From 5b9ba51263e0349c0f3669af91cd4842e7455f21 Mon Sep 17 00:00:00 2001 From: Yohei Demachi <55367533+yoheidemachi@users.noreply.github.com> Date: Sun, 1 Mar 2026 10:52:29 +0900 Subject: [PATCH] Replace ~~placeholder strings with readable tool names in user-facing text The ~~category convention is used internally for tool-agnostic references, but user-facing text (welcome messages, error messages, examples) should show actual tool names for clarity. - bio-research/commands/start.md: Replace ~~literature database, ~~chemical database, etc. with PubMed, ChEMBL, BioRender and other actual server names - enterprise-search/commands/search.md: Replace ~~chat, ~~email etc. in the "no sources connected" message with readable examples (e.g. Slack, Jira) - sales/skills/draft-outreach/SKILL.md: Replace "check ~~email" with "check your email client" Fixes #71 Co-Authored-By: Claude Opus 4.6 --- bio-research/commands/start.md | 25 ++++++++++++------------- enterprise-search/commands/search.md | 5 +++-- sales/skills/draft-outreach/SKILL.md | 4 ++-- 3 files changed, 17 insertions(+), 17 deletions(-) diff --git a/bio-research/commands/start.md b/bio-research/commands/start.md index d180433a..f2c014cb 100644 --- a/bio-research/commands/start.md +++ b/bio-research/commands/start.md @@ -25,20 +25,19 @@ and scientific strategy — all in one place. Test which MCP servers are connected by listing available tools. Group the results: **Literature & Data Sources:** -- ~~literature database — biomedical literature search -- ~~literature database — preprint access (biology and medicine) -- ~~journal access — academic publications -- ~~data repository — collaborative research data (Sage Bionetworks) +- PubMed (~~literature) — biomedical literature search +- bioRxiv (~~literature) — preprint access (biology and medicine) +- Wiley Scholar Gateway (~~journal access) — academic publications +- Synapse (~~data repository) — collaborative research data (Sage Bionetworks) **Drug Discovery & Clinical:** -- ~~chemical database — bioactive compound database -- ~~drug target database — drug target discovery platform +- ChEMBL (~~chemical database) — bioactive compound database +- Open Targets (~~drug targets) — drug target discovery platform - ClinicalTrials.gov — clinical trial registry -- ~~clinical data platform — clinical trial site ranking and platform help **Visualization & AI:** -- ~~scientific illustration — create scientific figures and diagrams -- ~~AI research platform — AI for biology (histopathology, drug discovery) +- BioRender (~~scientific illustration) — create scientific figures and diagrams +- Owkin (~~AI research) — AI for biology (histopathology, drug discovery) Report which servers are connected and which are not yet set up. @@ -58,9 +57,9 @@ List the analysis skills available in this plugin: Mention that two additional MCP servers are available as separate installations: -- **~~genomics platform** — Access cloud analysis data and workflows +- **10x Genomics** (~~genomics platform) — Access cloud analysis data and workflows Install: Download `txg-node.mcpb` from https://github.com/10XGenomics/txg-mcp/releases -- **~~tool database** (Harvard MIMS) — AI tools for scientific discovery +- **ToolUniverse** (~~tool database, Harvard MIMS) — AI tools for scientific discovery Install: Download `tooluniverse.mcpb` from https://github.com/mims-harvard/ToolUniverse/releases These require downloading binary files and are optional. @@ -69,9 +68,9 @@ These require downloading binary files and are optional. Ask the researcher what they're working on today. Suggest starting points based on common workflows: -1. **Literature review** — "Search ~~literature database for recent papers on [topic]" +1. **Literature review** — "Search PubMed for recent papers on [topic]" 2. **Analyze sequencing data** — "Run QC on my single-cell data" or "Set up an RNA-seq pipeline" -3. **Drug discovery** — "Search ~~chemical database for compounds targeting [protein]" or "Find drug targets for [disease]" +3. **Drug discovery** — "Search ChEMBL for compounds targeting [protein]" or "Find drug targets for [disease]" 4. **Data standardization** — "Convert my instrument data to Allotrope format" 5. **Research strategy** — "Help me evaluate a new project idea" diff --git a/enterprise-search/commands/search.md b/enterprise-search/commands/search.md index 3d3d2bca..c6b33f96 100644 --- a/enterprise-search/commands/search.md +++ b/enterprise-search/commands/search.md @@ -25,9 +25,10 @@ Before searching, determine which MCP sources are available. Attempt to identify If no MCP sources are connected: ``` To search across your tools, you'll need to connect at least one source. -Check your MCP settings to add ~~chat, ~~email, ~~cloud storage, or other tools. +Check your MCP settings to add a chat tool (e.g. Slack), email, cloud storage, or other tools. -Supported sources: ~~chat, ~~email, ~~cloud storage, ~~project tracker, ~~CRM, ~~knowledge base, +Supported sources: chat (e.g. Slack), email (e.g. Microsoft 365), cloud storage, +project tracker (e.g. Jira), CRM, knowledge base (e.g. Notion), and any other MCP-connected service. ``` diff --git a/sales/skills/draft-outreach/SKILL.md b/sales/skills/draft-outreach/SKILL.md index 12ac491f..c1b67fcb 100644 --- a/sales/skills/draft-outreach/SKILL.md +++ b/sales/skills/draft-outreach/SKILL.md @@ -100,7 +100,7 @@ Research first, then draft. This skill never sends generic outreach - it always ## Email Draft Status -[Draft created - check ~~email] +[Draft created - check your email client] [Email not connected - copy email above] [No email found - use LinkedIn approach] @@ -436,5 +436,5 @@ Best, --- ## Email Draft Status -Draft created - check ~~email +Draft created - check your email client ```