Thanks in advance.
", "messages": [ { "id": "2239219", "postDate": "04/29/2023 09:19:07", "content": "Thanks in advance.
", "rawMarkdown": "Thanks in advance.", "votes": null }, { "id": "2239240", "postDate": "04/29/2023 09:43:02", "content": "The primary difference between these two identifier systems is the database they are associated with. Generally speaking, UniProt is composed of two main sections: Swiss-Prot (6 digit) and TrEMBL (10 digit). TrEMBL contains computationally annotated protein sequences that are automatically derived from the translation of coding sequences in the EMBL-Bank/ENA/DDBJ nucleotide sequence databases. These protein sequences have not yet been manually reviewed and annotated by UniProt curators, unlike the entries in the Swiss-Prot section.
\nThis page is a good starting point https://www.uniprot.org/help/uniprot_data
", "rawMarkdown": "The primary difference between these two identifier systems is the database they are associated with. Generally speaking, UniProt is composed of two main sections: Swiss-Prot (6 digit) and TrEMBL (10 digit). TrEMBL contains computationally annotated protein sequences that are automatically derived from the translation of coding sequences in the EMBL-Bank/ENA/DDBJ nucleotide sequence databases. These protein sequences have not yet been manually reviewed and annotated by UniProt curators, unlike the entries in the Swiss-Prot section.\n\nThis page is a good starting point https://www.uniprot.org/help/uniprot_data", "votes": null }, { "id": "2239249", "postDate": "04/29/2023 09:50:02", "content": "Nothing really. If anything, it might be an indicator of how long the protein entry existed in UniProt. At first, all UniProt ACs started with O, P, or Q. Then, they allowed all 26 letters due to database growth. Finally, they extended the pattern to 10 characters.
\nI can't share the link (my account isn't old enough); simply google for \"uniprot accession number\" to find the regex patterns.
", "rawMarkdown": "Nothing really. If anything, it might be an indicator of how long the protein entry existed in UniProt. At first, all UniProt ACs started with O, P, or Q. Then, they allowed all 26 letters due to database growth. Finally, they extended the pattern to 10 characters.\n\nI can't share the link (my account isn't old enough); simply google for \"uniprot accession number\" to find the regex patterns.", "votes": null }, { "id": "2239252", "postDate": "04/29/2023 09:53:28", "content": "\n\nSwiss-Prot (6 digit) and TrEMBL (10 digit)
\n
That is not a hard rule. See for example A0A0B4J1F4 which is part of Swiss-Prot. A protein's UniProt AC stays constant. Thus, if it were to move from TrEMBL to Swiss-Prot, it would not change its AC.
Edit: Just to clarify, there is no rule (known to me) that says Swiss-Prot ACs are 6 characters long and TrEMBL ACs are 10. UniProt ACs simply started as 6-character combinations and later were extended to 10 characters.
\nThere might be some correlation, as the oldest entries are 6-character ACs and many of them might have been manually checked since then; thus moved to Swiss-Prot. While entries with 10-character ACs are newer and might not have been checked, i.e., are part of TrEMBL.
\nThe only information you could maybe interpolate is that:
\n1) Old entries have 6 characters, i.e., they were added before the extension(s).
\n2) Entries with 10 character ACs have been added more recently, i.e., after the extension(s).
However, as far as I know, new entries can still be assigned 6-character ACs. Thus, you cannot say all 6-character ACs are old. Finally, entries can be merged or split, which can result in a new primary AC (with the old AC(s) as secondary ones).
", "rawMarkdown": "> Swiss-Prot (6 digit) and TrEMBL (10 digit)\n\nThat is not a hard rule. See for example `A0A0B4J1F4` which is part of Swiss-Prot. A protein's UniProt AC stays constant. Thus, if it were to move from TrEMBL to Swiss-Prot, it would not change its AC.\n\nEdit: Just to clarify, there is no rule (known to me) that says Swiss-Prot ACs are 6 characters long and TrEMBL ACs are 10. UniProt ACs simply started as 6-character combinations and later were extended to 10 characters.\n\nThere might be some correlation, as the oldest entries are 6-character ACs and many of them might have been manually checked since then; thus moved to Swiss-Prot. While entries with 10-character ACs are newer and might not have been checked, i.e., are part of TrEMBL.\n\nThe only information you could maybe interpolate is that:\n1) Old entries have 6 characters, i.e., they were added before the extension(s).\n2) Entries with 10 character ACs have been added more recently, i.e., after the extension(s).\n\nHowever, as far as I know, new entries can still be assigned 6-character ACs. Thus, you cannot say all 6-character ACs are old. Finally, entries can be merged or split, which can result in a new primary AC (with the old AC(s) as secondary ones).", "votes": null }, { "id": "2239265", "postDate": "04/29/2023 10:17:35", "content": "The primary difference between these two identifier systems is the database they are associated with. Generally speaking, UniProt is composed of two main sections: Swiss-Prot (6 digit) and TrEMBL (10 digit). TrEMBL contains computationally annotated protein sequences that are automatically derived from the translation of coding sequences in the EMBL-Bank/ENA/DDBJ nucleotide sequence databases. These protein sequences have not yet been manually reviewed and annotated by UniProt curators, unlike the entries in the Swiss-Prot section.
", "rawMarkdown": "The primary difference between these two identifier systems is the database they are associated with. Generally speaking, UniProt is composed of two main sections: Swiss-Prot (6 digit) and TrEMBL (10 digit). TrEMBL contains computationally annotated protein sequences that are automatically derived from the translation of coding sequences in the EMBL-Bank/ENA/DDBJ nucleotide sequence databases. These protein sequences have not yet been manually reviewed and annotated by UniProt curators, unlike the entries in the Swiss-Prot section.", "votes": null }, { "id": "2239283", "postDate": "04/29/2023 10:30:27", "content": "\n\nSwiss-Prot (6 digit) and TrEMBL (10 digit)
\n
As demonstrated by A0A0B4J1F4, this is not true. For all I know, there is no meaning associated with a UniProt AC aside from it being a unique identifier. However, as you've posted the same text as MT, I'd be interested to know where this quote comes from?
Really appreciated. Thank you so much!
", "rawMarkdown": "ericka42 @mtinti @norixmb \n\nReally appreciated. Thank you so much!", "votes": null }, { "id": "2240331", "postDate": "04/30/2023 13:07:59", "content": "A few years back, when I was working with the UniProt database, I'm sure I was stumbling on 10-digit ids, and those ids were not uniprot/sprot. That impression was at the base of my wrong explanation, apology for that!
", "rawMarkdown": "A few years back, when I was working with the UniProt database, I'm sure I was stumbling on 10-digit ids, and those ids were not uniprot/sprot. That impression was at the base of my wrong explanation, apology for that!", "votes": null }, { "id": "2240359", "postDate": "04/30/2023 13:34:22", "content": "Don't worry, I can see how one could think that (simply going by the frequencies of 6 vs 10 character ACs in both databases). I was just surprised that both of you posted the exact same text, which to me would imply that there is a source for that quote somewhere.
", "rawMarkdown": "Don't worry, I can see how one could think that (simply going by the frequencies of 6 vs 10 character ACs in both databases). I was just surprised that both of you posted the exact same text, which to me would imply that there is a source for that quote somewhere.", "votes": null }, { "id": "2241826", "postDate": "05/01/2023 21:00:53", "content": "\n\nNothing really.
\n
This is the answer to the original question. For the purposes of this competition, there is no difference. Only those who wish to understand the history of protein naming would need to know more than that.
", "rawMarkdown": "> Nothing really.\n\nThis is the answer to the original question. For the purposes of this competition, there is no difference. Only those who wish to understand the history of protein naming would need to know more than that.", "votes": null } ], "comments": [ { "id": 2239240, "author_name": "mtinti", "author_url": "", "post_date": "04/29/2023 09:43:02", "content": "The primary difference between these two identifier systems is the database they are associated with. Generally speaking, UniProt is composed of two main sections: Swiss-Prot (6 digit) and TrEMBL (10 digit). TrEMBL contains computationally annotated protein sequences that are automatically derived from the translation of coding sequences in the EMBL-Bank/ENA/DDBJ nucleotide sequence databases. These protein sequences have not yet been manually reviewed and annotated by UniProt curators, unlike the entries in the Swiss-Prot section.
\nThis page is a good starting point https://www.uniprot.org/help/uniprot_data
", "votes": null, "replies": [ { "id": 2239252, "author_name": "norixmb", "author_url": "", "post_date": "04/29/2023 09:53:28", "content": "\n\nSwiss-Prot (6 digit) and TrEMBL (10 digit)
\n
That is not a hard rule. See for example A0A0B4J1F4 which is part of Swiss-Prot. A protein's UniProt AC stays constant. Thus, if it were to move from TrEMBL to Swiss-Prot, it would not change its AC.
Edit: Just to clarify, there is no rule (known to me) that says Swiss-Prot ACs are 6 characters long and TrEMBL ACs are 10. UniProt ACs simply started as 6-character combinations and later were extended to 10 characters.
\nThere might be some correlation, as the oldest entries are 6-character ACs and many of them might have been manually checked since then; thus moved to Swiss-Prot. While entries with 10-character ACs are newer and might not have been checked, i.e., are part of TrEMBL.
\nThe only information you could maybe interpolate is that:
\n1) Old entries have 6 characters, i.e., they were added before the extension(s).
\n2) Entries with 10 character ACs have been added more recently, i.e., after the extension(s).
However, as far as I know, new entries can still be assigned 6-character ACs. Thus, you cannot say all 6-character ACs are old. Finally, entries can be merged or split, which can result in a new primary AC (with the old AC(s) as secondary ones).
", "votes": null, "replies": [] } ] }, { "id": 2239249, "author_name": "norixmb", "author_url": "", "post_date": "04/29/2023 09:50:02", "content": "Nothing really. If anything, it might be an indicator of how long the protein entry existed in UniProt. At first, all UniProt ACs started with O, P, or Q. Then, they allowed all 26 letters due to database growth. Finally, they extended the pattern to 10 characters.
\nI can't share the link (my account isn't old enough); simply google for \"uniprot accession number\" to find the regex patterns.
", "votes": null, "replies": [ { "id": 2241826, "author_name": "tilii7", "author_url": "", "post_date": "05/01/2023 21:00:53", "content": "\n\nNothing really.
\n
This is the answer to the original question. For the purposes of this competition, there is no difference. Only those who wish to understand the history of protein naming would need to know more than that.
", "votes": null, "replies": [] } ] }, { "id": 2239265, "author_name": "ericka42", "author_url": "", "post_date": "04/29/2023 10:17:35", "content": "The primary difference between these two identifier systems is the database they are associated with. Generally speaking, UniProt is composed of two main sections: Swiss-Prot (6 digit) and TrEMBL (10 digit). TrEMBL contains computationally annotated protein sequences that are automatically derived from the translation of coding sequences in the EMBL-Bank/ENA/DDBJ nucleotide sequence databases. These protein sequences have not yet been manually reviewed and annotated by UniProt curators, unlike the entries in the Swiss-Prot section.
", "votes": null, "replies": [ { "id": 2239283, "author_name": "norixmb", "author_url": "", "post_date": "04/29/2023 10:30:27", "content": "\n\nSwiss-Prot (6 digit) and TrEMBL (10 digit)
\n
As demonstrated by A0A0B4J1F4, this is not true. For all I know, there is no meaning associated with a UniProt AC aside from it being a unique identifier. However, as you've posted the same text as MT, I'd be interested to know where this quote comes from?
A few years back, when I was working with the UniProt database, I'm sure I was stumbling on 10-digit ids, and those ids were not uniprot/sprot. That impression was at the base of my wrong explanation, apology for that!
", "votes": null, "replies": [ { "id": 2240359, "author_name": "norixmb", "author_url": "", "post_date": "04/30/2023 13:34:22", "content": "Don't worry, I can see how one could think that (simply going by the frequencies of 6 vs 10 character ACs in both databases). I was just surprised that both of you posted the exact same text, which to me would imply that there is a source for that quote somewhere.
", "votes": null, "replies": [] } ] } ] } ] }, { "id": 2239795, "author_name": "aesoptacit", "author_url": "", "post_date": "04/29/2023 21:45:51", "content": "\nReally appreciated. Thank you so much!
", "votes": null, "replies": [] } ], "raw_markdown_by_id": { "2239219": "Thanks in advance.", "2239240": "The primary difference between these two identifier systems is the database they are associated with. Generally speaking, UniProt is composed of two main sections: Swiss-Prot (6 digit) and TrEMBL (10 digit). TrEMBL contains computationally annotated protein sequences that are automatically derived from the translation of coding sequences in the EMBL-Bank/ENA/DDBJ nucleotide sequence databases. These protein sequences have not yet been manually reviewed and annotated by UniProt curators, unlike the entries in the Swiss-Prot section.\n\nThis page is a good starting point https://www.uniprot.org/help/uniprot_data", "2239249": "Nothing really. If anything, it might be an indicator of how long the protein entry existed in UniProt. At first, all UniProt ACs started with O, P, or Q. Then, they allowed all 26 letters due to database growth. Finally, they extended the pattern to 10 characters.\n\nI can't share the link (my account isn't old enough); simply google for \"uniprot accession number\" to find the regex patterns.", "2239252": "> Swiss-Prot (6 digit) and TrEMBL (10 digit)\n\nThat is not a hard rule. See for example `A0A0B4J1F4` which is part of Swiss-Prot. A protein's UniProt AC stays constant. Thus, if it were to move from TrEMBL to Swiss-Prot, it would not change its AC.\n\nEdit: Just to clarify, there is no rule (known to me) that says Swiss-Prot ACs are 6 characters long and TrEMBL ACs are 10. UniProt ACs simply started as 6-character combinations and later were extended to 10 characters.\n\nThere might be some correlation, as the oldest entries are 6-character ACs and many of them might have been manually checked since then; thus moved to Swiss-Prot. While entries with 10-character ACs are newer and might not have been checked, i.e., are part of TrEMBL.\n\nThe only information you could maybe interpolate is that:\n1) Old entries have 6 characters, i.e., they were added before the extension(s).\n2) Entries with 10 character ACs have been added more recently, i.e., after the extension(s).\n\nHowever, as far as I know, new entries can still be assigned 6-character ACs. Thus, you cannot say all 6-character ACs are old. Finally, entries can be merged or split, which can result in a new primary AC (with the old AC(s) as secondary ones).", "2239265": "The primary difference between these two identifier systems is the database they are associated with. Generally speaking, UniProt is composed of two main sections: Swiss-Prot (6 digit) and TrEMBL (10 digit). TrEMBL contains computationally annotated protein sequences that are automatically derived from the translation of coding sequences in the EMBL-Bank/ENA/DDBJ nucleotide sequence databases. These protein sequences have not yet been manually reviewed and annotated by UniProt curators, unlike the entries in the Swiss-Prot section.", "2239283": "> Swiss-Prot (6 digit) and TrEMBL (10 digit)\n\nAs demonstrated by `A0A0B4J1F4`, this is not true. For all I know, there is no meaning associated with a UniProt AC aside from it being a unique identifier. However, as you've posted the same text as MT, I'd be interested to know where this quote comes from?", "2239795": "ericka42 @mtinti @norixmb \n\nReally appreciated. Thank you so much!", "2240331": "A few years back, when I was working with the UniProt database, I'm sure I was stumbling on 10-digit ids, and those ids were not uniprot/sprot. That impression was at the base of my wrong explanation, apology for that!", "2240359": "Don't worry, I can see how one could think that (simply going by the frequencies of 6 vs 10 character ACs in both databases). I was just surprised that both of you posted the exact same text, which to me would imply that there is a source for that quote somewhere.", "2241826": "> Nothing really.\n\nThis is the answer to the original question. For the purposes of this competition, there is no difference. Only those who wish to understand the history of protein naming would need to know more than that." }, "source": "meta" }