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geneontology / amigo

AmiGO is the public interface for the Gene Ontology.
http://amigo.geneontology.org
BSD 3-Clause "New" or "Revised" License
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Definitions of molecular_function and cellular_component do not match in AmiGO and QuickGO #705

Closed addiehl closed 1 year ago

addiehl commented 1 year ago

Related to geneontology/go-ontology#26516

AmiGO CC A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).

QuickGO CC A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).

AmiGO MF A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.

QuickGO MF A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.

I don't know the history of these definition changes, but this is also concerning. (@giacomodecolle)

addiehl commented 1 year ago

I see that QuickGO registered a change to the molecular_function definition on 2023-03-06, so AmiGO is definitely behind on that.

On the other hand, I see that QuickGO registered a change to the cellular_component definition on 2023-10-28, so AmiGO will hopefully catch up on the next load.

kltm commented 1 year ago

@addiehl I'm pretty sure that this is related to geneontology/go-ontology#26516 and likely https://github.com/geneontology/go-ontology/issues/18870 via https://github.com/geneontology/pipeline/issues/162; definitely not a direct AmiGO issue. Would you mind if I close this out to keep the conversation compact?

kltm commented 1 year ago

Likely duplicate based on geneontology/go-ontology#26516; https://github.com/geneontology/go-ontology/issues/18870 via https://github.com/geneontology/pipeline/issues/162

addiehl commented 1 year ago

Thanks!