wotann 0.5.0 → 0.5.39

package/skills/scientific/markdown-mermaid-writing/templates/status_report.md

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+<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
+
+# Status Report / Executive Briefing Template
+
+> **Back to [Markdown Style Guide](../markdown_style_guide.md)** — Read the style guide first for formatting, citation, and emoji rules.
+
+**Use this template for:** Weekly/monthly status updates, executive briefings, project health reports, quarterly reviews, sprint retrospectives, or any document that updates stakeholders on progress, risks, and decisions needed. Designed to be read in under 5 minutes by someone with decision-making authority.
+
+**Key features:** TL;DR at the top for executives who won't read further, traffic-light health indicators, explicit "decisions needed" section that surfaces blockers, metrics table with trends, and risk register with mitigations.
+
+**Philosophy:** The #1 failure mode of status reports is burying the important stuff in a wall of accomplishments. Lead with what needs attention. If the reader only has 30 seconds, the TL;DR and health summary give them what they need. If they have 5 minutes, the full report answers every follow-up question they'd ask. Never make leadership dig for the thing they need to act on.
+
+---
+
+## How to Use
+
+1. Copy this file for each reporting period
+2. Name it by date: `status-2026-02-14.md` or `status-week-07.md`
+3. **Fill in the TL;DR first** — if you can't summarize it, you don't understand it yet
+4. Be honest about health status — green means green, not "green because I'm optimistic"
+5. Add [Mermaid diagrams](../mermaid_style_guide.md) for progress timelines, architecture changes, or risk impact flows
+
+---
+
+## The Template
+
+Everything below the line is the template. Copy from here:
+
+---
+
+# [Project/Team Name] — Status Report
+
+_[Reporting period: Week of Month DD, YYYY / Month YYYY / Q# YYYY]_
+_[Author] · [Date]_
+
+---
+
+## 📋 TL;DR
+
+[3–5 bullet points. One sentence each. The most important things leadership needs to know. If they read nothing else, this is it.]
+
+- **Overall:** [One-sentence project health summary]
+- **Progress:** [Key milestone hit or approaching]
+- **Blocker:** [The biggest risk or decision needed, or "None" if clear]
+- **Next:** [What happens in the next period]
+
+---
+
+## 🚦 Health Summary
+
+| Area         | Status       | Trend | Notes                     |
+| ------------ | ------------ | ----- | ------------------------- |
+| **Schedule** | 🟢 On track  | →     | [Brief context]           |
+| **Scope**    | 🟡 At risk   | ↓     | [What's causing concern]  |
+| **Budget**   | 🟢 On track  | →     | [Brief context]           |
+| **Quality**  | 🟢 Good      | ↑     | [What's improving]        |
+| **Team**     | 🟡 Stretched | →     | [Staffing or morale note] |
+
+**Status key:** 🟢 On track · 🟡 At risk · 🔴 Off track / blocked
+**Trend key:** ↑ Improving · → Stable · ↓ Declining
+
+---
+
+## ⚠️ Decisions Needed
+
+> **This section is for items that require action from leadership or stakeholders.** If nothing needs a decision, write "No decisions needed this period."
+
+### Decision 1: [Specific question that needs an answer]
+
+**Context:** [Why this decision is needed now — 2–3 sentences]
+
+**Options:**
+
+| Option     | Impact         | Recommendation                  |
+| ---------- | -------------- | ------------------------------- |
+| [Option A] | [What happens] | [Recommended / Not recommended] |
+| [Option B] | [What happens] | [Recommended / Not recommended] |
+
+**Deadline:** [When this decision is needed by and what happens if it's delayed]
+
+### Decision 2: [Another question]
+
+[Same structure as above]
+
+---
+
+## 📊 Key Metrics
+
+| Metric                             | Previous | Current | Target   | Trend   |
+| ---------------------------------- | -------- | ------- | -------- | ------- |
+| [Metric 1 — e.g., Sprint velocity] | [Value]  | [Value] | [Target] | [↑/→/↓] |
+| [Metric 2 — e.g., Open bugs]       | [Value]  | [Value] | [Target] | [↑/→/↓] |
+| [Metric 3 — e.g., Test coverage]   | [Value]  | [Value] | [Target] | [↑/→/↓] |
+| [Metric 4 — e.g., Uptime SLA]      | [Value]  | [Value] | [Target] | [↑/→/↓] |
+
+<details>
+<summary><strong>📊 Detailed Metrics</strong></summary>
+
+[Extended metrics, charts, or breakdowns that support the summary table but would overwhelm the main report.]
+
+</details>
+
+---
+
+## ✅ Accomplishments
+
+### Completed this period
+
+- **[Accomplishment 1]** — [Impact or outcome. Why it matters.]
+- **[Accomplishment 2]** — [Impact]
+- **[Accomplishment 3]** — [Impact]
+
+### Milestones
+
+| Milestone     | Planned date | Actual date | Status         |
+| ------------- | ------------ | ----------- | -------------- |
+| [Milestone 1] | [Date]       | [Date or —] | ✅ Complete    |
+| [Milestone 2] | [Date]       | [Date or —] | 🔄 In progress |
+| [Milestone 3] | [Date]       | —           | 📋 Upcoming    |
+
+---
+
+## 🔄 In Progress
+
+| Work item | Owner    | Started | Expected completion | Status                         |
+| --------- | -------- | ------- | ------------------- | ------------------------------ |
+| [Item 1]  | [Person] | [Date]  | [Date]              | [On track / At risk / Blocked] |
+| [Item 2]  | [Person] | [Date]  | [Date]              | [Status]                       |
+| [Item 3]  | [Person] | [Date]  | [Date]              | [Status]                       |
+
+---
+
+## 🚨 Risks and Issues
+
+### Active risks
+
+| Risk     | Likelihood | Impact  | Mitigation                  | Owner    |
+| -------- | ---------- | ------- | --------------------------- | -------- |
+| [Risk 1] | 🟡 Medium  | 🔴 High | [What we're doing about it] | [Person] |
+| [Risk 2] | [Level]    | [Level] | [Mitigation]                | [Person] |
+
+### Active blockers
+
+| Blocker                 | Impact           | Needed from       | Status                           |
+| ----------------------- | ---------------- | ----------------- | -------------------------------- |
+| [Blocker 1 — or "None"] | [What's delayed] | [Who can unblock] | [Escalated / Waiting / Resolved] |
+
+<details>
+<summary><strong>📋 Resolved Issues</strong></summary>
+
+| Issue     | Resolution            | Date resolved |
+| --------- | --------------------- | ------------- |
+| [Issue 1] | [How it was resolved] | [Date]        |
+| [Issue 2] | [Resolution]          | [Date]        |
+
+</details>
+
+---
+
+## 📍 Plan for Next Period
+
+### Priorities
+
+1. **[Priority 1]** — [What will be done and expected outcome]
+2. **[Priority 2]** — [What will be done]
+3. **[Priority 3]** — [What will be done]
+
+### Key dates
+
+| Date   | Event              |
+| ------ | ------------------ |
+| [Date] | [What's happening] |
+| [Date] | [What's happening] |
+
+---
+
+## 🔗 References
+
+- [Project board / Jira / Linear](https://example.com) — Live work tracking
+- [Previous status report](../../docs/project/kanban/sprint-2026-w07-agentic-template-modernization.md) — For context on trends
+- [Relevant decision record](../adr/ADR-001-agent-optimized-documentation-system.md) — Background on recent changes
+
+---
+
+_Next report due: [Date]_

package/skills/scientific/paper-lookup/SKILL.md

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+---
+name: sci-paper-lookup
+description: Search 10 academic paper databases via REST APIs for research papers, preprints, and scholarly articles. Covers PubMed, PMC (full text), bioRxiv, medRxiv, arXiv, OpenAlex, Crossref, Semantic Scholar, CORE, Unpaywall. Use when searching for papers, citations, DOI/PMID lookups, abstracts, full text, open access, preprints, citation graphs, author search, or any scholarly literature query. Triggers on mentions of any supported database or requests like "find papers on X" or "look up this DOI".
+metadata:
+  skill-author: K-Dense Inc.
+---
+
+# Paper Lookup
+
+You have access to 10 academic paper databases through their REST APIs. Your job is to figure out which database(s) best serve the user's query, call them, and return the results.
+
+## Core Workflow
+
+1. **Understand the query** -- What is the user looking for? A specific paper by DOI? Papers on a topic? An author's publications? Open access PDFs? Full text? This determines which database(s) to hit.
+
+2. **Select database(s)** -- Use the database selection guide below. Many queries benefit from hitting multiple databases -- for example, searching PubMed for papers and then checking Unpaywall for open access copies.
+
+3. **Read the reference file** -- Each database has a reference file in `references/` with endpoint details, query formats, and example calls. Read the relevant file(s) before making API calls.
+
+4. **Make the API call(s)** -- See the **Making API Calls** section below for which HTTP fetch tool to use on your platform.
+
+5. **Return results** -- Always return:
+   - The **raw JSON** (or parsed XML for arXiv) response from each database
+   - A **list of databases queried** with the specific endpoints used
+   - If a query returned no results, say so explicitly rather than omitting it
+
+## Database Selection Guide
+
+Match the user's intent to the right database(s).
+
+### By Use Case
+
+| User is asking about... | Primary database(s) | Also consider |
+|---|---|---|
+| Papers on a biomedical topic | PubMed | Semantic Scholar, OpenAlex |
+| Full text of a biomedical article | PMC | CORE |
+| Biology preprints | bioRxiv | Semantic Scholar, OpenAlex |
+| Health/medical preprints | medRxiv | Semantic Scholar, OpenAlex |
+| Physics, math, or CS preprints | arXiv | Semantic Scholar, OpenAlex |
+| Papers across all fields | OpenAlex | Semantic Scholar, Crossref |
+| A specific paper by DOI | Crossref | Unpaywall, Semantic Scholar |
+| Open access PDF for a paper | Unpaywall | CORE, PMC |
+| Citation graph (who cites whom) | Semantic Scholar | OpenAlex |
+| Author's publications | Semantic Scholar | OpenAlex |
+| Paper recommendations | Semantic Scholar | -- |
+| Full text (any field) | CORE | PMC (biomedical only) |
+| Journal/publisher metadata | Crossref | OpenAlex |
+| Funder information | Crossref | OpenAlex |
+| Convert between PMID/PMCID/DOI | PMC (ID Converter) | Crossref |
+| Recent preprints by date | bioRxiv, medRxiv | arXiv |
+
+### Cross-Database Queries
+
+| User is asking about... | Databases to query |
+|---|---|
+| Everything about a paper (metadata + citations + OA) | Crossref + Semantic Scholar + Unpaywall |
+| Comprehensive literature search | PubMed + OpenAlex + Semantic Scholar |
+| Find and read a paper | PubMed (find) + Unpaywall (OA link) + PMC or CORE (full text) |
+| Preprint and its published version | bioRxiv/medRxiv + Crossref |
+| Author overview with citation metrics | Semantic Scholar + OpenAlex |
+
+When a query spans multiple needs (e.g., "find papers about CRISPR and get me the PDFs"), query the relevant databases in parallel.
+
+## Common Identifier Formats
+
+Different databases use different identifier systems. If a query fails, the identifier format may be wrong.
+
+| Identifier | Format | Example | Used by |
+|---|---|---|---|
+| DOI | `10.xxxx/xxxxx` | `10.1038/nature12373` | All databases |
+| PMID | Integer | `34567890` | PubMed, PMC, Semantic Scholar |
+| PMCID | `PMC` + digits | `PMC7029759` | PMC, Europe PMC |
+| arXiv ID | `YYMM.NNNNN` | `2103.15348` | arXiv, Semantic Scholar |
+| OpenAlex ID | `W` + digits | `W2741809807` | OpenAlex |
+| Semantic Scholar ID | 40-char hex | `649def34f8be...` | Semantic Scholar |
+| ORCID | `0000-XXXX-XXXX-XXXX` | `0000-0001-6187-6610` | OpenAlex, Crossref |
+| ISSN | `XXXX-XXXX` | `0028-0836` | Crossref, OpenAlex |
+
+**Cross-referencing IDs:** Semantic Scholar accepts DOI, PMID, PMCID, and arXiv ID via prefixes (e.g., `DOI:10.1038/nature12373`, `PMID:34567890`, `ARXIV:2103.15348`). OpenAlex accepts DOI and PMID via prefixes (`doi:10.1038/...`, `pmid:34567890`). Use the PMC ID Converter to translate between PMID, PMCID, and DOI.
+
+## API Keys and Access
+
+Most of these databases are fully open. A few benefit from API keys for higher rate limits.
+
+### Databases requiring or benefiting from API keys
+
+| Database | Env Variable | Required? | Registration |
+|---|---|---|---|
+| NCBI (PubMed, PMC) | `NCBI_API_KEY` | No (3 req/s without, 10 with) | https://www.ncbi.nlm.nih.gov/account/settings/ |
+| CORE | `CORE_API_KEY` | Yes for full text | https://core.ac.uk/services/api |
+| Semantic Scholar | `S2_API_KEY` | No (shared pool without) | https://www.semanticscholar.org/product/api#api-key-form |
+| OpenAlex | `OPENALEX_API_KEY` | Recommended | https://openalex.org/settings/api |
+
+### Fully open databases (no key needed)
+
+| Database | Notes |
+|---|---|
+| bioRxiv / medRxiv | No auth, no documented rate limits |
+| arXiv | No auth, max 1 request per 3 seconds |
+| Crossref | No auth; add `mailto` param for polite pool (2x rate limit) |
+| Unpaywall | No auth; requires `email` parameter |
+
+### Loading API keys
+
+1. **Check the environment first** -- the key may already be exported (e.g., `$NCBI_API_KEY`).
+2. **Fall back to `.env`** -- check `.env` in the current working directory.
+3. **Proceed without** -- most APIs still work at lower rate limits. Tell the user which key is missing and how to get one.
+
+## Making API Calls
+
+Use your environment's HTTP fetch tool to call REST endpoints:
+
+| Platform | HTTP Fetch Tool | Fallback |
+|---|---|---|
+| Claude Code | `WebFetch` | `curl` via Bash |
+| Gemini CLI | `web_fetch` | `curl` via shell |
+| Windsurf | `read_url_content` | `curl` via terminal |
+| Cursor | No dedicated fetch tool | `curl` via `run_terminal_cmd` |
+| Codex CLI | No dedicated fetch tool | `curl` via `shell` |
+| Cline | No dedicated fetch tool | `curl` via `execute_command` |
+
+If the fetch tool fails, fall back to `curl` via whatever shell tool is available.
+
+### Special cases
+
+- **arXiv returns Atom XML**, not JSON. Parse it or use `curl` and extract the relevant fields. Consider piping through a simple parser if available.
+- **PMC eFetch returns JATS XML** for full text. This is expected -- full text articles are in XML format.
+- **Crossref and Unpaywall** benefit from including a `mailto` parameter or email for the polite/fast pool.
+
+### Request guidelines
+
+- For **NCBI APIs** (PubMed, PMC): max 3 req/sec without key, 10 with key. Make requests sequentially.
+- For **arXiv**: max 1 request every 3 seconds. Be patient.
+- For **Crossref**: 5 req/sec (public), 10 req/sec (polite pool with `mailto`).
+- For other APIs with no strict limits, you can query multiple databases in parallel.
+- If you get HTTP 429 (rate limit), wait briefly and retry once.
+
+### Error recovery
+
+1. **Check the identifier format** -- use the Common Identifier Formats table. A PMID won't work in arXiv, an arXiv ID won't work in PubMed directly.
+2. **Try alternative identifiers** -- if a DOI fails in one database, try the title or PMID instead.
+3. **Try a different database** -- if PubMed returns nothing for a CS paper, try Semantic Scholar or OpenAlex.
+4. **Report the failure** -- tell the user which database failed, the error, and what you tried instead.
+
+## Output Format
+
+Structure your response like this:
+
+```
+## Databases Queried
+- **PubMed** -- esearch + esummary for "CRISPR gene therapy"
+- **Unpaywall** -- DOI lookup for 10.1038/...
+
+## Results
+
+### PubMed
+[raw JSON response or formatted results]
+
+### Unpaywall
+[raw JSON response]
+```
+
+If results are very large, present the most relevant portion and note that more data is available. But default to showing the full raw JSON -- the user asked for it.
+
+## Available Databases
+
+Read the relevant reference file before making any API call.
+
+### Biomedical Literature
+| Database | Reference File | What it covers |
+|---|---|---|
+| PubMed | `references/pubmed.md` | 37M+ biomedical citations, abstracts, MeSH terms |
+| PMC | `references/pmc.md` | 10M+ full-text biomedical articles (JATS XML), ID conversion |
+
+### Preprint Servers
+| Database | Reference File | What it covers |
+|---|---|---|
+| bioRxiv | `references/biorxiv.md` | Biology preprints (browse by date/DOI, no keyword search) |
+| medRxiv | `references/medrxiv.md` | Health sciences preprints (browse by date/DOI, no keyword search) |
+| arXiv | `references/arxiv.md` | Physics, math, CS, biology, economics preprints (keyword search, Atom XML) |
+
+### Multidisciplinary Indexes
+| Database | Reference File | What it covers |
+|---|---|---|
+| OpenAlex | `references/openalex.md` | 250M+ works, authors, institutions, topics, citation data |
+| Crossref | `references/crossref.md` | 150M+ DOI metadata, journals, funders, references |
+| Semantic Scholar | `references/semantic-scholar.md` | 200M+ papers, citation graphs, AI-generated TLDRs, recommendations |
+
+### Open Access & Full Text
+| Database | Reference File | What it covers |
+|---|---|---|
+| CORE | `references/core.md` | 37M+ full texts from OA repositories worldwide |
+| Unpaywall | `references/unpaywall.md` | OA status and PDF links for any DOI |

package/skills/scientific/paper-lookup/references/arxiv.md

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+# arXiv API
+
+arXiv is a preprint server for physics, mathematics, computer science, quantitative biology, quantitative finance, statistics, electrical engineering, and economics.
+
+**Important:** The arXiv API returns **Atom XML**, not JSON. There is no JSON option.
+
+## Base URL
+
+```
+https://export.arxiv.org/api/query
+```
+
+## Authentication
+
+None required. Fully public.
+
+## Query Parameters
+
+```
+GET https://export.arxiv.org/api/query?search_query={query}&start={n}&max_results={n}
+```
+
+| Parameter | Required | Default | Description |
+|-----------|----------|---------|-------------|
+| `search_query` | Yes* | -- | Search using field prefixes + boolean operators |
+| `id_list` | Yes* | -- | Comma-separated arXiv IDs (e.g., `2103.15348,2005.14165`) |
+| `start` | No | 0 | Pagination offset (0-based) |
+| `max_results` | No | 10 | Results per request (max 2000; absolute max 30000) |
+| `sortBy` | No | `relevance` | `relevance`, `lastUpdatedDate`, `submittedDate` |
+| `sortOrder` | No | `descending` | `ascending` or `descending` |
+
+*At least one of `search_query` or `id_list` must be provided. They can be combined (intersection).
+
+## Search Field Prefixes
+
+| Prefix | Searches |
+|--------|----------|
+| `ti:` | Title |
+| `au:` | Author |
+| `abs:` | Abstract |
+| `co:` | Comment |
+| `jr:` | Journal reference |
+| `cat:` | Subject category |
+| `rn:` | Report number |
+| `all:` | All fields |
+
+## Boolean Operators
+
+- `AND` -- both conditions
+- `OR` -- either condition
+- `ANDNOT` -- exclude
+- Parentheses for grouping (URL-encode as `%28` / `%29`)
+- Quoted phrases (URL-encode as `%22`)
+
+## Example Queries
+
+**Search all fields:**
+```
+https://export.arxiv.org/api/query?search_query=all:transformer+attention&max_results=5
+```
+
+**Author + category:**
+```
+https://export.arxiv.org/api/query?search_query=au:hinton+AND+cat:cs.LG&max_results=10
+```
+
+**Title search:**
+```
+https://export.arxiv.org/api/query?search_query=ti:%22attention+is+all+you+need%22
+```
+
+**By ID:**
+```
+https://export.arxiv.org/api/query?id_list=2103.15348
+```
+
+**Multiple IDs:**
+```
+https://export.arxiv.org/api/query?id_list=2103.15348,2005.14165,1706.03762
+```
+
+**Date range:**
+```
+https://export.arxiv.org/api/query?search_query=cat:cs.AI+AND+submittedDate:[202401010000+TO+202412312359]
+```
+
+## Response Format (Atom XML)
+
+```xml
+<feed xmlns="http://www.w3.org/2005/Atom">
+  <opensearch:totalResults>1234</opensearch:totalResults>
+  <opensearch:startIndex>0</opensearch:startIndex>
+  <opensearch:itemsPerPage>10</opensearch:itemsPerPage>
+
+  <entry>
+    <id>http://arxiv.org/abs/1706.03762v7</id>
+    <title>Attention Is All You Need</title>
+    <summary>The dominant sequence transduction models are based on...</summary>
+    <published>2017-06-12T17:57:34Z</published>
+    <updated>2023-08-02T00:00:12Z</updated>
+    <author><name>Ashish Vaswani</name></author>
+    <author><name>Noam Shazeer</name></author>
+    <!-- more authors -->
+    <category term="cs.CL" scheme="http://arxiv.org/schemas/atom"/>
+    <arxiv:primary_category term="cs.CL"/>
+    <link rel="alternate" href="http://arxiv.org/abs/1706.03762v7"/>
+    <link rel="related" type="application/pdf" href="http://arxiv.org/pdf/1706.03762v7"/>
+    <arxiv:doi>10.48550/arXiv.1706.03762</arxiv:doi>
+    <arxiv:comment>15 pages, 5 figures</arxiv:comment>
+    <arxiv:journal_ref>Advances in Neural Information Processing Systems 30 (NIPS 2017)</arxiv:journal_ref>
+  </entry>
+</feed>
+```
+
+### Key XML elements per entry
+
+| Element | Description |
+|---------|-------------|
+| `<id>` | arXiv URL: `http://arxiv.org/abs/{id}` |
+| `<title>` | Paper title |
+| `<summary>` | Abstract |
+| `<published>` | Original submission date (ISO 8601) |
+| `<updated>` | Date of latest version |
+| `<author><name>` | One per author |
+| `<category term="...">` | Subject categories |
+| `<arxiv:primary_category>` | Primary classification |
+| `<link rel="alternate">` | Abstract page URL |
+| `<link rel="related" title="pdf">` | PDF URL |
+| `<arxiv:doi>` | DOI (when available) |
+| `<arxiv:comment>` | Author comments |
+| `<arxiv:journal_ref>` | Journal reference |
+
+## Parsing Tips
+
+Since arXiv returns XML, you'll need to parse it. With `curl`, you can pipe the output and extract what you need. The XML namespace is `http://www.w3.org/2005/Atom` with arXiv extensions in `http://arxiv.org/schemas/atom`.
+
+For practical extraction, the key data is in `<entry>` elements. Each entry's `<id>` contains the arXiv ID in the URL path.
+
+## Common Categories
+
+| Category | Field |
+|----------|-------|
+| `cs.AI` | Artificial Intelligence |
+| `cs.CL` | Computation and Language (NLP) |
+| `cs.CV` | Computer Vision |
+| `cs.LG` | Machine Learning |
+| `stat.ML` | Machine Learning (Statistics) |
+| `q-bio` | Quantitative Biology |
+| `physics` | Physics (all subcategories) |
+| `math` | Mathematics (all subcategories) |
+| `econ` | Economics |
+| `eess` | Electrical Engineering and Systems Science |
+
+Full list: https://arxiv.org/category_taxonomy
+
+## Rate Limits
+
+- **1 request every 3 seconds** (hard limit)
+- Single connection at a time
+- Search results are cached daily -- same query won't show new results within 24 hours
+- For bulk data, use the OAI-PMH interface instead

package/skills/scientific/paper-lookup/references/biorxiv.md

@@ -0,0 +1,118 @@
+# bioRxiv API
+
+bioRxiv is a preprint server for biology. The API provides metadata for preprints, including title, authors, abstract, DOI, and publication status.
+
+**Important:** The bioRxiv API has **no keyword search**. It supports date-range browsing and DOI lookup only. For keyword search of bioRxiv preprints, use Semantic Scholar, OpenAlex, or CORE instead.
+
+## Base URL
+
+```
+https://api.biorxiv.org
+```
+
+## Authentication
+
+None required. Fully public API.
+
+## Key Endpoints
+
+### 1. Content Detail -- Browse by date range
+
+```
+GET /details/biorxiv/{interval}/{cursor}/{format}
+```
+
+| Parameter | Values | Description |
+|-----------|--------|-------------|
+| `interval` | `YYYY-MM-DD/YYYY-MM-DD` | Date range (inclusive). Keep ranges narrow (1-3 days) to avoid timeouts. |
+| | `N` (integer) | N most recent preprints |
+| | `Nd` (integer + "d") | Last N days |
+| `cursor` | Integer (default `0`) | Pagination offset (100 results per page) |
+| `format` | `json` (default), `xml` | Response format |
+
+Optional query parameter: `?category=neuroscience` (filter by category, use underscores for spaces)
+
+**Examples:**
+```
+https://api.biorxiv.org/details/biorxiv/2024-01-01/2024-01-31/0
+https://api.biorxiv.org/details/biorxiv/5
+https://api.biorxiv.org/details/biorxiv/10d
+https://api.biorxiv.org/details/biorxiv/2024-01-01/2024-01-31?category=neuroscience
+```
+
+### 2. Content Detail -- DOI lookup
+
+```
+GET /details/biorxiv/{doi}/na/{format}
+```
+
+**Example:**
+```
+https://api.biorxiv.org/details/biorxiv/10.1101/2024.01.16.575895/na/json
+```
+
+### 3. Published Article Links
+
+```
+GET /pubs/biorxiv/{interval}/{cursor}
+GET /pubs/biorxiv/{doi}/na
+```
+
+Links preprints to their published journal versions. Accepts both preprint DOI and published DOI.
+
+### 4. Publisher Filter
+
+```
+GET /publisher/{prefix}/{interval}/{cursor}
+```
+
+Find bioRxiv papers published by a specific publisher (by DOI prefix).
+
+**Example:**
+```
+https://api.biorxiv.org/publisher/10.15252/2024-01-01/2024-06-01/0
+```
+
+## Response Format
+
+```json
+{
+  "messages": [{
+    "status": "ok",
+    "count": 100,
+    "total": "1029",
+    "cursor": 0
+  }],
+  "collection": [{
+    "title": "Paper title...",
+    "authors": "Surname, A.; Surname, B.",
+    "author_corresponding": "Full Name",
+    "author_corresponding_institution": "Institution",
+    "doi": "10.1101/2024.01.16.575895",
+    "date": "2024-01-20",
+    "version": "1",
+    "type": "new results",
+    "license": "cc_no",
+    "category": "cancer biology",
+    "jatsxml": "https://www.biorxiv.org/content/early/.../source.xml",
+    "abstract": "Full abstract text...",
+    "published": "10.1158/2159-8290.CD-24-0187",
+    "server": "bioRxiv"
+  }]
+}
+```
+
+- `published` is `"NA"` if not yet published in a journal, or the published DOI if it has been.
+- `type` values: `new results`, `confirmatory results`, `contradictory results`
+
+## Pagination
+
+All multi-result endpoints return **100 results per page**. Use `cursor` to paginate. The `messages` object tells you the `total` count.
+
+## Rate Limits
+
+No documented rate limits. No authentication required. Be reasonable with request frequency.
+
+## Categories
+
+`animal-behavior-and-cognition`, `biochemistry`, `bioengineering`, `bioinformatics`, `biophysics`, `cancer-biology`, `cell-biology`, `clinical-trials`, `developmental-biology`, `ecology`, `epidemiology`, `evolutionary-biology`, `genetics`, `genomics`, `immunology`, `microbiology`, `molecular-biology`, `neuroscience`, `paleontology`, `pathology`, `pharmacology-and-toxicology`, `physiology`, `plant-biology`, `scientific-communication-and-education`, `synthetic-biology`, `systems-biology`, `zoology`