This is likely explained somewhere in the overview or many papers and links thereafter, but it may be useful to some of you who don't necessarily read the fine print.
\nGene ontology (GO) annotations represent different levels of knowledge about proteins. GO categories with smaller numbers tend to have broad functional annotations, while GOs with larger numbers correspond to more specific functions. It is not a perfect analogy, but it may be easiest to understand by comparing GO annotations to taxonomic classification of organisms.
\nHere are taxonomic assignments for human species:
\nKingdom - Animalia
\nPhylum - Chordata
\nClass - Mammalia
\nOrder -Primates
\nFamily - Hominidae
\nGenus - Homo
\nSpecies - sapiens
Saying that humans belong to animal kingdom is accurate, but so do hundreds of thousands of other species. Our membership to the phylum of chordates (animals with backbone or backbone-like structures) narrows it down within animal kingdom, but is still fairly broad. So is our membership to mammalian class. Once we get to the family of hominids (great apes), it becomes a clearly defined group of terrestrial animals who socialize, care for their young and with higher brain functions. Note that taxonomic classification works upward/backward automatically, but not downward/forward. A member of primate order has to belong to mammals, chordates and animals, which are all categories above it. Yet it doesn't have to belong to a family of hominids, as there are other families within that order.
\nA similar approach is in play with GO annotations. Knowing that a protein is involved in DNA repair is a broad functional designation, as there are different types of DNA damage. If we can say that a protein's function is DNA synthesis involved in UV-damage excision repair, it becomes more clearly defined.
\nBroader protein functions (small GO numbers) are generally easier to predict, yet they don't necessarily help in defining specific molecular functions (larger GO numbers). Knowing specific protein functions can in many cases unambiguously define broader functional categories.
", "messages": [ { "id": "2227635", "postDate": "04/19/2023 22:18:06", "content": "This is likely explained somewhere in the overview or many papers and links thereafter, but it may be useful to some of you who don't necessarily read the fine print.
\nGene ontology (GO) annotations represent different levels of knowledge about proteins. GO categories with smaller numbers tend to have broad functional annotations, while GOs with larger numbers correspond to more specific functions. It is not a perfect analogy, but it may be easiest to understand by comparing GO annotations to taxonomic classification of organisms.
\nHere are taxonomic assignments for human species:
\nKingdom - Animalia
\nPhylum - Chordata
\nClass - Mammalia
\nOrder -Primates
\nFamily - Hominidae
\nGenus - Homo
\nSpecies - sapiens
Saying that humans belong to animal kingdom is accurate, but so do hundreds of thousands of other species. Our membership to the phylum of chordates (animals with backbone or backbone-like structures) narrows it down within animal kingdom, but is still fairly broad. So is our membership to mammalian class. Once we get to the family of hominids (great apes), it becomes a clearly defined group of terrestrial animals who socialize, care for their young and with higher brain functions. Note that taxonomic classification works upward/backward automatically, but not downward/forward. A member of primate order has to belong to mammals, chordates and animals, which are all categories above it. Yet it doesn't have to belong to a family of hominids, as there are other families within that order.
\nA similar approach is in play with GO annotations. Knowing that a protein is involved in DNA repair is a broad functional designation, as there are different types of DNA damage. If we can say that a protein's function is DNA synthesis involved in UV-damage excision repair, it becomes more clearly defined.
\nBroader protein functions (small GO numbers) are generally easier to predict, yet they don't necessarily help in defining specific molecular functions (larger GO numbers). Knowing specific protein functions can in many cases unambiguously define broader functional categories.
", "rawMarkdown": "This is likely explained somewhere in the overview or many papers and links thereafter, but it may be useful to some of you who don't necessarily read the fine print.\n\nGene ontology (GO) annotations represent different levels of knowledge about proteins. GO categories with smaller numbers tend to have broad functional annotations, while GOs with larger numbers correspond to more specific functions. It is not a perfect analogy, but it may be easiest to understand by comparing GO annotations to taxonomic classification of organisms.\n\nHere are taxonomic assignments for human species:\n\nKingdom - *Animalia*\nPhylum - *Chordata*\nClass - *Mammalia*\nOrder -*Primates*\nFamily - *Hominidae*\nGenus - *Homo*\nSpecies - *sapiens*\n\nSaying that humans belong to animal kingdom is accurate, but so do hundreds of thousands of other species. Our membership to the phylum of chordates (animals with backbone or backbone-like structures) narrows it down within animal kingdom, but is still fairly broad. So is our membership to mammalian class. Once we get to the family of hominids (great apes), it becomes a clearly defined group of terrestrial animals who socialize, care for their young and with higher brain functions. Note that taxonomic classification works upward/backward automatically, but not downward/forward. A member of primate order has to belong to mammals, chordates and animals, which are all categories above it. Yet it doesn't have to belong to a family of hominids, as there are other families within that order.\n\nA similar approach is in play with GO annotations. Knowing that a protein is involved in DNA repair is a broad functional designation, as there are different types of DNA damage. If we can say that a protein's function is [**DNA synthesis involved in UV-damage excision repair**](https://www.ebi.ac.uk/QuickGO/term/GO:1904161), it becomes more clearly defined.\n\nBroader protein functions (small GO numbers) are generally easier to predict, yet they don't necessarily help in defining specific molecular functions (larger GO numbers). Knowing specific protein functions can in many cases unambiguously define broader functional categories.", "votes": null }, { "id": "2235126", "postDate": "04/25/2023 18:49:33", "content": "Copied from a different post of mine as it relates to this particular topic.
\nThink about human body. All the bones, muscles and internal organs are body parts, but only some of them are parts of the left arm or the right eye. Similarly, all cellular proteins are part of the cell, but only some of them are in mitochondria or in cell membrane. There are different levels of specificity with which we describe a function, and that determines which subset of cellular proteins (or our body parts) is involved in it. If we try to describe a general function such as object manipulation, it would be fair to assume that human arms are performing that function. If we describe it more specifically, say fine-motor skills, chances are that we can narrow the function to our hands. If we want to be more specific, say buttoning a shirt as a subset of fine-motor skills, most people can do it with either or both hands. If we pick a skill subset such as handwriting, most people are better at writing with one hand than the other. So my right hand may belong to structural classification groups such as body part and right arm, while being functionally capable of object manipulation, fine-motor skills, buttoning a shirt and handwriting. My left hand would belong to body part and left arm, and functionally to object manipulation, fine-motor skills, buttoning a shirt and driving a car.
Copied from a different post of mine as it relates to this particular topic.
\nThink about human body. All the bones, muscles and internal organs are body parts, but only some of them are parts of the left arm or the right eye. Similarly, all cellular proteins are part of the cell, but only some of them are in mitochondria or in cell membrane. There are different levels of specificity with which we describe a function, and that determines which subset of cellular proteins (or our body parts) is involved in it. If we try to describe a general function such as object manipulation, it would be fair to assume that human arms are performing that function. If we describe it more specifically, say fine-motor skills, chances are that we can narrow the function to our hands. If we want to be more specific, say buttoning a shirt as a subset of fine-motor skills, most people can do it with either or both hands. If we pick a skill subset such as handwriting, most people are better at writing with one hand than the other. So my right hand may belong to structural classification groups such as body part and right arm, while being functionally capable of object manipulation, fine-motor skills, buttoning a shirt and handwriting. My left hand would belong to body part and left arm, and functionally to object manipulation, fine-motor skills, buttoning a shirt and driving a car.