From 4f87c9aaef356f1bab6421c056e3789583936ea0 Mon Sep 17 00:00:00 2001 From: cmungall Date: Wed, 10 Aug 2022 16:24:52 -0700 Subject: [PATCH 1/2] Docker docs --- README.md | 33 ++++++++++++++++++++++++++++----- 1 file changed, 28 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index a94f4fb..b80c556 100644 --- a/README.md +++ b/README.md @@ -30,20 +30,43 @@ Or simply download using URL of the form: ## Creating a SQLite database from an OWL file -Requirements; EITHER: +There are two protocols for doing this: + +1. install build dependencies +2. use Docker + +In either case: + +- The input MUST be in RDF/XML serialization and have the suffix `.owl`: +- use robot to convert if format is different + +### 1. Build a SQLite database directly + +Requirements: - [rdftab.rs](https://github.com/ontodev/rdftab.rs) - [relation-graph](https://github.com/balhoff/relation-graph) -OR use the ODK docker image - -The input MUST be in RDF/XML serialization and have the suffix `.owl`: +After installing these and putting both in your path: ```bash semsql make foo.db ``` -foo.db must be in the same directory +This assumes `foo.owl` is in the same folder + +### 2. Use Docker + +There are two docker images that can be used: + +- ODK +- [semantic-sql](https://hub.docker.com/repository/docker/linkml/semantic-sql) + +The ODK image may lag behind + +```bash +docker run -v $PWD:/work -w /work -ti linkml/semantic-sql semsql make foo.db +``` ## Schema From 0dd31f330ed9fcb14eecf1da4fb3b1c2d9e20300 Mon Sep 17 00:00:00 2001 From: cmungall Date: Wed, 10 Aug 2022 16:25:01 -0700 Subject: [PATCH 2/2] prefixes --- src/semsql/builder/prefixes/prefixes.csv | 5 +++++ src/semsql/builder/prefixes/prefixes_curated.csv | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/src/semsql/builder/prefixes/prefixes.csv b/src/semsql/builder/prefixes/prefixes.csv index d208919..3c4bb23 100644 --- a/src/semsql/builder/prefixes/prefixes.csv +++ b/src/semsql/builder/prefixes/prefixes.csv @@ -30,6 +30,11 @@ BAO,http://www.bioassayontology.org/bao#BAO_ biopax,http://www.biopax.org/release/biopax-level3.owl# reactome.biopax,http://www.reactome.org/biopax/81/48887# sweet,http://sweetontology.net/ +qudt,http://qudt.org/schema/qudt# +allotrope.property,http://purl.allotrope.org/ontologies/property# +allotrope.role,http://purl.allotrope.org/ontologies/role# +allotrope.equipment,http://purl.allotrope.org/ontologies/equipment# +allotrope,http://purl.allotrope.org/ontologies/ PSO,http://purl.obolibrary.org/obo/PSO_ CHIRO,http://purl.obolibrary.org/obo/CHIRO_ PW,http://purl.obolibrary.org/obo/PW_ diff --git a/src/semsql/builder/prefixes/prefixes_curated.csv b/src/semsql/builder/prefixes/prefixes_curated.csv index 7fc6765..2aa4327 100644 --- a/src/semsql/builder/prefixes/prefixes_curated.csv +++ b/src/semsql/builder/prefixes/prefixes_curated.csv @@ -30,3 +30,8 @@ BAO,http://www.bioassayontology.org/bao#BAO_ biopax,http://www.biopax.org/release/biopax-level3.owl# reactome.biopax,http://www.reactome.org/biopax/81/48887# sweet,http://sweetontology.net/ +qudt,http://qudt.org/schema/qudt# +allotrope.property,http://purl.allotrope.org/ontologies/property# +allotrope.role,http://purl.allotrope.org/ontologies/role# +allotrope.equipment,http://purl.allotrope.org/ontologies/equipment# +allotrope,http://purl.allotrope.org/ontologies/