[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill-google-deepmind-clinical-trials-database":3,"mdc--da6f66-key":33,"related-repo-google-deepmind-clinical-trials-database":3830,"related-org-google-deepmind-clinical-trials-database":3933},{"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},"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},"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},"Clinical Trials","clinical-trials",{"name":20,"slug":21,"type":15},"Life Sciences","life-sciences",2333,"https:\u002F\u002Fgithub.com\u002Fgoogle-deepmind\u002Fscience-skills","2026-07-12T07:52:06.846705",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\u002Fclinical_trials_database","---\nname: clinical-trials-database\ndescription: >\n  Query ClinicalTrials.gov via APIv2. Use when you want to search for trials by\n  condition, drug, location, status, or phase; retrieve trial details by NCT ID;\n  check eligibility\u002Finclusion criteria; count trials across conditions or time\n  periods; identify a sponsor's trial portfolio; find recruiting trials for\n  patient matching.\n---\n\n# Clinical Trials 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\u002Fclinical_trials_database_LICENSE.txt\n    does not already exist in the workspace root directory then (1) prominently\n    notify the user to check the terms at https:\u002F\u002Fclinicaltrials.gov\u002F, then (2)\n    create the file recording the notification text and timestamp.\n\n## Overview\n\nAccess worldwide clinical trial data from ClinicalTrials.gov via the REST API\nv2. The CLI script at `scripts\u002Fclinical_trials_api.py` wraps the API with\ndedicated flags for common filters (phase, age group, status, intervention,\nsponsor, etc.) so you rarely need to construct raw queries.\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-   **Always use `--fields`** — trial JSON records can be very large; restrict\n    to the data points you need.\n-   **Use `--count-total` first** — check result volume before fetching all\n    records.\n-   **Paginate large result sets** — use `--limit` with `--page-token` to\n    iterate.\n-   **Trust Search Filters**: Do not manually re-filter results unless\n    explicitly asked to verify detailed eligibility.\n-   **Notification**: If this skill is used, ensure this is mentioned in the\n    output.\n\n## Context Efficiency Warning\n\nTrial JSON records can be very large. **Always** use the `--fields` parameter to\nrestrict the response to only the data points you need. After writing to file,\nread only the fields you need rather than the entire file.\n\n> [!TIP] Use `references\u002Fstudies_schema.md` to identify exact field paths for\n> `--fields`.\n\n## Response Layout Summary\n\nAPI responses contain a list of studies (usually in a `studies[]` array). Each\nstudy is split into `protocolSection` and optional `resultsSection`.\n\n> [!Tip] Use the **shorthand aliases** below with the `--fields` parameter to\n> request specific data and keep responses small.\n\n### Top-Level Fields\n\n-   `totalCount` — Total studies matching query (integer)\n-   `studies[]` — Array of study objects\n-   `nextPageToken` — cursor string for pagination\n\n### Common Study Fields (and shorthand alias)\n\n-   **Identification**\n    -   `protocolSection.identificationModule.nctId` (`NCTId`) — Unique trial ID\n    -   `protocolSection.identificationModule.briefTitle` (`BriefTitle`) — Short\n        title\n-   **Status**\n    -   `protocolSection.statusModule.overallStatus` (`OverallStatus`) —\n        Recruitment status\n-   **Description**\n    -   `protocolSection.descriptionModule.briefSummary` (`BriefSummary`) —\n        Short description\n-   **Arms & Interventions**\n    -   `protocolSection.armsInterventionsModule.interventions`\n        (`ArmsInterventionsModule`)\n-   **Eligibility**\n    -   `protocolSection.eligibilityModule.eligibilityCriteria`\n        (`EligibilityCriteria`) — Inclusion\u002FExclusion\n    -   `protocolSection.eligibilityModule.stdAges` (`StdAge`) — CHILD, ADULT,\n        etc.\n\nConsult `references\u002Fstudies_schema.md` for full paths (Locations, Outcomes,\nResults) and common `--fields` recipes.\n\n## Commands\n\n### Search for studies\n\nUse for: finding trials by disease, drug, phase, status, age group, or any\ncombination of these filters.\n\n```bash\nuv run scripts\u002Fclinical_trials_api.py search \\\n  --condition \"\u003Cdisease>\" \\\n  --intervention \"\u003Cdrug_or_treatment>\" \\\n  --status \"\u003Cstatus>\" \\\n  --phase \"\u003Cphase>\" \\\n  --age-group \"\u003Cage_group>\" \\\n  --study-type \"\u003Cstudy_type>\" \\\n  --sponsor \"\u003Csponsor_name>\" \\\n  --has-results \\\n  --sort \"\u003Cfield>:\u003Casc|desc>\" \\\n  --fields \"\u003Cfields>\" \\\n  --limit \u003CN> \\\n  --count-total \\\n  --page-token \"\u003Ctoken>\" \\\n  --output \u002Ftmp\u002Fsearch_results.json\n```\n\nAll flags are optional and combine via AND logic.\n\n**Flag reference:**\n\n-   `--condition` — Disease or condition to search for (e.g. `\"cystic\n    fibrosis\"`).\n-   `--intervention` — Drug, device, or treatment name (e.g. `\"pembrolizumab\"`).\n-   `--status` — Recruitment status filter. Values: RECRUITING, COMPLETED,\n    NOT_YET_RECRUITING, ACTIVE_NOT_RECRUITING, ENROLLING_BY_INVITATION,\n    TERMINATED, SUSPENDED, WITHDRAWN.\n-   `--phase` — Trial phase filter. Values: PHASE1, PHASE2, PHASE3, PHASE4,\n    EARLY_PHASE1, NA.\n-   `--age-group` — Patient age group filter. Values: CHILD (0–17), ADULT\n    (18–64), OLDER_ADULT (65+).\n-   `--study-type` — Type of study. Values: INTERVENTIONAL, OBSERVATIONAL,\n    EXPANDED_ACCESS.\n-   `--sponsor` — Lead sponsor or institution name (e.g. `\"National Cancer\n    Institute\"`).\n-   `--has-results` — Boolean flag (no value needed). When present, filters for\n    studies that have results available on ClinicalTrials.gov.\n-   `--sort` — Sort order as `FieldName:asc` or `FieldName:desc`. Common fields:\n    `LastUpdatePostDate`, `EnrollmentCount`, `StudyFirstPostDate`, `StartDate`.\n-   `--fields` — Comma-separated list of JSON field names to include in the\n    response. Use this to keep responses small (e.g.\n    `\"NCTId,BriefTitle,OverallStatus,Phase\"`). See\n    `references\u002Fstudies_schema.md` for available field paths.\n-   `--limit` — Maximum number of studies to return per request (1–1000, default\n    10).\n-   `--count-total` — Boolean flag (no value needed). When present, the response\n    includes a `totalCount` field showing the total number of matching studies\n    across all pages.\n-   `--page-token` — An opaque cursor string used to fetch the next page of\n    results. Obtain this value from the `nextPageToken` field in a previous\n    search response. Do not construct this string yourself; always copy it\n    verbatim from the API response. See the Pagination section below.\n-   `--advanced` — Raw Essie filter expression for structured queries beyond the\n    dedicated flags (e.g. `\"AREA[LocationCountry]United States\"`). Combined with\n    other flags via AND. See `references\u002Fclinical_trials_api.md` for syntax.\n-   `--output` — **(Required)** File path where the JSON response is written.\n\n**Example — actively recruiting Phase 3 pediatric cystic fibrosis trials:**\n\n```bash\nuv run scripts\u002Fclinical_trials_api.py search \\\n  --condition \"cystic fibrosis\" \\\n  --status RECRUITING \\\n  --phase PHASE3 \\\n  --age-group CHILD \\\n  --fields \"NCTId,BriefTitle,OverallStatus,Phase\" \\\n  --limit 10 \\\n  --output \u002Ftmp\u002Fcf_trials.json\n```\n\n**Example — recruiting atezolizumab trials for esophageal cancer:**\n\n```bash\nuv run scripts\u002Fclinical_trials_api.py search \\\n  --condition \"esophageal cancer\" \\\n  --intervention \"Atezolizumab\" \\\n  --status RECRUITING \\\n  --fields \"NCTId,BriefTitle,Phase\" \\\n  --limit 10 \\\n  --output \u002Ftmp\u002Fatezolizumab_trials.json\n```\n\n### Retrieve a study by NCT ID\n\nUse for: fetching full details of a specific trial when you already have the NCT\nidentifier.\n\n```bash\nuv run scripts\u002Fclinical_trials_api.py get-study \\\n  \u003Cnct_id> [--fields \"\u003Cfields>\"] \\\n  --output \u002Ftmp\u002Fstudy.json\n```\n\nReturns a useful default set of fields if `--fields` is omitted:\n`NCTId,BriefTitle,OverallStatus,Phase,BriefSummary,`\n`ConditionsModule,ArmsInterventionsModule,EligibilityModule`\n\n**Structure of the default response:**\n\n```json\n{\n  \"protocolSection\": {\n    \"identificationModule\": {\n      \"nctId\": \"NCT00000000\",\n      \"briefTitle\": \"Study Title\"\n    },\n    \"statusModule\": {\n      \"overallStatus\": \"RECRUITING\"\n    },\n    \"descriptionModule\": {\n      \"briefSummary\": \"This study is about...\"\n    },\n    \"conditionsModule\": {\n      \"conditions\": [ \"Condition Name\" ]\n    },\n    \"armsInterventionsModule\": {\n      \"interventions\": [ { \"type\": \"DRUG\", \"name\": \"Drug Name\" } ]\n    },\n    \"eligibilityModule\": {\n      \"eligibilityCriteria\": \"Inclusion:\\n- ...\",\n      \"stdAges\": [ \"ADULT\" ]\n    }\n  }\n}\n```\n\n### Get eligibility \u002F inclusion criteria\n\nUse for: pulling inclusion\u002Fexclusion rules, age ranges, and sex requirements for\npatient-matching tasks.\n\n```bash\nuv run scripts\u002Fclinical_trials_api.py \\\n  get-eligibility \u003Cnct_id> \\\n  --output \u002Ftmp\u002Feligibility.json\n```\n\nShortcut that returns title and the full eligibility module (inclusion\u002Fexclusion\ncriteria, age range, sex).\n\n**Example — inclusion criteria for NCT04886804:**\n\n```bash\nuv run scripts\u002Fclinical_trials_api.py \\\n  get-eligibility NCT04886804 \\\n  --output \u002Ftmp\u002Feligibility_NCT04886804.json\n```\n\n### Count matching studies\n\nUse for: exploring the trial landscape — checking how many trials exist for a\ncondition, phase, or status before fetching full records.\n\n```bash\nuv run scripts\u002Fclinical_trials_api.py count \\\n  --condition \"\u003Cdisease>\" \\\n  [--status \"\u003Cstatus>\"] [--phase \"\u003Cphase>\"] ... \\\n  --output \u002Ftmp\u002Fcount.json\n```\n\nReturns only the total count of clinical trials matching the search criteria\nwithout fetching study records. Accepts the same filter flags as `search`.\n\n### Search by location \u002F geography\n\nUse for: narrowing trials to a specific country, state, or city.\n\nUse `--advanced` with `AREA[LocationCountry]` or `AREA[LocationCity]` to\nrestrict results by geography:\n\n```bash\nuv run scripts\u002Fclinical_trials_api.py search \\\n  --condition \"cystic fibrosis\" \\\n  --status RECRUITING \\\n  --advanced \"AREA[LocationCity]New York\" \\\n  --fields \"NCTId,BriefTitle\" \\\n  --limit 20 \\\n  --output \u002Ftmp\u002Fnyc_cf_trials.json\n```\n\n### Search by sponsor \u002F organization\n\nUse for: identifying a sponsor's or institution's trial portfolio.\n\nUse `--sponsor` to find trials run by a specific institution or company:\n\n```bash\nuv run scripts\u002Fclinical_trials_api.py search \\\n  --sponsor \"National Cancer Institute\" \\\n  --fields \"NCTId,BriefTitle,LeadSponsorName\" \\\n  --limit 20 \\\n  --output \u002Ftmp\u002Fnci_trials.json\n```\n\n### Combined multi-criteria search\n\nUse for: complex queries that layer multiple filters (condition and drug and\nphase and geography and sponsor, etc.).\n\nAll flags combine via AND, so you can layer conditions, interventions, status,\nphase, geography, and sponsor in a single query:\n\n```bash\nuv run scripts\u002Fclinical_trials_api.py search \\\n  --condition \"pancreatic cancer\" \\\n  --intervention \"immunotherapy\" \\\n  --status RECRUITING \\\n  --phase PHASE3 \\\n  --advanced \"AREA[LocationCountry]United States\" \\\n  --fields \"NCTId,BriefTitle,Phase,LeadSponsorName\" \\\n  --limit 20 \\\n  --output \u002Ftmp\u002Fpanc_trials.json\n```\n\n### Raw API query (escape hatch)\n\nUse for: uncommon endpoints or parameter combinations not covered by the\ndedicated flags.\n\n```bash\nuv run scripts\u002Fclinical_trials_api.py raw-query \\\n  --endpoint \u003Cpath> \\\n  --params '\u003Cjson_dict>' \\\n  --output \u002Ftmp\u002Fraw_result.json\n```\n\n## Pagination\n\nWhen results exceed `--limit`, the response includes a `nextPageToken`. Pass it\nwith `--page-token` to fetch the next page:\n\n```bash\nuv run scripts\u002Fclinical_trials_api.py search \\\n  --condition \"breast cancer\" \\\n  --status RECRUITING \\\n  --limit 50 --count-total \\\n  --output \u002Ftmp\u002Fbreast_cancer_p1.json\n\nuv run scripts\u002Fclinical_trials_api.py search \\\n  --condition \"breast cancer\" \\\n  --status RECRUITING \\\n  --limit 50 --page-token \"CAo=\" \\\n  --output \u002Ftmp\u002Fbreast_cancer_p2.json\n```\n\n## Advanced Querying\n\nFor complex filtering beyond the dedicated flags, use `--advanced` with an Essie\nexpression.\n\n**What is an Essie Expression?** Essie is the search engine powering\nClinicalTrials.gov. An Essie expression is a structured query that targets\nspecific fields (e.g., country, phase) rather than doing general keyword\nsearches.\n\n-   **`AREA[Field]Value`**: Targets a specific field.\n    -   `AREA[LocationCountry]United States`\n    -   `AREA[Phase]PHASE3`\n-   **Boolean operators**: Combine with `AND`, `OR`, `NOT`.\n-   **`RANGE[min, max]`**: For numeric\u002Fdate fields (e.g. `RANGE[500, MAX]`).\n\nSee `references\u002Fclinical_trials_api.md` for syntax and available fields.\n\nIt is combined with other flags via AND:\n\n```bash\nuv run scripts\u002Fclinical_trials_api.py search \\\n  --condition \"diabetes\" \\\n  --advanced \"AREA[LocationCountry]United States \\\n    AND AREA[EnrollmentCount]RANGE[500, MAX]\" \\\n  --fields \"NCTId,BriefTitle,EnrollmentCount\" \\\n  --output \u002Ftmp\u002Fdiabetes_us_large.json\n```\n\n## References\n\n-   **API parameters, enum values, and Essie syntax:**\n    `references\u002Fclinical_trials_api.md`\n-   **JSON field paths and `--fields` recipes:** `references\u002Fstudies_schema.md`\n",{"data":34,"body":35},{"name":4,"description":6},{"type":36,"children":37},"root",[38,46,53,108,114,128,134,228,234,253,283,289,317,344,351,386,392,578,597,603,609,614,988,993,1001,1284,1292,1447,1455,1599,1605,1610,1701,1725,1733,2365,2371,2376,2442,2447,2455,2509,2515,2520,2640,2652,2658,2663,2688,2833,2839,2844,2855,2960,2966,2971,2976,3159,3165,3170,3270,3276,3302,3519,3525,3537,3547,3636,3648,3653,3780,3786,3824],{"type":39,"tag":40,"props":41,"children":42},"element","h1",{"id":4},[43],{"type":44,"value":45},"text","Clinical Trials 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],{"type":39,"tag":62,"props":92,"children":93},{},[94],{"type":44,"value":95},"User Notification",{"type":44,"value":97},": If .licenses\u002Fclinical_trials_database_LICENSE.txt\ndoes not already exist in the workspace root directory then (1) prominently\nnotify the user to check the terms at ",{"type":39,"tag":99,"props":100,"children":104},"a",{"href":101,"rel":102},"https:\u002F\u002Fclinicaltrials.gov\u002F",[103],"nofollow",[105],{"type":44,"value":101},{"type":44,"value":107},", then (2)\ncreate the file recording the notification text and timestamp.",{"type":39,"tag":47,"props":109,"children":111},{"id":110},"overview",[112],{"type":44,"value":113},"Overview",{"type":39,"tag":115,"props":116,"children":117},"p",{},[118,120,126],{"type":44,"value":119},"Access worldwide clinical trial data from ClinicalTrials.gov via the REST API\nv2. 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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},[3868,3871,3874,3877,3880],{"name":3869,"slug":3870,"type":15},"ChEMBL","chembl",{"name":3872,"slug":3873,"type":15},"Chemistry","chemistry",{"name":3875,"slug":3876,"type":15},"Database","database",{"name":3878,"slug":3879,"type":15},"Pharmacology","pharmacology",{"name":13,"slug":14,"type":15},"2026-07-12T07:51:35.544306",{"slug":4,"name":4,"fn":5,"description":6,"org":3883,"tags":3884,"stars":22,"repoUrl":23,"updatedAt":24},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[3885,3886,3887],{"name":17,"slug":18,"type":15},{"name":20,"slug":21,"type":15},{"name":13,"slug":14,"type":15},{"slug":3889,"name":3889,"fn":3890,"description":3891,"org":3892,"tags":3893,"stars":22,"repoUrl":23,"updatedAt":3902},"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},[3894,3897,3898,3901],{"name":3895,"slug":3896,"type":15},"ClinVar","clinvar",{"name":3855,"slug":3856,"type":15},{"name":3899,"slug":3900,"type":15},"Healthcare","healthcare",{"name":13,"slug":14,"type":15},"2026-07-12T07:51:36.86094",{"slug":3904,"name":3904,"fn":3905,"description":3906,"org":3907,"tags":3908,"stars":22,"repoUrl":23,"updatedAt":3918},"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},[3909,3912,3915],{"name":3910,"slug":3911,"type":15},"Compliance","compliance",{"name":3913,"slug":3914,"type":15},"Operations","operations",{"name":3916,"slug":3917,"type":15},"Security","security","2026-07-12T07:52:17.355491",{"slug":3920,"name":3920,"fn":3921,"description":3922,"org":3923,"tags":3924,"stars":22,"repoUrl":23,"updatedAt":3931},"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},[3925,3926,3927,3930],{"name":3839,"slug":3840,"type":15},{"name":3855,"slug":3856,"type":15},{"name":3928,"slug":3929,"type":15},"NCBI","ncbi",{"name":13,"slug":14,"type":15},"2026-07-12T07:51:33.054229",38,{"items":3934,"total":3932},[3935,3942,3949,3957,3963,3970,3976,3983,3995,4010,4021,4031],{"slug":3833,"name":3833,"fn":3834,"description":3835,"org":3936,"tags":3937,"stars":22,"repoUrl":23,"updatedAt":3846},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[3938,3939,3940,3941],{"name":3839,"slug":3840,"type":15},{"name":3842,"slug":3843,"type":15},{"name":20,"slug":21,"type":15},{"name":13,"slug":14,"type":15},{"slug":3848,"name":3848,"fn":3849,"description":3850,"org":3943,"tags":3944,"stars":22,"repoUrl":23,"updatedAt":3861},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[3945,3946,3947,3948],{"name":3839,"slug":3840,"type":15},{"name":3855,"slug":3856,"type":15},{"name":13,"slug":14,"type":15},{"name":3859,"slug":3860,"type":15},{"slug":3863,"name":3863,"fn":3864,"description":3865,"org":3950,"tags":3951,"stars":22,"repoUrl":23,"updatedAt":3881},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[3952,3953,3954,3955,3956],{"name":3869,"slug":3870,"type":15},{"name":3872,"slug":3873,"type":15},{"name":3875,"slug":3876,"type":15},{"name":3878,"slug":3879,"type":15},{"name":13,"slug":14,"type":15},{"slug":4,"name":4,"fn":5,"description":6,"org":3958,"tags":3959,"stars":22,"repoUrl":23,"updatedAt":24},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[3960,3961,3962],{"name":17,"slug":18,"type":15},{"name":20,"slug":21,"type":15},{"name":13,"slug":14,"type":15},{"slug":3889,"name":3889,"fn":3890,"description":3891,"org":3964,"tags":3965,"stars":22,"repoUrl":23,"updatedAt":3902},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[3966,3967,3968,3969],{"name":3895,"slug":3896,"type":15},{"name":3855,"slug":3856,"type":15},{"name":3899,"slug":3900,"type":15},{"name":13,"slug":14,"type":15},{"slug":3904,"name":3904,"fn":3905,"description":3906,"org":3971,"tags":3972,"stars":22,"repoUrl":23,"updatedAt":3918},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[3973,3974,3975],{"name":3910,"slug":3911,"type":15},{"name":3913,"slug":3914,"type":15},{"name":3916,"slug":3917,"type":15},{"slug":3920,"name":3920,"fn":3921,"description":3922,"org":3977,"tags":3978,"stars":22,"repoUrl":23,"updatedAt":3931},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[3979,3980,3981,3982],{"name":3839,"slug":3840,"type":15},{"name":3855,"slug":3856,"type":15},{"name":3928,"slug":3929,"type":15},{"name":13,"slug":14,"type":15},{"slug":3984,"name":3984,"fn":3985,"description":3986,"org":3987,"tags":3988,"stars":22,"repoUrl":23,"updatedAt":3994},"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},[3989,3990,3993],{"name":3839,"slug":3840,"type":15},{"name":3991,"slug":3992,"type":15},"Ontology","ontology",{"name":13,"slug":14,"type":15},"2026-07-12T07:51:59.368324",{"slug":3996,"name":3996,"fn":3997,"description":3998,"org":3999,"tags":4000,"stars":22,"repoUrl":23,"updatedAt":4009},"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},[4001,4002,4005,4006],{"name":3839,"slug":3840,"type":15},{"name":4003,"slug":4004,"type":15},"GraphQL","graphql",{"name":13,"slug":14,"type":15},{"name":4007,"slug":4008,"type":15},"REST API","rest-api","2026-07-12T07:52:10.597139",{"slug":4011,"name":4011,"fn":4012,"description":4013,"org":4014,"tags":4015,"stars":22,"repoUrl":23,"updatedAt":4020},"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},[4016,4017,4018,4019],{"name":3839,"slug":3840,"type":15},{"name":3855,"slug":3856,"type":15},{"name":20,"slug":21,"type":15},{"name":13,"slug":14,"type":15},"2026-07-12T07:51:41.645835",{"slug":4022,"name":4022,"fn":4023,"description":4024,"org":4025,"tags":4026,"stars":22,"repoUrl":23,"updatedAt":4030},"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},[4027,4028,4029],{"name":3839,"slug":3840,"type":15},{"name":20,"slug":21,"type":15},{"name":13,"slug":14,"type":15},"2026-07-12T07:52:09.354992",{"slug":4032,"name":4032,"fn":4033,"description":4034,"org":4035,"tags":4036,"stars":22,"repoUrl":23,"updatedAt":4041},"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},[4037,4038,4039,4040],{"name":3839,"slug":3840,"type":15},{"name":3855,"slug":3856,"type":15},{"name":20,"slug":21,"type":15},{"name":13,"slug":14,"type":15},"2026-07-12T07:51:38.213009"]