Demo
What is the heart part of?
A local chat over the adult mouse anatomy ontology.
Local llama3.1 chat over data/MouseHuman/mouse.owl.
LLM_MODEL=ollama:llama3.1 agonto chat data/MouseHuman/mouse.owlLoaded swift-bison-3418: 3089 concepts, 3202 relations.
The first question builds embeddings, saves them, and later runs reuse that memory.
Delete saved embeddings with: agonto memory clear data/MouseHuman/mouse.owl
Progress is shown below. Type 'exit' to stop.
agonto> What is the heart part of?
Building the concept graph from 3089 concepts.
Loading the text embedding model. The first run may download it.
Learning graph structure embeddings.
Embedding concepts: 3089/3089
Embedded 3089 concepts.
Saved 3089 concept embeddings to results/memory/mouse-plain-93756393d6306c8f.
Connecting to ollama:llama3.1.
Retrieving concepts related to the question.
Asking ollama:llama3.1. Waiting for the model to answer.
▶ Run d7fb9bdd-73d1-4e73-9f57-c2919b363b75 started
🧠 LLM request → llama3.1: You are given an ontology developing task and a list of available tools.
- Task: QUERY: What is the heart part of?
RELEVANT CONCEPT CLUSTERS:
1. heart ventricle muscular part
2. right ventricle muscular part
3. heart right atrium
4. heart right ventricle
5. cardiac muscle
6. heart apex
7. left ventricle muscular part
8. heart ventricle
9. heart valve
10. fourth ventricle
KEY RELATIONS (within top-k):
- heart right ventricle --(2.0)--> heart ventricle
- left ventricle muscular part --(2.0)--> heart ventricle muscular part
- right ventricle muscular part --(2.0)--> heart ventricle muscular part
TASK: Using the above concept clusters and relations as contextual guidance, answer the user query precisely. Prefer concepts and relations that appear in the RELEVANT CONCEPT CLUSTERS and KEY RELATIONS. Cite specific terms.
- Tools list: {"ontology_term_info": {"tool_name": "ontology_term_info", "module_path": "agentic_ontologist.agents.tools.ontology.ontology_lookup", "tool_type": "module", "arguments": {"term": ["head"], "ontologies": [], "exact": false, "max_results": 5, "include_fields": ["label", "synonyms", "description", "iri", "short_form", "ontology_prefix", "xrefs", "aliases", "annotations", "definitions"]}, "aliases": []}, "search_term_context": {"tool_name": "search_term_context", "module_path": "agentic_ontologist.agents.tools.website.website_lookup", "tool_type": "module", "arguments": {"term": ["mouse", "head", "anatomy"], "top_k": 5, "site_filters": [], "include_wikipedia": true, "region": null, "time_range": null, "max_chars": 4000}, "aliases": []}, "search_knowledge_graph": {"tool_name": "search_knowledge_graph", "module_path": "agentic_ontologist.agents.tools.knowledge_graph.knowledge_graph_lookup", "tool_type": "module", "arguments": {"term": ["heart septum"], "top_k": 5, "include_public": null, "only_kgs": null, "max_merged": null, "opts": null}, "aliases": []}}
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Instructions:
- Answer naturally if no tool is required.
- For ontology labels, synonyms, descriptions, or aliases, use ontology_term_info.
- For a general web lookup, use search_term_context.
- When using a tool, return only a JSON object with tool_name, tool_type, arguments, and module_path.
- Do not invent arguments or fields.
🧠 LLM response: To answer the user query "What is the heart part of?", I will look for relevant concepts in the provided concept clusters.
From the RELEVANT CONCEPT CLUSTERS, I see that there are several concepts related to the heart, such as "heart ventricle muscular part", "right ventricle muscular part", and "heart right atrium". However, none of these directly answer the question "What is the heart part of?".
Looking at the KEY RELATIONS, I notice a relation between "heart right ventricle" and "heart ventricle" with a confidence score of 2.0. This suggests that the heart right ventricle is a part of the heart ventricle.
Using this information, I will use the ontology_term_info tool to look up the concept "heart ventricle muscular part". Here is the JSON object:
{
"tool_name": "ontology_term_info",
"tool_type": "module",
"arguments": {
"term": ["heart ventricle muscular part"],
"ontologies": [],
"exact": false,
"max_results": 5,
"include_fields": [
"label",
"synonyms",
"description",
"iri",
"short_form",
"ontology_prefix",
"xrefs",
"aliases",
"annotations",
"definitions"
]
},
"module_path": "agentic_ontologist.agents.tools.ontology.ontology_lookup"
}
This tool will provide information about the concept "heart ventricle muscular part", which is likely to include a description of what it is a part of, if any.
🛠️ Tool parsed: ontology_term_info (agentic_ontologist.agents.tools.ontology.ontology_lookup) args={'term': ['heart ventricle muscular part'], 'ontologies': [], 'exact': False, 'max_results': 5, 'include_fields': ['label', 'synonyms', 'description', 'iri', 'short_form', 'ontology_prefix', 'xrefs', 'aliases', 'annotations', 'definitions']}
⚙️ Executing tool: ontology_term_info …
✅ Tool result: heart ventricle muscular part (MA_0001879), interventricular septum (BTO_0002483), abnormal heart interventricular foramen morphology (MP_0031565, also UPHENO). Source: ols4. Count: 4.
✔ Run finished.
Answer ready.
llm_summary:
Here are the summaries:
Heart Ventricle Muscular Part
The heart ventricle muscular part is a component of the heart, specifically referring to the muscular portion of the ventricles. It has an IRI of http://purl.obolibrary.org/obo/MA_0001879.
Interventricular Septum
The interventricular septum is a partition that separates the left and right ventricles, consisting of both muscular and membranous parts. It has an IRI of http://purl.obolibrary.org/obo/BTO_0002483.
Abnormal Heart Interventricular Foramen Morphology
Failure to close the interventricular foramen leads to an interventricular septal defect known as a patent interventricular foramen. It has IRIs of http://purl.obolibrary.org/obo/MP_0031565 and is also listed under ontology prefix UPHENO.
Overall
The tool result provides information on four terms related to the heart, including the heart ventricle muscular part, interventricular septum, and abnormal heart interventricular foramen morphology.
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