| app: |
| description: '' |
| icon: 🤖 |
| icon_background: '#FFEAD5' |
| mode: advanced-chat |
| name: CECs_annotating |
| use_icon_as_answer_icon: false |
| dependencies: |
| - current_identifier: null |
| type: marketplace |
| value: |
| marketplace_plugin_unique_identifier: langgenius/openai:0.2.6@e2665624a156f52160927bceac9e169bd7e5ae6b936ae82575e14c90af390e6e |
| version: null |
| kind: app |
| version: 0.4.0 |
| workflow: |
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| features: |
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| - .JPEG |
| - .PNG |
| - .GIF |
| - .WEBP |
| - .SVG |
| allowed_file_types: |
| - image |
| allowed_file_upload_methods: |
| - local_file |
| - remote_url |
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| enabled: false |
| number_limits: 3 |
| transfer_methods: |
| - local_file |
| - remote_url |
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| sourceHandle: source |
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| targetHandle: target |
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| targetHandle: target |
| type: custom |
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| sourceType: start |
| targetType: knowledge-retrieval |
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| sourceHandle: source |
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| targetType: tool |
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| sourceHandle: source |
| target: '1764904930952' |
| targetHandle: target |
| type: custom |
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| sourceType: llm |
| targetType: code |
| id: 1764831451652-source-1764831538955-target |
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| sourceHandle: source |
| target: '1764831538955' |
| targetHandle: target |
| type: custom |
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| sourceType: tool |
| targetType: llm |
| id: 1764904930952-source-1766991784354-target |
| selected: false |
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| sourceHandle: source |
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| targetHandle: target |
| type: custom |
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| target: '1766991784354' |
| targetHandle: target |
| type: custom |
| zIndex: 0 |
| - data: |
| isInLoop: false |
| sourceType: knowledge-retrieval |
| targetType: llm |
| id: 1763020657891-source-1766991784354-target |
| selected: false |
| source: '1763020657891' |
| sourceHandle: source |
| target: '1766991784354' |
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| - data: |
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| sourceType: llm |
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| selected: false |
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| targetHandle: target |
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| type: start |
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| y: 251 |
| selected: false |
| sourcePosition: right |
| targetPosition: left |
| type: custom |
| width: 242 |
| - data: |
| code: "import re\n\ndef main(arg1: str) -> dict:\n arg1 = re.sub(r'<sql>\\\ |
| s*</sql>', '', arg1)\n arg1 = arg1.replace('\\n', ' ')\n sql_pattern\ |
| \ = r'<sql>(?:(?!<sql>).)*?</sql>'\n matches = re.findall(sql_pattern,\ |
| \ arg1, re.DOTALL)\n if matches:\n last_sql_tag = matches[-1].strip()\n\ |
| \ pure_sql = last_sql_tag.replace('<sql>', '').replace('</sql>',\ |
| \ '').strip()\n return {\"result\": pure_sql}\n else:\n \ |
| \ return {\"error\": \"No SQL statement wrapped in <sql> tags found\"}" |
| code_language: python3 |
| outputs: |
| result: |
| children: null |
| type: string |
| selected: false |
| title: executecode2 |
| type: code |
| variables: |
| - value_selector: |
| - '1760433170399' |
| - text |
| value_type: string |
| variable: arg1 |
| height: 52 |
| id: '1760431395870' |
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| x: 632 |
| y: 251 |
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| sourcePosition: right |
| targetPosition: left |
| type: custom |
| width: 242 |
| - data: |
| context: |
| enabled: true |
| variable_selector: |
| - sys |
| - query |
| model: |
| completion_params: {} |
| mode: chat |
| name: gpt-5 |
| provider: langgenius/openai/openai |
| prompt_template: |
| - id: abc810d5-7d5d-486e-9c65-26a8e231aa2a |
| role: system |
| text: '# Role |
| |
| You are a professional MySQL generation assistant, specializing in generating |
| SQL statements for the 【pubchemlite_exposomics_20251226】 database. Please |
| generate SQL query statements based on user requirements {{#context#}}. |
| You must strictly follow the requirements below and are not allowed to |
| deviate from the rules or generate irrelevant content. |
| |
| |
| # Core Rules |
| |
| - Must convert users'' natural language questions into valid MySQL query |
| statements that only target the "local compound database". Forbidden to |
| generate write operations such as creating tables, modifying tables, or |
| deleting data; only SELECT queries are supported. |
| |
| - The generated MySQL statements must be completely enclosed within <sql> |
| and </sql> tags. Necessary explanations can be added outside the tags |
| (non-mandatory), but only pure SQL statements should be kept inside the |
| tags. |
| |
| - Only allowed to use existing tables in the current compound database |
| (fixed table name: pubchemlite_ccs) and the fields XLogP, BioPathway, |
| ToxicityInfo, KnownUse, DisorderDisease. Forbidden to generate irrelevant |
| tables or fields on your own; field spellings must strictly correspond, |
| no errors, additions, or deletions allowed. |
| |
| - If the user''s question does not specify query conditions, default to |
| querying the above five columns of information for all compounds. If other |
| fields are involved, you must explain outside the tags: "Currently only |
| the XLogP, BioPathway, ToxicityInfo, KnownUse, and DisorderDisease columns |
| are supported for querying; other fields cannot be queried", and do not |
| generate invalid SQL. |
| |
| |
| # Database Table Relationship Description |
| |
| The current compound database only involves a single compound data table |
| (no multi-table associations). All queries are based on this single table, |
| and multi-table operations such as JOIN are not required. |
| |
| |
| # Example Reference |
| |
| 1. User question: “1,2,4-trichlorobenzene” |
| |
| Generated result: |
| |
| <sql> SELECT CompoundName, XLogP, BioPathway, ToxicityInfo, KnownUse, |
| DisorderDisease FROM pubchemlite_exposomics_20251226 WHERE CompoundName |
| = ''1,2,4-trichlorobenzene'' LIMIT 10 </sql>' |
| selected: false |
| title: LLM_pubchemlite |
| type: llm |
| vision: |
| enabled: false |
| height: 94 |
| id: '1760433170399' |
| position: |
| x: 331 |
| y: 251 |
| positionAbsolute: |
| x: 331 |
| y: 251 |
| selected: true |
| sourcePosition: right |
| targetPosition: left |
| type: custom |
| width: 242 |
| - data: |
| dataset_ids: |
| - CuV6X2iaXQgYHKfOjA5DAlyvVPpmF6fPFkrgIBjHqUpD7ENMHgaNSYgwMFm2I99Y |
| multiple_retrieval_config: |
| reranking_enable: false |
| reranking_mode: reranking_model |
| score_threshold: null |
| top_k: 4 |
| query_variable_selector: |
| - '1760360355141' |
| - sys.query |
| retrieval_mode: multiple |
| selected: false |
| title: 知识检索 |
| type: knowledge-retrieval |
| height: 90 |
| id: '1763020657891' |
| position: |
| x: 331 |
| y: 526.5353719125708 |
| positionAbsolute: |
| x: 331 |
| y: 526.5353719125708 |
| selected: false |
| sourcePosition: right |
| targetPosition: left |
| type: custom |
| width: 242 |
| - data: |
| context: |
| enabled: true |
| variable_selector: |
| - sys |
| - query |
| model: |
| completion_params: {} |
| mode: chat |
| name: gpt-5 |
| provider: langgenius/openai/openai |
| prompt_template: |
| - id: b9a3fcd8-9a77-47fe-9c25-2a60a0c014eb |
| role: system |
| text: "# Role\nYou are a professional MySQL generation assistant, specialized\ |
| \ in generating query statements for the [InvitroDB v4.3] toxicity database.\n\ |
| \n# Core Task\nWhen a user inputs a compound name{{#context#}}, automatically\ |
| \ generate the corresponding SQL query statement to retrieve toxicity\ |
| \ test data for that compound.\n\n# Output Format\nThe generated SQL statement\ |
| \ must be completely enclosed within `<sql>` and `</sql>` tags.\n\n# Query\ |
| \ Template (Fixed)\nUse the following SQL template, replacing [Compound\ |
| \ Name] with the actual compound name entered by the user:\n\n<sql>\n\ |
| SELECT DISTINCT \n c.chnm AS compound_name,\n c.casn AS CASRN, \n\ |
| \ ace.assay_component_endpoint_name AS endpoint_name\nFROM chemical\ |
| \ c, chemical_analytical_qc caq, mc0 m, assay_component_endpoint ace\n\ |
| WHERE c.dsstox_substance_id = caq.dsstox_substance_id\n AND caq.spid\ |
| \ = m.spid\n AND m.acid = ace.acid\n AND c.chnm = 'Acetamide'\nORDER\ |
| \ BY endpoint_name;\n</sql>\n\n# Operation Rules\n1. Users only need to\ |
| \ input the compound name, e.g.: Dehydroacetic acid\n2. You only need\ |
| \ to replace the user's input compound name into WHERE c.chnm = '[User-Entered\ |
| \ Compound Name]'\n3. Keep all other parts of the SQL statement completely\ |
| \ unchanged\n4. The output should only contain the <sql>...</sql> tags\ |
| \ and the SQL statement within them\n\n# Example\nUser input: Dehydroacetic\ |
| \ acid\n\nYour output should be:\n<sql>\nSELECT DISTINCT \n c.chnm\ |
| \ AS compound_name,\n c.casn AS CASRN, \n ace.assay_component_endpoint_name\ |
| \ AS endpoint_name\nFROM chemical c, chemical_analytical_qc caq, mc0 m,\ |
| \ assay_component_endpoint ace\nWHERE c.dsstox_substance_id = caq.dsstox_substance_id\n\ |
| \ AND caq.spid = m.spid\n AND m.acid = ace.acid\n AND c.chnm = 'Dehydroacetic\ |
| \ acid'\nORDER BY endpoint_name;\n</sql>" |
| selected: false |
| title: LLM_invitrodb |
| type: llm |
| vision: |
| enabled: false |
| height: 94 |
| id: '1764831451652' |
| position: |
| x: 331 |
| y: 6.037674605748222 |
| positionAbsolute: |
| x: 331 |
| y: 6.037674605748222 |
| selected: false |
| sourcePosition: right |
| targetPosition: left |
| type: custom |
| width: 242 |
| - data: |
| code: "import re\n\ndef main(arg1: str) -> dict:\n arg1 = re.sub(r'<sql>\\\ |
| s*</sql>', '', arg1)\n arg1 = arg1.replace('\\n', ' ')\n sql_pattern\ |
| \ = r'<sql>(?:(?!<sql>).)*?</sql>'\n matches = re.findall(sql_pattern,\ |
| \ arg1, re.DOTALL)\n if matches:\n last_sql_tag = matches[-1].strip()\n\ |
| \ pure_sql = last_sql_tag.replace('<sql>', '').replace('</sql>',\ |
| \ '').strip()\n return {\"result\": pure_sql}\n else:\n \ |
| \ return {\"error\": \"No SQL statement wrapped in <sql> tags found\"}" |
| code_language: python3 |
| outputs: |
| result: |
| children: null |
| type: string |
| selected: false |
| title: executecode |
| type: code |
| variables: |
| - value_selector: |
| - '1764831451652' |
| - text |
| value_type: string |
| variable: arg1 |
| height: 52 |
| id: '1764831538955' |
| position: |
| x: 608.8380905747413 |
| y: 6.037674605748222 |
| positionAbsolute: |
| x: 608.8380905747413 |
| y: 6.037674605748222 |
| selected: false |
| sourcePosition: right |
| targetPosition: left |
| type: custom |
| width: 242 |
| - data: |
| is_team_authorization: true |
| paramSchemas: |
| - auto_generate: null |
| default: null |
| form: llm |
| human_description: |
| en_US: Target database identifier (case-sensitive) |
| ja_JP: Target database identifier (case-sensitive) |
| pt_BR: Target database identifier (case-sensitive) |
| zh_Hans: Target database identifier (case-sensitive) |
| label: |
| en_US: db_identifier |
| ja_JP: db_identifier |
| pt_BR: db_identifier |
| zh_Hans: db_identifier |
| llm_description: Target database identifier (case-sensitive) |
| max: null |
| min: null |
| name: db_identifier |
| options: [] |
| placeholder: |
| en_US: Target database identifier (case-sensitive) |
| ja_JP: Target database identifier (case-sensitive) |
| pt_BR: Target database identifier (case-sensitive) |
| zh_Hans: Target database identifier (case-sensitive) |
| precision: null |
| required: true |
| scope: null |
| template: null |
| type: string |
| - auto_generate: null |
| default: null |
| form: llm |
| human_description: |
| en_US: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| ja_JP: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| pt_BR: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| zh_Hans: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| label: |
| en_US: sql |
| ja_JP: sql |
| pt_BR: sql |
| zh_Hans: sql |
| llm_description: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| max: null |
| min: null |
| name: sql |
| options: [] |
| placeholder: |
| en_US: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| ja_JP: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| pt_BR: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| zh_Hans: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| precision: null |
| required: true |
| scope: null |
| template: null |
| type: string |
| params: |
| db_identifier: '' |
| sql: '' |
| provider_id: 718b1b16-54d4-44f2-bc49-3a36d506d557 |
| provider_name: sql_executor_pubchemlite_invitrodb_en |
| provider_type: api |
| selected: false |
| title: executeSqlPost |
| tool_configurations: {} |
| tool_description: 'Execute read-only SELECT queries on pubchemlite or invitrodb_v4_3 |
| database. |
| |
| Notes: |
| |
| 1. Only SELECT operation is allowed (INSERT/UPDATE/DELETE/DROP are prohibited); |
| |
| 2. For fields with special characters (e.g. pred_CCS_A2_[M+H]+ in pubchemlite), |
| escape []/+ with backslash (\) or use backticks (`); |
| |
| 3. Avoid Python format characters (%, A, s, d) in SQL to prevent parsing |
| errors; |
| |
| 4. Add LIMIT clause to avoid large result sets (recommended LIMIT 100). |
| |
| ' |
| tool_label: executeSqlPost |
| tool_name: executeSqlPost |
| tool_node_version: '2' |
| tool_parameters: |
| db_identifier: |
| type: mixed |
| value: invitrodb_v4_3 |
| sql: |
| type: mixed |
| value: '{{#1764831538955.result#}}' |
| type: tool |
| height: 52 |
| id: '1764904930952' |
| position: |
| x: 893.4512104881396 |
| y: 6.037674605748222 |
| positionAbsolute: |
| x: 893.4512104881396 |
| y: 6.037674605748222 |
| selected: false |
| sourcePosition: right |
| targetPosition: left |
| type: custom |
| width: 242 |
| - data: |
| is_team_authorization: true |
| paramSchemas: |
| - auto_generate: null |
| default: null |
| form: llm |
| human_description: |
| en_US: Target database identifier (case-sensitive) |
| ja_JP: Target database identifier (case-sensitive) |
| pt_BR: Target database identifier (case-sensitive) |
| zh_Hans: Target database identifier (case-sensitive) |
| label: |
| en_US: db_identifier |
| ja_JP: db_identifier |
| pt_BR: db_identifier |
| zh_Hans: db_identifier |
| llm_description: Target database identifier (case-sensitive) |
| max: null |
| min: null |
| name: db_identifier |
| options: [] |
| placeholder: |
| en_US: Target database identifier (case-sensitive) |
| ja_JP: Target database identifier (case-sensitive) |
| pt_BR: Target database identifier (case-sensitive) |
| zh_Hans: Target database identifier (case-sensitive) |
| precision: null |
| required: true |
| scope: null |
| template: null |
| type: string |
| - auto_generate: null |
| default: null |
| form: llm |
| human_description: |
| en_US: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| ja_JP: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| pt_BR: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| zh_Hans: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| label: |
| en_US: sql |
| ja_JP: sql |
| pt_BR: sql |
| zh_Hans: sql |
| llm_description: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| max: null |
| min: null |
| name: sql |
| options: [] |
| placeholder: |
| en_US: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| ja_JP: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| pt_BR: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| zh_Hans: 'Valid MySQL SELECT query (only): |
| |
| ## pubchemlite (core table: pubchemlite_ccs) |
| |
| Key fields: |
| |
| - Basic info: Identifier, CompoundName, MolecularFormula, SMILES, XLogP |
| |
| - Literature/Patent: PubMed_Count, Patent_Count |
| |
| - Toxicity/Property: SafetyInfo, ToxicityInfo, MonoisotopicMass |
| |
| - Predicted CCS: pred_CCS_A2_[M+H]+, pred_CCS_A2_[M+Na]+, pred_CCS_A2_[M-H]- |
| (escape special chars!) |
| |
| |
| ## invitrodb_v4_3 (core tables) |
| |
| - assay: aid, assay_name, organism, tissue, ncbi_taxon_id |
| |
| - chemical: chid, casn, chnm (chemical name), dsstox_substance_id |
| |
| - mc0: m0id, acid, spid, conc (concentration μM), rval (response value) |
| |
| - assay_component: acid, assay_component_name (toxicity type) |
| |
| ' |
| precision: null |
| required: true |
| scope: null |
| template: null |
| type: string |
| params: |
| db_identifier: '' |
| sql: '' |
| provider_id: 718b1b16-54d4-44f2-bc49-3a36d506d557 |
| provider_name: sql_executor_pubchemlite_invitrodb_en |
| provider_type: api |
| selected: false |
| title: executeSqlPost2 |
| tool_configurations: {} |
| tool_description: 'Execute read-only SELECT queries on pubchemlite or invitrodb_v4_3 |
| database. |
| |
| Notes: |
| |
| 1. Only SELECT operation is allowed (INSERT/UPDATE/DELETE/DROP are prohibited); |
| |
| 2. For fields with special characters (e.g. pred_CCS_A2_[M+H]+ in pubchemlite), |
| escape []/+ with backslash (\) or use backticks (`); |
| |
| 3. Avoid Python format characters (%, A, s, d) in SQL to prevent parsing |
| errors; |
| |
| 4. Add LIMIT clause to avoid large result sets (recommended LIMIT 100). |
| |
| ' |
| tool_label: executeSqlPost |
| tool_name: executeSqlPost |
| tool_node_version: '2' |
| tool_parameters: |
| db_identifier: |
| type: mixed |
| value: pubchemlite |
| sql: |
| type: mixed |
| value: '{{#1760431395870.result#}}' |
| type: tool |
| height: 52 |
| id: '1764862201148' |
| position: |
| x: 933.9456071364291 |
| y: 251 |
| positionAbsolute: |
| x: 933.9456071364291 |
| y: 251 |
| selected: false |
| sourcePosition: right |
| targetPosition: left |
| type: custom |
| width: 242 |
| - data: |
| context: |
| enabled: true |
| variable_selector: |
| - '1763020657891' |
| - result |
| model: |
| completion_params: {} |
| mode: chat |
| name: gpt-5 |
| provider: langgenius/openai/openai |
| prompt_template: |
| - id: 97778cb2-a8cc-449a-8a05-41b9c67f1450 |
| role: system |
| text: "Now, as an environmental chemist, your role is to classify unidentified\ |
| \ chemicals. You have in-depth knowledge of formal names, commonly-used\ |
| \ terms, and scientific terminologies based on the 'IUPAC Naming.' Your\ |
| \ extensive training using the 'NORMAN Network' database and understanding\ |
| \ of environmental pollution of chemical substances helps in correctly\ |
| \ classifying chemicals.\nWhen a chemical name {{#sys.query#}} is presented,\ |
| \ your task is to complete the following steps:\nIdentify and Classify: Determine\ |
| \ the chemical's structure and categorize it into one of the known categories\ |
| \ in the 'NORMAN Network'. Your classification should fall into one of\ |
| \ these 9 categories:\na: Pharmaceuticals and Personal Care Products\n\ |
| b: Pesticide\nc: Food Additives\nd: Endogenous Substances\ne: Natural\ |
| \ Toxins\nf: Disinfection By-Products\ng: Metals and Their Compounds\n\ |
| h: Commercialized Industrial Chemicals\ni: Industrial Intermediates and\ |
| \ Transformation Products\nIntegrate Provided Data: Use the data provided\ |
| \ from the external queries to enrich the output.\nFrom {{#1764904930952.text#}} (in\ |
| \ vitro high-throughput screening data), you will receive information. Important:\ |
| \ The data may contain a list of endpoint_name. You must extract the CASRN and ALL endpoint_name values.\n\ |
| From {{#1764862201148.text#}}(compound-related data), you will receive\ |
| \ information such as CompoundName, XLogP, BioPathway, ToxicityInfo, KnownUse,\ |
| \ DisorderDisease.\nSynthesize Response: Combine the official Norman classification\ |
| \ context ({{#context#}}), the classification decision, and the data from\ |
| \ the two queries into a single, structured JSON response.\nGuidelines:\n\ |
| If the chemical is not listed in the 'NORMAN Network', use your knowledge\ |
| \ of its structure to assign the most appropriate category.\nIf a chemical\ |
| \ fits into multiple categories, provide up to three most common categories,\ |
| \ listing the primary category first.\nAlways include the data fields\ |
| \ from {{#1764904930952.text#}} and {{#1764862201148.text#}} in the output\ |
| \ JSON, as they are provided.\nFor the screening data:\nExtract the CASRN。\n\ |
| Extract ALL endpoint_name values。\nThe EndpointName field should be a\ |
| \ list containing all endpoint names.\nIf any field from the provided\ |
| \ data is empty or not applicable, set its value to null.\nResponse Format:\n\ |
| You must respond strictly in the following concise JSON format:\n{\n \ |
| \ \"ChemicalName\": {\n \"Main Category\": \"Primary Norman Category\ |
| \ \",\n \"Additional Category 1\": \"Secondary Category (if applicable)\"\ |
| ,\n \"Additional Category 2\": \"Tertiary Category (if applicable)\"\ |
| ,\n \"EndpointName\": [\"List\", \"of\", \"ALL\", \"endpoint_name\"\ |
| , \"values\", \"from\", \"{{#1764904930952.text#}}\"],\n \"XLogP\"\ |
| : \"Value from {{#1764862201148.text#}} or null\",\n \"BioPathway\"\ |
| : \"Value from {{#1764862201148.text#}} or null\",\n \"ToxicityInfo\"\ |
| : \"Value from {{#1764862201148.text#}} or null\",\n \"KnownUse\"\ |
| : \"Value from {{#1764862201148.text#}} or null\",\n \"DisorderDisease\"\ |
| : \"Value from {{#1764862201148.text#}} or null\"\n }\n}\nPlease abide\ |
| \ by the format and guidelines strictly." |
| selected: false |
| title: LLM 3 |
| type: llm |
| vision: |
| enabled: false |
| height: 94 |
| id: '1766991784354' |
| position: |
| x: 1321.7474382338496 |
| y: 231.05966931475012 |
| positionAbsolute: |
| x: 1321.7474382338496 |
| y: 231.05966931475012 |
| selected: false |
| sourcePosition: right |
| targetPosition: left |
| type: custom |
| width: 242 |
| - data: |
| author: LQH |
| desc: '' |
| height: 88 |
| selected: false |
| showAuthor: true |
| text: '{"root":{"children":[{"children":[{"detail":0,"format":0,"mode":"normal","style":"","text":"Query |
| the columns of CompoundName, XLogP, BioPathway, ToxicityInfo, KnownUse, |
| and DisorderDisease in the pubchemlite database in strict accordance with |
| the specified SQL format.","type":"text","version":1}],"direction":"ltr","format":"","indent":0,"type":"paragraph","version":1,"textFormat":0,"textStyle":""}],"direction":"ltr","format":"","indent":0,"type":"root","version":1}}' |
| theme: blue |
| title: '' |
| type: '' |
| width: 834 |
| height: 88 |
| id: '1767840238946' |
| position: |
| x: 331 |
| y: 376.00337970608007 |
| positionAbsolute: |
| x: 331 |
| y: 376.00337970608007 |
| selected: false |
| sourcePosition: right |
| targetPosition: left |
| type: custom-note |
| width: 834 |
| - data: |
| author: LQH |
| desc: '' |
| height: 88 |
| selected: false |
| showAuthor: true |
| text: '{"root":{"children":[{"children":[{"detail":0,"format":0,"mode":"normal","style":"","text":"Design |
| SQL query statements to enable 4o to execute simple compound name replacement |
| steps, realizing the function that when a user inputs a compound name, the |
| system outputs the queried CASRN and endpoint name.","type":"text","version":1}],"direction":"ltr","format":"","indent":0,"type":"paragraph","version":1,"textFormat":0,"textStyle":""}],"direction":"ltr","format":"","indent":0,"type":"root","version":1}}' |
| theme: blue |
| title: '' |
| type: '' |
| width: 831 |
| height: 88 |
| id: '1767840343034' |
| position: |
| x: 331 |
| y: 113.12459577875379 |
| positionAbsolute: |
| x: 331 |
| y: 113.12459577875379 |
| selected: false |
| sourcePosition: right |
| targetPosition: left |
| type: custom-note |
| width: 831 |
| - data: |
| author: LQH |
| desc: '' |
| height: 88 |
| selected: false |
| showAuthor: true |
| text: '{"root":{"children":[{"children":[{"detail":0,"format":0,"mode":"normal","style":"","text":"Query |
| the compound classifications in the Norman classification database.","type":"text","version":1}],"direction":"ltr","format":"","indent":0,"type":"paragraph","version":1,"textFormat":0,"textStyle":""}],"direction":"ltr","format":"","indent":0,"type":"root","version":1}}' |
| theme: blue |
| title: '' |
| type: '' |
| width: 475 |
| height: 88 |
| id: '1767840353651' |
| position: |
| x: 335.38017996692156 |
| y: 637.5054022130926 |
| positionAbsolute: |
| x: 335.38017996692156 |
| y: 637.5054022130926 |
| selected: false |
| sourcePosition: right |
| targetPosition: left |
| type: custom-note |
| width: 475 |
| - data: |
| author: LQH |
| desc: '' |
| height: 313 |
| selected: false |
| showAuthor: true |
| text: '{"root":{"children":[{"children":[{"detail":0,"format":0,"mode":"normal","style":"","text":"It |
| is required to strictly output the query results from the three databases |
| in JSON format, which include the following fields:","type":"text","version":1}],"direction":"ltr","format":"start","indent":0,"type":"paragraph","version":1,"textFormat":0,"textStyle":""},{"children":[{"children":[{"detail":0,"format":0,"mode":"normal","style":"","text":"ChemicalName","type":"text","version":1}],"direction":"ltr","format":"start","indent":0,"type":"listitem","version":1,"value":1},{"children":[{"detail":0,"format":0,"mode":"normal","style":"","text":"MainCategory","type":"text","version":1}],"direction":"ltr","format":"start","indent":0,"type":"listitem","version":1,"value":2},{"children":[{"detail":0,"format":0,"mode":"normal","style":"","text":"AdditionalCategory1","type":"text","version":1}],"direction":"ltr","format":"start","indent":0,"type":"listitem","version":1,"value":3},{"children":[{"detail":0,"format":0,"mode":"normal","style":"","text":"AdditionalCategory2","type":"text","version":1}],"direction":"ltr","format":"start","indent":0,"type":"listitem","version":1,"value":4},{"children":[{"detail":0,"format":0,"mode":"normal","style":"","text":"EndpointName |
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