hmdb-database SKILL.md skillA
hmdb-database from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/hmdb-database@git:20260428.81ea2d2Pins git:20260428.81ea2d2 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/proteomics-protein-engineering/hmdb-database/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260428.81ea2d2, committed Apr 28, 2026
- First version recorded
- Feb 18, 2026
- Size
- 24,509 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping. No REST API — uses ~6 GB XML download. Use drugbank-database-access for drugs; pubchem-compound-search for live lookups.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# HMDB Database — Local XML Access ## Overview Query the Human Metabolome Database (HMDB, 220,000+ metabolite entries) by parsing locally downloaded XML with Python's ElementTree. Covers metabolite lookup, chemical properties, biological context (pathways, enzymes, biofluids), disease/biomarker associations, spectral data for metabolite identification, and cross-database ID mapping to KEGG, PubChem, ChEBI, and DrugBank. ## When to Use - Looking up metabolite information (description, chemical class, cellular location) by HMDB ID or name - Retrieving chemical properties (molecular weight, formula, SMILES, InChI, logP, PSA) for metabolomics analysis - Finding pathway associations and enzyme links for a set of metabolites - Identifying biofluid/tissue locations of metabolites (blood, urine, CSF, saliva) - Querying disease associations and normal/abnormal concentration ranges for biomarker discovery - Extracting NMR or MS spectral peak lists for metabolite identification - Mapping HMDB IDs to KEGG, PubChem, ChEBI, DrugBank, or other databases - For drug-specific data (interactions, targets, pharmacology) use `drugbank-database-access` instead …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/hmdb-database@sha256:0856c39f0c920e3cThe line at the top of this page pins the label git:20260428.81ea2d2, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_vz5kn4swgwzrlcko)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between Feb 18, 2026 and Apr 28, 2026, about one every 34 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260428.81ea2d2 latest | 2026-04-28 | 81ea2d2 | 24,509 B | A | view · diff |
| git:20260409.a3b01d0 | 2026-04-09 | a3b01d0 | 24,602 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 24,623 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (24509 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_vz5kn4swgwzrlcko GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/hmdb-database GET https://markdownregistry.com/api/v1/blob/0856c39f0c920e3c1ead4f39ec1348fe2cf34c2829c84663a1a88a517744ab2d
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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