FoodOn

https://foodon.org/
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FoodOn is an open-source ontology representing knowledge about food from farm to fork, covering...
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### OntoFox Configuration for FoodOn Import

Source: https://foodon.org/reuse-project/reuse-technical/ontofox

Configuration file for OntoFox to fetch terms from the FoodOn ontology, including specific terms, their children, and annotations like labels and definitions. This file is used to generate an OWL import file.

```text
[URI of the OWL(RDF/XML) output file]
http://purl.obolibrary.org/obo/generic/foodon_import.owl

[Source ontology]
FOODON

[Low level source term URIs]
http://purl.obolibrary.org/obo/FOODON_03411564 #food source
includeAllChildren

[Top level source term URIs and target direct superclass URIs]


[Source term retrieval setting]
includeNoIntermediates

[Source annotation URIs]
http://www.w3.org/2000/01/rdf-schema#label
http://purl.obolibrary.org/obo/IAO_0000115 #iao:definition
http://www.geneontology.org/formats/oboInOwl#hasSynonym

[Source annotation URIs to be excluded]

[Source ontology]
SOME_OTHER_ONTOLOGY
...
```

--------------------------------

### Generate OWL Ontology Include File from TSV Template

Source: https://foodon.org/design/robot-managed-vocabularies

Use this command to convert a ROBOT TSV template into an OWL ontology include file. Ensure the input OWL file and prefixes are correctly specified for ID resolution and namespace expansion.

```bash
robot template --template wine.tsv \
  --input "../ro_import.owl" \
  --prefix "FOODON:http://purl.obolibrary.org/obo/FOODON_" \
  --prefix "RO:http://purl.obolibrary.org/obo/RO_" \
  --prefix "oboInOwl:http://www.geneontology.org/formats/oboInOwl#" \
  --prefix "schema:http://schema.org/" \
  --ontology-iri "http://purl.obolibrary.org/obo/foodon/imports/wine.owl" \
  --output wine.owl
```

--------------------------------

### Execute SPARQL Query with Robot CLI

Source: https://foodon.org/reuse-project/reuse-technical/query-with-sparql

Run a SPARQL query against an OWL file using the 'robot query' command. Specify the input ontology, the query file, an output file, and the desired format (e.g., TSV).

```bash
> robot query --input foodon.owl --query foodon_labels.sparql temp.tsv --format TSV
```

--------------------------------

### Robot CLI Command for SPARQL Query

Source: https://foodon.org/reuse-project/reuse-technical/query-with-sparql

This command executes a SPARQL query using the Robot tool, specifying input ontology, query file, output file, and desired format.

```bash
> robot query --input foodon-merged.owl --query foodon_synonyms.sparql output.tsv --format TSV
```

--------------------------------

### Reasoning with ROBOT (HermiT)

Source: https://foodon.org/reuse-project/reuse-technical/ontofox

Command to perform logical consistency checks on an ontology file using the HermiT reasoner. This helps identify and fix logical problems in the ontology.

```bash
robot reason --input myonto-edit.owl --reasoner hermit
```

--------------------------------

### Reasoning with ROBOT (ELK)

Source: https://foodon.org/reuse-project/reuse-technical/ontofox

Command to perform logical consistency checks on an ontology file using the ELK reasoner, which is faster than HermiT. This is useful for quick checks during ontology development.

```bash
robot reason --input myonto-edit.owl --reasoner ELK
```

--------------------------------

### Update OntoFox Import File using cURL

Source: https://foodon.org/reuse-project/reuse-technical/ontofox

Command to update the general_ontofox.owl file by sending the OntoFox configuration file to the OntoFox service. This fetches the latest terms from the specified sources.

```bash
curl -s -F file=@imports/general_ontofox.txt -o imports/general_ontofox.owl http://ontofox.hegroup.org/service.php
```

--------------------------------

### Execute SPARQL Query with Optional Annotations

Source: https://foodon.org/reuse-project/reuse-technical/query-with-sparql

Execute a SPARQL query that includes optional annotations against a merged ontology file using the 'robot query' command. This command is similar to the basic query execution but targets a different ontology file.

```bash
robot query --input foodon-merged.owl --query foodon_labels_alts.sparql temp.tsv --format TSV
```

--------------------------------

### Unpack OWL Equivalency Statements

Source: https://foodon.org/reuse-project/reuse-technical/teasing-facts-out-of-owl

Use the ROBOT command-line tool to relax an OWL file, making complex equivalency statements explicit as simpler SubClassOf conditions. This prepares the file for easier SPARQL querying.

```bash
robot relax --input imports/robot_plant_parts.owl --output reasoned.owl
```

--------------------------------

### Basic SPARQL Query for Ontology Labels

Source: https://foodon.org/reuse-project/reuse-technical/query-with-sparql

Use this SPARQL query to select distinct ontology IDs and their labels. It requires the rdfs:label predicate and defines a prefix for the RDF schema namespace.

```sparql
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT ?ontology_id ?label

WHERE {?ontology_id rdfs:label ?label}
```

--------------------------------

### Merge OWL Ontologies with Robot

Source: https://foodon.org/reuse-project/reuse-technical/ontofox

Use the robot merge command to combine an OWL file with its imported ontologies. The --xml-entities option is optional and helps in substituting ontology prefixes for full URIs.

```bash
robot merge --input myonto-edit.owl --xml-entities --output myonto.owl
```

--------------------------------

### Count FoodOn Facets with SPARQL

Source: https://foodon.org/reuse-project/reuse-technical/query-with-sparql

This query counts the number of classes that are subclasses of specified FoodOn facets. It uses prefixes for common ontologies and selects the search term, its label, and the total count of related classes.

```sparql
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX foodon: <http://purl.obolibrary.org/obo/FOODON_>
SELECT
	?search	
	(STR(?label) AS ?name) 
	(count(?class) as ?total) 
	WHERE {
	values ?search {
		fodon:03411041 # Chemical food component
		obo:OBI_0100026 # Organism (NCBI taxonomy)
		fodon:03411564 # Food product organismal source
	fodon:03420116 # Part of organism (anatomy)
		fodon:00002381 # Food product by organism (~single component food)
		fodon:00002501 # Multi-component food product
	fodon:00002451 # Food transformation process
	fodon:00003368 # Food contact material
	fodon:03400361 # Agency food product type
	}
	{?class rdfs:subClassOf+ ?search}
	OPTIONAL {?search rdfs:label ?label.}
}
GROUP BY ?search ?label
```

--------------------------------

### Defining Liver as a Food Product

Source: https://foodon.org/foodon-and-anatomy

Defines 'liver' as a food product using 'has part' to allow for flexibility in defining wholes and parts. The 'only liver' constraint ensures no other parts are included.

```owl
liver (food product): 'has part' some liver and ‘has part’ only liver.
```

--------------------------------

### Retrieve Labels and Synonyms with UNION

Source: https://foodon.org/reuse-project/reuse-technical/query-with-sparql

This SPARQL query uses UNION to retrieve labels, synonyms, and parent information for terms and their subclasses. It's designed to handle entities with multiple synonyms or labels.

```sparql
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX obo:  <http://purl.obolibrary.org/obo/>
PREFIX oboInOwl:  <http://www.geneontology.org/formats/oboInOwl#>

SELECT DISTINCT ?class ?parent ?type ?label 
WHERE {

	# Enter ontology term identifier here to start report with:
	# obo:BFO_0000001 entity includes every term in ontology
	# obo:BFO_0000040 material entity, including chemical food components and food products
	# obo:ENVO_00010483  environmental material terms, including food materials
	# obo:FOODON_00002403 food material terms, including all food products and additives
	BIND (obo:BFO_0000040 as ?search). 

	# Retrieve term and all subclass terms.
	?class rdfs:subClassOf* ?search.

	{
		# Retrieve one or more explicit parents of given entity
		{ 
			?class rdfs:subClassOf ?parent.
			# Ignore blank node parent (subclass axiom) 
			FILTER (isBlank(?parent)) 
		}

		# Retrieve entity's label(s). Might be multilingual.
		UNION { 
			?class rdfs:label ?label.
			BIND ('label' as ?type).
		}

		# Retrieve types of synonym
		UNION { 
			?class oboInOwl:hasSynonym ?label.
			BIND ('synonym' as ?type).
		}
		UNION {
			?class oboInOwl:hasBroadSynonym ?label.
			BIND ('synonym (broad)' as ?type).
		}
		UNION {
			?class oboInOwl:hasExactSynonym ?label.
			BIND ('synonym (exact)' as ?type).
		}
		UNION {
			?class oboInOwl:hasNarrowSynonym ?label.
			BIND ('synonym (narrow)' as ?type).
		}
		UNION {
			?class obo:IAO_0000118 ?label.
			BIND ('label (alternative)' as ?type).
		}
	}
}
ORDER BY ?class ?type
```

--------------------------------

### SPARQL Query with Optional Alternative Labels

Source: https://foodon.org/reuse-project/reuse-technical/query-with-sparql

This SPARQL query retrieves ontology IDs, labels, and optional alternative labels (using obo:IAO_0000118). The OPTIONAL clause ensures terms without alternative labels are still included.

```sparql
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT DISTINCT ?ontology_id ?label ?alt_label

WHERE { ?ontology_id rdfs:label ?label 
  OPTIONAL {?ontology_id obo:IAO_0000118 ?alt_label.}
}
```

--------------------------------

### Retrieve Entity Labels and Alternative Labels

Source: https://foodon.org/reuse-project/reuse-technical/query-with-sparql

This query retrieves the ontology ID, label, and alternative label for entities. It's useful for obtaining basic information about terms.

```sparql
SELECT ?ontology_id ?label ?alt_label
WHERE {
  ?ontology_id ?label ?alt_label
}
LIMIT 100
```

--------------------------------

### Defining Whole Liver as a Food Product

Source: https://foodon.org/foodon-and-anatomy

Defines 'whole liver' as a food product that is specifically 'liver (food product)' and possesses the quality of being 'whole'. This is used to express intactness.

```owl
whole liver (food product): 'liver (food product)' and 'has quality' whole.
```

--------------------------------

### Query for Subclass and Taxonomic Relationships

Source: https://foodon.org/reuse-project/reuse-technical/teasing-facts-out-of-owl

This SPARQL query retrieves direct subclass relationships and 'derives from' taxonomic links for a given food item. It uses UNION to combine results from different relationship types.

```sparql
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX foodon: <http://purl.obolibrary.org/obo/>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT ?search ?type ?parent
WHERE {
	BIND (obo:FOODON_00002473 as ?search) .
	{
		?search rdfs:subClassOf ?parent .
		FILTER (!isBlank(?parent)) .
		BIND ('subClassOf' as ?type) .
	}
	UNION {
		?search rdfs:subClassOf ?restriction .
		?restriction owl:onProperty obo:RO_0001000 . # derives from
              	?restriction owl:someValuesFrom ?parent .
		BIND ('taxon' as ?type) .
	}
}
```

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### Defining Pig Liver Derivation

Source: https://foodon.org/foodon-and-anatomy

Defines 'pig liver' as a food product that derives from a 'pig (organism)'. This establishes a relationship between the food product and its biological source.

```owl
pig liver: liver (food product) and 'derives from’ some pig (organism).
```
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