From b858312a173a5c3453ad35caa3ba581d98b24382 Mon Sep 17 00:00:00 2001 From: Ben Gyori Date: Tue, 12 Mar 2024 00:01:04 -0400 Subject: [PATCH 1/2] Add list of default grounding terms --- README.md | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/README.md b/README.md index 503333b..e1715e1 100644 --- a/README.md +++ b/README.md @@ -144,6 +144,23 @@ run the container based on the `docker-compose.yml` configuration: $ docker-compose up ``` +## Default grounding resources + +Gilda is customizable with terms coming from different vocabularies. However, +Gilda comes with a default set of resources from which terms are collected +(almost 2 million entries as of v1.1.0), without any additional configuration +needed. These resources include: +- [HGNC](https://bioregistry.io/hgnc) (human genes) +- [UniProt](https://bioregistry.io/uniprot) (human and model organism proteins) +- [FamPlex](https://bioregistry.io/famplex) (human protein families and complexes) +- [CHeBI](https://bioregistry.io/chebi) (small molecules, metabolites, etc.) +- [GO](https://bioregistry.io/go) (biological processes, molecular functions, complexes) +- [DOID](https://bioregistry.io/doid) (diseases) +- [EFO](https://bioregistry.io/efo) (experimental factors) +- [HP](https://bioregistry.io/hp) (human phenotypes) +- [MeSH](https://bioregistry.io/mesh) (general) +- [Adeft](https://github.com/gyorilab/adeft) (misc. terms corresponding to ambiguous acronyms) + ## Citation ```bibtex From 3ad4b2529b5dc3fa8f8b6159cf54a03b49905755 Mon Sep 17 00:00:00 2001 From: Ben Gyori Date: Tue, 12 Mar 2024 00:04:24 -0400 Subject: [PATCH 2/2] Add more examples to resources in README --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index e1715e1..05ec98d 100644 --- a/README.md +++ b/README.md @@ -156,9 +156,9 @@ needed. These resources include: - [CHeBI](https://bioregistry.io/chebi) (small molecules, metabolites, etc.) - [GO](https://bioregistry.io/go) (biological processes, molecular functions, complexes) - [DOID](https://bioregistry.io/doid) (diseases) -- [EFO](https://bioregistry.io/efo) (experimental factors) +- [EFO](https://bioregistry.io/efo) (experimental factors: cell lines, cell types, anatomical entities, etc.) - [HP](https://bioregistry.io/hp) (human phenotypes) -- [MeSH](https://bioregistry.io/mesh) (general) +- [MeSH](https://bioregistry.io/mesh) (general: diseases, proteins, small molecules, cell types, etc.) - [Adeft](https://github.com/gyorilab/adeft) (misc. terms corresponding to ambiguous acronyms) ## Citation