PubChem Ingest File format
edges.tsv
Fields
| Field | Corresponding element in UBKG | Accepted formats | Examples |
|---|---|---|---|
| subject | Code node | PUBCHEM PubChem CID | [PUBCHEM 9549299](https://pubchem.ncbi.nlm.nih.gov/compound/9549299 |
| predicate | relationships | For hierarchical relationships, the IRI http://www.w3.org/2000/01/rdf-schema#subClassOf OR the string “isa” | http://www.w3.org/2000/01/rdf-schema#subClassOf |
| For non-hierarchical relationships, an IRI for a relationship property in RO | http://purl.obolibrary.org/obo/RO_0002292 | ||
| Custom string | drinks milkshake of | ||
| object | Code node | same as for subject |
Relationships (predicates)
The definition of relationships is the principle informatics task of assertion. An appropriate selection of concept in the node_dbxrefs field of nodes.tsv will associate cross-referenced assertions.
## An example for PUBCHEM 9549299:
An EGFR inhibitor inhibits the expression of EGFR (UNIPROTKB ID P00533), so a possible assertion is
| subject | predicate | object |
|---|---|---|
| PUBCHEM 9549299 | http://purl.obolibrary.org/obo/RO_0002449 | UNIPROTKB P00533 |
| 1 | 2 | 3 |
RO_0002449 = directly inhibits
Because UNIPROTKB is already integrated into the UBKG, any relationship with P00533 would also get the link to HGNC 3236:
nodes.tsv
Fields
| Field | Corresponding element in UBKG | Accepted formats | Examples |
|---|---|---|---|
| node_id | Code node | PUBCHEM PubChem CID | [PUBCHEM 9549299](https://pubchem.ncbi.nlm.nih.gov/compound/9549299 |
| node_label | Term node, Preferred Term (PT) relationship | Text string for the Compound Name | EGFR Inhibitor |
| node_definition (optional) | Definition node, DEF relationship | Text string - IUPAC Name? | N-[3-[[6-[3-(trifluoromethyl)anilino]pyrimidin-4-yl]amino]phenyl]cyclopropanecarboxamide |
| node_synonyms (optional) | Term node; Synonym (SYN) relationship | Pipe-delimited list of synonyms | See example (pipes are also used to format table cells) |
| node_dbxrefs (optional) | Cross-references | Pipe-delimited list of references to cross-referenced concepts. Each cross-reference should be in format SAB:code or UMLS:CUI | UMLS:C5574906 |
Example of synonyms for EGFR inhibitor
N-[3-[[6-[3-(trifluoromethyl)anilino]pyrimidin-4-yl]amino]phenyl]cyclopropanecarboxamide|1S/C21H18F3N5O/c22-21(23,24)14-3-1-4-15(9-14)27-18-11-19(26-12-25-18)28-16-5-2-6-17(10-16)29-20(30)13-7-8-13/h1-6,9-13H,7-8H2,(H,29,30)(H2,25,26,27,28)|YOHYSYJDKVYCJI-UHFFFAOYSA-N|C1CC1C(=O)NC2=CC=CC(=C2)NC3=NC=NC(=C3)NC4=CC=CC(=C4)C(F)(F)F
i.e., 2.1.1IUPAC Name|2.1.2InChI|2.1.3InChIKey|2.1.4Canonical SMILES