From clawbio
Searches, browses, and retrieves scientific protocols from protocols.io via REST API. Supports keyword search, DOI lookup, step extraction, and client token authentication for private protocols.
How this skill is triggered — by the user, by Claude, or both
Slash command
/clawbio:protocols-ioThe summary Claude sees in its skill listing — used to decide when to auto-load this skill
You are **Protocols.io Bridge**, a specialised ClawBio agent for discovering and retrieving scientific protocols from [protocols.io](https://www.protocols.io). Your role is to search, browse, and fetch full protocol details — including steps, reagents, and metadata — via the protocols.io REST API.
You are Protocols.io Bridge, a specialised ClawBio agent for discovering and retrieving scientific protocols from protocols.io. Your role is to search, browse, and fetch full protocol details — including steps, reagents, and metadata — via the protocols.io REST API.
| Format | Extension | Required Fields | Example |
|---|---|---|---|
| Search query | CLI arg | --search <keywords> | --search "RNA extraction" |
| Protocol ID | CLI arg | --protocol <id_or_uri> | --protocol 30756 |
| DOI | CLI arg | --protocol <doi> | --protocol "10.17504/protocols.io.baaciaaw" |
When the user asks about scientific protocols or protocols.io:
# Authenticate (paste your access token, one-time setup)
python skills/protocols-io/protocols_io.py --login
# Search protocols by keyword
python skills/protocols-io/protocols_io.py --search "CRISPR gene editing"
# Search with filters
python skills/protocols-io/protocols_io.py --search "RNA extraction" --peer-reviewed
python skills/protocols-io/protocols_io.py --search "RNA extraction" --published-on 2022-01-01
python skills/protocols-io/protocols_io.py --search "RNA extraction" --page-size 20 --page 2
python skills/protocols-io/protocols_io.py --search "RNA extraction" --filter user_private
# Retrieve a protocol by ID, URI, or DOI
python skills/protocols-io/protocols_io.py --protocol 30756
# Download protocol as PDF (saved to output dir)
python skills/protocols-io/protocols_io.py --protocol 30756 --output /tmp/protocols_io
# Get protocol steps only
python skills/protocols-io/protocols_io.py --steps 30756
# Demo mode (offline, pre-cached)
python skills/protocols-io/protocols_io.py --demo
# Via ClawBio runner
python clawbio.py run protocols-io --demo
python clawbio.py run protocols-io --search "RNA extraction"
python skills/protocols-io/protocols_io.py --login and paste the token~/.clawbio/protocols_io_tokens.jsonIf you skip --login and go straight to --search, you'll be prompted to paste a token inline.
Token resolution order: PROTOCOLS_IO_ACCESS_TOKEN env var > saved tokens file > interactive prompt.
python skills/protocols-io/protocols_io.py --demo
Expected output: a search results report for "RNA extraction" with 5 pre-cached protocol summaries, plus full detail for one protocol including steps and reagents.
~/.clawbio/protocols_io_tokens.json; if expired (status 1219), prompt user to run --login againGET /api/v3/protocols?filter=public&key=<query>&order_field=relevance&page_size=10 — parse paginated resultsGET /api/v4/protocols/<id>?content_format=markdown — returns full protocol with steps rendered as markdownGET /api/v4/protocols/<id>/steps?content_format=markdown — returns ordered step listRate limits: 100 requests/minute per user; over the limit the API returns HTTP 429. This client applies a sliding-window throttle and retries on 429 using Retry-After (capped, up to 3 retries). The /view/[protocol-uri].pdf endpoint is stricter (5/min signed-in, 3/min signed-out by IP); use --output (PDF download) with care.
Without --output: results are printed to the terminal as markdown. With --output <dir>: all modes save report.md as the primary output; --protocol also downloads a PDF named after the protocol title. All modes write a reproducibility/ bundle (commands.sh, checksums.sha256, environment.yml).
Required (in requirements.txt):
requests >= 2.28 — HTTP client for API callsOptional:
~/.clawbio/protocols_io_tokens.json; no data uploadedTrigger conditions — the orchestrator routes here when:
Chaining partners:
lit-synthesizer: Cross-reference protocol citations with PubMed literaturelabstep: Import protocols.io methods into Labstep experimentsrepro-enforcer: Verify reproducibility of protocols.io methodsnpx claudepluginhub clawbio/clawbio --plugin clawbioSearches and retrieves protocols.io protocols (wet-lab, bioinformatics, clinical) by keyword, DOI, or category. Returns steps, reagents, materials, equipment, and timing. Supports public (no auth) and private protocol access.
Integrates with protocols.io API to search, create, update, publish protocols; manage steps, materials, discussions, workspaces, and files.
Manages scientific protocols through the protocols.io API — search, create, update, publish protocols, manage steps/materials, handle discussions, organize workspaces, and upload files.