hmdb-database
Parses the Human Metabolome Database XML for detailed metabolite information, aiding in metabolomics research and analysis.
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The hmdb-database skill was audited on May 24, 2026 and we found 13 security issues across 1 threat category. Review the findings below before installing.
Categories Tested
Security Issues
low line 27
External URL reference
SourceSKILL.md
| 27 | - **HMDB XML download**: Register at https://hmdb.ca/downloads — download `hmdb_metabolites.xml.zip` (~6 GB uncompressed) |
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External URL reference
SourceSKILL.md
| 42 | NS = {'hmdb': 'http://www.hmdb.ca'} |
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SourceSKILL.md
| 75 | NS = {'hmdb': 'http://www.hmdb.ca'} |
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SourceSKILL.md
| 87 | if elem.tag == '{http://www.hmdb.ca}metabolite': |
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External URL reference
SourceSKILL.md
| 88 | acc = elem.find('{http://www.hmdb.ca}accession') |
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External URL reference
SourceSKILL.md
| 89 | name = elem.find('{http://www.hmdb.ca}name') |
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External URL reference
SourceSKILL.md
| 452 | | `NS` (namespace dict) | All XPath queries | `{'hmdb': 'http://www.hmdb.ca'}` | Required for all `find`/`findall` calls | |
low line 462
External URL reference
SourceSKILL.md
| 462 | 2. **Always pass the namespace dict**: Every `find()`/`findall()` needs `NS = {'hmdb': 'http://www.hmdb.ca'}`. Omitting it returns empty results |
low line 528
External URL reference
SourceSKILL.md
| 528 | | `find()` returns `None` for known elements | Missing XML namespace | Always pass `NS = {'hmdb': 'http://www.hmdb.ca'}` | |
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External URL reference
SourceSKILL.md
| 551 | - HMDB website and downloads: https://hmdb.ca/ |
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External URL reference
SourceSKILL.md
| 552 | - Wishart DS et al. (2022). HMDB 5.0: the Human Metabolome Database for 2022. *Nucleic Acids Res.* 50(D1):D801-D816. https://doi.org/10.1093/nar/gkab1062 |
low line 553
External URL reference
SourceSKILL.md
| 553 | - HMDB data download page: https://hmdb.ca/downloads |
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External URL reference
SourceSKILL.md
| 554 | - MetaboAnalyst (complementary tool): https://www.metaboanalyst.ca/ |
Scanned on May 24, 2026
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Categorydata analytics
UpdatedJune 15, 2026
openclawdatabaseapidata-analystdata-scientistresearcherclinical-researcherdata analyticseducation researchhealthcare
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