{ "id": 424726, "title": "Why protein's terms are different with UniProtKB", "url": "/competitions/cafa-5-protein-function-prediction/discussion/424726", "author_name": "", "post_date": "2023-07-15T13:14:08.766443100Z", "votes": 4, "comment_count": 7, "views": 0, "content": "

Such as uid='P20536'

\n

In train set, the terms are

\n

\n

But in UniProtKB, they are

\n

\n

@iddux1 @damianopiovesan

", "messages": [ { "id": "2345521", "postDate": "07/15/2023 13:14:08", "content": "

Such as uid='P20536'

\n

In train set, the terms are

\n

\n

But in UniProtKB, they are

\n

\n

@iddux1 @damianopiovesan

", "rawMarkdown": "Such as uid='P20536'\n\nIn train set, the terms are \n\n\n\n\nBut in UniProtKB, they are\n\n\n\n@iddux1 @damianopiovesan", "votes": null }, { "id": "2345765", "postDate": "07/15/2023 17:06:36", "content": "

Have you done propagation ?

", "rawMarkdown": "Have you done propagation ?", "votes": null }, { "id": "2346069", "postDate": "07/16/2023 02:01:42", "content": "

No, the GO:0003677 can be found only in UniProtKB, it's odd.

", "rawMarkdown": "No, the GO:0003677 can be found only in UniProtKB, it's odd.", "votes": null }, { "id": "2346097", "postDate": "07/16/2023 02:52:57", "content": "

Because UniProtKB might have IEA annoation, and the DNA binding for this EntryID is inferred from electronic annotation.

", "rawMarkdown": "Because UniProtKB might have IEA annoation, and the DNA binding for this EntryID is inferred from electronic annotation.", "votes": null }, { "id": "2347469", "postDate": "07/17/2023 02:11:52", "content": "

But the number of annotations in trainset is more than UniProtKB. If only IDA(Inferred from Direct Assay) annoation in trainset, the number should be less.

", "rawMarkdown": "But the number of annotations in trainset is more than UniProtKB. If only IDA(Inferred from Direct Assay) annoation in trainset, the number should be less.", "votes": null }, { "id": "2347472", "postDate": "07/17/2023 02:17:42", "content": "

Did you consider the propagation? All terms in the trainset are propagated through is_a and part_of relationship. This is the reason why the number of annotations in trainsets is more than UniProtKB.

", "rawMarkdown": "Did you consider the propagation? All terms in the trainset are propagated through is_a and part_of relationship. This is the reason why the number of annotations in trainsets is more than UniProtKB.", "votes": null }, { "id": "2349574", "postDate": "07/18/2023 14:23:40", "content": "

Hi @daishu,

\n

As confirmed by the competition host here,

\n
\n

We include experimental (EXP, IDA, IPI, IMP, IGI, IEP), high-throughput (HTP,HDA, HMP,HGI,HEP) as well as TAS and IC.

\n
\n

These are all the evidence codes used by the host to filter the terms. Hope this helps.

", "rawMarkdown": "Hi @daishu,\n\nAs confirmed by the competition host [here](https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/405362#2342145),\n\n> We include experimental (EXP, IDA, IPI, IMP, IGI, IEP), high-throughput (HTP,HDA, HMP,HGI,HEP) as well as TAS and IC.\n\nThese are all the evidence codes used by the host to filter the terms. Hope this helps.", "votes": null }, { "id": "2350104", "postDate": "07/19/2023 02:16:23", "content": "

Thanks, i missed it

", "rawMarkdown": "Thanks, i missed it", "votes": null } ], "comments": [ { "id": 2345765, "author_name": "alexandervc", "author_url": "", "post_date": "07/15/2023 17:06:36", "content": "

Have you done propagation ?

", "votes": null, "replies": [ { "id": 2346069, "author_name": "daishu", "author_url": "", "post_date": "07/16/2023 02:01:42", "content": "

No, the GO:0003677 can be found only in UniProtKB, it's odd.

", "votes": null, "replies": [ { "id": 2346097, "author_name": "evansliu", "author_url": "", "post_date": "07/16/2023 02:52:57", "content": "

Because UniProtKB might have IEA annoation, and the DNA binding for this EntryID is inferred from electronic annotation.

", "votes": null, "replies": [ { "id": 2347469, "author_name": "daishu", "author_url": "", "post_date": "07/17/2023 02:11:52", "content": "

But the number of annotations in trainset is more than UniProtKB. If only IDA(Inferred from Direct Assay) annoation in trainset, the number should be less.

", "votes": null, "replies": [ { "id": 2347472, "author_name": "evansliu", "author_url": "", "post_date": "07/17/2023 02:17:42", "content": "

Did you consider the propagation? All terms in the trainset are propagated through is_a and part_of relationship. This is the reason why the number of annotations in trainsets is more than UniProtKB.

", "votes": null, "replies": [] }, { "id": 2349574, "author_name": "abaojiang", "author_url": "", "post_date": "07/18/2023 14:23:40", "content": "

Hi @daishu,

\n

As confirmed by the competition host here,

\n
\n

We include experimental (EXP, IDA, IPI, IMP, IGI, IEP), high-throughput (HTP,HDA, HMP,HGI,HEP) as well as TAS and IC.

\n
\n

These are all the evidence codes used by the host to filter the terms. Hope this helps.

", "votes": null, "replies": [ { "id": 2350104, "author_name": "daishu", "author_url": "", "post_date": "07/19/2023 02:16:23", "content": "

Thanks, i missed it

", "votes": null, "replies": [] } ] } ] } ] } ] } ] } ], "raw_markdown_by_id": { "2345521": "Such as uid='P20536'\n\nIn train set, the terms are \n\n\n\n\nBut in UniProtKB, they are\n\n\n\n@iddux1 @damianopiovesan", "2345765": "Have you done propagation ?", "2346069": "No, the GO:0003677 can be found only in UniProtKB, it's odd.", "2346097": "Because UniProtKB might have IEA annoation, and the DNA binding for this EntryID is inferred from electronic annotation.", "2347469": "But the number of annotations in trainset is more than UniProtKB. If only IDA(Inferred from Direct Assay) annoation in trainset, the number should be less.", "2347472": "Did you consider the propagation? All terms in the trainset are propagated through is_a and part_of relationship. This is the reason why the number of annotations in trainsets is more than UniProtKB.", "2349574": "Hi @daishu,\n\nAs confirmed by the competition host [here](https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/405362#2342145),\n\n> We include experimental (EXP, IDA, IPI, IMP, IGI, IEP), high-throughput (HTP,HDA, HMP,HGI,HEP) as well as TAS and IC.\n\nThese are all the evidence codes used by the host to filter the terms. Hope this helps.", "2350104": "Thanks, i missed it" }, "source": "meta" }