Agent skill

Bioc Pmc API

by wentorai in wentorai/research-plugins

Access PMC Open Access articles in BioC format for text mining

MITAuto-check passedAI & LLM Engineering

Install Bioc Pmc API

skills CLI

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

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

GitHub CLI

$ gh skill install wentorai/research-plugins bioc-pmc-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/literature/fulltext/bioc-pmc-api .claude/skills/bioc-pmc-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 "bioc-pmc-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/fulltext/bioc-pmc-api into .claude/skills/bioc-pmc-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioc-pmc-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/literature/fulltext/bioc-pmc-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 bioc-pmc-api -a codex

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

GitHub CLI

$ gh skill install wentorai/research-plugins bioc-pmc-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/literature/fulltext/bioc-pmc-api .agents/skills/bioc-pmc-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 "bioc-pmc-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/fulltext/bioc-pmc-api into .agents/skills/bioc-pmc-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioc-pmc-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 bioc-pmc-api -a cursor

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

GitHub CLI

$ gh skill install wentorai/research-plugins bioc-pmc-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/literature/fulltext/bioc-pmc-api .cursor/skills/bioc-pmc-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 "bioc-pmc-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/fulltext/bioc-pmc-api into .cursor/skills/bioc-pmc-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioc-pmc-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/literature/fulltext/bioc-pmc-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 bioc-pmc-api -a gemini-cli

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

GitHub CLI

$ gh skill install wentorai/research-plugins bioc-pmc-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/literature/fulltext/bioc-pmc-api .gemini/skills/bioc-pmc-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 "bioc-pmc-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/fulltext/bioc-pmc-api into .gemini/skills/bioc-pmc-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioc-pmc-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 bioc-pmc-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 bioc-pmc-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/literature/fulltext/bioc-pmc-api .github/skills/bioc-pmc-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 "bioc-pmc-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/fulltext/bioc-pmc-api into .github/skills/bioc-pmc-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioc-pmc-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 bioc-pmc-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 bioc-pmc-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/literature/fulltext/bioc-pmc-api .opencode/skills/bioc-pmc-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 "bioc-pmc-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/fulltext/bioc-pmc-api into .opencode/skills/bioc-pmc-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioc-pmc-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: bioc-pmc-api
GitHub stars: 298
Used in: 1 other repo
Token cost: ~1.2k tokens
SKILL.md length: 204 words
Files: 1
Skills in repo: 405
Repo updated: Jun 19, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Access PMC Open Access articles in BioC format for text mining

Tasks that involve Natural language processing
SKILL.md covers Overview, API Endpoints, BioC JSON Structure and Python Usage, plus 4 more sections
Calls curl; reaches ncbi.nlm.nih.gov

What it does

Bioc Pmc API is an agent skill from wentorai/research-plugins. Access PMC Open Access articles in BioC format for text mining

Its SKILL.md is about 1.2k 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 AI & LLM Engineering, covering Natural language processing. 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

Tasks that involve Natural language processing

Example prompts

“/bioc-pmc-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
Hosts in commands or code, which the agent is likely to contact:
- ncbi.nlm.nih.gov
Also links to:
- bioc.sourceforge.net
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

Bioc Pmc API loads about 1.2k tokens when it runs. Until then it costs about 19 tokens; SKILL.md has 204 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: ~1.2k

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). 204 words, ~1,160 tokens.

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

name: bioc-pmc-api
description: Access PMC Open Access articles in BioC format for text mining

BioC API for PMC Open Access

Overview

The BioC API provides full-text articles from PubMed Central (PMC) in the BioC format — a simplified XML/JSON structure designed specifically for biomedical text mining. Unlike the standard PMC OAI service (which returns JATS XML), BioC pre-segments text into passages with offset annotations, making it ideal for NLP pipelines, named entity recognition, relation extraction, and other text mining tasks. Free, no authentication required.

API Endpoints

Base URL

https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_json/{PMCID}/unicode

Retrieve by PMC ID

bash

# JSON format (recommended for programmatic use)
curl "https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_json/PMC6267067/unicode"

# XML format
curl "https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_xml/PMC6267067/unicode"

# ASCII encoding (strips non-ASCII characters)
curl "https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_json/PMC6267067/ascii"

Retrieve by PubMed ID

bash

# Convert PMID to PMCID first, then query
curl "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?ids=29346600&format=json"
# Returns: {"records": [{"pmid": "29346600", "pmcid": "PMC6267067", ...}]}

BioC JSON Structure

json

{
  "source": "PMC",
  "date": "2024-01-15",
  "key": "collection.key",
  "documents": [
    {
      "id": "PMC6267067",
      "passages": [
        {
          "infons": {
            "section_type": "TITLE",
            "type": "title"
          },
          "offset": 0,
          "text": "Article Title Here"
        },
        {
          "infons": {
            "section_type": "ABSTRACT",
            "type": "abstract"
          },
          "offset": 25,
          "text": "Background: This study investigates..."
        },
        {
          "infons": {
            "section_type": "INTRO",
            "type": "paragraph"
          },
          "offset": 350,
          "text": "The introduction text..."
        }
      ]
    }
  ]
}

Key fields:

passages[].infons.section_type: TITLE, ABSTRACT, INTRO, METHODS, RESULTS, DISCUSS, CONCL, REF, FIG, TABLE
passages[].offset: Character offset from document start
passages[].text: Plain text content of the passage

Python Usage

python

import requests
import json

def get_bioc_article(pmcid: str, fmt: str = "json") -> dict:
    """Fetch a PMC article in BioC format."""
    url = f"https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_{fmt}/{pmcid}/unicode"
    resp = requests.get(url, timeout=30)
    resp.raise_for_status()
    return resp.json() if fmt == "json" else resp.text

def extract_sections(bioc_doc: dict) -> dict:
    """Extract text organized by section type."""
    sections = {}
    for doc in bioc_doc.get("documents", []):
        for passage in doc.get("passages", []):
            section = passage.get("infons", {}).get("section_type", "OTHER")
            text = passage.get("text", "")
            sections.setdefault(section, []).append(text)
    return {k: "\n".join(v) for k, v in sections.items()}

# Example: fetch and parse
article = get_bioc_article("PMC6267067")
sections = extract_sections(article)
print(f"Title: {sections.get('TITLE', 'N/A')}")
print(f"Abstract length: {len(sections.get('ABSTRACT', ''))} chars")
print(f"Sections found: {list(sections.keys())}")

Data Coverage

PMC Open Access Subset: ~4M+ articles with CC licenses
Author Manuscript Collection: NIH-funded author manuscripts
Updates: New articles added daily

Rate Limits

Follow NCBI standard: 3 requests per second
For bulk access, use the PMC FTP service instead
Add tool=your_tool_name&email=your@email.com to requests for priority queue

Citation

When using this API in publications, cite:

Comeau DC, Wei CH, Islamaj Dogan R, Lu Z. PMC text mining subset in BioC: about 3 million full text articles and growing. Bioinformatics, btz070, 2019.

References

Files

Just SKILL.md in skills/literature/fulltext/bioc-pmc-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/literature/fulltext/bioc-pmc-api

Compare with similar skills

Bioc Pmc 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.

Bioc Pmc API compared with similar skills
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Bioconductor VissebioMate-AI/biomate-bioconductor-kb	804	—	~1.4k	Automated safety check: Pass	Custom licence	3 mo ago
Hugging Face TokenizersOrchestra-Research/AI-Research-SKILLs	13k	6 repos	~3.4k	Automated safety check: Pass	MIT	3 mo ago
OpenMed Model Card Writermaziyarpanahi/openmed	5.5k	—	~1.8k	Automated safety check: Pass	Apache-2.0	today

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Questions about Bioc Pmc API

What does Bioc Pmc API do?

Access PMC Open Access articles in BioC format for text mining. Bioc Pmc API is an agent skill from wentorai/research-plugins.

When should I use Bioc Pmc API?

Bioc Pmc API fits situations like: tasks that involve Natural language processing.

How do I install Bioc Pmc API in Claude Code?

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

How do I install Bioc Pmc API in Codex?

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

Can I use Bioc Pmc 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 bioc-pmc-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/bioc-pmc-api, .gemini/skills/bioc-pmc-api, .github/skills/bioc-pmc-api and .opencode/skills/bioc-pmc-api in your project.

What does Bioc Pmc API need to run?

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

Does Bioc Pmc API access the network?

SKILL.md names 2 domains. In commands or code: ncbi.nlm.nih.gov; the agent is likely to contact it when it follows the instructions. As links in the text: bioc.sourceforge.net. This is read from the text; nothing was executed.

Is Bioc Pmc 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 Bioc Pmc API use?

Bioc Pmc 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 Bioc Pmc API use?

About 1.2k tokens (SKILL.md is roughly 4.6k 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 Bioc Pmc API?

Skills that share tags, products or a category with Bioc Pmc API: Building With Openmed (maziyarpanahi/openmed, 5.5k stars), Annual Meeting Of The Association For Computational Linguistics (franklee16/academic-research-skills, 223 stars), Bioconductor Visse (bioMate-AI/biomate-bioconductor-kb, 804 stars) and Hugging Face Tokenizers (Orchestra-Research/AI-Research-SKILLs, 13k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bioc Pmc 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 Bioc Pmc 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

BioC API for PMC Open Access

Overview

API Endpoints

Base URL

Retrieve by PMC ID

Retrieve by PubMed ID

BioC JSON Structure

Python Usage

Data Coverage

Rate Limits

Citation

References

Files

Used in 1 other repository

Compare with similar skills

Similar skills

More from wentorai/research-plugins

Related

Questions about Bioc Pmc API