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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,145 +1,144 @@ | ||
| --- | ||
| name: ld50_catmos | ||
| description: |- | ||
| Acute toxicity LD50 measures | ||
| the most conservative dose that can lead to lethal adverse effects. | ||
| The higher the dose, the more lethal of a drug. | ||
| We aggregated the data from multiple SMILES by computing the mean. | ||
| Acute toxicity LD50 measures | ||
| the most conservative dose that can lead to lethal adverse effects. | ||
| The higher the dose, the more lethal of a drug. | ||
| We aggregated the data from multiple SMILES by computing the mean. | ||
| targets: | ||
| - id: CATMoS_LD50_mgkg | ||
| description: Acute Toxicity LD50. | ||
| units: mg/kg | ||
| type: continuous | ||
| names: | ||
| - noun: acute oral toxicity rat LD50 | ||
| - noun: acute oral toxicity (LD50 in rats) | ||
| uris: | ||
| - http://www.bioassayontology.org/bao#BAO_0002117 | ||
| significant_digits: 1 | ||
| - id: log10_LD50 | ||
| description: Acute Toxicity LD50. | ||
| units: log10(mg/kg) | ||
| type: continuous | ||
| names: | ||
| - noun: log10 acute oral toxicity rat LD50 | ||
| - noun: log10 acute oral toxicity (LD50 in rats) | ||
| - noun: log10 LD50 in rats (oral exposure) | ||
| - noun: log10 rat LD50 (oral exposure) | ||
| significant_digits: 2 | ||
| - id: num_ghose_violations | ||
| description: Ghose filter violations | ||
| type: ordinal | ||
| significant_digits: 0 | ||
| names: | ||
| - noun: Ghose filter violations | ||
| - noun: violations of the Ghose filter | ||
| - id: num_lead_likeness_violations | ||
| description: Lead likeness filter violations | ||
| type: ordinal | ||
| significant_digits: 0 | ||
| names: | ||
| - noun: lead likeness filter violations | ||
| - noun: violations of the lead likeness filter | ||
| - id: num_lipinski_violations | ||
| description: Lipinski filter violations | ||
| type: ordinal | ||
| significant_digits: 0 | ||
| names: | ||
| - noun: Lipinski rule violations | ||
| - noun: violations of the Lipinski rules | ||
| - id: molecular_mass | ||
| description: Molecular mass | ||
| type: continuous | ||
| units: g/mol | ||
| names: | ||
| - noun: molecular mass | ||
| - noun: molecular weight | ||
| - id: num_carbon_atoms | ||
| description: Number of carbon atoms | ||
| type: ordinal | ||
| significant_digits: 0 | ||
| names: | ||
| - noun: carbon atoms | ||
| - id: num_oxygen_atoms | ||
| description: Number of oxygen atoms | ||
| type: ordinal | ||
| significant_digits: 0 | ||
| names: | ||
| - noun: oxygen atoms | ||
| - id: CATMoS_LD50_mgkg | ||
| description: Acute Toxicity LD50. | ||
| units: mg/kg | ||
| type: continuous | ||
| names: | ||
| - noun: acute oral toxicity rat LD50 | ||
| - noun: acute oral toxicity (LD50 in rats) | ||
| uris: | ||
| - http://www.bioassayontology.org/bao#BAO_0002117 | ||
| significant_digits: 1 | ||
| - id: log10_LD50 | ||
| description: Acute Toxicity LD50. | ||
| units: log10(mg/kg) | ||
| type: continuous | ||
| names: | ||
| - noun: log10 acute oral toxicity rat LD50 | ||
| - noun: log10 acute oral toxicity (LD50 in rats) | ||
| - noun: log10 LD50 in rats (oral exposure) | ||
| - noun: log10 rat LD50 (oral exposure) | ||
| significant_digits: 2 | ||
| - id: num_ghose_violations | ||
| description: Ghose filter violations | ||
| type: ordinal | ||
| significant_digits: 0 | ||
| names: | ||
| - noun: Ghose filter violations | ||
| - noun: violations of the Ghose filter | ||
| - id: num_lead_likeness_violations | ||
| description: Lead likeness filter violations | ||
| type: ordinal | ||
| significant_digits: 0 | ||
| names: | ||
| - noun: lead likeness filter violations | ||
| - noun: violations of the lead likeness filter | ||
| - id: num_lipinski_violations | ||
| description: Lipinski filter violations | ||
| type: ordinal | ||
| significant_digits: 0 | ||
| names: | ||
| - noun: Lipinski rule violations | ||
| - noun: violations of the Lipinski rules | ||
| - id: molecular_mass | ||
| description: Molecular mass | ||
| type: continuous | ||
| units: g/mol | ||
| names: | ||
| - noun: molecular mass | ||
| - noun: molecular weight | ||
| - id: num_carbon_atoms | ||
| description: Number of carbon atoms | ||
| type: ordinal | ||
| significant_digits: 0 | ||
| names: | ||
| - noun: carbon atoms | ||
| - id: num_oxygen_atoms | ||
| description: Number of oxygen atoms | ||
| type: ordinal | ||
| significant_digits: 0 | ||
| names: | ||
| - noun: oxygen atoms | ||
| identifiers: | ||
| - id: SMILES | ||
| type: SMILES | ||
| description: SMILES | ||
| - id: SMILES | ||
| type: SMILES | ||
| description: SMILES | ||
| license: CC BY 4.0 | ||
| links: | ||
| - url: https://ehp.niehs.nih.gov/doi/full/10.1289/EHP8495#supplementary-materials | ||
| description: corresponding publication | ||
| - url: https://ehp.niehs.nih.gov/doi/full/10.1289/EHP8495#supplementary-materials | ||
| description: corresponding publication | ||
| num_points: 9032 | ||
| bibtex: | ||
| - |- | ||
| @article{Mansouri_2021, title={CATMoS: Collaborative Acute Toxicity Modeling Suite}, | ||
| volume={129}, | ||
| ISSN={1552-9924}, | ||
| url={http://dx.doi.org/10.1289/EHP8495}, | ||
| DOI={10.1289/ehp8495}, | ||
| number={4}, | ||
| journal={Environmental Health Perspectives}, | ||
| publisher={Environmental Health Perspectives}, | ||
| author={Mansouri, Kamel and Karmaus, Agnes L. and Fitzpatrick, Jeremy | ||
| and Patlewicz, Grace and Pradeep, Prachi and Alberga, Domenico and | ||
| Alepee, Nathalie and Allen, Timothy E.H. and Allen, Dave and Alves, Vinicius M. | ||
| and Andrade, Carolina H. and Auernhammer, Tyler R. and Ballabio, Davide and | ||
| Bell, Shannon and Benfenati, Emilio and Bhattacharya, Sudin and | ||
| Bastos, Joyce V. and Boyd, Stephen and Brown, J.B. and Capuzzi, Stephen J. and | ||
| Chushak, Yaroslav and Ciallella, Heather and Clark, Alex M. and | ||
| Consonni, Viviana and Daga, Pankaj R. and Ekins, Sean and Farag, Sherif and | ||
| Fedorov, Maxim and Fourches, Denis and Gadaleta, Domenico and Gao, Feng and | ||
| Gearhart, Jeffery M. and Goh, Garett and Goodman, Jonathan M. and | ||
| Grisoni, Francesca and Grulke, Christopher M. and Hartung, Thomas and | ||
| Hirn, Matthew and Karpov, Pavel and Korotcov, Alexandru and | ||
| Lavado, Giovanna J. and Lawless, Michael and Li, Xinhao and | ||
| Luechtefeld, Thomas and Lunghini, Filippo and Mangiatordi, Giuseppe F. and | ||
| Marcou, Gilles and Marsh, Dan and Martin, Todd and Mauri, Andrea and | ||
| Muratov, Eugene N. and Myatt, Glenn J. and Nguyen, Dac-Trung and | ||
| Nicolotti, Orazio and Note, Reine and Pande, Paritosh and | ||
| Parks, Amanda K. and Peryea, Tyler and Polash, Ahsan H. and | ||
| Rallo, Robert and Roncaglioni, Alessandra and Rowlands, Craig and | ||
| Ruiz, Patricia and Russo, Daniel P. and Sayed, Ahmed and Sayre, Risa and | ||
| Sheils, Timothy and Siegel, Charles and Silva, Arthur C. and Simeonov, Anton and | ||
| Sosnin, Sergey and Southall, Noel and Strickland, Judy and Tang, Yun and | ||
| Teppen, Brian and Tetko, Igor V. and Thomas, Dennis and Tkachenko, Valery and | ||
| Todeschini, Roberto and Toma, Cosimo and Tripodi, Ignacio and | ||
| Trisciuzzi, Daniela and Tropsha, Alexander and Varnek, Alexandre and | ||
| Vukovic, Kristijan and Wang, Zhongyu and Wang, Liguo and | ||
| Waters, Katrina M. and Wedlake, Andrew J. and Wijeyesakere, Sanjeeva J. and | ||
| Wilson, Dan and Xiao, Zijun and Yang, Hongbin and Zahoranszky-Kohalmi, Gergely and | ||
| Zakharov, Alexey V. and Zhang, Fagen F. and Zhang, Zhen and Zhao, Tongan and | ||
| Zhu, Hao and Zorn, Kimberley M. and Casey, Warren and Kleinstreuer, Nicole C.}, | ||
| year={2021}, month=apr } | ||
| - |- | ||
| @article{Mansouri_2021, title={CATMoS: Collaborative Acute Toxicity Modeling Suite}, | ||
| volume={129}, | ||
| ISSN={1552-9924}, | ||
| url={http://dx.doi.org/10.1289/EHP8495}, | ||
| DOI={10.1289/ehp8495}, | ||
| number={4}, | ||
| journal={Environmental Health Perspectives}, | ||
| publisher={Environmental Health Perspectives}, | ||
| author={Mansouri, Kamel and Karmaus, Agnes L. and Fitzpatrick, Jeremy | ||
| and Patlewicz, Grace and Pradeep, Prachi and Alberga, Domenico and | ||
| Alepee, Nathalie and Allen, Timothy E.H. and Allen, Dave and Alves, Vinicius M. | ||
| and Andrade, Carolina H. and Auernhammer, Tyler R. and Ballabio, Davide and | ||
| Bell, Shannon and Benfenati, Emilio and Bhattacharya, Sudin and | ||
| Bastos, Joyce V. and Boyd, Stephen and Brown, J.B. and Capuzzi, Stephen J. and | ||
| Chushak, Yaroslav and Ciallella, Heather and Clark, Alex M. and | ||
| Consonni, Viviana and Daga, Pankaj R. and Ekins, Sean and Farag, Sherif and | ||
| Fedorov, Maxim and Fourches, Denis and Gadaleta, Domenico and Gao, Feng and | ||
| Gearhart, Jeffery M. and Goh, Garett and Goodman, Jonathan M. and | ||
| Grisoni, Francesca and Grulke, Christopher M. and Hartung, Thomas and | ||
| Hirn, Matthew and Karpov, Pavel and Korotcov, Alexandru and | ||
| Lavado, Giovanna J. and Lawless, Michael and Li, Xinhao and | ||
| Luechtefeld, Thomas and Lunghini, Filippo and Mangiatordi, Giuseppe F. and | ||
| Marcou, Gilles and Marsh, Dan and Martin, Todd and Mauri, Andrea and | ||
| Muratov, Eugene N. and Myatt, Glenn J. and Nguyen, Dac-Trung and | ||
| Nicolotti, Orazio and Note, Reine and Pande, Paritosh and | ||
| Parks, Amanda K. and Peryea, Tyler and Polash, Ahsan H. and | ||
| Rallo, Robert and Roncaglioni, Alessandra and Rowlands, Craig and | ||
| Ruiz, Patricia and Russo, Daniel P. and Sayed, Ahmed and Sayre, Risa and | ||
| Sheils, Timothy and Siegel, Charles and Silva, Arthur C. and Simeonov, Anton and | ||
| Sosnin, Sergey and Southall, Noel and Strickland, Judy and Tang, Yun and | ||
| Teppen, Brian and Tetko, Igor V. and Thomas, Dennis and Tkachenko, Valery and | ||
| Todeschini, Roberto and Toma, Cosimo and Tripodi, Ignacio and | ||
| Trisciuzzi, Daniela and Tropsha, Alexander and Varnek, Alexandre and | ||
| Vukovic, Kristijan and Wang, Zhongyu and Wang, Liguo and | ||
| Waters, Katrina M. and Wedlake, Andrew J. and Wijeyesakere, Sanjeeva J. and | ||
| Wilson, Dan and Xiao, Zijun and Yang, Hongbin and Zahoranszky-Kohalmi, Gergely and | ||
| Zakharov, Alexey V. and Zhang, Fagen F. and Zhang, Zhen and Zhao, Tongan and | ||
| Zhu, Hao and Zorn, Kimberley M. and Casey, Warren and Kleinstreuer, Nicole C.}, | ||
| year={2021}, month=apr } | ||
| templates: | ||
| - The {#molecule|chemical|compound!} with the {SMILES__description} {#representation of |!}{SMILES#} {#shows|exhibits|displays!} an {CATMoS_LD50_mgkg__names__noun} of {CATMoS_LD50_mgkg#} {CATMoS_LD50_mgkg__units}. | ||
| - The {#molecule|chemical|compound!} with the {SMILES__description} {#representation of |!}{SMILES#} {#shows|exhibits|displays!} a {log10_LD50__names__noun} of {log10_LD50#} {log10_LD50__units}. | ||
| - | | ||
| Task: Determine the acute oral toxicity and molecular properties of a {#molecule|chemical|compound!} given the {SMILES__description}. | ||
| Input: {SMILES#} | ||
| Desired Output: {CATMoS_LD50_mgkg__names__noun}, {log10_LD50__names__noun}, {num_ghose_violations__names__noun}, {num_lead_likeness_violations__names__noun}, {num_lipinski_violations__names__noun}, {molecular_mass__names__noun}, {num_carbon_atoms__names__noun}, {num_oxygen_atoms__names__noun} | ||
| Output: {CATMoS_LD50_mgkg#} {CATMoS_LD50_mgkg__units}, {log10_LD50#} {log10_LD50__units}, {num_ghose_violations#}, {num_lead_likeness_violations#}, {num_lipinski_violations#}, {molecular_mass#} {molecular_mass__units}, {num_carbon_atoms#}, {num_oxygen_atoms#} | ||
| - | | ||
| Context: You are {#an assistant|researcher|scientist!} in a pharmaceutical company. Your {#boss|superior|department head!} has asked you to {#design|create|synthesize!} a new drug. | ||
| User: The {#drug|compound|chemical!} should have a {CATMoS_LD50_mgkg__names__noun} of {CATMoS_LD50_mgkg#} {CATMoS_LD50_mgkg__units}, {num_ghose_violations#} {num_ghose_violations__names__noun}, {num_lead_likeness_violations#} {num_lead_likeness_violations__names__noun}, {num_lipinski_violations#} {num_lipinski_violations__names__noun}, {molecular_mass#} {molecular_mass__names__noun} {molecular_mass__units}, {num_carbon_atoms#} {num_carbon_atoms__names__noun}, and {num_oxygen_atoms#} {num_oxygen_atoms__names__noun}. | ||
| Assistant: {#Happy to help!|Sure!|Of course!} The {#molecule|chemical|compound!} with the {SMILES__description} {#representation of |!}{SMILES#} {#shows|exhibits|displays!} the desired properties. | ||
| - | | ||
| User: I need a {#drug|compound|chemical!} with a {log10_LD50__names__noun} of {log10_LD50#} {log10_LD50__units}. | ||
| Assistant: {#Happy to help!|Sure!|Of course!} Can you provide me with more {#constraints|details|information!}? | ||
| User: The {#drug|compound|chemical!} should have {num_ghose_violations#} {num_ghose_violations__names__noun}, {num_lead_likeness_violations#} {num_lead_likeness_violations__names__noun}, {num_lipinski_violations#} {num_lipinski_violations__names__noun}, {num_carbon_atoms#} {num_carbon_atoms__names__noun}, and {num_oxygen_atoms#} {num_oxygen_atoms__names__noun}. | ||
| Assistant: The {#molecule|chemical|compound!} with the {SMILES__description} {#representation of |!}{SMILES#} {#shows|exhibits|displays!} the desired properties. | ||
| - | | ||
| User: I need a {#drug|compound|chemical!} with a {CATMoS_LD50_mgkg__names__noun} of {CATMoS_LD50_mgkg#} {CATMoS_LD50_mgkg__units}. | ||
| Assistant: {#Happy to help!|Sure!|Of course!} Can you provide me with more {#constraints|details|information!}? | ||
| User: The {#drug|compound|chemical!} should have a {num_carbon_atoms#} {num_carbon_atoms__names__noun}, {num_oxygen_atoms#} {num_oxygen_atoms__names__noun}, and a {molecular_mass__names__noun} of {molecular_mass#} {molecular_mass__units}. Could you please only provide me with the {SMILES__description} and return no other information? | ||
| Assistant: {SMILES#} | ||
| - | | ||
| User: I am looking for a {#drug|compound|chemical!} with a {log10_LD50__names__noun} of {log10_LD50#} {log10_LD50__units}. | ||
| Assistant: {#That's interesting!|Interesting!|I see!} Can you provide me with more {#constraints|details|information!}? | ||
| User: The {#drug|compound|chemical!} should have {num_ghose_violations#} {num_ghose_violations__names__noun}, {num_lead_likeness_violations#} {num_lead_likeness_violations__names__noun}, {num_lipinski_violations#} {num_lipinski_violations__names__noun}, {num_carbon_atoms#} {num_carbon_atoms__names__noun}, and {num_oxygen_atoms#} {num_oxygen_atoms__names__noun}. Please return only the {SMILES__description} wrapped as follows [ANSWER]<SMILES>[/ANSWER]. | ||
| Assistant: [ANSWER]{SMILES#}[/ANSWER] | ||
| - The {#molecule|chemical|compound!} with the {SMILES__description} {#representation of |!}{SMILES#} {#shows|exhibits|displays!} an {CATMoS_LD50_mgkg__names__noun} of {CATMoS_LD50_mgkg#} {CATMoS_LD50_mgkg__units}. | ||
| - The {#molecule|chemical|compound!} with the {SMILES__description} {#representation of |!}{SMILES#} {#shows|exhibits|displays!} a {log10_LD50__names__noun} of {log10_LD50#} {log10_LD50__units}. | ||
| - | | ||
| Task: Determine the acute oral toxicity and molecular properties of a {#molecule|chemical|compound!} given the {SMILES__description}. | ||
| Input: {SMILES#} | ||
| Desired Output: {CATMoS_LD50_mgkg__names__noun}, {log10_LD50__names__noun}, {num_ghose_violations__names__noun}, {num_lead_likeness_violations__names__noun}, {num_lipinski_violations__names__noun}, {molecular_mass__names__noun}, {num_carbon_atoms__names__noun}, {num_oxygen_atoms__names__noun} | ||
| Output: {CATMoS_LD50_mgkg#} {CATMoS_LD50_mgkg__units}, {log10_LD50#} {log10_LD50__units}, {num_ghose_violations#}, {num_lead_likeness_violations#}, {num_lipinski_violations#}, {molecular_mass#} {molecular_mass__units}, {num_carbon_atoms#}, {num_oxygen_atoms#} | ||
| - | | ||
| Context: You are {#an assistant|researcher|scientist!} in a pharmaceutical company. Your {#boss|superior|department head!} has asked you to {#design|create|synthesize!} a new drug. | ||
| User: The {#drug|compound|chemical!} should have a {CATMoS_LD50_mgkg__names__noun} of {CATMoS_LD50_mgkg#} {CATMoS_LD50_mgkg__units}, {num_ghose_violations#} {num_ghose_violations__names__noun}, {num_lead_likeness_violations#} {num_lead_likeness_violations__names__noun}, {num_lipinski_violations#} {num_lipinski_violations__names__noun}, {molecular_mass#} {molecular_mass__names__noun} {molecular_mass__units}, {num_carbon_atoms#} {num_carbon_atoms__names__noun}, and {num_oxygen_atoms#} {num_oxygen_atoms__names__noun}. | ||
| Assistant: {#Happy to help!|Sure!|Of course!} The {#molecule|chemical|compound!} with the {SMILES__description} {#representation of |!}{SMILES#} {#shows|exhibits|displays!} the desired properties. | ||
| - | | ||
| User: I need a {#drug|compound|chemical!} with a {log10_LD50__names__noun} of {log10_LD50#} {log10_LD50__units}. | ||
| Assistant: {#Happy to help!|Sure!|Of course!} Can you provide me with more {#constraints|details|information!}? | ||
| User: The {#drug|compound|chemical!} should have {num_ghose_violations#} {num_ghose_violations__names__noun}, {num_lead_likeness_violations#} {num_lead_likeness_violations__names__noun}, {num_lipinski_violations#} {num_lipinski_violations__names__noun}, {num_carbon_atoms#} {num_carbon_atoms__names__noun}, and {num_oxygen_atoms#} {num_oxygen_atoms__names__noun}. | ||
| Assistant: The {#molecule|chemical|compound!} with the {SMILES__description} {#representation of |!}{SMILES#} {#shows|exhibits|displays!} the desired properties. | ||
| - | | ||
| User: I need a {#drug|compound|chemical!} with a {CATMoS_LD50_mgkg__names__noun} of {CATMoS_LD50_mgkg#} {CATMoS_LD50_mgkg__units}. | ||
| Assistant: {#Happy to help!|Sure!|Of course!} Can you provide me with more {#constraints|details|information!}? | ||
| User: The {#drug|compound|chemical!} should have a {num_carbon_atoms#} {num_carbon_atoms__names__noun}, {num_oxygen_atoms#} {num_oxygen_atoms__names__noun}, and a {molecular_mass__names__noun} of {molecular_mass#} {molecular_mass__units}. Could you please only provide me with the {SMILES__description} and return no other information? | ||
| Assistant: {SMILES#} | ||
| - | | ||
| User: I am looking for a {#drug|compound|chemical!} with a {log10_LD50__names__noun} of {log10_LD50#} {log10_LD50__units}. | ||
| Assistant: {#That's interesting!|Interesting!|I see!} Can you provide me with more {#constraints|details|information!}? | ||
| User: The {#drug|compound|chemical!} should have {num_ghose_violations#} {num_ghose_violations__names__noun}, {num_lead_likeness_violations#} {num_lead_likeness_violations__names__noun}, {num_lipinski_violations#} {num_lipinski_violations__names__noun}, {num_carbon_atoms#} {num_carbon_atoms__names__noun}, and {num_oxygen_atoms#} {num_oxygen_atoms__names__noun}. Please return only the {SMILES__description} wrapped as follows [ANSWER]<SMILES>[/ANSWER]. | ||
| Assistant: [ANSWER]{SMILES#}[/ANSWER] |
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