug":14,"type":15},"2026-07-12T07:51:38.213009"]