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jaechang-hitsjaechang-hits/SciAgent-Skills/skills/proteomics-protein-engineering/hmdb-database/SKILL.md

hmdb-database

Skill386 starsChanged 4 months agoLicence not identifiedView on GitHub

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.

  • Installs packages

9 other projects use a version of this.

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Projects with it also use simpy, torch-geometric and 6 more.

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  • tondevrelSkill

    simpy

    A process-based discrete-event simulation framework. Use for modeling queuing systems, supply chains, manufacturing processes, network simulation, project management, and any system where events occur at specific points in time. Load when working with discrete event simulation, process modeling, resource allocation, virtual time, simpy.Environment, simpy.Resource, or event-driven simulation.

    Also in 5 projects that use this

  • Hongyu-yuSkill

    torch-geometric

    Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.

    Also in 6 projects that use this

  • refly-aiSkill

    alpha-vantage

    Get financial data from Alpha Vantage. Use when you need to: (1) retrieve stock quotes and prices, (2) get forex or crypto rates, or (3) access market analytics data.

    Also in 4 projects that use this

  • yf8578Skill

    usfiscaldata

    Query the U.S. Treasury Fiscal Data API for federal financial data including national debt, government spending, revenue, interest rates, exchange rates, and savings bonds. Access 54 datasets and 182 data tables with no API key required. Use when working with U.S. federal fiscal data, national debt tracking (Debt to the Penny), Daily Treasury Statements, Monthly Treasury Statements, Treasury securities auctions, interest rates on Treasury securities, foreign exchange rates, savings bonds, or any U.S. government financial statistics.

    Also in 4 projects that use this

  • Google DeepMindSkill

    string-database

    Query the STRING database for protein-protein interactions (PPIs), functional enrichment, and homology. Use when the user asks about interactions between specific proteins, interaction evidence, confidence scores, protein interaction partners, or pathway enrichments.

    Also in 6 projects that use this

  • Google DeepMindSkill

    uniprot-database

    Access protein metadata, function, taxonomy, and sequences across UniProtKB, UniParc, and UniRef. Use when searching for proteins, mapping identifiers, or retrieving functional annotations and publications. Don't use for sequence alignment, protein folding, or sequence similarity search (use specialized skills for those tasks).

    Also in 5 projects that use this

The file

We split this skill into the rules it gives an agent

6 rules. 0 are common, 5 are distinctive, and 1 is very specific to this project.

  • 0

    Common

    Most of the 9 edited versions we read keep these.

  • 5

    Distinctive

    This author's own choices. Worth a look.

  • 1

    Very specific

    Tied to their project's names, files or tools. Probably skip.

The licence could not be identified — read it at the source. We count its rules but don't quote them. Read them on GitHub.

“Common” is measured: kept by at least 6 in 10 of the 9 edited versions of this file we could read. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.

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