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Merge pull request #531 from EBISPOT/issue-527
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issue-527: update documentation page to add some sample requests
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@serjoshua
serjoshua authored Oct 3, 2023
2 parents 616e14d + 8e5f33f commit 36a3bb2
Showing 1 changed file with 32 additions and 20 deletions.
52 changes: 32 additions & 20 deletions frontend/src/pages/Help.tsx
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<span className="text-code">page</span> parameter for accessing a
specific page of items.
</p>
<div className="text-xl italic my-3">Paging resources</div>
<div className="text-xl font-bold italic my-3">Paging resources</div>
<p className="mb-2">
Links will be provided in the response to navigate the resources.
</p>
Expand Down Expand Up @@ -328,7 +328,7 @@ Content-Type: application/json
<p className="mb-2">
The api endpoint provides the entry point into the service.
</p>
<div className="text-xl italic my-3">Accessing the API</div>
<div className="text-xl font-bold italic my-3">Accessing the API</div>
<p className="mb-2">
A&thinsp;<span className="text-code">GET</span> request is used to
access the API
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<p className="mb-2">
The Ontologies resources is used to list ontologies in OLS
</p>
<div className="text-xl italic my-3">Listing ontologies</div>
<div className="text-xl font-bold italic my-3">Listing ontologies</div>
<p className="mb-2">
A&thinsp;<span className="text-code">GET</span> request will list all
of the OLS ontologies.
Expand All @@ -422,7 +422,7 @@ Content-Type: application/json
&thinsp;field.
</p>
<div className="text-xl text-petrol-600 font-bold my-3">Ontology</div>
<div className="text-xl italic my-3">Retrieve an ontology</div>
<div className="text-xl font-bold italic my-3">Retrieve an ontology</div>
<div className="text-lg text-petrol-600 my-3">Request structure</div>
<code className="break-words">
GET&nbsp;/api/ontologies/&#123;ontology&#125;
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},
]}
/>
<div className="text-xl italic my-3">Roots terms</div>
<div className="text-xl font-bold italic my-3">Roots terms</div>
<div className="text-lg text-petrol-600 my-3">Request structure</div>
<code className="break-words">
GET&nbsp;/api/ontologies/&#123;ontology&#125;/terms/roots
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The terms resources is used to list terms (or classes) in OLS from a
particular ontology
</p>
<div className="text-xl italic my-3">Listing ontology terms</div>
<div className="text-xl font-bold italic my-3">Listing ontology terms</div>
<div className="text-lg text-petrol-600 my-3">Request structure</div>
<code className="break-words">
GET&nbsp;/api/ontologies/&#123;ontology&#125;/terms
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the&thinsp;<span className="text-code">_embedded.terms</span> field.
</p>
<div className="text-xl text-petrol-600 font-bold my-3">Term</div>
<div className="text-xl italic my-3">Retrieve a term</div>
<div className="text-xl font-bold italic my-3">Retrieve a term</div>
<div className="text-lg text-petrol-600 my-3">Request structure</div>
<code className="break-words">
GET&nbsp;/api/ontologies/&#123;ontology&#125;/terms/&#123;iri&#125;
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},
]}
/>
<div className="text-xl italic my-3">
<div className="text-xl font-bold italic my-3">
Parent/child relationships for terms
</div>
<p className="mb-2">
Expand Down Expand Up @@ -805,7 +805,7 @@ $ curl -L 'http://www.ebi.ac.uk/ols4/api/ontologies/go/hierarchicalAncestors?id=
`}
</pre>
</Banner>
<div className="text-xl italic my-3">Other related terms</div>
<div className="text-xl font-bold italic my-3">Other related terms</div>
<p className="mb-2">
In cases where a term has a direct relation to another term (single
existential to a named class in OBO), for example a "part of"
Expand All @@ -815,7 +815,13 @@ $ curl -L 'http://www.ebi.ac.uk/ols4/api/ontologies/go/hierarchicalAncestors?id=
<code className="break-words">
GET&nbsp;/api/ontologies/&#123;ontology_id&#125;/terms/&#123;term_iri&#125;/&#123;property_iri&#125;
</code>
<div className="text-xl italic my-3">
<div className="text-lg text-petrol-600 my-3">Sample requests</div>
<Banner type="code">
<pre>
{`$ curl -L 'http://www.ebi.ac.uk/ols4/api/ontologies/uberon/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUBERON_0000016/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000050' -i -H 'Accept: application/json'`}
</pre>
</Banner>
<div className="text-xl font-bold italic my-3">
Term matching across ontologies
</div>
<p className="mb-2">
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}`}
</pre>
</Banner>
<div className="text-xl italic my-3">
<div className="text-xl font-bold italic my-3">
Terms based on defining ontology
</div>
<p className="mb-2">
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You can access property (relationships) and ontology individuals
(instances) following similar methods to terms.
</p>
<div className="text-xl italic my-3">Retrieve a property</div>
<div className="text-xl font-bold italic my-3">Retrieve a property</div>
<div className="text-lg text-petrol-600 my-3">Request structure</div>
<code className="break-words">
GET&nbsp;/api/ontologies/&#123;ontology&#125;/properties/&#123;iri&#125;
Expand All @@ -1024,7 +1030,7 @@ Content-Length: 3052
},
]}
/>
<div className="text-xl italic my-3">
<div className="text-xl font-bold italic my-3">
Property matching across ontologies
</div>
<p className="mb-2">
Expand All @@ -1042,7 +1048,7 @@ Content-Length: 3052
$ curl -L 'http://www.ebi.ac.uk/ols4/api/properties?iri=http://www.ebi.ac.uk/efo/EFO_0000784' -i -H 'Accept: application/json'`}
</pre>
</Banner>
<div className="text-xl italic my-3">
<div className="text-xl font-bold italic my-3">
Properties based on defining ontology
</div>
<p className="mb-2">
Expand All @@ -1057,11 +1063,17 @@ $ curl -L 'http://www.ebi.ac.uk/ols4/api/properties?iri=http://www.ebi.ac.uk/efo
$ curl -L 'http://www.ebi.ac.uk/ols4/api/properties/findByIdAndIsDefiningOntology?iri=http://www.ebi.ac.uk/efo/EFO_0000784' -i -H 'Accept: application/json'`}
</pre>
</Banner>
<div className="text-xl italic my-3">Retrieve an individual</div>
<div className="text-xl font-bold italic my-3">Retrieve an individual</div>
<div className="text-lg text-petrol-600 my-3">Request structure</div>
<code className="break-words">
GET&nbsp;/api/ontologies/&#123;ontology&#125;/individuals/&#123;iri&#125;
</code>
<div className="text-lg text-petrol-600 my-3">Sample requests</div>
<Banner type="code">
<pre>
{`$ curl -L 'http://www.ebi.ac.uk/ols4/api/ontologies/iao/individuals/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FIAO_0000002' -i -H 'Accept: application/json'`}
</pre>
</Banner>
<DataTable
columns={columnsParamDesc}
data={[
Expand All @@ -1076,7 +1088,7 @@ $ curl -L 'http://www.ebi.ac.uk/ols4/api/properties/findByIdAndIsDefiningOntolog
},
]}
/>
<div className="text-xl italic my-3">
<div className="text-xl font-bold italic my-3">
Individual matching across ontologies
</div>
<p className="mb-2">
Expand All @@ -1094,7 +1106,7 @@ $ curl -L 'http://www.ebi.ac.uk/ols4/api/properties/findByIdAndIsDefiningOntolog
$ curl -L 'http://www.ebi.ac.uk/ols4/api/individuals?iri=http://purl.obolibrary.org/obo/IAO_0000125' -i -H 'Accept: application/json'`}
</pre>
</Banner>
<div className="text-xl italic my-3">
<div className="text-xl font-bold italic my-3">
Individual based on defining ontology
</div>
<p className="mb-2">
Expand All @@ -1110,7 +1122,7 @@ $ curl -L 'http://www.ebi.ac.uk/ols4/api/individuals/findByIdAndIsDefiningOntolo
</pre>
</Banner>
<div className="text-xl text-petrol-600 font-bold my-3">Search</div>
<div className="text-xl italic my-3">Search terms</div>
<div className="text-xl font-bold italic my-3">Search terms</div>
<p className="mb-2">
The search API is independent of the REST API and supports free text
search over the ontologies. The default search is across all textual
Expand Down Expand Up @@ -1210,7 +1222,7 @@ $ curl -L 'http://www.ebi.ac.uk/ols4/api/individuals/findByIdAndIsDefiningOntolo
},
]}
/>
<div className="text-xl italic my-3">Select terms</div>
<div className="text-xl font-bold italic my-3">Select terms</div>
<p className="mb-2">
We provide an additional search endopint that is designed specifically
for selecting ontology terms. This has been tuned specifically to
Expand Down Expand Up @@ -1277,7 +1289,7 @@ $ curl -L 'http://www.ebi.ac.uk/ols4/api/individuals/findByIdAndIsDefiningOntolo
},
]}
/>
<div className="text-xl italic my-3">Suggest terms</div>
<div className="text-xl font-bold italic my-3">Suggest terms</div>
<p className="mb-2">
We also provide a generic suggester endpoint. This endpoint aims to
provide traditional autosuggest based on all the vocabulary in OLS
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