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Agent skill

Analytical Grounding

by exon-research in exon-research/genomi

Retrieve canonical pathway members, cell-type marker records, and genomic interval feature overlaps from declared analytical sources.

Apache-2.0Auto-check passedResearch & Science

Install Analytical Grounding

skills CLI
$ npx skills add exon-research/genomi --skill analytical-grounding -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install exon-research/genomi analytical-grounding --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/analytical-grounding .claude/skills/analytical-grounding && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
analytical-grounding
GitHub stars
484
Token cost
~1.2k tokens
SKILL.md length
540 words
Files
1
Skills in repo
20
Repo updated
First seen
Licence
Apache-2.0

At a glance

Retrieve canonical pathway members, cell-type marker records, and genomic interval feature overlaps from declared analytical sources.

  • Tasks that involve Bioinformatics
  • SKILL.md covers Use When, Operations, Boundaries and Examples, plus 2 more sections
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Analytical Grounding is an agent skill from exon-research/genomi. Retrieve canonical pathway members, cell-type marker records, and genomic interval feature overlaps from declared analytical sources.

Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Bioinformatics. The repository describes itself as: Local-first, open-source Claude Science alternative, before Claude Science is a thing. Turn your AI agent into personal DNA expert. The licence is Apache-2.0.

When your agent uses it

  • Tasks that involve Bioinformatics

Example prompts

  • “/analytical-grounding”

What it can do on your machine

Read from SKILL.md and the folder at commit 1df4f5b. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md.

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Analytical Grounding loads about 1.2k tokens when it runs. Until then it costs about 39 tokens; SKILL.md has 540 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~39
When it runs · the whole SKILL.md, loaded when a task matches
~1.2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from exon-research/genomi at commit 1df4f5b, republished under its Apache-2.0 licence (© exon-research). 540 words, ~1,214 tokens.

Download SKILL.mdSave it as .claude/skills/analytical-grounding/SKILL.md (or your agent's skills folder).
name
analytical-grounding
description
Retrieve canonical pathway members, cell-type marker records, and genomic interval feature overlaps from declared analytical sources.
tools
pathway.retrieve_members, cell_type.retrieve_markers, region.retrieve_features
mutating
false

Analytical Grounding

Use this skill for source-declared records that ground an analytical statement, without asking Genomi to choose the interpretation.

Use When

  • The input is a controlled pathway or gene-set name/id and the agent needs its canonical member genes.
  • The input is a controlled cell type and the agent needs marker-gene records.
  • The input is a genomic interval and the agent needs overlaps against declared GENCODE or ENCODE annotation files.

Operations

  • pathway.retrieve_members: retrieve Reactome, KEGG human pathway, or supplied or installed MSigDB Hallmark GMT member genes. Use a source for free-text pathway names unless the identifier prefix makes the source clear.
  • cell_type.retrieve_markers: retrieve HPA single-cell marker records, installed CellMarker/PanglaoDB tables, or supplied marker tables.
  • region.retrieve_features: retrieve interval overlaps from supplied or installed GENCODE GTF and/or ENCODE cCRE BED files for GRCh37/GRCh38. Supply assembly; without it the tool reports unsupported assembly instead of guessing a genome build.

Boundaries

  • These are retrieval verbs over declared source coverage.
  • Do not use them as experimental protocol recommendations, workflow templates, or free-text biological interpretation.
  • Treat coverage_status literally:
    • data_returned: declared source records were returned.
    • in_scope_empty: the input was in declared scope, and no records matched.
    • out_of_scope_for_input: the source, assembly, identifier, or required source file is outside declared coverage.
  • Preserve source priors. A pathway member, marker gene, interval overlap, or druggable-target membership row is evidence context, not a selected answer.

Examples

  • pathway.retrieve_members with {"pathway_id_or_name":"R-HSA-70635"}
  • pathway.retrieve_members with {"pathway_id_or_name":"hsa00010"}
  • cell_type.retrieve_markers with {"cell_type_id_or_name":"hepatocytes","source":"hpa"}
  • cell_type.retrieve_markers with {"cell_type_id_or_name":"Hepatocyte","source":"cellmarker"}
  • region.retrieve_features with {"region":"1:1000-1250","assembly":"GRCh38"}

The installer can cache gencode-grch38, gencode-grch37, encode-ccre-grch38, panglaodb-markers, and cellmarker-human under GENOMI_HOME. MSigDB Hallmark requires a user-supplied official GMT export.

Cross-Capability Synthesis

A scope-limited result from this capability is not a final user-facing answer when other Genomi capabilities can contribute orthogonal evidence to the same question. Returning "cannot answer" while applicable capabilities remain unexamined is a host-agent failure mode.

Tools

Show full SKILL.md (241 more words)Show less
cell_type.retrieve_markers

Retrieve canonical marker genes for a controlled cell-type source entity.

Use when: Returns source-declared marker genes for HPA single-cell records or supplied CellMarker, PanglaoDB, or ENCODE marker tables.

Why necessary: Cell-type identity questions need marker records, not disease genetics or GWAS evidence.

Result semantics: Returns marker records only; it does not annotate clusters, assign cell identities, rank cell types, or interpret cell states. Free-text cluster IDs and hypothetical cell-state labels are out of scope.

pathway.retrieve_members

Retrieve canonical member genes for a controlled pathway or gene-set source entity.

Use when: Returns source-declared member genes for Reactome pathways, KEGG human pathways, or supplied MSigDB Hallmark GMT gene sets.

Why necessary: Pathway membership is a grounding fact and should be retrieved separately from disease or variant claims.

Result semantics: Returns pathway membership records only; it does not infer pathway activity, choose genes, or summarize pathway biology. Free-text pathway names should include source unless the identifier prefix implies a declared source.

region.retrieve_features

Retrieve genomic-region feature annotations from supplied or installed GENCODE and ENCODE annotation files.

Use when: The user or an upstream tool supplies a genomic interval and the agent needs transcript or regulatory-feature overlaps for an explicit GRCh37 or GRCh38 assembly.

Why necessary: Genomic coordinates need gene and regulatory feature context before they can be biologically discussed.

Result semantics: Returns source-declared interval overlaps for the assembly shown in query. Empty results mean no overlap in declared files, not biological absence outside declared coverage.

© exon-research, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/analytical-grounding of exon-research/genomi.

Open the folder on GitHubat commit 1df4f5b

Compare with similar skills

Analytical Grounding next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Analytical Grounding compared with similar skills
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Analytical Grounding this skillexon-research/genomi484—~1.2kAutomated safety check: PassApache-2.0
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Clinvar Databasegoogle-deepmind/science-skills3.2k2 repos~3.9kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
Dbsnp Databasegoogle-deepmind/science-skills3.2k2 repos~3.4kAutomated safety check: NotesApache-2.0

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Categories

Questions about Analytical Grounding

What does Analytical Grounding do?

Retrieve canonical pathway members, cell-type marker records, and genomic interval feature overlaps from declared analytical sources. Analytical Grounding is an agent skill from exon-research/genomi. Retrieve canonical pathway members, cell-type marker records, and genomic interval feature overlaps from declared analytical sources.

When should I use Analytical Grounding?

Analytical Grounding fits situations like: tasks that involve Bioinformatics.

How do I install Analytical Grounding in Claude Code?

Run `npx skills add exon-research/genomi --skill analytical-grounding -a claude-code`. Or copy the skill folder (skills/analytical-grounding in exon-research/genomi) into .claude/skills/analytical-grounding in your project. Claude Code loads it when a task matches its description.

How do I install Analytical Grounding in Codex?

Run `npx skills add exon-research/genomi --skill analytical-grounding -a codex`. Or copy the skill folder (skills/analytical-grounding in exon-research/genomi) into .agents/skills/analytical-grounding in your project. Codex loads it when a task matches its description.

Can I use Analytical Grounding in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add exon-research/genomi --skill analytical-grounding -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/analytical-grounding, .gemini/skills/analytical-grounding, .github/skills/analytical-grounding and .opencode/skills/analytical-grounding in your project.

What does Analytical Grounding need to run?

SKILL.md names no scripts, command-line tools or credentials: Analytical Grounding is instructions for the agent only.

Does Analytical Grounding access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Analytical Grounding safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Analytical Grounding use?

Analytical Grounding is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Analytical Grounding use?

About 1.2k tokens (SKILL.md is roughly 4.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Analytical Grounding?

Skills that share tags, products or a category with Analytical Grounding: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Analytical Grounding?

exon-research (a GitHub organization) maintains it in exon-research/genomi, which has 484 GitHub stars. The repository holds 20 skills in this directory. The repository was last updated on August 31, 2026.

Source: exon-research/genomi on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.