clearai-dsh 0.3.0 → 0.4.0

package/presets/clearai/template/skills/paper-lookup/references/medrxiv.md

@@ -1,104 +0,0 @@
-# medRxiv API
-
-medRxiv is a preprint server for health sciences. The API is identical to bioRxiv's API -- same endpoints, same response format -- just use `medrxiv` as the server parameter.
-
-**Important:** Like bioRxiv, there is **no keyword search**. Use Semantic Scholar, OpenAlex, or PubMed for keyword searches of medRxiv content.
-
-## Base URL
-
-```
-https://api.biorxiv.org
-```
-
-(Same base URL as bioRxiv -- the server is specified in the path.)
-
-## Authentication
-
-None required. Fully public API.
-
-## Key Endpoints
-
-### 1. Content Detail -- Browse by date range
-
-```
-GET /details/medrxiv/{interval}/{cursor}/{format}
-```
-
-| Parameter | Values | Description |
-|-----------|--------|-------------|
-| `interval` | `YYYY-MM-DD/YYYY-MM-DD` | Date range (inclusive) |
-| | `N` (integer) | N most recent preprints |
-| | `Nd` (integer + "d") | Last N days |
-| `cursor` | Integer (default `0`) | Pagination offset (100 per page) |
-| `format` | `json` (default), `xml` | Response format |
-
-Optional: `?category=cardiovascular%20medicine` (use URL-encoding for spaces)
-
-**Examples:**
-```
-https://api.biorxiv.org/details/medrxiv/2024-01-01/2024-01-31/0
-https://api.biorxiv.org/details/medrxiv/5
-https://api.biorxiv.org/details/medrxiv/10d
-```
-
-### 2. Content Detail -- DOI lookup
-
-```
-GET /details/medrxiv/{doi}/na/{format}
-```
-
-**Example:**
-```
-https://api.biorxiv.org/details/medrxiv/10.1101/2021.04.29.21256344/na/json
-```
-
-### 3. Published Article Links
-
-```
-GET /pubs/medrxiv/{interval}/{cursor}
-GET /pubs/medrxiv/{doi}/na
-```
-
-Links preprints to their published journal versions. Accepts both preprint DOI and published DOI.
-
-## Response Format
-
-Same as bioRxiv:
-
-```json
-{
-  "messages": [{
-    "status": "ok",
-    "count": 100,
-    "total": "502",
-    "cursor": 0
-  }],
-  "collection": [{
-    "title": "Paper title...",
-    "authors": "Surname, A.; Surname, B.",
-    "author_corresponding": "Full Name",
-    "author_corresponding_institution": "Institution",
-    "doi": "10.1101/2021.04.29.21256344",
-    "date": "2021-05-03",
-    "version": "1",
-    "type": "PUBLISHAHEADOFPRINT",
-    "license": "cc_by_nc_nd",
-    "category": "cardiovascular medicine",
-    "abstract": "Full abstract text...",
-    "published": "10.1371/journal.pone.0256482",
-    "server": "medRxiv"
-  }]
-}
-```
-
-## Pagination
-
-100 results per page. Use `cursor` parameter to paginate.
-
-## Rate Limits
-
-No documented rate limits. No authentication required.
-
-## Categories
-
-`addiction-medicine`, `allergy-and-immunology`, `anesthesia`, `cardiovascular-medicine`, `dentistry-and-oral-medicine`, `dermatology`, `emergency-medicine`, `endocrinology`, `epidemiology`, `forensic-medicine`, `gastroenterology`, `genetic-and-genomic-medicine`, `geriatric-medicine`, `health-economics`, `health-informatics`, `health-policy`, `health-systems-and-quality-improvement`, `hematology`, `hiv-aids`, `infectious-diseases`, `intensive-care-and-critical-care-medicine`, `medical-education`, `medical-ethics`, `nephrology`, `neurology`, `nursing`, `nutrition`, `obstetrics-and-gynecology`, `occupational-and-environmental-health`, `oncology`, `ophthalmology`, `orthopedics`, `otolaryngology`, `pain-medicine`, `palliative-medicine`, `pathology`, `pediatrics`, `pharmacology-and-therapeutics`, `primary-care-research`, `psychiatry-and-clinical-psychology`, `public-and-global-health`, `radiology-and-imaging`, `rehabilitation-medicine-and-physical-therapy`, `respiratory-medicine`, `rheumatology`, `sexual-and-reproductive-health`, `sports-medicine`, `surgery`, `toxicology`, `transplantation`, `urology`

package/presets/clearai/template/skills/paper-lookup/references/openalex.md

@@ -1,174 +0,0 @@
-# OpenAlex API
-
-OpenAlex is a comprehensive index of 250M+ scholarly works, authors, institutions, sources, and topics. It's the broadest multidisciplinary database in this skill.
-
-## Base URL
-
-```
-https://api.openalex.org
-```
-
-## Authentication
-
-- **API key recommended** (free). Get one at https://openalex.org/settings/api
-- Pass as: `?api_key=YOUR_KEY`
-- Legacy polite pool still works: add `?mailto=you@example.com` for better rate limits
-
-## Rate Limits
-
-- **100 requests/second** max
-- Usage-based pricing with $1/day free allowance
-- Single entity lookups by ID/DOI are free (unlimited)
-- List + filter queries: ~$0.0001 each (~10,000/day free)
-- Search queries: ~$0.001 each (~1,000/day free)
-
-## Key Endpoints
-
-### 1. Get a single work
-
-```
-GET /works/{id}
-```
-
-Accepts multiple ID formats:
-```
-/works/W2741809807                              (OpenAlex ID)
-/works/doi:10.7717/peerj.4375                  (DOI)
-/works/pmid:29456894                            (PMID)
-/works/https://doi.org/10.7717/peerj.4375      (full DOI URL)
-```
-
-### 2. Search works
-
-```
-GET /works?search={query}&per_page={n}&page={n}
-```
-
-| Parameter | Default | Description |
-|-----------|---------|-------------|
-| `search` | -- | Full-text search (title, abstract, fulltext). Supports boolean: `AND`, `OR`, `NOT` (uppercase) |
-| `search.exact` | -- | No stemming |
-| `search.semantic` | -- | AI embedding search (beta, 1 req/s, max 50 results) |
-| `filter` | -- | Comma-separated `field:value` pairs |
-| `sort` | relevance | `cited_by_count:desc`, `publication_date:desc`, `relevance_score:desc` |
-| `per_page` | 25 | Results per page (max 100) |
-| `page` | 1 | Page number (max `page * per_page` = 10,000) |
-| `cursor` | -- | Use `*` for first page of deep pagination |
-| `select` | -- | Comma-separated fields to return |
-| `group_by` | -- | Aggregate by field |
-
-**Advanced search:** Supports wildcards (`machin*`), fuzzy (`machin~1`), proximity (`"climate change"~5`), boolean grouping.
-
-**Example:**
-```
-https://api.openalex.org/works?search=CRISPR+gene+therapy&filter=from_publication_date:2023-01-01&sort=cited_by_count:desc&per_page=10
-```
-
-### 3. Filter works
-
-```
-GET /works?filter={filters}
-```
-
-Key filter fields:
-| Filter | Example | Description |
-|--------|---------|-------------|
-| `from_publication_date` | `2023-01-01` | Published after date |
-| `to_publication_date` | `2024-12-31` | Published before date |
-| `publication_year` | `2024` | Exact year |
-| `type` | `article` | Work type |
-| `cited_by_count` | `>100` | Citation threshold |
-| `is_oa` | `true` | Open access only |
-| `has_abstract` | `true` | Has abstract |
-| `authorships.author.id` | `A5048491430` | By author ID |
-| `primary_location.source.id` | `S137773608` | By journal/source |
-| `institutions.country_code` | `us` | By country |
-| `concepts.id` | `C41008148` | By concept/topic |
-| `doi` | `10.1038/nature12373` | By DOI |
-
-**Operators:** `>`, `<`, `!` (negation), `|` (OR within filter)
-
-**Example:**
-```
-https://api.openalex.org/works?filter=from_publication_date:2024-01-01,type:article,is_oa:true,cited_by_count:>50
-```
-
-### 4. Other entities
-
-```
-GET /authors?search={name}
-GET /authors/{id}
-GET /sources?search={name}          (journals, repositories)
-GET /sources/{id}
-GET /institutions?search={name}
-GET /institutions/{id}
-GET /topics/{id}
-```
-
-Authors and institutions accept similar filter/sort/pagination parameters.
-
-### 5. Cursor pagination (for >10,000 results)
-
-```
-GET /works?filter=publication_year:2024&cursor=*&per_page=100
-```
-
-Response includes `meta.next_cursor`. Pass it as `cursor={value}` in the next request. Stop when `next_cursor` is null.
-
-## Response Format
-
-### Work object (key fields)
-
-```json
-{
-  "id": "https://openalex.org/W2741809807",
-  "doi": "https://doi.org/10.7717/peerj.4375",
-  "title": "The state of OA",
-  "publication_year": 2018,
-  "publication_date": "2018-02-13",
-  "type": "article",
-  "language": "en",
-  "is_retracted": false,
-  "cited_by_count": 1169,
-  "open_access": {
-    "is_oa": true,
-    "oa_status": "gold",
-    "oa_url": "https://doi.org/10.7717/peerj.4375"
-  },
-  "authorships": [{
-    "author": {"id": "https://openalex.org/A5048491430", "display_name": "Heather Piwowar"},
-    "institutions": [{"display_name": "Impactstory"}]
-  }],
-  "primary_location": {
-    "source": {"display_name": "PeerJ", "issn_l": "2167-8359"}
-  },
-  "abstract_inverted_index": {"Despite": [0], "growing": [1], "interest": [2], ...},
-  "referenced_works": ["https://openalex.org/W123...", ...],
-  "ids": {"openalex": "...", "doi": "...", "pmid": "..."}
-}
-```
-
-### Abstract inverted index
-
-Abstracts are stored as `{word: [positions]}`. To reconstruct:
-```python
-def reconstruct(inverted_index):
-    positions = {}
-    for word, indices in inverted_index.items():
-        for idx in indices:
-            positions[idx] = word
-    return ' '.join(positions[i] for i in sorted(positions.keys()))
-```
-
-### List response
-
-```json
-{
-  "meta": {"count": 3771834, "page": 1, "per_page": 10},
-  "results": [...]
-}
-```
-
-## Error Format
-
-HTTP 403 for invalid API key, 429 for rate limit exceeded. Error responses include a message field.

package/presets/clearai/template/skills/paper-lookup/references/pmc.md

@@ -1,152 +0,0 @@
-# PMC (PubMed Central)
-
-PMC is a **full-text archive** of biomedical and life sciences articles. It is separate from PubMed -- PubMed has citations/abstracts, PMC has full text. Not all PubMed articles are in PMC, and vice versa.
-
-## E-utilities for PMC
-
-### Base URL
-
-```
-https://eutils.ncbi.nlm.nih.gov/entrez/eutils/
-```
-
-Same E-utilities as PubMed, but with `db=pmc`.
-
-### eSearch -- Search PMC
-
-```
-GET /esearch.fcgi?db=pmc&term={query}&retmode=json
-```
-
-Same parameters as PubMed eSearch. Returns PMC UIDs (numeric, e.g., `13033346`). You need to prepend "PMC" to get a PMCID (e.g., `PMC13033346`).
-
-### eFetch -- Get Full Text XML
-
-```
-GET /efetch.fcgi?db=pmc&id={pmcid}&retmode=xml
-```
-
-| rettype | retmode | Returns |
-|---------|---------|---------|
-| *(omit)* | `xml` | **Full text JATS XML** (body, figures, references) |
-| `medline` | `text` | MEDLINE format |
-
-**Example:**
-```
-https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=7029759&retmode=xml
-```
-
-The XML uses JATS (Journal Article Tag Suite) format:
-- `<front>` -- journal metadata, article metadata, author info
-- `<body>` -- full article text with `<sec>` sections, `<p>` paragraphs, `<fig>` figures
-- `<back>` -- `<ref-list>` with all references
-
-Pass numeric IDs only (not "PMC7029759", just "7029759").
-
-## BioC API -- Structured Full Text
-
-An alternative way to get full text in a structured passage format.
-
-### Base URL
-
-```
-https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/
-```
-
-### Endpoint
-
-```
-GET /BioC_{format}/{id}/{encoding}
-```
-
-| Parameter | Values |
-|-----------|--------|
-| `format` | `json` or `xml` |
-| `id` | PMID (e.g., `17299597`) or PMCID (e.g., `PMC7029759`) |
-| `encoding` | `unicode` or `ascii` |
-
-**Example:**
-```
-https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_json/PMC7029759/unicode
-```
-
-**Response structure (JSON):**
-```json
-{
-  "source": "PMC",
-  "documents": [{
-    "id": "PMC7029759",
-    "infons": {"license": "...", "doi": "..."},
-    "passages": [
-      {
-        "offset": 0,
-        "infons": {"section_type": "TITLE"},
-        "text": "Article title..."
-      },
-      {
-        "offset": 42,
-        "infons": {"section_type": "ABSTRACT"},
-        "text": "Abstract text..."
-      },
-      {
-        "offset": 500,
-        "infons": {"section_type": "INTRO"},
-        "text": "Introduction text..."
-      }
-    ]
-  }]
-}
-```
-
-Section types: `TITLE`, `ABSTRACT`, `INTRO`, `METHODS`, `RESULTS`, `DISCUSS`, `CONCL`, `REF`, `SUPPL`, `FIG`, `TABLE`
-
-**Coverage:** ~3 million articles from the PMC Open Access Subset.
-
-## PMC ID Converter API
-
-Converts between PMID, PMCID, DOI, and Manuscript ID.
-
-### Base URL
-
-```
-https://pmc.ncbi.nlm.nih.gov/tools/idconv/api/v1/articles/
-```
-
-### Parameters
-
-| Parameter | Required | Description |
-|-----------|----------|-------------|
-| `ids` | Yes | Up to 200 comma-separated IDs |
-| `idtype` | No | `pmcid`, `pmid`, `mid`, `doi` (default: auto-detect) |
-| `format` | No | `json`, `xml`, `csv` (default: xml) |
-| `tool` | Recommended | Your application name |
-| `email` | Recommended | Your contact email |
-
-**Example:**
-```
-https://pmc.ncbi.nlm.nih.gov/tools/idconv/api/v1/articles/?ids=PMC7029759&format=json
-```
-
-**Response:**
-```json
-{
-  "status": "ok",
-  "records": [{
-    "pmcid": "PMC7029759",
-    "pmid": "32117569",
-    "doi": "10.12688/f1000research.22211.2"
-  }]
-}
-```
-
-Only returns results for articles that are in PMC. If an article is in PubMed but not PMC, no PMCID will be returned.
-
-## Rate Limits
-
-| Service | Limit |
-|---------|-------|
-| E-utilities (`db=pmc`) | 3/sec without key, 10/sec with key |
-| BioC API | Follow general NCBI policy (3/sec without key) |
-| ID Converter | Follow general NCBI policy |
-
-Include `tool` and `email` parameters on E-utility requests. Large batch jobs should run outside peak hours (Mon-Fri 5AM-9PM ET).

package/presets/clearai/template/skills/paper-lookup/references/pubmed.md

@@ -1,124 +0,0 @@
-# PubMed (NCBI E-utilities)
-
-PubMed provides citations, abstracts, and metadata for 37M+ biomedical and life science articles. It does NOT contain full text -- for that, use PMC.
-
-## Base URL
-
-```
-https://eutils.ncbi.nlm.nih.gov/entrez/eutils/
-```
-
-## Authentication
-
-- **API key optional** but recommended. Without: 3 req/sec. With: 10 req/sec.
-- Pass as: `&api_key=YOUR_KEY`
-- Also include `&tool=your_app_name&email=your@email.com` on all requests.
-
-## Key Endpoints
-
-### 1. eSearch -- Search and get PMIDs
-
-```
-GET /esearch.fcgi?db=pubmed&term={query}&retmode=json
-```
-
-| Parameter | Required | Default | Description |
-|-----------|----------|---------|-------------|
-| `db` | Yes | -- | `pubmed` |
-| `term` | Yes | -- | Search query. Supports PubMed syntax: field tags `[AU]`, `[TI]`, `[TA]`, `[MH]` (MeSH), boolean AND/OR/NOT |
-| `retmax` | No | 20 | Max PMIDs returned (max 10,000) |
-| `retstart` | No | 0 | Pagination offset |
-| `retmode` | No | `xml` | `json` or `xml` |
-| `rettype` | No | `uilist` | `uilist` (IDs) or `count` (count only) |
-| `sort` | No | `relevance` | `relevance`, `pub_date`, `Author`, `JournalName` |
-| `datetype` | No | -- | `pdat` (publication), `mdat` (modification), `edat` (entrez) |
-| `mindate` / `maxdate` | No | -- | Date range `YYYY/MM/DD` |
-| `reldate` | No | -- | Items from last N days |
-| `usehistory` | No | -- | `y` to store on History Server for large result sets |
-
-**Example:**
-```
-https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CRISPR+gene+therapy&retmode=json&retmax=5&sort=pub_date
-```
-
-**Response:**
-```json
-{
-  "esearchresult": {
-    "count": "224107",
-    "retmax": "5",
-    "retstart": "0",
-    "idlist": ["39984857", "39984678", "39984543", "39984210", "39983901"]
-  }
-}
-```
-
-### 2. eSummary -- Get document summaries
-
-```
-GET /esummary.fcgi?db=pubmed&id={pmids}&retmode=json
-```
-
-| Parameter | Required | Description |
-|-----------|----------|-------------|
-| `db` | Yes | `pubmed` |
-| `id` | Yes | Comma-separated PMIDs (max 10,000) |
-| `retmode` | No | `json` or `xml` |
-
-**Example:**
-```
-https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=39984857,39984678&retmode=json
-```
-
-**Response fields:** `uid`, `pubdate`, `source` (journal), `authors`, `title`, `volume`, `issue`, `pages`, `fulljournalname`, `elocationid` (DOI), `articleids` (PMC, DOI, etc.), `pubtype`, `pmcrefcount`
-
-### 3. eFetch -- Retrieve full records (abstracts, MEDLINE)
-
-```
-GET /efetch.fcgi?db=pubmed&id={pmids}&rettype={type}&retmode={mode}
-```
-
-| rettype | retmode | Returns |
-|---------|---------|---------|
-| *(omit)* | `xml` | Full PubMed XML (citation + abstract) |
-| `medline` | `text` | MEDLINE format |
-| `abstract` | `text` | Plain text abstract |
-| `uilist` | `text` | PMID list |
-
-**Example -- get abstracts as XML:**
-```
-https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=39984857&retmode=xml
-```
-
-The XML contains `<PubmedArticle>` with `<MedlineCitation>` (title, abstract, MeSH terms, authors) and `<PubmedData>` (article IDs, publication history).
-
-### 4. eLink -- Find related articles
-
-```
-GET /elink.fcgi?dbfrom=pubmed&db=pubmed&id={pmid}&cmd=neighbor_score&retmode=json
-```
-
-Returns related PMIDs with relevance scores.
-
-## Search Syntax Tips
-
-- **Field tags:** `aspirin[TI]` (title), `Smith J[AU]` (author), `Nature[TA]` (journal), `neoplasms[MH]` (MeSH heading)
-- **Boolean:** `CRISPR AND (therapy OR treatment)`
-- **Date range:** `2020/01/01:2024/12/31[PDAT]`
-- **Publication type:** `review[PT]`, `clinical trial[PT]`
-- **Organism:** `humans[MH]`, `mice[MH]`
-
-## Rate Limits
-
-- **3 requests/second** without API key
-- **10 requests/second** with API key
-- Include `tool` and `email` parameters on every request
-- Large batch jobs should run outside peak hours (Mon-Fri 5AM-9PM ET)
-
-## Error Format
-
-```json
-{"error": "API rate limit exceeded", "count": "11"}
-```
-
-HTTP 400 for bad requests, 429 for rate limiting.