diff --git a/content/20.sup.methods.md b/content/20.sup.methods.md index a33b836..f07ea10 100644 --- a/content/20.sup.methods.md +++ b/content/20.sup.methods.md @@ -1,4 +1,4 @@ -## 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. diff --git a/content/30.sup.table.1.md b/content/30.sup.table.1.md index 7afdd58..4e1d479 100644 --- a/content/30.sup.table.1.md +++ b/content/30.sup.table.1.md @@ -1,38 +1,24 @@ -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} \ No newline at end of file