README.md

---
license: mit
language:
- en
pretty_name: "MrGO Anatomist"  # Example: SQuAD
task_categories:
  - question-answering
model_creator: Chime Ogbuji
size_categories:
  - "10K<n<100K"
source_datasets:
- "FMA"  # Example: wikipedia
tags:
- medical
- health  
- instruct
- finetune
---

# Mr. Grammatical Ontology: Anatomist

This dataset was extracted from the [Web Ontology Language (OWL)](https://en.wikipedia.org/wiki/Web_Ontology_Language) 
[representation](http://purl.org/sig/ont/fma.owl) of the [Foundational Model of Anatomy](http://si.washington.edu/projects/fma) [1] using 
[Owlready2](https://owlready2.readthedocs.io/en/v0.47/#) to facilitate the extraction of the logical axioms in the FMA
into a Controlled Natural Language (CNL) for use in training Medical Large Language Models to be conversant in 
canonical human anatomy.

So, Description Logic expressions such as the following in FMA about fma13245 (Surface of left ventricle):

```console
fma13245 ⊑ fma222938 (Surface of cardiac chamber)
fma13245 ⊑ ∃ bounds .fma7101 (Left ventricle)
fma13245 ⊑ ∃ bounds .fma7166 (Left side of heart)
fma13245 ⊑ ∃ bounds .fma73704 (Wall of left side of heart)
fma13245 ⊑ ∃ bounds .fma83473 (Wall of biventricular part of heart)
fma13245 ⊑ fma222938 (Surface of cardiac chamber)
```

can be rendered as the following textual definition:


```
The Surface of left ventricle is defined in the Foundational Model Anatomy (FMA) as a surface of cardiac chamber.
It bounds a left ventricle, a left side of heart, a wall of left side of heart, and a wall of biventricular part of heart
```

This dataset includes full definition instructions such as the following, generated from the logical axioms of the FMA ontology:

```json
{"input": "What is the Cardiac vein?", 
 "output": "The Cardiac vein is defined in the Foundational Model Anatomy (FMA) as a systemic vein. It is a compositionally distinct anatomical element of a heart. It is the venous drainage of a left ventricle, a wall of right side of heart, a wall of left side of heart, a wall of biventricular part of heart, a free wall of left ventricle, a myocardium of basal zone of left ventricle, a myocardium of mid zone of left ventricle, a myocardium of apical zone of left ventricle, a myocardial zone 17, a septal wall of left ventricle, a myocardium, an anterior wall of left ventricle, an inferior wall of left ventricle, and a lateral wall of left ventricle"}
```

As well as fine-grained definition instructions such as:

```json
{"input": "What is the Cardiac vein a compositionally distinct anatomical element of?", 
 "output": "It is a compositionally distinct anatomical element of a heart"}
```

The full definition instructions for _15,807 FMA_ terms were extracted into *train.json* and _4,807_ fine-grained 
definition instructions were extracted into *valid.json*

[1] __Rosse, Cornelius, and José LV Mejino Jr. "A reference ontology for biomedical informatics: the Foundational Model of Anatomy." Journal of biomedical informatics 36.6 (2003): 478-500.__