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## Supplementary Methods
## Supplementary Methods {.page_break_before}

BioCypher is implemented as a Python package.
Its structure follows the purpose of a threefold modularity of inputs, ontology, and outputs.
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60 changes: 23 additions & 37 deletions content/30.sup.table.1.md
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Supplementary table 1. Recent biomedical knowledge graph solutions (non-comprehensive).
Database
Reference
Biological Insight Knowledge Graph
[@doi:10.1101/2021.10.28.466262]
Bioteque
[@doi:10.1038/s41467-022-33026-0]
Clinical Knowledge Graph
[@doi:10.1038/s41587-021-01145-6]
CROssBAR
[@doi:10.1093/nar/gkab543]
Dependency Map
[@doi:10.1038/s41467-021-21898-7]
GenomicKB
[@doi:10.1093/nar/gkac957]
HealthECCO Covidgraph
[@doi:10.1093/bioinformatics/btac592]
INDRA CogEx
https://github.com/bgyori/indra_cogex
KG-COVID-19
[@doi:10.1101/2020.08.17.254839]
NIH Funding knowledge graph
[@doi:10.1186/s13023-021-02120-9]
OmniPath
[@doi:10.1038/nmeth.4077]
Open Targets
[@doi:10.1093/nar/gkw1055]
PheKnowLator
[@doi:10.1101/2020.04.30.071407]
PORI (Platform for Oncogenic Reporting and Interpretation)
[@doi:10.1038/s41467-022-28348-y]
PrimeKG
[@doi:10.1101/2022.05.01.489928]
RTX-KG2
[@doi:10.1186/s12859-022-04932-3]
TypeDB
https://github.com/typedb-osi/typedb-bio
## Supplementary tables

| Database | Reference |
| -------- | --------- |
| Biological Insight Knowledge Graph | [@doi:10.1101/2021.10.28.466262] |
| Bioteque | [@doi:10.1038/s41467-022-33026-0] |
| Clinical Knowledge Graph | [@doi:10.1038/s41587-021-01145-6] |
| CROssBAR | [@doi:10.1093/nar/gkab543] |
| Dependency Map | [@doi:10.1038/s41467-021-21898-7] |
| GenomicKB | [@doi:10.1093/nar/gkac957] |
| HealthECCO Covidgraph | [@doi:10.1093/bioinformatics/btac592] |
| INDRA CogEx | [https://github.com/bgyori/indra_cogex] |
| KG-COVID-19 | [@doi:10.1101/2020.08.17.254839] |
| NIH Funding knowledge graph | [@doi:10.1186/s13023-021-02120-9] |
| OmniPath | [@doi:10.1038/nmeth.4077] |
| Open Targets | [@doi:10.1093/nar/gkw1055] |
| PheKnowLator | [@doi:10.1101/2020.04.30.071407] |
| PORI (Platform for Oncogenic Reporting and Interpretation) | [@doi:10.1038/s41467-022-28348-y] |
| PrimeKG | [@doi:10.1101/2022.05.01.489928] |
| RTX-KG2 | [@doi:10.1186/s12859-022-04932-3] |
| TypeDB | [https://github.com/typedb-osi/typedb-bio] |

Table: Supplementary table 1. Recent biomedical knowledge graph solutions (non-comprehensive).
{#tbl:sup.table.1}

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