From d948bf9c3ee2e04f404004666eb173f92dad9d09 Mon Sep 17 00:00:00 2001 From: James McLaughlin Date: Thu, 7 Nov 2024 18:15:28 +0000 Subject: [PATCH] add biomappings to readme --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ffa89c3..6afbe7b 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ Note that the purpose of this pipeline is not to supply another knowledge graph, ## Mapping sets used -The following SSSOM tables are loaded: +The following mapping tables are loaded: * https://data.monarchinitiative.org/mappings/latest/gene_mappings.sssom.tsv * https://data.monarchinitiative.org/mappings/latest/hp_mesh.sssom.tsv @@ -27,8 +27,9 @@ The following SSSOM tables are loaded: * https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/master/mappings/mp_hp_mgi_all.sssom.tsv * https://raw.githubusercontent.com/obophenotype/bio-attribute-ontology/master/src/mappings/oba-efo.sssom.tsv * https://raw.githubusercontent.com/obophenotype/bio-attribute-ontology/master/src/mappings/oba-vt.sssom.tsv +* https://github.com/biopragmatics/biomappings/raw/refs/heads/master/src/biomappings/resources/mappings.tsv -In all of the currently configured outputs, `skos:exactMatch` mappings cause clique merging. In `ebi_monarch_xspecies`, `semapv:crossSpeciesExactMatch` also causes clique merging (so e.g. corresponding HP and MP terms will share a graph node). As this is not always desirable a separate graph `ebi_monarch` is also provided where `semapv:crossSpeciesExactMatch` mappings are represented as edges. +In all of the currently configured outputs, `skos:exactMatch` mappings cause clique merging. In `ebi_monarch_xspecies`, `semapv:crossSpeciesExactMatch` also causes clique merging (so e.g. corresponding HP and MP terms will share a graph node). As this is not always desirable, a separate graph `ebi_monarch` is also provided where `semapv:crossSpeciesExactMatch` mappings are represented as edges. ## Full list of datasources