A compressed folder containing serialized dataset associations ready for knowledge graph ingestion in multiple formats:
gobp23.rdf
@prefix gene: ncbi.nlm.nih.gov/gene/
@prefix RO: purl.obolibrary.org/RO_
@prefix GO: amigo.geneontology.org/amigo/term/GO:
gene:28655 RO:0000056 GO:0050830 .
gene:728637 RO:0000056 GO:0010789 .
gene:728637 RO:0000056 GO:0045143 .
gene:728637 RO:0000056 GO:0051754 .
gene:1564 RO:0000056 GO:0042178 .
gene:101928527 RO:0000056 GO:1900101 .
gene:100130520 RO:0000056 GO:0030593 .
gene:550643 RO:0000056 GO:0000956 .
gene:550643 RO:0000056 GO:0010607 .
gene:100507043 RO:0000056 GO:0032469 .
gene:100507043 RO:0000056 GO:0035774 .
gene:100507043 RO:0000056 GO:0045665 .
gene:100507043 RO:0000056 GO:0048812 .
gene:100507043 RO:0000056 GO:0051480 .
gene:101929726 RO:0000056 GO:0007520 .
gene:101929726 RO:0000056 GO:0014905 .
...
gobp23.json
"Version": "1",
"nodes": {
"28655": {
"type": "gene",
"properties": {
"id": 28655,
"label": "TRAV27"
}
},
...,
"GO:0002222": {
"type": "biological process",
"properties": {
"id": "GO:0002222",
"label": "stimulatory killer cell immunoglobulin-like receptor signaling pathway"
}
}}
"edges": [
{
"source": 28655,
"relation": "participates in",
"target": "GO:0050830",
"properties": {
"id": "28655:GO:0050830",
"source_id": 28655,
"source_label": "TRAV27",
"target_label": "defense response to Gram-positive bacterium",
"target_id": "GO:0050830",
"directed": true,
"threshold": 1
}
},
...,
{
"source": 728637,
"relation": "participates in",
"target": "GO:0010789",
"properties": {
"id": "728637:GO:0010789",
"source_id": 728637,
"source_label": "MEIKIN",
"target_label": "meiotic sister chromatid cohesion involved in meiosis I",
"target_id": "GO:0010789",
"directed": true,
"threshold": 1
}
}
]
gobp23_tsv/nodes.tsv| namespace | id | label | |
|---|---|---|---|
| 0 | NCBI Entrez | 28655 | TRAV27 |
| 1 | NCBI Entrez | 728637 | MEIKIN |
| 2 | NCBI Entrez | 1564 | CYP2D7 |
| 3 | NCBI Entrez | 101928527 | PIGBOS1 |
| 4 | NCBI Entrez | 100130520 | CD300H |
gobp23_tsv/edges.tsv| source | relation | target | threshold | |
|---|---|---|---|---|
| 0 | 28655 | participates in | GO:0050830 | 1 |
| 1 | 728637 | participates in | GO:0010789 | 1 |
| 2 | 728637 | participates in | GO:0045143 | 1 |
| 3 | 728637 | participates in | GO:0051754 | 1 |
| 4 | 1564 | participates in | GO:0042178 | 1 |
Visualization of Tabula Sapiens Gene-Cell Type Associations and PANTHER Pathways
Documentation has been written to help users navigate the site and use each of the visualization and analysis modules. Screenshots from each page are included to help illustrate and explain useful features.
A tool to compare the similarity of attributes from two datasets based on the similarity of their associated gene sets. Selecting two datasets will return a table of gene sets from those datasets with information about their overlapping genes. Visit the Cross page to begin crossing datasets.
An AI chatbot powered by OpenAI's GPT-4o model. Using natural language, users can interact with the Harmonizome knowledgebase to find connections between genes and attributes from different datasets and resources. Visit the Chatbot page to begin chatting.
A knowledge graph application to serve the serialized Harmonizome datasets in a Neo4j database. We have developed a UI that allows users to access this information and create customized subnetworks without any coding necessary. Subnetworks can be created based on a search term, selecting types of edges available from different resources integrated in Harmonizome, and selecting pairs of terms to find paths between nodes. Visit the Knowledge Graph to begin creating subnetworks.
