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Update with BioSamples inferred disease #360

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71 changes: 71 additions & 0 deletions webapps/core/src/main/asciidoc/guides_curation.adoc
Original file line number Diff line number Diff line change
Expand Up @@ -134,6 +134,77 @@ ____

It takes up to 24 hours to generate the curation.

== Curation projects, add BioSamples inferred disease

BioSamples uses automated curation based on manual rules. This project has been done to improve the metadata representation in Phenopackets and the query for disease in BioSamples. Those rules are not applied for a specific project.

For the samples containing the attributes ‘is tumor :yes’ and study disease corresponding to a cancer, BioSamples adds the attributes ‘Biosamples inferred disease :cancer’.

For example, when the user submits:

[source,json]
----
"characteristics" : {
"is tumor" : [ {
"text" : "Yes"
} ],
"study disease" : [ {
"text" : "Carcinoma, Renal Cell"
} ]
}
----


BioSamples adds the inferred disease with ontology term :

[source,json]
----
"characteristics" : {
"BioSamples inferred disease" : [ {
"text" : "cancer",
"ontologyTerms" : [ "http://www.ebi.ac.uk/efo/EFO_0000311" ]
} ],
"is tumor" : [ {
"text" : "Yes"
} ],
"study disease" : [ {
"text" : "Carcinoma, Renal Cell"
} ]
}
----

For the samples containing the attributes ‘diabetes’ and/or ‘diabetes type’, Biosamples adds the ontology term of diabetes.

For example, when the user submits:

[source,json]
----
"characteristics" : {
"diabetes" : [ {
"text" : " yes.type.I"
} ]
}
----

BioSamples adds the inferred disease with ontology term :

[source,json]
----
"characteristics" : {
"BioSamples inferred disease" : [ {
"text" : " Type I diabetes",
"ontologyTerms" : [ "http://www.ebi.ac.uk/efo/EFO_0001359" ]
} ],
"diabetes" : [ {
"text" : " yes.type.I"
} ]
}
----

____
[.emoji]#💡# BioSamples has done the curation on December 16th 2020. All samples submitted after this date are not curated.
____

== Manual curation

Users can also provide their manual curation. See details
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