Data Source
Optional. Name of the preferred source for this data. E.g. OMIM, DrugBank
Main Entity Type
What kind of entity are you interested in? Biolink type preferred, e.g. variant, disease, gene
Connected Entity Type
What kind of thing should the subject be connected to? E.g. for drug-disease links this would be 'disease'. Biolink type preferred
Example statement
Enter one or more examples of statements/edges you would expect to retrieve using this source. For example, "aldehydes exacerbates Fanconi anemia". In future this could be used to drive integration tests
- EXAMPLE 1: CDK2 is phosphorylated by CDK7
From https://research.bioinformatics.udel.edu/iptmnet/api/P24941/substrate, this snippet asserts that CDK7 phosphorylates CDK2 with various bits of provenance
{
"residue": "T",
"site": "T165",
"ptm_type": "Phosphorylation",
"score": 3,
"sources": [
{
"name": "RLIMS-P",
"label": "rlimsp",
"url": "http://research.bioinformatics.udel.edu/rlimsp/"
},
{
"name": "PSP",
"label": "psp",
"url": "http://www.phosphosite.org/"
}
],
"enzymes": [
{
"id": "P50613",
"enz_type": "uniprot_ac",
"name": "CDK7"
}
],
"pmids": [
"18396144"
]
}
- EXAMPLE 2: CDK2 phosphorylates MCM4
From https://research.bioinformatics.udel.edu/iptmnet/api/P24941/as-enzyme, this snippet asserts that CDK2 phosphorylates MCM4 with various bits of provenance
{
"substrate": "P33991",
"substrate_symbol": "MCM4",
"site": "S3",
"score": 0,
"sources": [
{
"name": "HPRD",
"label": "hprd",
"url": "http://www.hprd.org/"
}
],
"pmids": [
"19651622",
"16519687",
"20068231"
]
}
Preferred format or ingest method
How would you prefer to get the data? Via API or Data dump that can be ingested into your KG? Would you prefer a smart API registry entry, a neo4j dump, biolink-compliant CSV/RDF/JSON that can be loaded with KGX?
Data Source
Optional. Name of the preferred source for this data. E.g. OMIM, DrugBank
Main Entity Type
What kind of entity are you interested in? Biolink type preferred, e.g. variant, disease, gene
Connected Entity Type
What kind of thing should the subject be connected to? E.g. for drug-disease links this would be 'disease'. Biolink type preferred
OBJECT: Protein
RELATION: entity regulated by entity / entity regulates entity
Example statement
Enter one or more examples of statements/edges you would expect to retrieve using this source. For example, "aldehydes exacerbates Fanconi anemia". In future this could be used to drive integration tests
From https://research.bioinformatics.udel.edu/iptmnet/api/P24941/substrate, this snippet asserts that CDK7 phosphorylates CDK2 with various bits of provenance
From https://research.bioinformatics.udel.edu/iptmnet/api/P24941/as-enzyme, this snippet asserts that CDK2 phosphorylates MCM4 with various bits of provenance
Preferred format or ingest method
How would you prefer to get the data? Via API or Data dump that can be ingested into your KG? Would you prefer a smart API registry entry, a neo4j dump, biolink-compliant CSV/RDF/JSON that can be loaded with KGX?