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Main relations used in Gene Ontology(GO):
\n
1. is a
\nThe is a relation forms the basic structure of GO. If we say A is a B, we mean that node A is a subtype of node B. For example, mitotic cell cycle is a cell cycle, or lyase activity is a catalytic activity.
\nIt is safe to use is a to group annotations. For example if a gene product X is annotated as having tyrosine kinase activity and the ontology records that tyrosine kinase activity is a (type of) kinase activity, then we can safely conclude that gene product X has kinase activity.
\n2. part of
\nThe part of relation is used to represent part-whole relationships. part of has a specific meaning in GO, and a part of relation would only be added between A and B if B is necessarily part of A: wherever B exists, it is as part of A, and the presence of the B implies the presence of A. However, given the occurrence of A, we cannot say for certain that B exists.
\nIt is safe to use part of to group annotations. For example if a gene product X is annotated as located in the inner mitochondrial membrane and the ontology records a part of relation between inner mitochondrial membrane and mitochondrion, we can safely conclude that X is located in a mitochondrion.
\n3. has part
\nThe logical complement to the part of relation is has part, which represents a part-whole relationship from the perspective of the parent. As with part of, the GO relation has part is only used in cases where A always has B as a part, i.e. where A necessarily has part B. If A exists, B will always exist; however, if B exists, we cannot say for certain that A exists. i.e. all A have part B; some B part of A.
\nIt is NOT correct to use has part for grouping annotations. For example, we might assert in the ontology that a receptor tyrosine kinase activity has part ATP hydrolysis activity. However it would not then be correct to group all annotations to kinase activity under ATPase activity.
\n4. regulates
\nA relation that describes case in which one process directly affects the manifestation of another process or quality, i.e. the former regulates the latter. The target of the regulation may be another process, for e.g., regulation of a pathway or an enzymatic reaction, or it may be a quality, such as cell size or pH. Analogously to part of, this relation is used specifically to mean necessarily regulates: if both A and B are present, B always regulates A, but A may not always be regulated by B., i.e. all B regulate A; some A are regulated by B.
\nUnlike is a and part of, grouping annotations to gene products grouped via regulates changes the relationship between the GO term and the gene product over the is a and part of relations. If gene product X is annotated as involved in a process that regulates glycolysis, it would not be correct to conclude that X participates in glycolysis. Nevertheless, some tools use regulates relations to group annotations. This can be useful for gene-set enrichment. The resulting gene sets include genes that are involved in processes that are causally related to the grouping term.
\n", "messages": [ { "id": "2227453", "postDate": "04/19/2023 19:04:44", "content": "Main relations used in Gene Ontology(GO):
\n
1. is a
\nThe is a relation forms the basic structure of GO. If we say A is a B, we mean that node A is a subtype of node B. For example, mitotic cell cycle is a cell cycle, or lyase activity is a catalytic activity.
\nIt is safe to use is a to group annotations. For example if a gene product X is annotated as having tyrosine kinase activity and the ontology records that tyrosine kinase activity is a (type of) kinase activity, then we can safely conclude that gene product X has kinase activity.
\n2. part of
\nThe part of relation is used to represent part-whole relationships. part of has a specific meaning in GO, and a part of relation would only be added between A and B if B is necessarily part of A: wherever B exists, it is as part of A, and the presence of the B implies the presence of A. However, given the occurrence of A, we cannot say for certain that B exists.
\nIt is safe to use part of to group annotations. For example if a gene product X is annotated as located in the inner mitochondrial membrane and the ontology records a part of relation between inner mitochondrial membrane and mitochondrion, we can safely conclude that X is located in a mitochondrion.
\n3. has part
\nThe logical complement to the part of relation is has part, which represents a part-whole relationship from the perspective of the parent. As with part of, the GO relation has part is only used in cases where A always has B as a part, i.e. where A necessarily has part B. If A exists, B will always exist; however, if B exists, we cannot say for certain that A exists. i.e. all A have part B; some B part of A.
\nIt is NOT correct to use has part for grouping annotations. For example, we might assert in the ontology that a receptor tyrosine kinase activity has part ATP hydrolysis activity. However it would not then be correct to group all annotations to kinase activity under ATPase activity.
\n4. regulates
\nA relation that describes case in which one process directly affects the manifestation of another process or quality, i.e. the former regulates the latter. The target of the regulation may be another process, for e.g., regulation of a pathway or an enzymatic reaction, or it may be a quality, such as cell size or pH. Analogously to part of, this relation is used specifically to mean necessarily regulates: if both A and B are present, B always regulates A, but A may not always be regulated by B., i.e. all B regulate A; some A are regulated by B.
\nUnlike is a and part of, grouping annotations to gene products grouped via regulates changes the relationship between the GO term and the gene product over the is a and part of relations. If gene product X is annotated as involved in a process that regulates glycolysis, it would not be correct to conclude that X participates in glycolysis. Nevertheless, some tools use regulates relations to group annotations. This can be useful for gene-set enrichment. The resulting gene sets include genes that are involved in processes that are causally related to the grouping term.
\n", "rawMarkdown": "Main relations used in Gene Ontology(GO):\n\n\n\n**1. is a**\n\nThe is a relation forms the basic structure of GO. If we say A is a B, we mean that node A is a subtype of node B. For example, mitotic cell cycle is a cell cycle, or lyase activity is a catalytic activity.\n\nIt is safe to use is a to group annotations. For example if a gene product X is annotated as having tyrosine kinase activity and the ontology records that tyrosine kinase activity is a (type of) kinase activity, then we can safely conclude that gene product X has kinase activity.\n\t \n**2. part of**\n\nThe part of relation is used to represent part-whole relationships. part of has a specific meaning in GO, and a part of relation would only be added between A and B if B is necessarily part of A: wherever B exists, it is as part of A, and the presence of the B implies the presence of A. However, given the occurrence of A, we cannot say for certain that B exists.\n\nIt is safe to use part of to group annotations. For example if a gene product X is annotated as located in the inner mitochondrial membrane and the ontology records a part of relation between inner mitochondrial membrane and mitochondrion, we can safely conclude that X is located in a mitochondrion.\t \n\n**3. has part**\n\nThe logical complement to the part of relation is has part, which represents a part-whole relationship from the perspective of the parent. As with part of, the GO relation has part is only used in cases where A always has B as a part, i.e. where A necessarily has part B. If A exists, B will always exist; however, if B exists, we cannot say for certain that A exists. i.e. all A have part B; some B part of A.\n\nIt is NOT correct to use has part for grouping annotations. For example, we might assert in the ontology that a receptor tyrosine kinase activity has part ATP hydrolysis activity. However it would not then be correct to group all annotations to kinase activity under ATPase activity.\t \n\n**4. regulates**\n\nA relation that describes case in which one process directly affects the manifestation of another process or quality, i.e. the former regulates the latter. The target of the regulation may be another process, for e.g., regulation of a pathway or an enzymatic reaction, or it may be a quality, such as cell size or pH. Analogously to part of, this relation is used specifically to mean necessarily regulates: if both A and B are present, B always regulates A, but A may not always be regulated by B., i.e. all B regulate A; some A are regulated by B.\n\nUnlike is a and part of, grouping annotations to gene products grouped via regulates changes the relationship between the GO term and the gene product over the is a and part of relations. If gene product X is annotated as involved in a process that regulates glycolysis, it would not be correct to conclude that X participates in glycolysis. Nevertheless, some tools use regulates relations to group annotations. This can be useful for gene-set enrichment. The resulting gene sets include genes that are involved in processes that are causally related to the grouping term.\t\n\n[source](http://geneontology.org/docs/ontology-relations/)", "votes": null }, { "id": "2227467", "postDate": "04/19/2023 19:16:29", "content": "@serangu Great starting resource, thank you!
", "rawMarkdown": "serangu Great starting resource, thank you!", "votes": null }, { "id": "2227816", "postDate": "04/20/2023 03:31:52", "content": "@luisfrentzen thanks. I hope this topic will help to understand how relations work.
", "rawMarkdown": "luisfrentzen thanks. I hope this topic will help to understand how relations work.", "votes": null }, { "id": "2364685", "postDate": "07/29/2023 14:29:25", "content": "Thanks you enlighten me,😀
", "rawMarkdown": "Thanks you enlighten me,😀", "votes": null }, { "id": "3129302", "postDate": "02/20/2025 13:33:17", "content": "This is a clear and well structured explanation of the main relationships in GeneOntology. The distinctions between 'is a', 'part of', 'has part', and 'regulates' are well articulated, especially in terms of how they impact annotation grouping. The note on the cautious use of 'has part' and 'regulates' for grouping is particularly insightful. Great summary.
", "rawMarkdown": "This is a clear and well structured explanation of the main relationships in GeneOntology. The distinctions between 'is a', 'part of', 'has part', and 'regulates' are well articulated, especially in terms of how they impact annotation grouping. The note on the cautious use of 'has part' and 'regulates' for grouping is particularly insightful. Great summary.", "votes": null } ], "comments": [ { "id": 2227467, "author_name": "luisfrentzen", "author_url": "", "post_date": "04/19/2023 19:16:29", "content": "@serangu Great starting resource, thank you!
", "votes": null, "replies": [ { "id": 2227816, "author_name": "serangu", "author_url": "", "post_date": "04/20/2023 03:31:52", "content": "@luisfrentzen thanks. I hope this topic will help to understand how relations work.
", "votes": null, "replies": [] } ] }, { "id": 2364685, "author_name": "bitguber", "author_url": "", "post_date": "07/29/2023 14:29:25", "content": "Thanks you enlighten me,😀
", "votes": null, "replies": [] }, { "id": 3129302, "author_name": "mohammad1ziyar", "author_url": "", "post_date": "02/20/2025 13:33:17", "content": "This is a clear and well structured explanation of the main relationships in GeneOntology. The distinctions between 'is a', 'part of', 'has part', and 'regulates' are well articulated, especially in terms of how they impact annotation grouping. The note on the cautious use of 'has part' and 'regulates' for grouping is particularly insightful. Great summary.
", "votes": null, "replies": [] } ], "raw_markdown_by_id": { "2227453": "Main relations used in Gene Ontology(GO):\n\n\n\n**1. is a**\n\nThe is a relation forms the basic structure of GO. If we say A is a B, we mean that node A is a subtype of node B. For example, mitotic cell cycle is a cell cycle, or lyase activity is a catalytic activity.\n\nIt is safe to use is a to group annotations. For example if a gene product X is annotated as having tyrosine kinase activity and the ontology records that tyrosine kinase activity is a (type of) kinase activity, then we can safely conclude that gene product X has kinase activity.\n\t \n**2. part of**\n\nThe part of relation is used to represent part-whole relationships. part of has a specific meaning in GO, and a part of relation would only be added between A and B if B is necessarily part of A: wherever B exists, it is as part of A, and the presence of the B implies the presence of A. However, given the occurrence of A, we cannot say for certain that B exists.\n\nIt is safe to use part of to group annotations. For example if a gene product X is annotated as located in the inner mitochondrial membrane and the ontology records a part of relation between inner mitochondrial membrane and mitochondrion, we can safely conclude that X is located in a mitochondrion.\t \n\n**3. has part**\n\nThe logical complement to the part of relation is has part, which represents a part-whole relationship from the perspective of the parent. As with part of, the GO relation has part is only used in cases where A always has B as a part, i.e. where A necessarily has part B. If A exists, B will always exist; however, if B exists, we cannot say for certain that A exists. i.e. all A have part B; some B part of A.\n\nIt is NOT correct to use has part for grouping annotations. For example, we might assert in the ontology that a receptor tyrosine kinase activity has part ATP hydrolysis activity. However it would not then be correct to group all annotations to kinase activity under ATPase activity.\t \n\n**4. regulates**\n\nA relation that describes case in which one process directly affects the manifestation of another process or quality, i.e. the former regulates the latter. The target of the regulation may be another process, for e.g., regulation of a pathway or an enzymatic reaction, or it may be a quality, such as cell size or pH. Analogously to part of, this relation is used specifically to mean necessarily regulates: if both A and B are present, B always regulates A, but A may not always be regulated by B., i.e. all B regulate A; some A are regulated by B.\n\nUnlike is a and part of, grouping annotations to gene products grouped via regulates changes the relationship between the GO term and the gene product over the is a and part of relations. If gene product X is annotated as involved in a process that regulates glycolysis, it would not be correct to conclude that X participates in glycolysis. Nevertheless, some tools use regulates relations to group annotations. This can be useful for gene-set enrichment. The resulting gene sets include genes that are involved in processes that are causally related to the grouping term.\t\n\n[source](http://geneontology.org/docs/ontology-relations/)", "2227467": "serangu Great starting resource, thank you!", "2227816": "luisfrentzen thanks. I hope this topic will help to understand how relations work.", "2364685": "Thanks you enlighten me,😀", "3129302": "This is a clear and well structured explanation of the main relationships in GeneOntology. The distinctions between 'is a', 'part of', 'has part', and 'regulates' are well articulated, especially in terms of how they impact annotation grouping. The note on the cautious use of 'has part' and 'regulates' for grouping is particularly insightful. Great summary." }, "source": "meta" }