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* fix: use SMILES__description instead of SMILES__names__noun for mol. repr. sampling * fix: mol_repr_transl/transform.py w/o SMILES with H and with split col only * fix: exclude uniprot binding .. * fix: missing ! and wrong variable name in template * fix: missing ! in templates * fix: and rheadb and sort exclude_from_standard_tabular_text_templates * fix: RedDB templates and fully export to meta.yaml * fix: aminoacids templates var name * fix: polymer_data templates var name * fix: var dtypes * fix: name and id * fix: add rdkit_features to /exclude_from_standard_tabular_text_templates * fix: # missing in template var * fix: # missing in template var 2 * fix: fix dialogue template in compound_protein_compound_* * fix: QC templates 1 * update reddb * update zhu * add description of representation * orexin1_receptor_butkiewicz * smiles__description * molecule with SMILES * fix: QC templates 2 * fix: QC templates 3 * fix: QC templates 3 * fix: QC templates * fix: QC templates * fix: QC templates * fix: QC templates * add organism * make explicit * add representation name * add representation name * update standard templates * add representation name * add representation names * representation name use * smiles usage * must to * add representation name * Update data/kg/compound_protein_protein/meta.yaml Co-authored-by: Michael Pieler <[email protected]> * Update data/tabular/freesolv/meta.yaml Co-authored-by: Michael Pieler <[email protected]> * Update data/tabular/freesolv/transform.py Co-authored-by: Michael Pieler <[email protected]> * Update data/tabular/freesolv/transform.py Co-authored-by: Michael Pieler <[email protected]> * Update data/tabular/sr_p53_tox21/meta.yaml Co-authored-by: Michael Pieler <[email protected]> * Update data/kg/compound_protein_protein/meta.yaml * Update data/kg/compound_protein_protein/meta.yaml * Update data/kg/compound_protein_protein/meta.yaml * Update data/tabular/freesolv/meta.yaml * Update data/tabular/sr_p53_tox21/meta.yaml * Update data/kg/compound_protein_compound_1/meta.yaml * Update data/kg/compound_protein_compound_1/meta.yaml * Update data/kg/compound_protein_compound_1/meta.yaml * Update data/kg/compound_protein_compound_1/meta.yaml * Update data/kg/compound_protein_compound_1/meta.yaml * Update data/kg/compound_protein_compound_3/meta.yaml * Update data/kg/compound_protein_compound_3/meta.yaml * Update data/kg/compound_protein_compound_3/meta.yaml * Update data/kg/compound_protein_compound_3/meta.yaml * Update data/kg/compound_protein_compound_3/meta.yaml * Update data/kg/compound_protein_go_term_1/meta.yaml * Update data/kg/compound_protein_go_term_1/meta.yaml * Update data/kg/compound_protein_go_term_2/meta.yaml * Update data/kg/compound_protein_go_term_2/meta.yaml * Update data/kg/compound_protein_go_term_3/meta.yaml * Update data/kg/compound_protein_go_term_3/meta.yaml * Update data/kg/compound_protein_go_term_4/meta.yaml * Update data/kg/compound_protein_go_term_4/meta.yaml * Update data/kg/compound_protein_pathway_disease_2/meta.yaml * Update data/kg/drug_protein_hpo_disease/meta.yaml * Update data/tabular/chemcaption_rdkit/meta.yaml * Update data/tabular/mona/meta.yaml * Update data/tabular/mona/transform.py --------- Co-authored-by: Michael Pieler <[email protected]> Co-authored-by: Kevin Maik Jablonka <[email protected]> Co-authored-by: Michael Pieler <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,55 +1,55 @@ | ||
| --- | ||
| name: half_life_obach | ||
| description: |- | ||
| Half life of a drug is the duration for the concentration of the drug | ||
| in the body to be reduced by half. It measures the duration of actions of a drug. | ||
| This dataset deposited version under CHEMBL assay 1614674. | ||
| Half life of a drug is the duration for the concentration of the drug | ||
| in the body to be reduced by half. It measures the duration of actions of a drug. | ||
| This dataset deposited version under CHEMBL assay 1614674. | ||
| targets: | ||
| - id: half_life_duration | ||
| description: the time it takes for the plasma concentration of a drug in the body to be reduced by half | ||
| units: hours | ||
| type: continuous | ||
| significant_digits: 2 | ||
| names: | ||
| - noun: half life in humans after IV administration | ||
| - noun: half life time in humans after IV administration | ||
| - noun: drug half life time in humans after IV administration | ||
| uris: | ||
| - http://purl.bioontology.org/ontology/MESH/D006207 | ||
| - id: half_life_duration | ||
| description: the time it takes for the plasma concentration of a drug in the body | ||
| to be reduced by half | ||
| units: hours | ||
| type: continuous | ||
| significant_digits: 2 | ||
| names: | ||
| - noun: half life in humans after IV administration | ||
| - noun: half life time in humans after IV administration | ||
| - noun: drug half life time in humans after IV administration | ||
| uris: | ||
| - http://purl.bioontology.org/ontology/MESH/D006207 | ||
| benchmarks: | ||
| - name: TDC | ||
| link: https://tdcommons.ai/ | ||
| split_column: split | ||
| - name: TDC | ||
| link: https://tdcommons.ai/ | ||
| split_column: split | ||
| identifiers: | ||
| - id: SMILES | ||
| type: SMILES | ||
| description: SMILES | ||
| - id: chembl_id | ||
| type: Other | ||
| names: | ||
| - noun: ChEMBL database id | ||
| - noun: ChEMBL identifier number | ||
| description: ChEMBL ids | ||
| sample: false | ||
| - id: SMILES | ||
| type: SMILES | ||
| description: SMILES | ||
| - id: chembl_id | ||
| type: Other | ||
| names: | ||
| - noun: ChEMBL database id | ||
| - noun: ChEMBL identifier number | ||
| description: ChEMBL ids | ||
| sample: false | ||
| license: CC BY 4.0 | ||
| links: | ||
| - url: https://doi.org/10.1124/dmd.108.020479 | ||
| description: corresponding publication | ||
| - url: https://tdcommons.ai/single_pred_tasks/adme/#half-life-obach-et-al | ||
| description: data source | ||
| - url: https://doi.org/10.1124/dmd.108.020479 | ||
| description: corresponding publication | ||
| - url: https://tdcommons.ai/single_pred_tasks/adme/#half-life-obach-et-al | ||
| description: data source | ||
| num_points: 667 | ||
| bibtex: | ||
| - |- | ||
| @article{Obach2008, | ||
| doi = {10.1124/dmd.108.020479}, | ||
| url = {https://doi.org/10.1124/dmd.108.020479}, | ||
| year = {2008}, | ||
| month = apr, | ||
| publisher = {American Society for Pharmacology and Experimental Therapeutics (ASPET)}, | ||
| volume = {36}, | ||
| number = {7}, | ||
| pages = {1385--1405}, | ||
| author = {R. Scott Obach and Franco Lombardo and Nigel J. Waters}, | ||
| title = {Trend Analysis of a Database of Intravenous Pharmacokinetic | ||
| Parameters in Humans for 670 Drug Compounds}, | ||
| journal = {Drug Metabolism and Disposition} | ||
| - |- | ||
| @article{Obach2008, | ||
| doi = {10.1124/dmd.108.020479}, | ||
| url = {https://doi.org/10.1124/dmd.108.020479}, | ||
| year = {2008}, | ||
| month = apr, | ||
| publisher = {American Society for Pharmacology and Experimental Therapeutics (ASPET)}, | ||
| volume = {36}, | ||
| number = {7}, | ||
| pages = {1385--1405}, | ||
| author = {R. Scott Obach and Franco Lombardo and Nigel J. Waters}, | ||
| title = {Trend Analysis of a Database of Intravenous Pharmacokinetic | ||
| Parameters in Humans for 670 Drug Compounds}, | ||
| journal = {Drug Metabolism and Disposition} |
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