Agent skill

Biothings API

by wentorai in wentorai/research-plugins

Query gene, variant, and drug annotations via BioThings APIs

Install Biothings API

skills CLI

$ npx skills add wentorai/research-plugins --skill biothings-api -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins biothings-api --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/domains/biomedical/biothings-api .claude/skills/biothings-api && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "biothings-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/biothings-api into .claude/skills/biothings-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biothings-api", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/biothings-api

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add wentorai/research-plugins --skill biothings-api -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins biothings-api --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/domains/biomedical/biothings-api .agents/skills/biothings-api && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "biothings-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/biothings-api into .agents/skills/biothings-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biothings-api", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add wentorai/research-plugins --skill biothings-api -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins biothings-api --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/domains/biomedical/biothings-api .cursor/skills/biothings-api && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "biothings-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/biothings-api into .cursor/skills/biothings-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biothings-api", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/wentorai/research-plugins.git --path skills/domains/biomedical/biothings-api

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add wentorai/research-plugins --skill biothings-api -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins biothings-api --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/domains/biomedical/biothings-api .gemini/skills/biothings-api && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "biothings-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/biothings-api into .gemini/skills/biothings-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biothings-api", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install wentorai/research-plugins biothings-api

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add wentorai/research-plugins --skill biothings-api -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/domains/biomedical/biothings-api .github/skills/biothings-api && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "biothings-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/biothings-api into .github/skills/biothings-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biothings-api", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add wentorai/research-plugins --skill biothings-api -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins biothings-api --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/domains/biomedical/biothings-api .opencode/skills/biothings-api && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "biothings-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/biothings-api into .opencode/skills/biothings-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biothings-api", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: biothings-api
GitHub stars: 298
Used in: 1 other repo
Token cost: ~2.2k tokens
SKILL.md length: 487 words
Files: 1
Skills in repo: 405
Repo updated: Jun 19, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Query gene, variant, and drug annotations via BioThings APIs

Research & Science work in your project
SKILL.md covers Overview, Authentication, MyGene.info — Gene Annotations and MyVariant.info — Variant…, plus 6 more sections
Calls curl

What it does

Biothings API is an agent skill from wentorai/research-plugins. Query gene, variant, and drug annotations via BioThings APIs

Its SKILL.md is about 2.2k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science. It works with NCBI. The repository describes itself as: 350+ academic research skills, MCP configs, and plugins for Research-Claw and AI agents. The licence is MIT.

When your agent uses it

Research & Science work in your project

Example prompts

“/biothings-api”

Requirements

Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit bf44b3c. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
- curl
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- biothings.io
- doi.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Biothings API loads about 2.2k tokens when it runs. Until then it costs about 19 tokens; SKILL.md has 487 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~19
When it runs · the whole SKILL.md, loaded when a task matches: ~2.2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from wentorai/research-plugins at commit bf44b3c, republished under its MIT licence (© wentorai). 487 words, ~2,222 tokens.

Download SKILL.mdSave it as .claude/skills/biothings-api/SKILL.md (or your agent's skills folder).

name: biothings-api
description: Query gene, variant, and drug annotations via BioThings APIs

BioThings API Suite

Overview

BioThings is a family of high-performance biomedical annotation APIs developed at the Scripps Research Institute. The suite provides unified, up-to-date access to gene, variant, and chemical/drug annotations aggregated from dozens of authoritative sources. Three primary services cover the core entities in translational research:

MyGene.info — Gene annotations from NCBI Entrez, Ensembl, UniProt, GO, KEGG, Reactome, and 20+ sources.
MyVariant.info — Variant annotations from dbSNP, ClinVar, gnomAD, CADD, COSMIC, and 15+ sources.
MyChem.info — Drug and chemical annotations from NDC, DrugBank, ChEMBL, FDA, PubChem, and 10+ sources.

All three share identical query syntax, require no authentication, and return JSON. Free for academic and commercial use.

Authentication

No authentication or API keys are required. All endpoints are open-access.

bash

# No API key needed — just query directly
curl "https://mygene.info/v3/query?q=BRCA1&size=1"

MyGene.info — Gene Annotations

Search Genes

GET https://mygene.info/v3/query?q={query}&size={n}

Query by gene symbol, name, Entrez ID, Ensembl ID, or keyword. Supports boolean operators (AND, OR, NOT) and field-specific queries like symbol:CDK2.

bash

curl -s "https://mygene.info/v3/query?q=BRCA1&size=1"

Response:

json

{
  "took": 178,
  "total": 13223,
  "hits": [
    {
      "_id": "672",
      "_score": 145.6796,
      "entrezgene": "672",
      "name": "BRCA1 DNA repair associated",
      "symbol": "BRCA1",
      "taxid": 9606
    }
  ]
}

Get Gene by ID

GET https://mygene.info/v3/gene/{entrez_id}

Returns comprehensive annotations for a single gene. Use the fields parameter to select specific data sources.

bash

# Full annotation (large response)
curl -s "https://mygene.info/v3/gene/1017"

# Selective fields
curl -s "https://mygene.info/v3/gene/1017?fields=symbol,name,summary,genomic_pos,go"

Response (key fields for CDK2, Entrez ID 1017):

json

{
  "_id": "1017",
  "symbol": "CDK2",
  "name": "cyclin dependent kinase 2",
  "HGNC": "1771",
  "MIM": "116953",
  "AllianceGenome": "1771",
  "taxid": 9606,
  "type_of_gene": "protein-coding"
}

The full response includes accessions, Gene Ontology terms, pathway memberships (KEGG, Reactome, WikiPathways), protein domains (InterPro, Pfam), homology data, and genomic coordinates.

MyVariant.info — Variant Annotations

Search Variants

GET https://myvariant.info/v1/query?q={query}&size={n}

Query by rsID, HGVS notation (e.g., chr7:g.140453136A>T), gene symbol, or ClinVar significance. Returns aggregated annotations from 15+ sources.

bash

curl -s "https://myvariant.info/v1/query?q=rs58991260&size=1"

Response (truncated):

json

{
  "took": 20,
  "total": 1,
  "hits": [
    {
      "_id": "chr1:g.218631822G>A",
      "_score": 21.382616,
      "dbsnp": {
        "rsid": "rs58991260",
        "vartype": "snv",
        "ref": "G",
        "alt": "A",
        "chrom": "1"
      },
      "cadd": {
        "phred": 1.679,
        "consequence": "INTERGENIC",
        "chrom": 1,
        "pos": 218631822
      },
      "gnomad_genome": {
        "af": { "af": 0.0150338, "af_afr": 0.0528007, "af_eas": 0.0, "af_nfe": 0.00032417 },
        "alt": "A",
        "ref": "G"
      }
    }
  ]
}

Get Variant by HGVS ID

GET https://myvariant.info/v1/variant/{hgvs_id}

bash

curl -s "https://myvariant.info/v1/variant/chr1:g.218631822G>A?fields=dbsnp,cadd,clinvar"

MyChem.info — Drug & Chemical Annotations

Search Drugs/Chemicals

GET https://mychem.info/v1/query?q={query}&size={n}

Query by drug name, NDC code, InChIKey, or active ingredient. Aggregates data from FDA NDC, DrugBank, ChEMBL, PubChem, SIDER, and more.

bash

curl -s "https://mychem.info/v1/query?q=aspirin&size=1"

Response (truncated):

json

{
  "took": 82,
  "total": 248,
  "hits": [
    {
      "_id": "0615-8613",
      "_score": 13.657401,
      "ndc": {
        "substancename": "ASPIRIN",
        "nonproprietaryname": "Aspirin",
        "proprietaryname": "Adult Low Dose Aspirin",
        "active_numerator_strength": "81",
        "active_ingred_unit": "mg/1",
        "dosageformname": "TABLET, DELAYED RELEASE",
        "routename": "ORAL",
        "producttypename": "HUMAN OTC DRUG",
        "pharm_classes": [
          "Cyclooxygenase Inhibitors [MoA]",
          "Decreased Platelet Aggregation [PE]",
          "Anti-Inflammatory Agents, Non-Steroidal [CS]",
          "Nonsteroidal Anti-inflammatory Drug [EPC]",
          "Platelet Aggregation Inhibitor [EPC]"
        ]
      }
    }
  ]
}

Get Chemical by ID

GET https://mychem.info/v1/chem/{id}

bash

curl -s "https://mychem.info/v1/chem/CHEMBL25?fields=drugbank,chembl,pubchem"

Query Syntax (Shared Across All Three APIs)

All BioThings APIs share the same query engine. Key features:

Feature	Syntax	Example
Field-specific	`field:value`	`symbol:TP53`
Boolean	`AND`, `OR`, `NOT`	`BRCA1 AND cancer`
Wildcard	`*`	`CDK*`
Range	`[min TO max]`	`exac.af:[0.01 TO 0.05]`
Pagination	`size`, `from`	`size=20&from=40`
Field selection	`fields`	`fields=symbol,name,go`
Sorting	`sort`	`sort=_score:desc`
Batch POST	POST with `ids`	Up to 1000 IDs per request

Show full SKILL.md (168 more words)Show less

Rate Limits

GET requests: 3 per second sustained; bursts up to 10/s tolerated
POST batch requests: 1 per second; up to 1000 IDs per batch
No daily cap for reasonable academic usage
Best practice: Add 350ms delays between sequential requests; use batch POST for bulk queries
User-Agent header: Set a descriptive User-Agent for priority support from the BioThings team

Python Example: Cross-API Gene-Variant-Drug Lookup

python

import requests, time

MYGENE = "https://mygene.info/v3"
MYVARIANT = "https://myvariant.info/v1"
MYCHEM = "https://mychem.info/v1"

def search_gene(symbol):
    resp = requests.get(f"{MYGENE}/query",
                        params={"q": f"symbol:{symbol}", "size": 1, "species": "human"})
    resp.raise_for_status()
    hits = resp.json().get("hits", [])
    return hits[0] if hits else {}

def search_variants(gene_symbol, size=5):
    resp = requests.get(f"{MYVARIANT}/query",
                        params={"q": f"clinvar.gene.symbol:{gene_symbol}",
                                "fields": "dbsnp.rsid,clinvar.rcv.clinical_significance,cadd.phred",
                                "size": size})
    resp.raise_for_status()
    return resp.json().get("hits", [])

def search_drug(name):
    resp = requests.get(f"{MYCHEM}/query",
                        params={"q": name, "size": 1,
                                "fields": "ndc.substancename,ndc.pharm_classes"})
    resp.raise_for_status()
    hits = resp.json().get("hits", [])
    return hits[0] if hits else {}

# Translational research pipeline: gene -> variants -> drug
gene = search_gene("BRCA1")
print(f"Gene: {gene.get('symbol')} (Entrez: {gene.get('entrezgene')})")
time.sleep(0.35)

variants = search_variants("BRCA1", size=3)
for v in variants:
    rsid = v.get("dbsnp", {}).get("rsid", v.get("_id"))
    print(f"  Variant: {rsid} | CADD: {v.get('cadd', {}).get('phred', 'N/A')}")
time.sleep(0.35)

drug = search_drug("olaparib")
print(f"  Drug: {drug.get('ndc', {}).get('substancename', 'N/A')}")

Academic Use Cases

GWAS follow-up: Annotate thousands of significant SNPs with allele frequencies (gnomAD), functional predictions (CADD, SIFT, PolyPhen), and clinical significance (ClinVar) via MyVariant.info batch queries.
Drug target mapping: Link gene symbols to pathway memberships (KEGG, Reactome) via MyGene.info, then find approved drugs targeting those pathways via MyChem.info.
Pharmacogenomics: Cross-reference variant annotations with drug metabolism data to identify clinically actionable gene-drug interactions.
Systematic reviews: Programmatically collect gene/variant metadata across large candidate lists to populate supplementary tables in genomics publications.

References

BioThings API Hub: https://biothings.io
MyGene.info Documentation: https://docs.mygene.info
MyVariant.info Documentation: https://docs.myvariant.info
MyChem.info Documentation: https://docs.mychem.info
Publication: Xin J et al. Genome Biology 17:91 (2016). https://doi.org/10.1186/s13059-016-0953-9

Files

Just SKILL.md in skills/domains/biomedical/biothings-api of wentorai/research-plugins.

Open the folder on GitHubat commit bf44b3c

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in wentorai/research-plugins, which our catalogue first saw on October 7, 2026.

brycewang-stanford/Auto-Empirical-Research-Skillsskills/43-wentorai-research-plugins/skills/domains/biomedical/biothings-api

Compare with similar skills

Biothings API next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Biothings API compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Biothings API this skillwentorai/research-plugins	298	1 repos	~2.2k	Automated safety check: Pass	MIT	3 mo ago
Dbsnp Databasegoogle-deepmind/science-skills	3.2k	2 repos	~3.4k	Automated safety check: Notes	Apache-2.0	24 days ago
Biopython Bioinformaticsaiming-lab/AutoResearchClaw	15k	—	~810	Automated safety check: Pass	MIT	1 mo ago
Bio Write SequencesGPTomics/bioSkills	1.2k	3 repos	~2.1k	Automated safety check: Pass	MIT	1 mo ago
Mako Loreliebaojun/MakoCode	155	—	~692	Automated safety check: Pass	Custom licence	1 mo ago
PubMed REST API Searchdavila7/claude-code-templates	32k	14 repos	~3.9k	Automated safety check: Pass	MIT	today

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Questions about Biothings API

What does Biothings API do?

Query gene, variant, and drug annotations via BioThings APIs. Biothings API is an agent skill from wentorai/research-plugins.

When should I use Biothings API?

Biothings API fits situations like: research & Science work in your project.

How do I install Biothings API in Claude Code?

Run `npx skills add wentorai/research-plugins --skill biothings-api -a claude-code`. Or copy the skill folder (skills/domains/biomedical/biothings-api in wentorai/research-plugins) into .claude/skills/biothings-api in your project. Claude Code loads it when a task matches its description.

How do I install Biothings API in Codex?

Run `npx skills add wentorai/research-plugins --skill biothings-api -a codex`. Or copy the skill folder (skills/domains/biomedical/biothings-api in wentorai/research-plugins) into .agents/skills/biothings-api in your project. Codex loads it when a task matches its description.

Can I use Biothings API in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add wentorai/research-plugins --skill biothings-api -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/biothings-api, .gemini/skills/biothings-api, .github/skills/biothings-api and .opencode/skills/biothings-api in your project.

What does Biothings API need to run?

Going by SKILL.md and its folder, Biothings API needs the command-line tools its instructions call (curl). Our summary lists: Python 3.

Does Biothings API access the network?

SKILL.md names 2 domains. As links in the text: biothings.io and doi.org. This is read from the text; nothing was executed.

Is Biothings API safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Biothings API use?

Biothings API is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Biothings API use?

About 2.2k tokens (SKILL.md is roughly 8.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Biothings API?

Skills that share tags, products or a category with Biothings API: Dbsnp Database (google-deepmind/science-skills, 3.2k stars), Biopython Bioinformatics (aiming-lab/AutoResearchClaw, 15k stars), Bio Write Sequences (GPTomics/bioSkills, 1.2k stars) and Mako Lore (liebaojun/MakoCode, 155 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Biothings API?

wentorai (a GitHub user) maintains it in wentorai/research-plugins, which has 298 GitHub stars. The repository holds 405 skills in this directory. The repository was last updated on June 19, 2026.

Source: wentorai/research-plugins on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Biothings API

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

BioThings API Suite

Overview

Authentication

MyGene.info — Gene Annotations

Search Genes

Get Gene by ID

MyVariant.info — Variant Annotations

Search Variants

Get Variant by HGVS ID

MyChem.info — Drug & Chemical Annotations

Search Drugs/Chemicals

Get Chemical by ID

Query Syntax (Shared Across All Three APIs)

Rate Limits

Python Example: Cross-API Gene-Variant-Drug Lookup

Academic Use Cases

References

Files

Used in 1 other repository

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