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Agent skills
agentic-search

Topic: agentic-search

36 skills in this topic.

graph Query citation graphs — view a paper's references, find which papers cite it, and analyze shared references between multiple papers. Use when the user asks about citation relationships, reference overlap, or bibliographic connections.
ZimoLiao/scholaraio 332
rename Rename paper directories to standardized Author-Year-Title format based on JSON metadata. Use when the user wants to normalize filenames after metadata corrections.
ZimoLiao/scholaraio 332
scientific-runtime Use when serving scientific CLI tasks through ScholarAIO, especially when the agent should prefer scholaraio toolref, handle partial coverage safely, and avoid turning user work into documentation maintenance.
ZimoLiao/scholaraio 332
topics Explore topic distribution in the paper library using BERTopic clustering. Build/rebuild topic models, view topic overview, list papers in a topic, merge similar topics, and generate HTML visualizations. Use when the user asks about research themes, topic distribution, or wants to discover cross-domain connections.
ZimoLiao/scholaraio 332
openfoam Use when working on CFD cases with OpenFOAM, especially solver selection, dictionary setup, mesh workflow decisions, turbulence-model choices, and verification of fluid-flow or heat-transfer simulations.
ZimoLiao/scholaraio 332
metrics View LLM token usage, API call timing, and runtime metrics. Use when the user asks about token consumption, API costs, or performance statistics.
ZimoLiao/scholaraio 332
literature-review Write a literature review based on papers in a workspace. Covers topic organization, narrative structure, gap identification, and BibTeX export. Use when the user wants to draft a literature review, survey a research area, or summarize the state of the art.
ZimoLiao/scholaraio 332
lammps Use when working on classical materials simulations with LAMMPS, especially interatomic-potential selection, shock or deformation setups, thermodynamic runs, and structure analysis for solids or nanomaterials.
ZimoLiao/scholaraio 332
insights Analyze research behavior data — search hot keywords, most-read papers, reading trends, and semantic neighbors you haven't read yet. Use when the user wants to understand their reading habits, discover overlooked papers, or review recent research activity.
ZimoLiao/scholaraio 332
ingest Use when the user wants to process new papers, patents, theses, documents, or proceedings from inbox into the knowledge base, run the ingest pipeline, or rebuild indexes.
ZimoLiao/scholaraio 332
scientific-tool-onboarding Use when adding or upgrading ScholarAIO support for a new scientific computing tool, especially when the work needs official docs ingestion, toolref integration, lightweight skill design, and end-to-end CLI verification
ZimoLiao/scholaraio 332
translate Translate paper markdown to a target language (default Chinese). Preserves LaTeX formulas, code blocks, and images. Supports single paper or batch translation. Use when the user wants to read papers in their native language or translate non-Chinese documents.
ZimoLiao/scholaraio 332
gromacs Use when working on biomolecular molecular dynamics with GROMACS, especially system setup, equilibration, production runs, trajectory analysis, or MM/PBSA-style post-processing.
ZimoLiao/scholaraio 332
review-response Draft point-by-point responses to peer review comments. Locates supporting evidence from workspace papers and the original manuscript. Use when the user receives reviewer feedback and needs to write a rebuttal or revision response letter.
ZimoLiao/scholaraio 332
export Export papers from the knowledge base to standard citation formats (BibTeX, RIS, Markdown reference list) or export any Markdown content as a Word DOCX file. Supports exporting all papers, specific papers, or filtered by year/journal. Use when the user needs citation files, wants to import into Zotero/Endnote/Mendeley, needs a reference list for writing, or wants to share a document as Word.
ZimoLiao/scholaraio 332
explore Explore literature by fetching papers from OpenAlex with multi-dimensional filters (ISSN, concept, author, institution, keyword, etc.), building local embeddings, running BERTopic clustering, and multi-mode search (semantic/keyword/unified). Data is isolated in data/explore/<name>/. Use when the user wants to survey a journal, explore a research field, analyze an author's output, or do landscape analysis.
ZimoLiao/scholaraio 332
enrich Enrich paper metadata using LLM extraction. Extract table of contents (TOC), conclusions (L3), and backfill abstracts. Use when the user wants to extract conclusions, build TOC, or backfill missing abstracts. For citation count updates, see the /citations skill.
ZimoLiao/scholaraio 332
draw Generate diagrams and vector graphics. Supports Mermaid (flowcharts, sequence diagrams, ER diagrams, Gantt charts, mind maps) via mermaid-py, and custom vector graphics (shapes, text, gradients, layers) via cli-anything-inkscape. Outputs PNG/SVG/PDF to workspace/. Use when the user wants to visualize workflows, architecture, data relationships, research timelines, concept maps, or create polished figures for papers.
ZimoLiao/scholaraio 332
writing-polish Polish academic writing — remove AI-generated patterns, improve clarity, and match a target style. Supports both English and Chinese. Use when the user wants to refine prose, remove AI artifacts, or adapt writing to a specific journal style.
ZimoLiao/scholaraio 332
workspace Manage workspace paper subsets — create workspaces, add/remove papers, search within a workspace, and export BibTeX. Workspaces are thin layers that reference papers in the main library by UUID. Use when the user wants to organize papers into groups for writing, review, or focused analysis.
ZimoLiao/scholaraio 332
citation-check Verify citations in AI-generated or human-written text against the local knowledge base. Catches hallucinated references, wrong metadata, and missing papers. Use when the user wants to check if citations are real and accurate.
ZimoLiao/scholaraio 332
bioinformatics Use when working on bioinformatics toolchains such as alignment, variant calling, phylogenetics, or protein-structure analysis, especially when the agent must route across BLAST, minimap2, samtools, bcftools, MAFFT, IQ-TREE, or ESMFold.
ZimoLiao/scholaraio 332
audit Audit paper data quality in the knowledge base. Checks for missing fields, filename issues, DOI duplicates, title mismatches, and more. Supports LLM-based deep diagnosis for title mismatches and automated repair. Use when the user wants to check data quality, find problems, or fix metadata issues.
ZimoLiao/scholaraio 332
arxiv Use when the user wants to browse arXiv preprints, search arXiv directly, fetch a PDF by arXiv ID or URL, or send a preprint straight into the ingest pipeline.
ZimoLiao/scholaraio 332