

# Otter UB Dataset Card
UB is a dataset comprising entities (Proteins/Drugs) from Uniprot (U) and BindingDB (B)

## Dataset details
#### Uniprot 
Uniprot comprises of 573,227 proteins from SwissProt, which is the subset of manually curated entries within UniProt, including attributes with different modalities like the sequence (567,483 of them), full name, organism, protein family, description of its function, catalytics activity, pathways and its length. The number of edges are 38,665 of type target_of from Uniprot ids to both ChEMBL and Drugbank ids, and 196,133 interactants between Uniprot protein ids.
#### BindingDB 
BindingDB consists of 2,656,221 data points, involving 1.2 million compounds and 9,000 targets. Instead of utilizing the affinity score, we generate a triple for each combination of drugs and proteins. In order to prevent any data leakage, we eliminate overlapping triples with the TDC DTI dataset. As a result, the dataset concludes with a total of 2,232,392 triples.

**Original datasets:**
- Uniprot: The UniProt Consortium. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Research, 51(D1):D523–D531, 11 2022. ISSN 0305-1048. doi: 10.1093/nar/gkac1052. URL https://doi.org/10.1093/nar/gkac1052
- BindingDB: Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N Jorissen, and Michael K Gilson. Bindingdb: a web-accessible database of experimentally determined protein–ligand binding affinities. Nucleic acids research, 35(suppl_1):D198–D201, 2007.

**Paper or resources for more information:**
- [GitHub Repo](https://github.com/IBM/otter-knowledge)
- [Paper](https://arxiv.org/abs/2306.12802)

**License:**

MIT

**Where to send questions or comments about the dataset:**
- [GitHub Repo](https://github.com/IBM/otter-knowledge)

license:mit arxiv:2306.12802 region:us
{"license": "mit"}
TAGS
#license-mit #arxiv-2306.12802 #region-us 



# Otter UB Dataset Card
UB is a dataset comprising entities (Proteins/Drugs) from Uniprot (U) and BindingDB (B)

## Dataset details
#### Uniprot 
Uniprot comprises of 573,227 proteins from SwissProt, which is the subset of manually curated entries within UniProt, including attributes with different modalities like the sequence (567,483 of them), full name, organism, protein family, description of its function, catalytics activity, pathways and its length. The number of edges are 38,665 of type target_of from Uniprot ids to both ChEMBL and Drugbank ids, and 196,133 interactants between Uniprot protein ids.
#### BindingDB 
BindingDB consists of 2,656,221 data points, involving 1.2 million compounds and 9,000 targets. Instead of utilizing the affinity score, we generate a triple for each combination of drugs and proteins. In order to prevent any data leakage, we eliminate overlapping triples with the TDC DTI dataset. As a result, the dataset concludes with a total of 2,232,392 triples.

Original datasets:
- Uniprot: The UniProt Consortium. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Research, 51(D1):D523–D531, 11 2022. ISSN 0305-1048. doi: 10.1093/nar/gkac1052. URL URL
- BindingDB: Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N Jorissen, and Michael K Gilson. Bindingdb: a web-accessible database of experimentally determined protein–ligand binding affinities. Nucleic acids research, 35(suppl_1):D198–D201, 2007.

Paper or resources for more information:
- GitHub Repo
- Paper

License:

MIT

Where to send questions or comments about the dataset:
- GitHub Repo

# Otter UB Dataset Card
UB is a dataset comprising entities (Proteins/Drugs) from Uniprot (U) and BindingDB (B) ## Dataset details #### Uniprot 
Uniprot comprises of 573,227 proteins from SwissProt, which is the subset of manually curated entries within UniProt, including attributes with different modalities like the sequence (567,483 of them), full name, organism, protein family, description of its function, catalytics activity, pathways and its length. The number of edges are 38,665 of type target_of from Uniprot ids to both ChEMBL and Drugbank ids, and 196,133 interactants between Uniprot protein ids. #### BindingDB 
BindingDB consists of 2,656,221 data points, involving 1.2 million compounds and 9,000 targets. Instead of utilizing the affinity score, we generate a triple for each combination of drugs and proteins. In order to prevent any data leakage, we eliminate overlapping triples with the TDC DTI dataset. As a result, the dataset concludes with a total of 2,232,392 triples.

Original datasets:
- Uniprot: The UniProt Consortium. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Research, 51(D1):D523–D531, 11 2022. ISSN 0305-1048. doi: 10.1093/nar/gkac1052. URL URL
- BindingDB: Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N Jorissen, and Michael K Gilson. Bindingdb: a web-accessible database of experimentally determined protein–ligand binding affinities. Nucleic acids research, 35(suppl_1):D198–D201, 2007.

Paper or resources for more information:
- GitHub Repo
- Paper

License:

MIT

Where to send questions or comments about the dataset:
- GitHub Repo
TAGS
#license-mit #arxiv-2306.12802 #region-us 
 # Otter UB Dataset Card
UB is a dataset comprising entities (Proteins/Drugs) from Uniprot (U) and BindingDB (B) ## Dataset details #### Uniprot 
Uniprot comprises of 573,227 proteins from SwissProt, which is the subset of manually curated entries within UniProt, including attributes with different modalities like the sequence (567,483 of them), full name, organism, protein family, description of its function, catalytics activity, pathways and its length. The number of edges are 38,665 of type target_of from Uniprot ids to both ChEMBL and Drugbank ids, and 196,133 interactants between Uniprot protein ids. #### BindingDB 
BindingDB consists of 2,656,221 data points, involving 1.2 million compounds and 9,000 targets. Instead of utilizing the affinity score, we generate a triple for each combination of drugs and proteins. In order to prevent any data leakage, we eliminate overlapping triples with the TDC DTI dataset. As a result, the dataset concludes with a total of 2,232,392 triples.

Original datasets:
- Uniprot: The UniProt Consortium. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Research, 51(D1):D523–D531, 11 2022. ISSN 0305-1048. doi: 10.1093/nar/gkac1052. URL URL
- BindingDB: Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N Jorissen, and Michael K Gilson. Bindingdb: a web-accessible database of experimentally determined protein–ligand binding affinities. Nucleic acids research, 35(suppl_1):D198–D201, 2007.

Paper or resources for more information:
- GitHub Repo
- Paper

License:

MIT

Where to send questions or comments about the dataset:
- GitHub Repo