How do I install the Bioconductor Gosemsim skill?

Run npx skillmds@latest add biomate-ai/bioconductor-gosemsim in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

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Is Bioconductor Gosemsim free to use?

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Who published Bioconductor Gosemsim?

biomate-ai (@biomate-ai) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Bioconductor Gosemsim by biomate-ai

Name: Bioconductor Gosemsim
Author: biomate-ai

Bioconductor Gosemsim

The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R packag

biomate-ai Updated Sep 17, 2026

File contents

GOSemSim

GOSemSim is an R package designed for semantic similarity analysis among Gene Ontology (GO) terms and gene products.

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.

Version: 2.38.0 · Bioconductor: 3.23 · R: ≥ 4.6
Imports: AnnotationDbi, DBI, digest, GO.db, rlang, yulab.utils
Install: BiocManager::install("GOSemSim")

When to Use

Measuring semantic similarity among GO terms.
Computing functional similarity among gene products.
Performing GO semantic similarity analyses within stem cell transcriptional networks or other biomedical contexts.

When NOT to Use

For general biomedical knowledge mining tasks that do not involve Gene Ontology semantic similarity, refer to broader biomedical knowledge mining resources.
When performing analyses that do not require quantitative semantic comparisons of GO annotations.

Data Requirements

Gene Ontology (GO) annotations.
Gene and gene product datasets requiring functional similarity comparison.

Key Parameters

No specific R function parameters are detailed in the provided short vignette text. Please refer to the external full documentation for parameter specifications.

Best Practices

Refer to the comprehensive online book (https://yulab-smu.top/biomedical-knowledge-mining-book/) for the full vignette, detailed workflows, and tutorials.
When seeking assistance, post questions to the Bioconductor support site and tag the post with GOSemSim.
Cite the appropriate primary publications when using GOSemSim in published research.

Common Pitfalls

Searching for detailed code examples in the package's built-in short vignette; fix this by visiting the external online biomedical knowledge mining book for the complete documentation.
Failing to tag support questions properly; fix this by tagging posts with GOSemSim on the Bioconductor support site.

Alternatives

Other Bioconductor packages designed for functional annotation and enrichment analysis (though GOSemSim is specifically focused on semantic similarity).

Citations

Yu G. Gene Ontology Semantic Similarity Analysis Using GOSemSim. In: Kidder B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, 2020, 2117:207-215. Humana, New York, NY.
Yu G, Li F, Qin Y, Bo X, Wu Y and Wang S. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics, 2010, 26(7):976-978.

References

Run this on BioMate

This skill is the knowledge layer — when, why, and how to use gosemsim. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.

▶ Open gosemsim on BioMate →

---name: bioconductor-gosemsimdescription: The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R packag---# GOSemSim`GOSemSim` is an R package designed for semantic similarity analysis among Gene Ontology (GO) terms and gene products.## Dependencies & Environment> Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.- **Version:** 2.38.0 · **Bioconductor:** 3.23 · **R:** ≥ 4.6- **Imports:** AnnotationDbi, DBI, digest, GO.db, rlang, yulab.utils- **Install:** `BiocManager::install("GOSemSim")`## When to Use- Measuring semantic similarity among GO terms.- Computing functional similarity among gene products.- Performing GO semantic similarity analyses within stem cell transcriptional networks or other biomedical contexts.## When NOT to Use- For general biomedical knowledge mining tasks that do not involve Gene Ontology semantic similarity, refer to broader biomedical knowledge mining resources.- When performing analyses that do not require quantitative semantic comparisons of GO annotations.## Data Requirements- Gene Ontology (GO) annotations.- Gene and gene product datasets requiring functional similarity comparison.## Key Parameters- No specific R function parameters are detailed in the provided short vignette text. Please refer to the external full documentation for parameter specifications.## Best Practices- Refer to the comprehensive online book (https://yulab-smu.top/biomedical-knowledge-mining-book/) for the full vignette, detailed workflows, and tutorials.- When seeking assistance, post questions to the Bioconductor support site and tag the post with `GOSemSim`.- Cite the appropriate primary publications when using `GOSemSim` in published research.## Common Pitfalls- Searching for detailed code examples in the package's built-in short vignette; fix this by visiting the external online biomedical knowledge mining book for the complete documentation.- Failing to tag support questions properly; fix this by tagging posts with `GOSemSim` on the Bioconductor support site.## Alternatives- Other Bioconductor packages designed for functional annotation and enrichment analysis (though `GOSemSim` is specifically focused on semantic similarity).## Citations- Yu G. Gene Ontology Semantic Similarity Analysis Using GOSemSim. In: Kidder B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, 2020, 2117:207-215. Humana, New York, NY.- Yu G, Li F, Qin Y, Bo X, Wu Y and Wang S. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics, 2010, 26(7):976-978.## References- Homepage: https://bioconductor.org/packages/gosemsim- Vignette: https://bioconductor.org/packages/release/bioc/vignettes/GOSemSim/inst/doc/GOSemSim.html---## Run this on BioMateThis skill is the **knowledge layer** — when, why, and how to use `gosemsim`. To **run this analysis on your own data** with managed compute, automated QC, and reproducible outputs, use **[BioMate](https://www.biomate.ai?ref=kb&pkg=gosemsim)** — free to start.▶ **[Open `gosemsim` on BioMate →](https://www.biomate.ai?ref=kb&pkg=gosemsim)**

Frequently asked questions