Implement mechanism to support integration with Dataverse #16

jonquet · 2023-01-11T12:34:54Z

Is your feature request related to a problem? Please describe.

We need a way to ease the selection of vocabulary/ontology term in Dataverse using OntoPortal instances.
For the moment the current intefcae requires 4 fields

In Data INRAE we can replace the fields above with only one, the concept search below:

Describe the solution you'd like

The plan is to :

Refactor our widgets to support easy integration with outside application like this. See also Fix Agroportal widgets agroportal/project-management#349
Implement a mechanism to change the 4 fields above by only one field with autocompletion with selected vocabularies hosted in a OntoPortal instance
Implement a mechanism to call the correspondant OntoPortal Annotator on the title/abstract fields of the data set to pre-propose some ontology/vocabulary terms in the UI that the user can only keep or discard.

Describe alternatives you've considered

Something similar has been done for SKOSMOS already. Lesson to be learned: https://osf.io/5af9q
Also in video : https://www.youtube.com/watch?v=mWMPxCwB2ys&t=1825s

Additional context

This is being done in the context of FAIR-IMPACT T4.5
CC @DS-INRA @xeniacs @IlariaRosati @saubin78

syphax-bouazzouni · 2023-11-08T05:40:07Z

Context

This is a Technical update, addinng details after discussing with the team at INRAE Dataverse.

Goal

Extend the dataverse-external-vocab-support interface to work with Ontoportal repositories, which mean in summary two thing:
1- Add a configuration file for ontoportal (as already done for authors, affiliations, or, skosmos,...)
2- Add a JS/Jquery script to render the results got from Ontoportal from JSON to HTML

Roadmap

1- Get a API key

In both cases you will need to have an apikey, (having anonymous can be discussed in the future ncbo/bioportal_web_ui#112)
Here is a doc, to how to get an API key

2- Use our search API, to have an autocomplete

GET "https://data.agroportal.lirmm.fr/search?q=<pattern_to_search>&include_properties=true&include_views=true&apikey=<your_apikey>&display_context=false"

example of a result

	{
	"prefLabel": "plant",
	"definition": [
	"Any living organism that typically synthesizes its food from inorganic substances, possesses cellulose cell walls, responds slowly and often permanently to a stimulus, lacks specialized sense organs and nervous system, and has no powers of locomotion. (Source: CED)",
	"http://opendata.inra.fr/anaeeThes/i_def_24509784-142a-4d0d-9deb-2c7c5869ebde"
	],
	"obsolete": false,
	"matchType": "prefLabel",
	"ontologyType": "ONTOLOGY",
	"provisional": false,
	"@id": "http://opendata.inra.fr/anaeeThes/c2_225",
	"@type": "http://www.w3.org/2002/07/owl#Class",
	"links": {
				"self": "https://data.agroportal.lirmm.fr/ontologies/ANAEETHES/classes/http%3A%2F%2Fopendata.inra.fr%2FanaeeThes%2Fc2_225",
				"ontology": "https://data.agroportal.lirmm.fr/ontologies/ANAEETHES",
				"children": "https://data.agroportal.lirmm.fr/ontologies/ANAEETHES/classes/http%3A%2F%2Fopendata.inra.fr%2FanaeeThes%2Fc2_225/children",
				"parents": "https://data.agroportal.lirmm.fr/ontologies/ANAEETHES/classes/http%3A%2F%2Fopendata.inra.fr%2FanaeeThes%2Fc2_225/parents",
				"descendants": "https://data.agroportal.lirmm.fr/ontologies/ANAEETHES/classes/http%3A%2F%2Fopendata.inra.fr%2FanaeeThes%2Fc2_225/descendants",
				"ancestors": "https://data.agroportal.lirmm.fr/ontologies/ANAEETHES/classes/http%3A%2F%2Fopendata.inra.fr%2FanaeeThes%2Fc2_225/ancestors",
				"instances": "https://data.agroportal.lirmm.fr/ontologies/ANAEETHES/classes/http%3A%2F%2Fopendata.inra.fr%2FanaeeThes%2Fc2_225/instances",
				"tree": "https://data.agroportal.lirmm.fr/ontologies/ANAEETHES/classes/http%3A%2F%2Fopendata.inra.fr%2FanaeeThes%2Fc2_225/tree",
				"notes": "https://data.agroportal.lirmm.fr/ontologies/ANAEETHES/classes/http%3A%2F%2Fopendata.inra.fr%2FanaeeThes%2Fc2_225/notes",
				"mappings": "https://data.agroportal.lirmm.fr/ontologies/ANAEETHES/classes/http%3A%2F%2Fopendata.inra.fr%2FanaeeThes%2Fc2_225/mappings",
				"ui": "http://agroportal.lirmm.fr/ontologies/ANAEETHES?p=classes&conceptid=http%3A%2F%2Fopendata.inra.fr%2FanaeeThes%2Fc2_225"
		}
}

From it you can extract two main information:

Concept ID: "@id": "http://opendata.inra.fr/anaeeThes/c2_225"
Ontology ACRONYM: from "ontology":"https://data.agroportal.lirmm.fr/ontologies/ANAEETHES" in the links block, you can extract ontology_acronym = ANAEETHES

3- Use the dataverse-external-vocab-support plugin to retrieve concept details

The dataverse external vocab support plugin, need one main field in its configuration file, the retrieval-uri, in the case of skosmos they use https://skosmos.dev.finto.fi/rest/v1/data?uri={0}, with {0} equal to the URI of a concept in skosmos.

In our case, as we don't identify elements not only by URI but also with its Òntoloy. The retrieval-uri will be tricky:

 "retrieval-uri": "https://data.agroportal.lirmm.fr/ontologies/{0}"

with {0}equal to ${ontology_acronym}/classes/${concept_id}?display=all&display_context=false&display_links=false&apikey=${your_apikey}

here is an a example of a result

{
	"id": "http://opendata.inra.fr/anaeeThes/c2_225",
	"synonym": [ ],
	"prefLabel": "plant",
	"definition": [
			"Any living organism that typically synthesizes its food from inorganic substances, possesses cellulose cell walls, responds slowly and often permanently to a stimulus, lacks specialized sense organs and nervous system, and has no powers of locomotion. (Source: CED)",
	],
	"obsolete": false,
	"inScheme": [
			"http://opendata.inra.fr/anaeeThes/"
	],
	"memberOf": [ ],
	"isInActiveScheme": [
			"http://opendata.inra.fr/anaeeThes/"
	],
	"isInActiveCollection": [ ],
	"created": null,
	"parents": [
			{
				"id": "http://opendata.inra.fr/anaeeThes/c2_2758",
				"synonym": [
					"eukaryotes",
					"eukaryota"
				],
				"prefLabel": "eukaryote",
				"definition": [ ],
				"obsolete": false,
				"inScheme": [
					"http://opendata.inra.fr/anaeeThes/"
				],
				"created": null,
				"modified": "2020-04-17T09:38:53+02:00",
				"notation": null,
				"label": [ ],
				"prefLabelXl": [ ],
				"altLabelXl": [ ],
				"hiddenLabelXl": [ ],
				"prefixIRI": null,
				"subClassOf": [ ],
				"semanticType": [ ],
				"cui": [ ],
				"xref": null,
				"@id": "http://opendata.inra.fr/anaeeThes/c2_2758",
				"@type": "http://www.w3.org/2004/02/skos/core#Concept"
			}
	],
	"modified": "2018-06-26T14:47:36+00:00",
	"notation": null,
	"label": [ ],
	"prefLabelXl": [ ],
	"altLabelXl": [ ],
	"hiddenLabelXl": [ ],
	"prefixIRI": null,
	"subClassOf": [ ],
	"semanticType": [ ],
	"cui": [ ],
	"xref": null,
	"properties": {
			"http://www.w3.org/2004/02/skos/core#narrower": [
					"http://opendata.inra.fr/anaeeThes/c2_226",
					"http://opendata.inra.fr/anaeeThes/c2_243",
					"http://opendata.inra.fr/anaeeThes/c_4d1cf953",
					"http://opendata.inra.fr/anaeeThes/c2_2440"
			],
			"http://www.w3.org/2004/02/skos/core#definition": [
					"Any living organism that typically synthesizes its food from inorganic substances, possesses cellulose cell walls, responds slowly and often permanently to a stimulus, lacks specialized sense organs and nervous system, and has no powers of locomotion. (Source: CED)",
					"http://opendata.inra.fr/anaeeThes/i_def_24509784-142a-4d0d-9deb-2c7c5869ebde"
			],
			"http://www.w3.org/2004/02/skos/core#prefLabel": [
					"plante",
					"plant"
			],
			"http://www.w3.org/2004/02/skos/core#inScheme": [
					"http://opendata.inra.fr/anaeeThes/"
			],
			"http://www.w3.org/2004/02/skos/core#broader": [
					"http://opendata.inra.fr/anaeeThes/c2_2758"
			],
			"http://art.uniroma2.it/ontologies/vocbench#hasStatus": [
					"Published"
			],
			"http://www.w3.org/1999/02/22-rdf-syntax-ns#type": [
					"http://www.w3.org/2004/02/skos/core#Concept",
					"http://www.w3.org/2002/07/owl#NamedIndividual"
			],
			"http://purl.org/dc/terms/modified": [
					"2018-06-26T14:47:36Z"
			],
			"http://www.w3.org/2004/02/skos/core#exactMatch": [
					"http://aims.fao.org/aos/agrovoc/c_5993"
			]
	},
	"@id": "http://opendata.inra.fr/anaeeThes/c2_225",
	"@type": "http://www.w3.org/2004/02/skos/core#Concept"
}

jonquet · 2023-11-08T12:45:12Z

Note that the config file must allow to specify a list of ontologies to deal with. If empty then all ontologies shall be used.
Then such a list can be used into the /search call at step 2 to avoid getting back results that we know will be filter out after.

jonquet added the feature request label Jan 11, 2023

jonquet assigned jonquet, saubin78 and syphax-bouazzouni Jan 11, 2023

jonquet mentioned this issue Jan 11, 2023

Feature Request/Idea:Implement mechanism to support integration with OntoPortal IQSS/dataverse#9276

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Implement mechanism to support integration with Dataverse #16

Implement mechanism to support integration with Dataverse #16

jonquet commented Jan 11, 2023 •

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syphax-bouazzouni commented Nov 8, 2023 •

edited

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jonquet commented Nov 8, 2023

Implement mechanism to support integration with Dataverse #16

Implement mechanism to support integration with Dataverse #16

Comments

jonquet commented Jan 11, 2023 • edited Loading

Is your feature request related to a problem? Please describe.

Describe the solution you'd like

Describe alternatives you've considered

Additional context

syphax-bouazzouni commented Nov 8, 2023 • edited Loading

Context

Goal

Roadmap

1- Get a API key

2- Use our search API, to have an autocomplete

3- Use the dataverse-external-vocab-support plugin to retrieve concept details

jonquet commented Nov 8, 2023

jonquet commented Jan 11, 2023 •

edited

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syphax-bouazzouni commented Nov 8, 2023 •

edited

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