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Knowledge-Graph-Hub / kg-idg

A Knowledge Graph to Illuminate the Druggable Genome
https://knowledge-graph-hub.github.io/kg-idg/
BSD 3-Clause "New" or "Revised" License
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MONARCH and MONARCH_NODE nodes - where are they coming from? #87

Open caufieldjh opened 2 years ago

caufieldjh commented 2 years ago

In meeting with @LucaCappelletti94 on Mar 28, we found that dendritic stars were present in the graph:

Dendritic stars
A dendritic star is a dendritic tree with a maximal depth of one, where nodes with maximal unique degree one are connected to a central root node with high degree and inside a strongly connected component. We have detected 76.57K dendritic stars in the graph, involving a total of 370.09K nodes (38.54%) and 370.09K edges (5.58%), with the largest one involving 1.62K nodes and 1.62K edges. The detected dendritic stars, sorted by decreasing size, are:

Dendritic star starting from the root node [MONARCH_NODE:GRCh38chr1](https://monarchinitiative.org/MONARCH_GRCh38chr1) (degree 3.27K), and containing 1.62K nodes, with a maximal depth of 1, which are [MONARCH:.well-known/genid/b001b2a08902a888b688](https://monarchinitiative.org/MONARCH_.well-known/genid/b001b2a08902a888b688), [MONARCH:.well-known/genid/b00240a6cd5c9ce72cfc](https://monarchinitiative.org/MONARCH_.well-known/genid/b00240a6cd5c9ce72cfc), [MONARCH:.well-known/genid/b00264d5500fc17abdb3](https://monarchinitiative.org/MONARCH_.well-known/genid/b00264d5500fc17abdb3), [MONARCH:.well-known/genid/b00314f5c8595c3c6090](https://monarchinitiative.org/MONARCH_.well-known/genid/b00314f5c8595c3c6090) and [MONARCH:.well-known/genid/b0031ce26f12079d8eda](https://monarchinitiative.org/MONARCH_.well-known/genid/b0031ce26f12079d8eda). Its nodes have a single node type, which is [biolink:NamedThing](https://biolink.github.io/biolink-model/docs/NamedThing.html). Its edges have a single edge type, which is [biolink:related_to](https://biolink.github.io/biolink-model/docs/related_to.html).

Dendritic star starting from the root node [MONARCH_NODE:GRCh38chr19](https://monarchinitiative.org/MONARCH_GRCh38chr19) (degree 2.08K), and containing 1.04K nodes, with a maximal depth of 1, which are [MONARCH:.well-known/genid/b0020b13d149a3ace335](https://monarchinitiative.org/MONARCH_.well-known/genid/b0020b13d149a3ace335), [MONARCH:.well-known/genid/b0034da11610011d83b6](https://monarchinitiative.org/MONARCH_.well-known/genid/b0034da11610011d83b6), [MONARCH:.well-known/genid/b00481884ceba59a184b](https://monarchinitiative.org/MONARCH_.well-known/genid/b00481884ceba59a184b), [MONARCH:.well-known/genid/b01061b745f09c7b17a0](https://monarchinitiative.org/MONARCH_.well-known/genid/b01061b745f09c7b17a0) and [MONARCH:.well-known/genid/b0112155b43b0392ab9e](https://monarchinitiative.org/MONARCH_.well-known/genid/b0112155b43b0392ab9e). Its nodes have a single node type, which is [biolink:NamedThing](https://biolink.github.io/biolink-model/docs/NamedThing.html). Its edges have a single edge type, which is [biolink:related_to](https://biolink.github.io/biolink-model/docs/related_to.html).

Dendritic star starting from the root node [MONARCH_NODE:GRCh38chr2](https://monarchinitiative.org/MONARCH_GRCh38chr2) (degree 2.05K), and containing 1.01K nodes, with a maximal depth of 1, which are [MONARCH:.well-known/genid/b00615c4b695fbaec504](https://monarchinitiative.org/MONARCH_.well-known/genid/b00615c4b695fbaec504), [MONARCH:.well-known/genid/b00640167c662a3d85cc](https://monarchinitiative.org/MONARCH_.well-known/genid/b00640167c662a3d85cc), [MONARCH:.well-known/genid/b0084aa562f0b8e874f7](https://monarchinitiative.org/MONARCH_.well-known/genid/b0084aa562f0b8e874f7), [MONARCH:.well-known/genid/b00f01967f08455b0230](https://monarchinitiative.org/MONARCH_.well-known/genid/b00f01967f08455b0230) and [MONARCH:.well-known/genid/b010b3222397837c92c1](https://monarchinitiative.org/MONARCH_.well-known/genid/b010b3222397837c92c1). Its nodes have a single node type, which is [biolink:NamedThing](https://biolink.github.io/biolink-model/docs/NamedThing.html). Its edges have a single edge type, which is [biolink:related_to](https://biolink.github.io/biolink-model/docs/related_to.html).

Dendritic star starting from the root node [MONARCH_NODE:GRCh38chr11](https://monarchinitiative.org/MONARCH_GRCh38chr11) (degree 1.96K), and containing 971 nodes, with a maximal depth of 1, which are [MONARCH:.well-known/genid/b005f4b408aacadc4052](https://monarchinitiative.org/MONARCH_.well-known/genid/b005f4b408aacadc4052), [MONARCH:.well-known/genid/b00d7e00405a3d304484](https://monarchinitiative.org/MONARCH_.well-known/genid/b00d7e00405a3d304484), [MONARCH:.well-known/genid/b01428224cf0b68106f2](https://monarchinitiative.org/MONARCH_.well-known/genid/b01428224cf0b68106f2), [MONARCH:.well-known/genid/b015611ec1932aee59c1](https://monarchinitiative.org/MONARCH_.well-known/genid/b015611ec1932aee59c1) and [MONARCH:.well-known/genid/b01c6b0056aa4a4ad4e8](https://monarchinitiative.org/MONARCH_.well-known/genid/b01c6b0056aa4a4ad4e8). Its nodes have a single node type, which is [biolink:NamedThing](https://biolink.github.io/biolink-model/docs/NamedThing.html). Its edges have a single edge type, which is [biolink:related_to](https://biolink.github.io/biolink-model/docs/related_to.html).

Dendritic star starting from the root node [MONARCH_NODE:GRCh38chr17](https://monarchinitiative.org/MONARCH_GRCh38chr17) (degree 1.92K), and containing 950 nodes, with a maximal depth of 1, which are [MONARCH:.well-known/genid/b003a20d29c1de3b50d7](https://monarchinitiative.org/MONARCH_.well-known/genid/b003a20d29c1de3b50d7), [MONARCH:.well-known/genid/b014f794d06917bf8acd](https://monarchinitiative.org/MONARCH_.well-known/genid/b014f794d06917bf8acd), [MONARCH:.well-known/genid/b01a0c2037bd0770892d](https://monarchinitiative.org/MONARCH_.well-known/genid/b01a0c2037bd0770892d), [MONARCH:.well-known/genid/b01b1f0127d3a52c2477](https://monarchinitiative.org/MONARCH_.well-known/genid/b01b1f0127d3a52c2477) and [MONARCH:.well-known/genid/b02097c939e7b03de65d](https://monarchinitiative.org/MONARCH_.well-known/genid/b02097c939e7b03de65d). Its nodes have a single node type, which is [biolink:NamedThing](https://biolink.github.io/biolink-model/docs/NamedThing.html). Its edges have a single edge type, which is [biolink:related_to](https://biolink.github.io/biolink-model/docs/related_to.html).

Dendritic star starting from the root node [MONARCH_NODE:GRCh38chr6](https://monarchinitiative.org/MONARCH_GRCh38chr6) (degree 1.80K), and containing 890 nodes, with a maximal depth of 1, which are [MONARCH:.well-known/genid/b000a2698b275276fc61](https://monarchinitiative.org/MONARCH_.well-known/genid/b000a2698b275276fc61), [MONARCH:.well-known/genid/b003500cbe0691866ca7](https://monarchinitiative.org/MONARCH_.well-known/genid/b003500cbe0691866ca7), [MONARCH:.well-known/genid/b003fa4fd2c425a02b14](https://monarchinitiative.org/MONARCH_.well-known/genid/b003fa4fd2c425a02b14), [MONARCH:.well-known/genid/b00a4bd069e6ea7ccd34](https://monarchinitiative.org/MONARCH_.well-known/genid/b00a4bd069e6ea7ccd34) and [MONARCH:.well-known/genid/b00fa6dadec685f40c9b](https://monarchinitiative.org/MONARCH_.well-known/genid/b00fa6dadec685f40c9b). Its nodes have a single node type, which is [biolink:NamedThing](https://biolink.github.io/biolink-model/docs/NamedThing.html). Its edges have a single edge type, which is [biolink:related_to](https://biolink.github.io/biolink-model/docs/related_to.html).

And other 76.56K dendritic stars.

Across the entire graph, there are 26 nodes with the MONARCH_NODE prefix - what is their origin?