PubMed REST API Search
davila7/claude-code-templates
Searches PubMed directly through its E-utilities REST API, with guidance on Boolean and MeSH query syntax, batch retrieval and citation data.
Recommends target journals for manuscript submission by analyzing the paper topic/abstract and the journal distribution of similar PubMed literature; use when users ask for journal…
Install Journal Skills
$ npx skills add aipoch/medical-research-skills --skill journal-skills -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aipoch/medical-research-skills journal-skills --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Evidence Insight/journal-skills' .claude/skills/journal-skills && rm -rf skills-srcUse ~/.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/
Install the "journal-skills" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/journal-skills into .claude/skills/journal-skills/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "journal-skills", 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 install https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/journal-skillsType 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.
$ npx skills add aipoch/medical-research-skills --skill journal-skills -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aipoch/medical-research-skills journal-skills --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/'scientific-skills/Evidence Insight/journal-skills' .agents/skills/journal-skills && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "journal-skills" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/journal-skills into .agents/skills/journal-skills/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "journal-skills", 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.
$ npx skills add aipoch/medical-research-skills --skill journal-skills -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aipoch/medical-research-skills journal-skills --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/'scientific-skills/Evidence Insight/journal-skills' .cursor/skills/journal-skills && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "journal-skills" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/journal-skills into .cursor/skills/journal-skills/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "journal-skills", 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 https://github.com/aipoch/medical-research-skills.git --path 'scientific-skills/Evidence Insight/journal-skills'--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add aipoch/medical-research-skills --skill journal-skills -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aipoch/medical-research-skills journal-skills --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/'scientific-skills/Evidence Insight/journal-skills' .gemini/skills/journal-skills && rm -rf skills-srcUse ~/.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/
Install the "journal-skills" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/journal-skills into .gemini/skills/journal-skills/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "journal-skills", 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.
$ gh skill install aipoch/medical-research-skills journal-skillsInstalls 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).
$ npx skills add aipoch/medical-research-skills --skill journal-skills -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/'scientific-skills/Evidence Insight/journal-skills' .github/skills/journal-skills && rm -rf skills-srcUse ~/.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/
Install the "journal-skills" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/journal-skills into .github/skills/journal-skills/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "journal-skills", 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.
$ npx skills add aipoch/medical-research-skills --skill journal-skills -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install aipoch/medical-research-skills journal-skills --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/'scientific-skills/Evidence Insight/journal-skills' .opencode/skills/journal-skills && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "journal-skills" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/journal-skills into .opencode/skills/journal-skills/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "journal-skills", 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
journal-skills- GitHub stars
- 1.9k
- Token cost
- ~1.7k tokens
- SKILL.md length
- 815 words
- Files
- 6 (incl. scripts, references, assets)
- Skills in repo
- 578
- Repo updated
- First seen
- Licence
- MIT
At a glance
Recommends target journals for manuscript submission by analyzing the paper topic/abstract and the journal distribution of similar PubMed literature; use when users ask for journal…
- Works in 5 steps: Prepare inputs → Configure the script → Run the recommender → …
- Users ask for journal recommendation/matching
- SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 8 more sections
- Runs Python scripts from its folder; calls python; needs API_KEY
What it does
Journal Skills is an agent skill from aipoch/medical-research-skills. Recommends target journals for manuscript submission by analyzing the paper topic/abstract and the journal distribution of similar PubMed literature; use when users ask for journal recommendation/matching, submission strategy, PubMed search, or similar-literature statistics.
Its SKILL.md is about 1.7k tokens, which your agent loads only when the skill is triggered. The skill folder holds 8 other files, including scripts, reference files and assets (for example `POLISH_CHANGELOG.md`, `eval_report_journal-skills_result.json` and `references/guide.md`).
It sits in Research & Science, covering Academic paper search and Statistics. It works with PubMed and NCBI. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.
When your agent uses it
- Users ask for journal recommendation/matching
- Submission strategy
- Similar-literature statistics
Example prompts
- “Use the journal-skills skill to recommend target journals for manuscript submission by analyzing the paper topic/abstract and the journal…”
- “/journal-skills”
Requirements
- Python 3
- A credential in API_KEY
Workflow steps
5 steps, taken from the step headings in SKILL.md.
What it can do on your machine
Read from SKILL.md and the folder at commit 686e09d. 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
Ships 1 file in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
python
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names these keys or tokens, usually read from environment variables:
API_KEY
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Journal Skills loads about 1.7k tokens when it runs, and up to ~1.9k if it reads all its reference files. Until then it costs about 73 tokens; SKILL.md has 815 words of instructions outside code blocks.
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); the scripts in this folder are not scanned.
SKILL.md
The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 815 words, ~1,747 tokens.
Download SKILL.mdSave it as
.claude/skills/journal-skills/SKILL.md (or your agent's skills folder). This skill also uses 5 other files; get the full folder from GitHub.- name
- journal-skills
- description
- Recommends target journals for manuscript submission by analyzing the paper topic/abstract and the journal distribution of similar PubMed literature; use when users ask for journal recommendation/matching, submission strategy, PubMed search, or similar-literature statistics.
- license
- MIT
- author
- AIPOCH
When to Use
- You have a manuscript title/abstract and need a shortlist of suitable journals to submit to.
- You want evidence-based journal matching using similar PubMed literature and journal distribution statistics.
- You need to compare candidate journals by scope fit, open access requirements, and review/publication timelines.
- You must provide a clear matching rationale (why each journal fits) for internal review or co-author alignment.
- You are planning a submission strategy (primary target + backups) and want to highlight risks and alternatives.
Key Features
- Topic- and abstract-driven journal recommendation workflow.
- PubMed-based similar literature search and journal frequency distribution compilation.
- Candidate journal screening using scope, policy constraints (e.g., OA), and practical considerations (e.g., review cycle).
- Structured recommendation output with rationale, risks, and backup options.
- Reusable CSV template for consistent reporting.
Dependencies
- Python 3.9+ (recommended)
- PubMed E-utilities access (NCBI)
EMAILrequired (per NCBI policy)API_KEYoptional (recommended for higher rate limits)
Example Usage
1) Prepare inputs
Have the manuscript title and abstract ready.
2) Configure the script
Open scripts/pubmed_journal_recommender.py and set the CONFIG values:
EMAIL: your email (required)API_KEY: your NCBI API key (optional)- Output directory (if the script supports/requests it)
3) Run the recommender
python scripts/pubmed_journal_recommender.pyWhen prompted, paste the manuscript title and abstract. The script will query PubMed for similar records and produce journal statistics.
4) Produce a structured recommendation table
Use the template below to standardize the final output:
- Template:
assets/journal_recommendation_template.csv
Fill it with:
- Candidate journals (from the script’s distribution + domain knowledge)
- Matching rationale (scope fit + audience + similarity evidence)
- Constraints (OA, policies)
- Practical notes (review cycle, risks)
- Primary target and backup options
5) Follow the checklist and formatting guidance
For recommended output formats, checklists, and key points, see:
references/guide.md
Implementation Details
Workflow Overview
Topic and Scope Definition
- Identify the research field, subfield, and intended readership.
- Confirm journal type preferences and constraints (e.g., OA mandates).
Similar Literature Analysis (PubMed)
- Use the manuscript title/abstract to retrieve similar PubMed records.
- Aggregate results by journal to compute a distribution (e.g., counts per journal).
- Prioritize journals that appear frequently among highly relevant records.
Journal Screening
- Cross-check each candidate against:
- Journal scope/aims
- Policy requirements (OA, data availability, ethics)
- Review/publication timelines (if available)
- Remove journals that are out-of-scope or non-compliant.
- Cross-check each candidate against:
Recommendation Output
- Provide a ranked list with:
- Fit rationale (topic alignment + similarity evidence)
- Risks (scope mismatch, policy conflicts, timeline concerns)
- Alternatives (backup journals)
- Provide a ranked list with:
Key Parameters / Notes
- NCBI
EMAIL: required to comply with NCBI E-utilities usage policy. - NCBI
API_KEY: optional but recommended to reduce throttling and improve throughput. - Output structuring: use
assets/journal_recommendation_template.csvto ensure consistent fields and downstream usability.
When Not to Use
- Do not proceed when required input files, identifiers, parameters, or context are missing — ask the user to provide them first.
- Do not assume capabilities beyond this skill's declared scope when the user requests external operations or inferences.
- Do not proceed without user confirmation when overwriting existing results, executing high-cost batch operations, or expanding task scope.
Show full SKILL.md (333 more words)Show less
Required Inputs
| Field | Required | Format/Source | Example | If Missing |
|---|---|---|---|---|
| User task description | Yes | Text | Research question, writing goal, analysis objective | Stop and ask user to provide |
| Primary input material | Depends on task | Text, file path, ID, table, or literature | PMID, PDF, CSV, DOCX, keywords, etc. | Specify which material type is missing |
| Output preference | No | Text | Language, format, target journal, template | Use skill default format |
Output Contract
- Primary output: Structured result or target file aligned with this skill's objective.
- Optional output: Intermediate check notes, issue list, supplementary suggestions, or generated file paths.
- Format requirement: Unless the user specifies otherwise, prefer stable, reviewable Markdown or JSON; if the skill's bundled script requires a fixed format, use that format.
- If partially complete: Must explicitly mark as PARTIAL and state which steps are completed and which remain.
Failure Handling
- Missing critical input: Explicitly state which fields, files, or identifiers are missing and pause.
- Script, template, or resource execution failure: Report the failing step, likely cause, and recovery suggestions — do not silently degrade.
- Partial completion only: Return the verified portion first, then list remaining blockers and suggested next steps.
User Checkpoints
- Before executing batch processing, overwriting files, long-running searches, or multi-stage generation, confirm scope and output format with the user.
- Before proceeding when a key judgment is ambiguous, evidence is insufficient, or the workflow is entering the next stage, confirm with the user.
Input Validation
This skill accepts requests that match the documented purpose of journal-skills and include enough context to complete the workflow safely.
Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:
journal-skillsonly handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.
Quick Validation
- Check that key scripts, templates, or reference file paths this skill depends on exist.
- Check that the final output contains the core fields, sections, or files specified for this task.
- Check that results clearly mark assumptions, limitations, and incomplete items.
© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 5 other files (scripts, references, assets) in scientific-skills/Evidence Insight/journal-skills of aipoch/medical-research-skills.
- SKILL.md
- POLISH_CHANGELOG.md
- assets/journal_recommendation_template.csv
- eval_report_journal-skills_result.json
- references/guide.md
- scripts/pubmed_journal_recommender.py
Open the folder on GitHubat commit 686e09d
Compare with similar skills
Journal Skills 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Journal Skills this skillaipoch/medical-research-skills | 1.9k | — | ~1.7k | Automated safety check: Pass | MIT | |
| PubMed REST API Searchdavila7/claude-code-templates | 33k | 14 repos | ~3.9k | Automated safety check: Pass | MIT | |
| Pubmed Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~2.1k | Automated safety check: Notes | Apache-2.0 | |
| Ncbi Sequence Fetchgoogle-deepmind/science-skills | 3.2k | 1 repos | ~2.3k | Automated safety check: Notes | Apache-2.0 | |
| Pubmed Databasejaechang-hits/SciAgent-Skills | 374 | 1 repos | ~4.4k | Automated safety check: Pass | CC-BY-4.0 | |
| Scientific DB Pubmed Databaseaffaan-m/ECC | 277k | 1 repos | ~1.2k | Automated safety check: Pass | MIT |
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Pubmed Database
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Ncbi Sequence Fetch
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Pubmed Database
jaechang-hits/SciAgent-Skills
Programmatic PubMed access via NCBI E-utilities REST API. An agent skill from jaechang-hits/SciAgent-Skills.
Scientific DB Pubmed Database
affaan-m/ECC
Direct PubMed and NCBI E-utilities search workflows for biomedical literature, MeSH queries, PMID lookup, citation retrieval, and API-backed literature monitoring.
Mining Pubmed Literature
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Categories
Questions about Journal Skills
What does Journal Skills do?
Recommends target journals for manuscript submission by analyzing the paper topic/abstract and the journal distribution of similar PubMed literature; use when users ask for journal…. Journal Skills is an agent skill from aipoch/medical-research-skills. Recommends target journals for manuscript submission by analyzing the paper topic/abstract and the journal distribution of similar PubMed literature; use when users ask for journal recommendation/matching, submission strategy, PubMed search, or similar-literature statistics.
When should I use Journal Skills?
Journal Skills fits situations like: users ask for journal recommendation/matching; submission strategy; similar-literature statistics.
How do I install Journal Skills in Claude Code?
Run `npx skills add aipoch/medical-research-skills --skill journal-skills -a claude-code`. Or copy the skill folder (scientific-skills/Evidence Insight/journal-skills in aipoch/medical-research-skills) into .claude/skills/journal-skills in your project. Claude Code loads it when a task matches its description.
How do I install Journal Skills in Codex?
Run `npx skills add aipoch/medical-research-skills --skill journal-skills -a codex`. Or copy the skill folder (scientific-skills/Evidence Insight/journal-skills in aipoch/medical-research-skills) into .agents/skills/journal-skills in your project. Codex loads it when a task matches its description.
Can I use Journal Skills 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 aipoch/medical-research-skills --skill journal-skills -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/journal-skills, .gemini/skills/journal-skills, .github/skills/journal-skills and .opencode/skills/journal-skills in your project.
What does Journal Skills need to run?
Going by SKILL.md and its folder, Journal Skills needs Python for the scripts in its folder, the command-line tools its instructions call (python) and credentials named API_KEY. Our summary lists: Python 3; A credential in API_KEY.
Does Journal Skills access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Journal Skills 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Journal Skills use?
Journal Skills is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Journal Skills use?
About 1.7k tokens (SKILL.md is roughly 7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 189 tokens, read only when the agent opens those files.
What are the alternatives to Journal Skills?
Skills that share tags, products or a category with Journal Skills: PubMed REST API Search (davila7/claude-code-templates, 33k stars), Pubmed Database (google-deepmind/science-skills, 3.2k stars), Ncbi Sequence Fetch (google-deepmind/science-skills, 3.2k stars) and Pubmed Database (jaechang-hits/SciAgent-Skills, 374 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Journal Skills?
aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,937 GitHub stars. The repository holds 578 skills in this directory. The repository was last updated on September 17, 2026.
Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.