organ formation vs anatomical structure formation

[gocentral]

Hi,

I am confused with these 2 terms:

organ formation GO:0048645 Def: The process that gives rise to an organ. This process pertains to the initial formation of a structure from unspecified parts.

anatomical structure formation GO:0048646 Def: The process that gives rise to an anatomical structure. This process pertains to the initial formation of a structure from unspecified parts.

I think if we are having these 2 terms, the difference between the two should be specified clearly more than saying 'organ' and 'anatomical part'. Also, looks like organ formation term is specifically for floral organ and what about other organs such as heart etc?

Again under anatomical structure formation, I don't see shoot or root formation which are anatomical parts. This whole distinction is confusing to me.

Can someone explain this distinction and choice of parentages?

Suparna

Reported by: smundodi

Original Ticket: "geneontology/ontology-requests/3195":https://sourceforge.net/p/geneontology/ontology-requests/3195

[gocentral]

• assigned_to: nobody --> jenclark

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=735846

Hi Suparna,

The terms were agreed in this item: [ 1247348 ] initiation of organ primordium https://sourceforge.net/tracker/index.php? func=detail&aid=1247348&group_id=36855&atid=440764 D'y want to have a read and let me know what you think?

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=835115

An organ is a specific type of anatomical structure, so 'organ formation' is_a 'anatomical structure formation'. This structure tries to distinguish between "organ" and "non-organ" anatomical structures. However, there are inconsistencies in how this is being used.

For example, 'otic vesicle formation' (GO:0030916) is a child of 'organ formation', while 'optic placode formation' is a child of 'anatomical structure formation' (GO:0048646).

I don't think either the otic vesicle or the optic placode would properly be considered organs..but instead would be considered to be anatomical structures.

Consequently, both should be children of 'anatomical structure formation'

-Doug

Original comment by: doughowe

[gocentral]

Logged In: YES user_id=735846

Hi Doug,

Thanks for pointing ou that missing relationship. I've fixed it. How would these do as a first shot at a definition:

organ:

A natural part or structure in an animal or a plant, capable of performing some special action (termed its function), which is essential to the life or well-being of the whole; as, the heart, lungs, etc, are organs of animals; the root, stem, foliage, etc, are organs of plants. In animals the organs are generally made up of several tissues, one of which usually predominates, and determines the principal function of the organ.

System:

Groups of organs working together to fullfill a discrete function constitute a system.

Anatomical structure:

Component parts of the body, which may include the whole or part of many organs or systems, but are not wholly composed of a single organ or system.

Anatomical structure is quite hard to define. I see the online dictionaries all woose out: 'a particular complex anatomical structure; "he has good bone structure" '

Jen

Original comment by: jenclark

[gocentral]

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Does anybody have any views on these possible defs?

Thanks,

Jen

Original comment by: jenclark

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Logged In: YES user_id=835115

These seem reasonable to me.

Original comment by: doughowe

[gocentral]

Logged In: YES user_id=735846

David came up with an improved definition for these terms.

organ formation ; GO:0048645 def: "The process pertaining to the initial formation of an organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment. Organs are a natural part or structure in an animal or a plant, capable of performing some special action (termed its function), which is essential to the life or well-being of the whole. The heart and lungs are organs of animals, and the petal and leaf are organs of plants. In animals the organs are generally made up of several tissues, one of which usually predominates, and determines the principal function of the organ." [GOC:dph, GOC:jic]

anatomical structure formation ; GO:0048646 def: "The process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GOC:dph, GOC:jic]

I have committed them.

Thanks,

Jennifer

Original comment by: jenclark

[gocentral]

• labels: --> Other term-related request
• milestone: --> Plant Ontology
• status: open --> closed-accepted

Original comment by: jenclark

[gocentral]

• assigned_to: Jennifer Deegan --> nobody
• Group: Plant Ontology --> None

Original comment by: cooperl09