#1 part_of in FMA

open
nobody
None
5
2007-07-18
2007-07-18
Chris Mungall
No

The OBO Relation ontology defines part_of using the standard ALL-SOME pattern. We had assumed the FMA was the same.

However, the FMA asserts:

Protoplasm part_of Parafollicular cell of thyroid gland
Protoplasm part_of Mucous cell of gastric gland
Protoplasm part_of . ...

and so on for many more classes. This is clearly incompatible with the RO definition of part_of.

This is not a problem with the Protege conversion - this can be seen on the FMA explorer too (make sure you choose subclass view, as you can't open Protoplasm in part_of view due to the explosion of parent terms)

It seems that the FMA chooses to interpret part_of in a SOME-SOME manner.

There are a good number of other suspicious classes, such as Intercellular matrix

According to FMA, Protoplasm is part_of all these things:

Paneth cell
Acinar cell of pancreas
Parafollicular cell of thyroid gland
Mucous cell of gastric gland
Type I cell of adrenal cortex
Vacuolar absorptive cell
Pancreatic centro-acinar cell
Langerhans cell
Type EC2 enteroendocrine cell
Type L enteroendocrine cell
Brush cell
Hepatic macrophage
Enteroendocrine cell
Basophil
Type I enteroendocrine cell
Type D enteroendocrine cell
Chromaffin cell of adrenal cortex
Type D1 enteroendocrine cell
Microfold cell
Surface mucous cell of stomach
Granular leukocyte
Inactive chief cell of parathyroid gland
Type S enteroendocrine cell
Type EC1 enteroendocrine cell
Bipolar cell of retina
Type X enteroendocrine cell
Type PP enteroendocrine cell
Type TG enteroendocrine cell
Pancreatic ductal cell
Type K enteroendocrine cell
B lymphocyte
Enterocyte
Type II cell of adrenal cortex
Chief cell of parathyroid gland
Epithelial cell of appendix
Natural killer cell
Goblet cell
Dense-core granulated cell
Lymphocyte
Mesothelial cell
Type EC enteroendocrine cell
Type N enteroendocrine cell
T lymphocyte

All the following classes have more than 5 part_of parents, which is not necessarily a problem, but points a finger of suspicion:

Articular cartilage of right superior articular process of second thoracic vertebra
Articular cartilage of left superior articular process of second thoracic vertebra
Intralobular stroma of lactiferous gland
Enterocyte
Organized mucosa-associated lymphoid tissue
Diffuse mucosa-associated lymphoid tissue
Basal lamina
Microfold cell
Epithelium of crypt of Lieberkuhn of large intestine
Epithelium proper of large intestine
Plasma membrane
Basement membrane
Areolar connective tissue
Myocyte of sinuatrial node
Myocyte of atrioventricular node
Transitional myocyte
Protoplasm
Type G enteroendocrine cell
Brush cell
Parafollicular cell of thyroid gland
Thyroid follicular cell
Active chief cell of parathyroid gland
Inactive chief cell of parathyroid gland
Tricuspid valve
Mitral valve
Anterolateral head of lateral papillary muscle of left ventricle
Trabecula carnea of left ventricle
Endocardium
Endocardium of right atrium
Endocardium of left atrium
Mesothelium of epicardium
Subepicardial layer of epicardium
Regular ventricular cardiac myocyte
Cardiac endomysium
Fibrocollagenous sheath of cardiac muscle fasciculus
Septal division of left branch of atrioventricular bundle
Transitional myocyte of internodal tract
Transitional myocyte of atrioventricular bundle
Purkinje myocyte of atrioventricular bundle
Dense collagenous reticulum of atrioventricular bundle
Myocardium of right atrium
Myocardium of left atrium
Endocardium of interatrial septum
Endocardium of interventricular septum
Endothelium of endocardium
Fibroelastic connective tissue of epicardium
Endocardium of papillary muscle of left ventricle
Fibroelastic connective tissue of semilunar valvule of aortic valve
Cardiac muscle tissue of interatrial septum
Cardiac muscle tissue of interventricular septum
Fibroelastic connective tissue of lunule of semilunar valvule
Fibroelastic connective tissue of endocardium
Fibrocollagenous connective tissue of lunule of semilunar valvule
Fibrocollagenous sheath of cardiac muscle tissue
Cardiac muscle tissue of papillary muscle of left ventricle
Epicardium of right atrium
Anterior division of left branch of atrioventricular bundle
Posterior division of left branch of atrioventricular bundle
Epicardium of left atrium
Epicardium of right ventricle
Myocardium of right ventricle
Endocardium of right ventricle
Epicardium of left ventricle
Endocardium of left ventricle
Intercellular matrix

Discussion

  • Onard Mejino
    Onard Mejino
    2007-07-19

    Logged In: YES
    user_id=1846212
    Originator: NO

    Thanks for the alert. The FMA authors intend to comply with RO's standard use of ALL-SOME pattern. In the next release the appropriate relation is enforced, e.g. Protoplasm of parafolliculat cell of thyroid gland part_of Parafollicular cell of thyroid gland.

     
  • Chris Mungall
    Chris Mungall
    2008-10-13

    Thanks Onard. I see most of these are fixed in FMA2. However, there are a few remaining. E.g.

    * Compartment of thorax regional_part_of Male body compartment
    * Compartment of thorax regional_part_of Female body compartment

    If it helps I can make a comprehensive list.

    Note this isn't an artefact of the conversion - the above relations are in the FMA explorer on:

    http://fme.biostr.washington.edu:8089/FME/index.html