[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill-google-deepmind-agentic-ecology-init":3,"mdc--kr7tzv-key":32,"related-repo-google-deepmind-agentic-ecology-init":447,"related-org-google-deepmind-agentic-ecology-init":517},{"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":30,"mdContent":31},"agentic-ecology-init","initialize Python projects for agentic ecology","Initializes a local uv-managed project directory for agentic ecology workloads. Sets up Python dependencies using reference pyproject.toml and uv.lock, configures workspace rules, and ensures Agentic Ecology skills are discoverable.",{"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},"Local Development","local-development","tag",{"name":17,"slug":18,"type":15},"Python","python",{"name":20,"slug":21,"type":15},"Engineering","engineering",2,"https:\u002F\u002Fgithub.com\u002Fgoogle-deepmind\u002Fagentic_ecology","2026-08-29T09:48:06.14295",null,0,[],{"repoUrl":23,"stars":22,"forks":26,"topics":29,"description":25},[],"https:\u002F\u002Fgithub.com\u002Fgoogle-deepmind\u002Fagentic_ecology\u002Ftree\u002FHEAD\u002Fskills\u002Fagentic-ecology-init","---\nname: agentic-ecology-init\ndescription: >-\n  Initializes a local uv-managed project directory for agentic ecology workloads.\n  Sets up Python dependencies using reference pyproject.toml and uv.lock, configures\n  workspace rules, and ensures Agentic Ecology skills are discoverable.\n---\n\n# Agentic Ecology Project Initialization Skill\n\nUse this skill when you need to initialize a fresh, local project directory for\necological modeling workflows (such as bioacoustics or camera trap analysis)\nwithout cloning the entire `agentic_ecology` repository into the user's project\nworkspace.\n\n## Workflow Overview\n\nFollow these sequential steps to set up the local workspace:\n\n1.  **Identify Target Working Directory**:\n    *   Confirm the root directory of the user's project workspace.\n2.  **Initialize Project & Scaffolding**:\n    *   Ensure the target project directory exists.\n    *   Run `uv init --python 3.12 --no-readme && rm main.py` in the project\n        directory if it has not already been initialized. This pins\n        `.python-version` to 3.12, generates `.gitignore`, initializes version\n        control tracking, and removes the placeholder entrypoint.\n    *   Install the `google-deepmind\u002Fagentic_ecology` and\n        `googlecolab\u002Fgoogle-colab-cli` (`colab-operator`) skills locally with\n        `npx skills add`.\n    *   Create standard working subdirectories:\n        *   `agent_workspace\u002F`: Sandboxed folder for agent scripts, server\n        *   `databases\u002F`: Destination folder for Hoplite vector databases.\n        *   `data\u002F`: Destination folder for raw datasets (e.g., audio, images).\n3.  **Copy Reference Dependency Configurations**:\n    *   Overwrite the generated `pyproject.toml` and copy `uv.lock` from\n        this skill's `references\u002F` directory into the target project root.\n    *   Adjust the package name in `pyproject.toml` to match the user's project\n        name if desired, keeping all core dependencies (`perch-hoplite`,\n        `speciesnet`), constraints, and build configurations intact.\n5.  **Install Workspace Rules (`AGENTS.md`)**:\n    *   Copy the reference `AGENTS.md` from this skill's `references\u002F` directory\n        into the appropriate location in the project workspace to establish\n        standard Agentic Ecology guidelines (compute assessment and offloading\n        protocols, macOS dynamic library deadlock rules, Linux\n        PyTorch\u002FTensorFlow import order rules, and SQL log suppression filters).\n6.  **Synchronize Environment with `uv`**:\n    *   Execute `uv sync` from the target project root to create the local\n        virtual environment (`.venv`) and install all pinned dependencies.\n7.  **Verify Environment Setup**:\n    *   Run a verification command via `uv run python` to confirm that key\n        libraries (`perch_hoplite`, `speciesnet`, `soundfile`, `tensorflow`)\n        import cleanly.\n\n## Technical Reference\n\nFor detailed command options, directory layout specifications, and verification\ncode snippets, see:\n\n*   [Initialization Technical Reference](references\u002Ftechnical_reference.md)\n",{"data":33,"body":34},{"name":4,"description":6},{"type":35,"children":36},"root",[37,46,61,68,73,423,429,434],{"type":38,"tag":39,"props":40,"children":42},"element","h1",{"id":41},"agentic-ecology-project-initialization-skill",[43],{"type":44,"value":45},"text","Agentic Ecology Project Initialization Skill",{"type":38,"tag":47,"props":48,"children":49},"p",{},[50,52,59],{"type":44,"value":51},"Use this skill when you need to initialize a fresh, local project directory for\necological modeling workflows (such as bioacoustics or camera trap analysis)\nwithout cloning the entire ",{"type":38,"tag":53,"props":54,"children":56},"code",{"className":55},[],[57],{"type":44,"value":58},"agentic_ecology",{"type":44,"value":60}," repository into the user's project\nworkspace.",{"type":38,"tag":62,"props":63,"children":65},"h2",{"id":64},"workflow-overview",[66],{"type":44,"value":67},"Workflow Overview",{"type":38,"tag":47,"props":69,"children":70},{},[71],{"type":44,"value":72},"Follow these sequential steps to set up the local workspace:",{"type":38,"tag":74,"props":75,"children":76},"ol",{},[77,98,222,291,330,369],{"type":38,"tag":78,"props":79,"children":80},"li",{},[81,87,89],{"type":38,"tag":82,"props":83,"children":84},"strong",{},[85],{"type":44,"value":86},"Identify Target Working Directory",{"type":44,"value":88},":\n",{"type":38,"tag":90,"props":91,"children":92},"ul",{},[93],{"type":38,"tag":78,"props":94,"children":95},{},[96],{"type":44,"value":97},"Confirm the root directory of the user's project workspace.",{"type":38,"tag":78,"props":99,"children":100},{},[101,106,107],{"type":38,"tag":82,"props":102,"children":103},{},[104],{"type":44,"value":105},"Initialize Project & Scaffolding",{"type":44,"value":88},{"type":38,"tag":90,"props":108,"children":109},{},[110,115,144,181],{"type":38,"tag":78,"props":111,"children":112},{},[113],{"type":44,"value":114},"Ensure the target project directory exists.",{"type":38,"tag":78,"props":116,"children":117},{},[118,120,126,128,134,136,142],{"type":44,"value":119},"Run ",{"type":38,"tag":53,"props":121,"children":123},{"className":122},[],[124],{"type":44,"value":125},"uv init --python 3.12 --no-readme && rm main.py",{"type":44,"value":127}," in the project\ndirectory if it has not already been initialized. This pins\n",{"type":38,"tag":53,"props":129,"children":131},{"className":130},[],[132],{"type":44,"value":133},".python-version",{"type":44,"value":135}," to 3.12, generates ",{"type":38,"tag":53,"props":137,"children":139},{"className":138},[],[140],{"type":44,"value":141},".gitignore",{"type":44,"value":143},", initializes version\ncontrol tracking, and removes the placeholder entrypoint.",{"type":38,"tag":78,"props":145,"children":146},{},[147,149,155,157,163,165,171,173,179],{"type":44,"value":148},"Install the ",{"type":38,"tag":53,"props":150,"children":152},{"className":151},[],[153],{"type":44,"value":154},"google-deepmind\u002Fagentic_ecology",{"type":44,"value":156}," and\n",{"type":38,"tag":53,"props":158,"children":160},{"className":159},[],[161],{"type":44,"value":162},"googlecolab\u002Fgoogle-colab-cli",{"type":44,"value":164}," (",{"type":38,"tag":53,"props":166,"children":168},{"className":167},[],[169],{"type":44,"value":170},"colab-operator",{"type":44,"value":172},") skills locally with\n",{"type":38,"tag":53,"props":174,"children":176},{"className":175},[],[177],{"type":44,"value":178},"npx skills add",{"type":44,"value":180},".",{"type":38,"tag":78,"props":182,"children":183},{},[184,186],{"type":44,"value":185},"Create standard working subdirectories:\n",{"type":38,"tag":90,"props":187,"children":188},{},[189,200,211],{"type":38,"tag":78,"props":190,"children":191},{},[192,198],{"type":38,"tag":53,"props":193,"children":195},{"className":194},[],[196],{"type":44,"value":197},"agent_workspace\u002F",{"type":44,"value":199},": Sandboxed folder for agent scripts, server",{"type":38,"tag":78,"props":201,"children":202},{},[203,209],{"type":38,"tag":53,"props":204,"children":206},{"className":205},[],[207],{"type":44,"value":208},"databases\u002F",{"type":44,"value":210},": Destination folder for Hoplite vector databases.",{"type":38,"tag":78,"props":212,"children":213},{},[214,220],{"type":38,"tag":53,"props":215,"children":217},{"className":216},[],[218],{"type":44,"value":219},"data\u002F",{"type":44,"value":221},": Destination folder for raw datasets (e.g., audio, images).",{"type":38,"tag":78,"props":223,"children":224},{},[225,230,231],{"type":38,"tag":82,"props":226,"children":227},{},[228],{"type":44,"value":229},"Copy Reference Dependency Configurations",{"type":44,"value":88},{"type":38,"tag":90,"props":232,"children":233},{},[234,263],{"type":38,"tag":78,"props":235,"children":236},{},[237,239,245,247,253,255,261],{"type":44,"value":238},"Overwrite the generated ",{"type":38,"tag":53,"props":240,"children":242},{"className":241},[],[243],{"type":44,"value":244},"pyproject.toml",{"type":44,"value":246}," and copy ",{"type":38,"tag":53,"props":248,"children":250},{"className":249},[],[251],{"type":44,"value":252},"uv.lock",{"type":44,"value":254}," from\nthis skill's ",{"type":38,"tag":53,"props":256,"children":258},{"className":257},[],[259],{"type":44,"value":260},"references\u002F",{"type":44,"value":262}," directory into the target project root.",{"type":38,"tag":78,"props":264,"children":265},{},[266,268,273,275,281,283,289],{"type":44,"value":267},"Adjust the package name in ",{"type":38,"tag":53,"props":269,"children":271},{"className":270},[],[272],{"type":44,"value":244},{"type":44,"value":274}," to match the user's project\nname if desired, keeping all core dependencies (",{"type":38,"tag":53,"props":276,"children":278},{"className":277},[],[279],{"type":44,"value":280},"perch-hoplite",{"type":44,"value":282},",\n",{"type":38,"tag":53,"props":284,"children":286},{"className":285},[],[287],{"type":44,"value":288},"speciesnet",{"type":44,"value":290},"), constraints, and build configurations intact.",{"type":38,"tag":78,"props":292,"children":293},{},[294,307,308],{"type":38,"tag":82,"props":295,"children":296},{},[297,299,305],{"type":44,"value":298},"Install Workspace Rules (",{"type":38,"tag":53,"props":300,"children":302},{"className":301},[],[303],{"type":44,"value":304},"AGENTS.md",{"type":44,"value":306},")",{"type":44,"value":88},{"type":38,"tag":90,"props":309,"children":310},{},[311],{"type":38,"tag":78,"props":312,"children":313},{},[314,316,321,323,328],{"type":44,"value":315},"Copy the reference ",{"type":38,"tag":53,"props":317,"children":319},{"className":318},[],[320],{"type":44,"value":304},{"type":44,"value":322}," from this skill's ",{"type":38,"tag":53,"props":324,"children":326},{"className":325},[],[327],{"type":44,"value":260},{"type":44,"value":329}," directory\ninto the appropriate location in the project workspace to establish\nstandard Agentic Ecology guidelines (compute assessment and offloading\nprotocols, macOS dynamic library deadlock rules, Linux\nPyTorch\u002FTensorFlow import order rules, and SQL log suppression filters).",{"type":38,"tag":78,"props":331,"children":332},{},[333,344,345],{"type":38,"tag":82,"props":334,"children":335},{},[336,338],{"type":44,"value":337},"Synchronize Environment with ",{"type":38,"tag":53,"props":339,"children":341},{"className":340},[],[342],{"type":44,"value":343},"uv",{"type":44,"value":88},{"type":38,"tag":90,"props":346,"children":347},{},[348],{"type":38,"tag":78,"props":349,"children":350},{},[351,353,359,361,367],{"type":44,"value":352},"Execute ",{"type":38,"tag":53,"props":354,"children":356},{"className":355},[],[357],{"type":44,"value":358},"uv sync",{"type":44,"value":360}," from the target project root to create the local\nvirtual environment (",{"type":38,"tag":53,"props":362,"children":364},{"className":363},[],[365],{"type":44,"value":366},".venv",{"type":44,"value":368},") and install all pinned dependencies.",{"type":38,"tag":78,"props":370,"children":371},{},[372,377,378],{"type":38,"tag":82,"props":373,"children":374},{},[375],{"type":44,"value":376},"Verify Environment Setup",{"type":44,"value":88},{"type":38,"tag":90,"props":379,"children":380},{},[381],{"type":38,"tag":78,"props":382,"children":383},{},[384,386,392,394,400,402,407,408,414,415,421],{"type":44,"value":385},"Run a verification command via ",{"type":38,"tag":53,"props":387,"children":389},{"className":388},[],[390],{"type":44,"value":391},"uv run python",{"type":44,"value":393}," to confirm that key\nlibraries (",{"type":38,"tag":53,"props":395,"children":397},{"className":396},[],[398],{"type":44,"value":399},"perch_hoplite",{"type":44,"value":401},", ",{"type":38,"tag":53,"props":403,"children":405},{"className":404},[],[406],{"type":44,"value":288},{"type":44,"value":401},{"type":38,"tag":53,"props":409,"children":411},{"className":410},[],[412],{"type":44,"value":413},"soundfile",{"type":44,"value":401},{"type":38,"tag":53,"props":416,"children":418},{"className":417},[],[419],{"type":44,"value":420},"tensorflow",{"type":44,"value":422},")\nimport cleanly.",{"type":38,"tag":62,"props":424,"children":426},{"id":425},"technical-reference",[427],{"type":44,"value":428},"Technical Reference",{"type":38,"tag":47,"props":430,"children":431},{},[432],{"type":44,"value":433},"For detailed command options, directory layout specifications, and verification\ncode snippets, see:",{"type":38,"tag":90,"props":435,"children":436},{},[437],{"type":38,"tag":78,"props":438,"children":439},{},[440],{"type":38,"tag":441,"props":442,"children":444},"a",{"href":443},"references\u002Ftechnical_reference.md",[445],{"type":44,"value":446},"Initialization Technical Reference",{"items":448,"total":516},[449,463,477,483,499],{"slug":450,"name":450,"fn":451,"description":452,"org":453,"tags":454,"stars":22,"repoUrl":23,"updatedAt":462},"agentic-ecology-bioacoustics","perform bioacoustic analysis for ecological research","Provides bioacoustic analysis capabilities for ecologists and researchers using the perch-hoplite Python package. A typical use case is to use agile modeling to bootstrap the creation and deployment of a bespoke detector for targeted species on an existing collection of passive acoustic monitoring recordings.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[455,458,459],{"name":456,"slug":457,"type":15},"Data Analysis","data-analysis",{"name":17,"slug":18,"type":15},{"name":460,"slug":461,"type":15},"Research","research","2026-08-29T09:48:06.668897",{"slug":464,"name":464,"fn":465,"description":466,"org":467,"tags":468,"stars":22,"repoUrl":23,"updatedAt":476},"agentic-ecology-camera-traps","classify and search camera trap images","Provides capabilities to run SpeciesNet detector and classifier on camera trap images, extract crop-level feature embeddings, and populate a Hoplite vector database for downstream search and agile modeling.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[469,472,473],{"name":470,"slug":471,"type":15},"Computer Vision","computer-vision",{"name":456,"slug":457,"type":15},{"name":474,"slug":475,"type":15},"Search","search","2026-08-29T09:48:07.220771",{"slug":4,"name":4,"fn":5,"description":6,"org":478,"tags":479,"stars":22,"repoUrl":23,"updatedAt":24},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[480,481,482],{"name":20,"slug":21,"type":15},{"name":13,"slug":14,"type":15},{"name":17,"slug":18,"type":15},{"slug":484,"name":484,"fn":485,"description":486,"org":487,"tags":488,"stars":22,"repoUrl":23,"updatedAt":498},"agentic-ecology-storage","upload local data to cloud storage","Provides guidelines and reference implementations for uploading local data (such as audio recordings or datasets) to cloud storage systems, focusing on Google Drive via rclone as the primary target.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[489,492,495],{"name":490,"slug":491,"type":15},"Data Engineering","data-engineering",{"name":493,"slug":494,"type":15},"Google Drive","google-drive",{"name":496,"slug":497,"type":15},"Storage","storage","2026-08-29T09:48:13.00055",{"slug":500,"name":500,"fn":501,"description":502,"org":503,"tags":504,"stars":22,"repoUrl":23,"updatedAt":515},"agentic-ecology-ui","visualize and annotate vector database results","Guidelines and templates for creating a generic web UI to visualize, rank, filter, and annotate vector databases. The UI has a hierarchical structure covering database selection, label selection\u002Fdefinition, ranking\u002Ffiltering configuration, and row visualization\u002Fannotation. Meant to be copied and adapted for specific downstream tasks like bioacoustics or camera traps.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[505,508,511,512],{"name":506,"slug":507,"type":15},"Dashboards","dashboards",{"name":509,"slug":510,"type":15},"Data Visualization","data-visualization",{"name":474,"slug":475,"type":15},{"name":513,"slug":514,"type":15},"UI Components","ui-components","2026-08-29T09:48:03.400711",5,{"items":518,"total":688},[519,538,553,573,585,600,616,629,641,656,667,677],{"slug":520,"name":520,"fn":521,"description":522,"org":523,"tags":524,"stars":535,"repoUrl":536,"updatedAt":537},"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},[525,528,531,534],{"name":526,"slug":527,"type":15},"Bioinformatics","bioinformatics",{"name":529,"slug":530,"type":15},"Genomics","genomics",{"name":532,"slug":533,"type":15},"Life Sciences","life-sciences",{"name":460,"slug":461,"type":15},2690,"https:\u002F\u002Fgithub.com\u002Fgoogle-deepmind\u002Fscience-skills","2026-07-12T07:51:51.827211",{"slug":539,"name":539,"fn":540,"description":541,"org":542,"tags":543,"stars":535,"repoUrl":536,"updatedAt":552},"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},[544,545,548,549],{"name":526,"slug":527,"type":15},{"name":546,"slug":547,"type":15},"Genetics","genetics",{"name":460,"slug":461,"type":15},{"name":550,"slug":551,"type":15},"RNA-seq","rna-seq","2026-07-12T07:51:39.494803",{"slug":554,"name":554,"fn":555,"description":556,"org":557,"tags":558,"stars":535,"repoUrl":536,"updatedAt":572},"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},[559,562,565,568,571],{"name":560,"slug":561,"type":15},"ChEMBL","chembl",{"name":563,"slug":564,"type":15},"Chemistry","chemistry",{"name":566,"slug":567,"type":15},"Database","database",{"name":569,"slug":570,"type":15},"Pharmacology","pharmacology",{"name":460,"slug":461,"type":15},"2026-07-12T07:51:35.544306",{"slug":574,"name":574,"fn":575,"description":576,"org":577,"tags":578,"stars":535,"repoUrl":536,"updatedAt":584},"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},[579,582,583],{"name":580,"slug":581,"type":15},"Clinical Trials","clinical-trials",{"name":532,"slug":533,"type":15},{"name":460,"slug":461,"type":15},"2026-07-12T07:52:06.846705",{"slug":586,"name":586,"fn":587,"description":588,"org":589,"tags":590,"stars":535,"repoUrl":536,"updatedAt":599},"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},[591,594,595,598],{"name":592,"slug":593,"type":15},"ClinVar","clinvar",{"name":546,"slug":547,"type":15},{"name":596,"slug":597,"type":15},"Healthcare","healthcare",{"name":460,"slug":461,"type":15},"2026-07-12T07:51:36.86094",{"slug":601,"name":601,"fn":602,"description":603,"org":604,"tags":605,"stars":535,"repoUrl":536,"updatedAt":615},"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},[606,609,612],{"name":607,"slug":608,"type":15},"Compliance","compliance",{"name":610,"slug":611,"type":15},"Operations","operations",{"name":613,"slug":614,"type":15},"Security","security","2026-07-12T07:52:17.355491",{"slug":617,"name":617,"fn":618,"description":619,"org":620,"tags":621,"stars":535,"repoUrl":536,"updatedAt":628},"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},[622,623,624,627],{"name":526,"slug":527,"type":15},{"name":546,"slug":547,"type":15},{"name":625,"slug":626,"type":15},"NCBI","ncbi",{"name":460,"slug":461,"type":15},"2026-07-12T07:51:33.054229",{"slug":630,"name":630,"fn":631,"description":632,"org":633,"tags":634,"stars":535,"repoUrl":536,"updatedAt":640},"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},[635,636,639],{"name":526,"slug":527,"type":15},{"name":637,"slug":638,"type":15},"Ontology","ontology",{"name":460,"slug":461,"type":15},"2026-07-12T07:51:59.368324",{"slug":642,"name":642,"fn":643,"description":644,"org":645,"tags":646,"stars":535,"repoUrl":536,"updatedAt":655},"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},[647,648,651,652],{"name":526,"slug":527,"type":15},{"name":649,"slug":650,"type":15},"GraphQL","graphql",{"name":460,"slug":461,"type":15},{"name":653,"slug":654,"type":15},"REST API","rest-api","2026-07-12T07:52:10.597139",{"slug":657,"name":657,"fn":658,"description":659,"org":660,"tags":661,"stars":535,"repoUrl":536,"updatedAt":666},"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},[662,663,664,665],{"name":526,"slug":527,"type":15},{"name":546,"slug":547,"type":15},{"name":532,"slug":533,"type":15},{"name":460,"slug":461,"type":15},"2026-07-12T07:51:41.645835",{"slug":668,"name":668,"fn":669,"description":670,"org":671,"tags":672,"stars":535,"repoUrl":536,"updatedAt":676},"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},[673,674,675],{"name":526,"slug":527,"type":15},{"name":532,"slug":533,"type":15},{"name":460,"slug":461,"type":15},"2026-07-12T07:52:09.354992",{"slug":678,"name":678,"fn":679,"description":680,"org":681,"tags":682,"stars":535,"repoUrl":536,"updatedAt":687},"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},[683,684,685,686],{"name":526,"slug":527,"type":15},{"name":546,"slug":547,"type":15},{"name":532,"slug":533,"type":15},{"name":460,"slug":461,"type":15},"2026-07-12T07:51:38.213009",43]