Feature: Add SKOSMOS integration

[fillies]

This PR implements the integration of the SLOSMOS search API to our API-Gateway.

Changes

1- Federated Search over ols,skosmos and ontoportal

Now by default, the search will be federated over ols (ebi), ontoportal(biodivportal) and skosmos(agrovoc) , for example this request http://localhost:8080/api-gateway/federatedSearch?query=milk*&targetDbSchema=ols will return
For OLS:

  {
    "iri": "http://purl.obolibrary.org/obo/CMO_0002537",
    "backend_type": "ols",
    "short_form": "CMO_0002537",
    "description": [
      "A calculated measurement in which amount of the alpha fraction of the casein phosphoprotein in a specified sample of milk is divided by corresponding amount of the beta fraction of the casein phosphoprotein, and the result presented as a ratio, fraction, quotient or percentage."
    ],
    "label": "milk alpha-casein content to beta-casein content ratio",
    "source": "https://ebi.ac.uk/ols4/api",
    "type": "class",
    "ontology": "cmo"
  },

For OntoPortal

  {
    "iri": "http://purl.obolibrary.org/obo/UBERON_0001913",
    "backend_type": "ontoportal",
    "short_form": "uberon_0001913",
    "label": "milk",
    "source": "https://data.biodivportal.gfbio.dev",
    "type": "class",
    "ontology": "oba"
  }

And now also SKOSMOS

 {
    "iri": "http://aims.fao.org/aos/agrovoc/c_25682",
    "backend_type": "skosmos",
    "short_form": "c_25682",
    "description": [
      "Used for transportation of milk"
    ],
    "label": "milk containers",
    "source": "https://agrovoc.fao.org/browse/rest/v1",
    "type": "individual",
    "ontology": "agrovoc"
  }

2- Output results to SKOSMOS format

Doing http://localhost:8080/api-gateway/federatedSearch?query=milk*&targetDbSchema=skosmos, will output all the results in the skosmos format
Bellow an example of results:

Format mappings

	OLS	SKOSMOS	ONTOPORTAL
iri	iri	uri	@id
label	label	prefLabel	prefLabel
synonym	synonym	altLabel	synonym
short_form	short_form	deducted from uri	deducted from uri
description	description	scopeNote	definition
ontology	ontology_name	vocab	links->ontology
type	class,property,individual,ontology	individual	class
source	ebi url	agrovoc url	biodiv url
backend_type	ols	skosmos	ontoportal

[rombaum]

@fillies

scopeNote is added as a description, please give me more input on what you want matched, especially for short form

type issue

there are two more changes for the prototype. The type in the Skosmos api response has to converted to individual for the ols api. This is a workaround and could be solved in the future on a better way.

type with not supported skos:concept

type with supported individual + short_form

short_form issue

For the short_form you could use the Jena library and use the local name to put it to the response. similar to this:

https://github.com/ts4nfdi/api-gateway/blob/50055f78d104b93ba853179425bdc9bbb978a530/src/main/java/org/semantics/apigateway/api/OlsTransformer.java#L21C1-L27C14

[syphax-bouazzouni]

@rombaum fixed the type and short_form issues, you can see the screenshot in the description.

[rombaum]

looks good. There is just this small request if we could directly use the information from the API instead of a static value.