General definitions

Please try to use the following templates for definitions of terms such as Atrophy of X that should be analogous for multiple organs. The template refers to the first sentence of the definition; if there are other particularities, they should be added after the first sentence.

Abscess

Exmaple: A circumscribed area of pus or necrotic debris in lung parenchyma, which leads to a cavity, and after formation of bronchopulmonary fistula, can manifest as an air-fluid level inside the cavity.

Atresia

A developmental defect resulting in complete obliteration of the lumen of a hollow (often tubular) organ. Here is the definition for atresia of the colon:

A developmental defect resulting in complete obliteration of the lumen of the colon. 
That is, there is an abnormal closure, or atresia of the tubular structure of the 
colon.

The corresponding logical definition is:

'has part' some 
    (atretic
     and ('inheres in' some colon)
     and ('has modifier' some abnormal))

Atrophy

Atrophy is the partial or complete wasting (loss) of tissue that was once present. Here is the definition for the HPO term Brain atrophy:

Partial or complete wasting (loss) of brain tissue that was once present.

Degeneration

Degeneration is the deterioration of a tissue or an organ in which its function is diminished or its structure is impaired.

Atrophy vs. Degeneration

Atrophy (nearly an opposite meaning of hypertrophy) is a decrease in size of an organ, tissue or cell, owing to a decrease in size of individual cells or a reduced number of cells in the affected organ or tissue. Atrophy usually refers to an acquired (and this is the meaning given in the HPO). Degeneration refers to a deterioration (gradual loss) of structure and function of organs, tissues, or cells. Since the HPO includes separate subhierarchies for morphology and function, we will encode "degeneration" as a morphological abnormality (since it is usually diagnosed histologically). If appropriate, associated functional anomalies need to be coded separately.

##Dysgenesis Dysgenesis refers to defective development of an organ. It is thus not really specific as to what the morphological defect is, but it implies that the defect was present from the beginning. Defective or abnormal development of an organ. This description, although not very specific, is common in clinical usage and thus the HPO has corresponding terms. Dysgenesis of the cerebellar vermis is defined as Defective development of the vermis of cerebellum.

'has part' some 
    (dysplastic
     and ('inheres in' some 'cerebellar vermis')
     and ('has modifier' some abnormal))

Fibrosis

For example, Hepatic fibrosis (HP:0001395): The presence of excessive fibrous connective tissue in the liver. Fibrosis is a reparative or reactive process.

'has part' some 
    ('increased amount'
     and ('inheres in' some 
        (fibrosis
         and ('part of' some liver)))
     and ('has modifier' some abnormal))

General definitions for organs

In general, each of the organs should have one general term and one morphology and one physiology term. For instance

Abnormality of the digestive system
'has part' some 
    (quality
     and ('inheres in part of' some 'cardiovascular system')
     and ('has modifier' some abnormal))

and

Abnormality of digestive system morphology
'has part' some 
    (morphology
     and ('inheres in part of' some 'digestive system')
     and ('has modifier' some abnormal))

and

Abnormality of digestive system physiology
'has part' some 
    (functionality
     and ('inheres in part of' some 'digestive system')
     and ('has modifier' some abnormal))