Add cell-free expression value sets for synthetic biology#70
Merged
Conversation
Add value sets for cell-free protein synthesis (CFPS) covering: - CellFreeExpressionSystemEnum: source extracts/reconstituted systems (E. coli, PURE, wheat germ, reticulocyte, insect, HeLa, CHO, yeast, Leishmania, V. natriegens, tobacco BY-2) - CellFreeReactionFormatEnum: batch, CECF, CFCF, bilayer, lyophilized - EnergyRegenerationSubstrateEnum: energy substrates mapped to CHEBI - CellFreeApplicationEnum: common applications Register the new module in valuesets.yaml imports. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016VM3wUFdmZ2gD7UW6A483j
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016VM3wUFdmZ2gD7UW6A483j
Add ontology mappings found via OBO/OLS search: - RABBIT_RETICULOCYTE_LYSATE -> BAO:0000255 (rabbit reticulocyte lysate format) - BIOSENSOR -> NCIT:C16350; HIGH_THROUGHPUT_SCREENING -> NCIT:C18472; VACCINE_PRODUCTION -> OBI:0000719 (with BAO/NCIT exact_mappings) - broad_mappings to BAO:0000366 (cell-free format) for all extract systems - related_mappings: CONTINUOUS_EXCHANGE -> OBI:0600052 (dialysis), LYOPHILIZED -> NCIT:C28150 (freeze-drying), DIAGNOSTICS -> NCIT:C209465 Declare BAO and NCIT prefixes. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016VM3wUFdmZ2gD7UW6A483j
Contributor
|
Claude encountered an error —— View job I'll analyze this and get back to you. |
Update the Claude Code GitHub Action workflows to the latest v1, matching the preferred settings in linkml/linkml-reference-validator: - claude-code-action@beta -> @v1; actions/checkout@v4 -> @v6 - claude-code-review: replace removed 'direct_prompt' with 'prompt' + 'track_progress: true' (restores PR-comment behavior in automation mode), pin model via 'claude_args: --model opus' - claude: move removed v0.x 'mcp_config'/'allowed_tools'/model inputs into 'claude_args' (--mcp-config / --allowedTools / --model opus) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016VM3wUFdmZ2gD7UW6A483j
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Adds comprehensive value sets for cell-free protein synthesis (CFPS), covering the systems, reaction formats, energy substrates, and applications used in synthetic biology, structural biology, and biomanufacturing.
Key Changes
New schema module:
src/valuesets/schema/bio/cell_free_expression.yamlwith 450 lines defining four enums:CellFreeExpressionSystemEnum: 11 permissible values covering prokaryotic (E. coli, V. natriegens, PURE) and eukaryotic (wheat germ, insect, mammalian, yeast, plant) expression systemsCellFreeReactionFormatEnum: 5 permissible values for batch, continuous-exchange, continuous-flow, bilayer, and lyophilized formatsEnergyRegenerationSubstrateEnum: 9 permissible values for ATP/GTP regeneration substrates (phosphocreatine, PEP, acetyl phosphate, glucose variants, etc.)CellFreeApplicationEnum: 13 permissible values spanning protein production, diagnostics, biosensors, structural biology, and vaccine/antibody synthesisOntology mappings: Integrated references to BAO, OBI, NCIT, and CHEBI ontologies with proper CURIE prefixes and
meaning:mappings for standardized termsSchema integration: Added import of the new module to
src/valuesets/schema/valuesets.yamlCache updates: Added 8 CHEBI chemical terms and 1 NCIT term to support energy substrate and application mappings
Implementation Details
https://claude.ai/code/session_016VM3wUFdmZ2gD7UW6A483j