I'm pretty curious about the usege of InChI instead of SMILES, even if in theory the first is more reliable, there are too few works that use it (a quick search on arxiv or biorxiv to confirm this). The notation it's not new like SELFIES (Krenn, 2020). Don't missunderstand me, i have no bad intentions doing the past question, is just pure curiosity.
\nP.S.: Thanks for host a competition related to chemistry so exciting.
", "messages": [ { "id": "1224658", "postDate": "03/03/2021 00:23:15", "content": "I'm pretty curious about the usege of InChI instead of SMILES, even if in theory the first is more reliable, there are too few works that use it (a quick search on arxiv or biorxiv to confirm this). The notation it's not new like SELFIES (Krenn, 2020). Don't missunderstand me, i have no bad intentions doing the past question, is just pure curiosity.
\nP.S.: Thanks for host a competition related to chemistry so exciting.
", "rawMarkdown": "I'm pretty curious about the usege of **InChI** instead of **SMILES**, even if in theory the first is more reliable, there are too few works that use it (a quick search on **arxiv** or **biorxiv** to confirm this). The notation it's not new like **SELFIES** ([Krenn, 2020](https://arxiv.org/pdf/1905.13741.pdf)). Don't missunderstand me, i have no bad intentions doing the past question, is just pure curiosity. \n\nP.S.: Thanks for host a competition related to chemistry so exciting.", "votes": null }, { "id": "1224668", "postDate": "03/03/2021 01:01:28", "content": "Hello Hiram, InChI is a unique identifier for molecules. However, you can create several SMILES for the same molecule.
\nFor example: CCO and OCC
\nFor the evaluation, there should be one valid answer, I guess that's why they use InChI.
\nYou can convert SMILES to InChI so you don't have to work with InChI. I recommend RDKit to convert molecules.
", "rawMarkdown": "Hello Hiram, InChI is a unique identifier for molecules. However, you can create several SMILES for the same molecule. \n\nFor example: CCO and OCC\n\nFor the evaluation, there should be one valid answer, I guess that's why they use InChI.\n\nYou can convert SMILES to InChI so you don't have to work with InChI. I recommend RDKit to convert molecules.", "votes": null }, { "id": "1224671", "postDate": "03/03/2021 01:05:25", "content": "\n\nInChI is a unique identifier for molecules. However, you can create several SMILES for the same molecule.
\n
I was thinking the same, InChI is more reliable due the reason that you mentioned. However, i still have the doubt of why is so unused even if is a unique identifier.
\n\n\nYou can convert SMILES to InChI so you don't have to work with InChI. I recommend RDKit to convert molecules.
\n
Maybe as an augmentation technique, and also SELFIES.
", "rawMarkdown": "> InChI is a unique identifier for molecules. However, you can create several SMILES for the same molecule.\n\nI was thinking the same, InChI is more reliable due the reason that you mentioned. However, i still have the doubt of why is so unused even if is a unique identifier. \n\n> You can convert SMILES to InChI so you don't have to work with InChI. I recommend RDKit to convert molecules.\n\nMaybe as an augmentation technique, and also **SELFIES**.", "votes": null }, { "id": "1224683", "postDate": "03/03/2021 01:23:00", "content": "I guess there are two reasons for SMILES domination:
\nAgain you hit the nail, especially at the number of datasets. After this competition, maybe more papers will be published.
", "rawMarkdown": "Again you hit the nail, especially at the number of datasets. After this competition, maybe more papers will be published.", "votes": null }, { "id": "1224821", "postDate": "03/03/2021 05:03:20", "content": "A brief introduction to SMILES vs InChi : http://molecularmodelingbasics.blogspot.com/2016/05/a-brief-introduction-to-smiles-and-inchi.html
", "rawMarkdown": "A brief introduction to SMILES vs InChi : http://molecularmodelingbasics.blogspot.com/2016/05/a-brief-introduction-to-smiles-and-inchi.html", "votes": null }, { "id": "1230320", "postDate": "03/08/2021 02:53:56", "content": "@hiramcho I found this particular Technical FAQ covering all questions like Why InCHI , its scope and also databases available etc
\nhttps://www.inchi-trust.org/technical-faq-2/#2.3
", "rawMarkdown": "hiramcho I found this particular Technical FAQ covering all questions like Why InCHI , its scope and also databases available etc \n\nhttps://www.inchi-trust.org/technical-faq-2/#2.3", "votes": null }, { "id": "1230804", "postDate": "03/08/2021 13:19:45", "content": "Thanks for your answer.
", "rawMarkdown": "Thanks for your answer.", "votes": null }, { "id": "1231340", "postDate": "03/08/2021 22:08:29", "content": "Very good question, in practice SMILES are often preferred for molecular representation, but there is no universal standard for the format. For this competition, InChI were selected to provide a canonical representation of the molecules. The winning submission will likely convert the text representation to another format, so with InChI we both avoid steering everyone to a single cheminformatics package, and provide a standard for submissions.
", "rawMarkdown": "Very good question, in practice SMILES are often preferred for molecular representation, but there is no universal standard for the format. For this competition, InChI were selected to provide a canonical representation of the molecules. The winning submission will likely convert the text representation to another format, so with InChI we both avoid steering everyone to a single cheminformatics package, and provide a standard for submissions.", "votes": null }, { "id": "1231399", "postDate": "03/09/2021 00:15:53", "content": "Thanks for answer my question, my curiosity is now satisfied.
", "rawMarkdown": "Thanks for answer my question, my curiosity is now satisfied.", "votes": null } ], "comments": [ { "id": 1224668, "author_name": "sorkun", "author_url": "", "post_date": "03/03/2021 01:01:28", "content": "Hello Hiram, InChI is a unique identifier for molecules. However, you can create several SMILES for the same molecule.
\nFor example: CCO and OCC
\nFor the evaluation, there should be one valid answer, I guess that's why they use InChI.
\nYou can convert SMILES to InChI so you don't have to work with InChI. I recommend RDKit to convert molecules.
", "votes": null, "replies": [ { "id": 1224671, "author_name": "hiramcho", "author_url": "", "post_date": "03/03/2021 01:05:25", "content": "\n\nInChI is a unique identifier for molecules. However, you can create several SMILES for the same molecule.
\n
I was thinking the same, InChI is more reliable due the reason that you mentioned. However, i still have the doubt of why is so unused even if is a unique identifier.
\n\n\nYou can convert SMILES to InChI so you don't have to work with InChI. I recommend RDKit to convert molecules.
\n
Maybe as an augmentation technique, and also SELFIES.
", "votes": null, "replies": [] }, { "id": 1224683, "author_name": "sorkun", "author_url": "", "post_date": "03/03/2021 01:23:00", "content": "I guess there are two reasons for SMILES domination:
\nAgain you hit the nail, especially at the number of datasets. After this competition, maybe more papers will be published.
", "votes": null, "replies": [] } ] }, { "id": 1224821, "author_name": "sarveswara", "author_url": "", "post_date": "03/03/2021 05:03:20", "content": "A brief introduction to SMILES vs InChi : http://molecularmodelingbasics.blogspot.com/2016/05/a-brief-introduction-to-smiles-and-inchi.html
", "votes": null, "replies": [] }, { "id": 1230320, "author_name": "usharengaraju", "author_url": "", "post_date": "03/08/2021 02:53:56", "content": "@hiramcho I found this particular Technical FAQ covering all questions like Why InCHI , its scope and also databases available etc
\nhttps://www.inchi-trust.org/technical-faq-2/#2.3
", "votes": null, "replies": [ { "id": 1230804, "author_name": "hiramcho", "author_url": "", "post_date": "03/08/2021 13:19:45", "content": "Thanks for your answer.
", "votes": null, "replies": [] } ] }, { "id": 1231340, "author_name": "jakealbrecht1337", "author_url": "", "post_date": "03/08/2021 22:08:29", "content": "Very good question, in practice SMILES are often preferred for molecular representation, but there is no universal standard for the format. For this competition, InChI were selected to provide a canonical representation of the molecules. The winning submission will likely convert the text representation to another format, so with InChI we both avoid steering everyone to a single cheminformatics package, and provide a standard for submissions.
", "votes": null, "replies": [ { "id": 1231399, "author_name": "hiramcho", "author_url": "", "post_date": "03/09/2021 00:15:53", "content": "Thanks for answer my question, my curiosity is now satisfied.
", "votes": null, "replies": [] } ] } ], "raw_markdown_by_id": { "1224658": "I'm pretty curious about the usege of **InChI** instead of **SMILES**, even if in theory the first is more reliable, there are too few works that use it (a quick search on **arxiv** or **biorxiv** to confirm this). The notation it's not new like **SELFIES** ([Krenn, 2020](https://arxiv.org/pdf/1905.13741.pdf)). Don't missunderstand me, i have no bad intentions doing the past question, is just pure curiosity. \n\nP.S.: Thanks for host a competition related to chemistry so exciting.", "1224668": "Hello Hiram, InChI is a unique identifier for molecules. However, you can create several SMILES for the same molecule. \n\nFor example: CCO and OCC\n\nFor the evaluation, there should be one valid answer, I guess that's why they use InChI.\n\nYou can convert SMILES to InChI so you don't have to work with InChI. I recommend RDKit to convert molecules.", "1224671": "> InChI is a unique identifier for molecules. However, you can create several SMILES for the same molecule.\n\nI was thinking the same, InChI is more reliable due the reason that you mentioned. However, i still have the doubt of why is so unused even if is a unique identifier. \n\n> You can convert SMILES to InChI so you don't have to work with InChI. I recommend RDKit to convert molecules.\n\nMaybe as an augmentation technique, and also **SELFIES**.", "1224683": "I guess there are two reasons for SMILES domination: \n- SMILES is an older representation and many available datasets contain SMILES. \n- SMILES is more human-friendly : )", "1224692": "Again you hit the nail, especially at the number of datasets. After this competition, maybe more papers will be published.", "1224821": "A brief introduction to SMILES vs InChi : http://molecularmodelingbasics.blogspot.com/2016/05/a-brief-introduction-to-smiles-and-inchi.html", "1230320": "hiramcho I found this particular Technical FAQ covering all questions like Why InCHI , its scope and also databases available etc \n\nhttps://www.inchi-trust.org/technical-faq-2/#2.3", "1230804": "Thanks for your answer.", "1231340": "Very good question, in practice SMILES are often preferred for molecular representation, but there is no universal standard for the format. For this competition, InChI were selected to provide a canonical representation of the molecules. The winning submission will likely convert the text representation to another format, so with InChI we both avoid steering everyone to a single cheminformatics package, and provide a standard for submissions.", "1231399": "Thanks for answer my question, my curiosity is now satisfied." }, "source": "meta" }