diff --git a/petagraph/data_dict.md b/petagraph/data_dict.md index b9e6eab..8cd95e9 100644 --- a/petagraph/data_dict.md +++ b/petagraph/data_dict.md @@ -83,7 +83,7 @@ return * limit 1 **Source**: The source of this data is the `GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct` from the GTEx Expression dataset above. -**Preproccessing**: Co-expression of genes were computed using Pearson’s correlation. Gene pairs were included if the Pearson correlation coefficient was greater than 0.99. Computing co-expression pairs for all genes in all tissues resulted in many pairs even after filtering for pairs with a score above 0.99. To reduce the size of the data we included only gene co-expression pairs that are highly co-expressed in at least 5 tissues. +**Preproccessing**: Co-expression of genes was computed using Pearson’s correlation. Gene pairs were included if the Pearson correlation coefficient was greater than 0.99. Computing co-expression pairs for all genes in all tissues resulted in many pairs even after filtering for pairs with a score above 0.99. To reduce the size of the data we included only gene co-expression pairs that are highly co-expressed in at least 5 tissues. drawing @@ -100,15 +100,13 @@ return * limit 1 --- ## Human-Mouse Orthologs (HGNCHCOP) -**Source**: -- Orthologs from HGNC Comparisons of Orthology Predictions (**HCOP**) [https://www.genenames.org/tools/hcop/](https://www.genenames.org/tools/hcop/) (scroll to the bottom, under Bulk Downloads. Select Human - Mouse ortholog data) - -**Preproccessing**: -- were obtained in April 2023 from the HGNC Comparisons of Orthology Predictions (HCOP) tool at https://www.genenames.org/tools/hcop/. We created new mouse gene Concepts and mapped them using the HCOP data to their corresponding human ortholog. Each orthologous pair share reciprocal relationships, ('has_human_ortholog', 'has_mouse_ortholog') and out of the 41,638 HGNC Codes in the UMLS, the HCOP tool found at least one mouse ortholog for 20,715 HGNC Codes. +**Source**: Mouse genes were downloaded from HGNC Comparisons of Orthology Predictions (**HCOP**) [https://www.genenames.org/tools/hcop/](https://www.genenames.org/tools/hcop/) (scroll to the bottom, under Bulk Downloads. Select Human - Mouse ortholog data) +The human to mouse orthology mapping data were also obtained in April 2023 from the HGNC HCOP tool. +**Preproccessing**: We created new mouse gene Concepts and mapped them using the HCOP data to their corresponding human ortholog. Each orthologous pair share reciprocal relationships. Out of the 41,638 HGNC Codes in the UMLS, the HCOP tool found at least one mouse ortholog for 20,715 of them. drawing -**Schema Description**: HGNC Concept (blue), Code (yellow) and Term (brown) from HGNC on the left and its corresponding Mouse gene Concept and code on the right. The SAB for this mapping dataset is `HGNCHCOP` and is located on the SAB property of the `in_1_to_1_relationship_with` and `inverse_in_1_to_1_relationship_with` relationships. +**Schema Description**: HGNC Concept (blue), Code (yellow) and Term (brown) from HGNC on the left and its corresponding Mouse gene Concept and Code (SAB = `HCOP`) on the right. The SAB for this mapping dataset is `HGNCHCOP` and is located on the SAB property of the `in_1_to_1_relationship_with` and `inverse_in_1_to_1_relationship_with` relationships. ```cypher @@ -121,16 +119,15 @@ return * limit 1 ## Human gene-phenotype (HGNCHPO) **Source**: -We use the Human Phenotype (HP) Ontology mappings for gene-to-phenotype and phenotype-to-genes. The HP annotations can be found here: [https://hpo.jax.org/app/data/annotations](https://hpo.jax.org/app/data/annotations). -These data are generated by the HP group to use OMIM disease-gene associations to map all HP phenotypes to genes with those phenotypes associated with diseases. Therefore, a gene can be associated with several phenotypes, and a phenotype can be associated with several genes. -- OMIM and Orphanet are combined together in the HPO database. +We use the Human Phenotype (HPO) Ontology mappings for `genes_to_phenotype.txt` and `phenotype_to_genes.txt`. The HPO annotations can be found here: [https://hpo.jax.org/app/data/annotations](https://hpo.jax.org/app/data/annotations). +These data are generated by the HPO group to use OMIM disease-gene associations to map all HPO phenotypes to genes with those phenotypes associated with diseases. Therefore, a gene can be associated with several phenotypes, and a phenotype can be associated with several genes. -**Preproccessing**: +**Preproccessing**: This dataset was not preprocessed at all. drawing -**Schema Description**: HGNC Concept (blue), Code (yellow) and Term (brown) nodes are connected to an HPO Concept node through an `associated_with` relationship. The SAB for this mapping dataset is HGNCHPO and it is located on the SAB property of the `associated_with` and `inverse_associated_with` relationships. +**Schema Description**: On the left hand side, an HGNC Concept (blue), Code (yellow) and Term (brown) nodes are connected to an HPO Concept node through an `associated_with` relationship. The SAB for this mapping dataset is HGNCHPO and it is located on the SAB property of the `associated_with` and `inverse_associated_with` relationships. In this example we can see that the ODAD2 gene is associated with Atelectasis. ```cypher // Cypher query to reproduce the schema figure