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ValTaxonomicAPIWoRMS_ValTaxonomicaAPIWoRMS.txt
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ValTaxonomicAPIWoRMS_ValTaxonomicaAPIWoRMS.txt
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--------------------------------------------------------------------------------
---Do not copy /No Copiar
--ENGLISH VERSION
SiB Colombia scripts for Biodiversity data validation and cleaning in OPEN REFINE
https://github.com/SIB-Colombia/data-quality-open-refine
Script Taxonomic Validation using Worms's API
Language: GREL 'General Refine Expression Language'
Created: 2019-05-01
Last Update:2019-06-12
Contributors: Camila Plata, Leonardo Buitrago
This script:
1-Matches original scientificName with Worms's taxonomic Backbone
2-Retrieves Worms's rank and status allowing the user to evaluate the state of each name
3-Retrieves Worms's higher taxonomy for all names
4-Retrieves Worms's habitat classification in DwC
5-Compares Worms's taxonomic suggestions with original taxonomy using a boolean descriptor (1,0)
Conventions boolean descriptor
0-Worms's suggested name DOES NOT match the original name
1-Worms's suggested name matches the original name
Conditions
Dataset with minimum the DwC element 'scientificName'
To obtain a validation of higher taxonomy, these DwC elements are also required: 'kingdom','phylum','class','order','family','genus'
New data will be stored in columns at the beginning of the dataset
Taxonomy elements are reorganized to facilitate the taxonomic validation
--VERSION EN ESPAÑOL
Rutinas del SiB Colombia para la validación y limpieza de datos primarios
de Biodiversidad en OPEN REFINE
https://github.com/SIB-Colombia/data-quality-open-refine
Nombre rutina: Validación taxonomica usando el API de Worms
Languaje: GREL 'General Refine Expression Language'
Creado:2019-05-01
Última Actualización:2019-06-12
Autores: Camila Plata, Leonardo Buitrago
Esta rutina:
1-Compara el elemento scientificName con el árbol taxonómico de Worms
2-Trae los elementos rank y status permitiendo al usuario evaluar el estado del nombre científico
3-Trae la taxonomia superior de cada nombre de acuerdo a Worms
4-Trae la clasificación del habitat de cada nombre en DwC según Worms
5-Compara las sugerencias taxonómicas de Worms con la taxonomia documentada usando descriptores booleanos (1,0)
Conventions boolean descriptor
0- El nombre sugerido por Worms NO coincide con el nombre documentado en el conjunto de datos
1- El nombre sugerido por Worms coincide con el nombre documentado en el conjunto de datose
Requerimientos:
Conjunto de datos con minimo el elemento DwC 'scientificName' documentado
Para obtener la validación de la taxonomía superior también se requieren los elementos DwC: 'kingdom','phylum','class','order','family','genus'
Los nuevos datos seran guardados en columnas el inicio del conjunto de datos
Los elementos taxonómicos son reorganizados para facilitar la validación taxonómicas
---Do not copy /No Copiar
--------------------------------------------------------------------------------
[
{
"op": "core/text-transform",
"description": "Text transform on cells in column scientificName",
"engineConfig": {
"mode": "row-based",
"facets": []
},
"columnName": "scientificName",
"expression": "grel:value.replace(/\\s+/,' ').trim()",
"onError": "keep-original",
"repeat": false,
"repeatCount": 10
},
{
"op": "core/column-addition",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"baseColumnName": "scientificName",
"expression": "grel:value.replace(' ','%20')",
"onError": "set-to-blank",
"newColumnName": "NomAPIw",
"columnInsertIndex": 2,
"description": "Create column NomAPIw at index 4 based on column scientificName using expression grel:value.replace(' ','%20')"
},
{
"op": "core/column-addition-by-fetching-urls",
"description": "Create column c at index 3 by fetching URLs based on column NomAPIw",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"newColumnName": "callAPIworms",
"columnInsertIndex": 3,
"baseColumnName": "NomAPIw",
"urlExpression": "grel:'http://www.marinespecies.org/rest/AphiaRecordsByMatchNames?scientificnames%5B%5D='+value+'&marine_only=false'",
"onError": "set-to-blank",
"delay": 0,
"cacheResponses": true,
"httpHeadersJson": [
{
"name": "authorization",
"value": ""
},
{
"name": "user-agent",
"value": "OpenRefine 3.1 [b90e413]"
},
{
"name": "accept",
"value": "*/*"
}
]
},
{
"op": "core/text-transform",
"description": "Text transform on cells in column callAPIworms",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "callAPIworms",
"expression": "grel:value.replace('[','').replace(']','')",
"onError": "keep-original",
"repeat": false,
"repeatCount": 10
},
{
"op": "core/column-addition",
"description": "Create column isTerrestrial at index 2 based on column callAPIworms",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"newColumnName": "isTerrestrial",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('isTerrestrial').toString()",
"onError": "set-to-blank"
},
{
"op": "core/column-addition",
"description": "Create column isFreshwater at index 2 based on column callAPIworms",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"newColumnName": "isFreshwater",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('isFreshwater').toString()",
"onError": "set-to-blank"
},
{
"op": "core/column-addition",
"description": "Create column isBrackish at index 2 based on column callAPIworms",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"newColumnName": "isBrackish",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('isBrackish').toString()",
"onError": "set-to-blank"
},
{
"op": "core/column-addition",
"description": "Create column isMarine at index 2 based on column callAPIworms",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"newColumnName": "isMarine",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('isMarine').toString()",
"onError": "set-to-blank"
},
{
"op": "core/column-addition",
"description": "Create column A at index 2 based on column callAPIworms",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"newColumnName": "nameAccordingToID",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('url')",
"onError": "set-to-blank"
},
{
"op": "core/column-addition",
"description": "Create column A at index 2 based on column callAPIworms",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"newColumnName": "nameAccordingTo",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('citation')",
"onError": "set-to-blank"
},
{
"op": "core/column-move",
"description": "Move column infraspecificEpithet to position 2",
"columnName": "infraspecificEpithet",
"index": 2
},
{
"op": "core/column-addition",
"description": "Create column specificEpithetSuggested at index 2 based on column callAPIworms",
"engineConfig": {
"mode": "row-based",
"facets": []
},
"newColumnName": "specificEpithetSuggested",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:split(value.parseJson().get(\"scientificname\"),' ')[1]",
"onError": "set-to-blank"
},
{
"op": "core/column-addition",
"description": "Create column specificEpithetValidation at index 2 based on column suggestedSpecificEpithet",
"engineConfig": {
"mode": "row-based",
"facets": []
},
"newColumnName": "specificEpithetValidation",
"columnInsertIndex": 2,
"baseColumnName": "specificEpithetSuggested",
"expression": "grel:if(value==cells[\"specificEpithet\"].value,'1','0').toString()",
"onError": "set-to-blank"
},
{
"op": "core/column-move",
"description": "Move column infraspecificEpithet to position 2",
"columnName": "specificEpithet",
"index": 2
},
{
"op": "core/column-addition",
"description": "Create column A at index 2 based on column callAPIworms",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"newColumnName": "genusSuggested",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('genus')",
"onError": "set-to-blank"
},
{
"op": "core/column-addition",
"description": "Create column genusValidation at index 2 based on column suggstedKingdom",
"engineConfig": {
"mode": "row-based",
"facets": []
},
"newColumnName": "genusValidation",
"columnInsertIndex": 2,
"baseColumnName": "genusSuggested",
"expression": "grel:if(value==cells[\"genus\"].value,'1','0').toString()",
"onError": "set-to-blank"
},
{
"op": "core/column-move",
"description": "Move column genus to position 2",
"columnName": "genus",
"index": 2
},
{
"op": "core/column-addition",
"description": "Create column familySuggested at index 2 based on column callAPIworms",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"newColumnName": "familySuggested",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('family')",
"onError": "set-to-blank"
},
{
"op": "core/column-addition",
"description": "Create column familyValidation at index 2 based on column familySuggested",
"engineConfig": {
"mode": "row-based",
"facets": []
},
"newColumnName": "familyValidation",
"columnInsertIndex": 2,
"baseColumnName": "familySuggested",
"expression": "grel:if(value==cells[\"family\"].value,'1','0').toString()",
"onError": "set-to-blank"
},
{
"op": "core/column-move",
"description": "Move column family to position 2",
"columnName": "family",
"index": 2
},
{
"op": "core/column-addition",
"description": "Create column A at index 2 based on column callAPIworms",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"newColumnName": "orderSuggested",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('order')",
"onError": "set-to-blank"
},
{
"op": "core/column-addition",
"description": "Create column orderValidation at index 2 based on column suggestedOrder",
"engineConfig": {
"mode": "row-based",
"facets": []
},
"newColumnName": "orderValidation",
"columnInsertIndex": 2,
"baseColumnName": "orderSuggested",
"expression": "grel:if(value==cells[\"order\"].value,'1','0').toString()",
"onError": "set-to-blank"
},
{
"op": "core/column-move",
"description": "Move column order to position 2",
"columnName": "order",
"index": 2
},
{
"op": "core/column-addition",
"description": "Create column A at index 2 based on column callAPIworms",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"newColumnName": "classSuggested",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('class')",
"onError": "set-to-blank"
},
{
"op": "core/column-addition",
"description": "Create column classValidation at index 2 based on column suggestedClass",
"engineConfig": {
"mode": "row-based",
"facets": []
},
"newColumnName": "classValidation",
"columnInsertIndex": 2,
"baseColumnName": "classSuggested",
"expression": "grel:if(value==cells[\"class\"].value,'1','0').toString()",
"onError": "set-to-blank"
},
{
"op": "core/column-move",
"description": "Move column class to position 2",
"columnName": "class",
"index": 2
},
{
"op": "core/column-addition",
"description": "Create column A at index 2 based on column callAPIworms",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"newColumnName": "phylumSuggested",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('phylum')",
"onError": "set-to-blank"
},
{
"op": "core/column-addition",
"description": "Create column phylumValidation at index 2 based on column suggestedPhylum",
"engineConfig": {
"mode": "row-based",
"facets": []
},
"newColumnName": "phylumValidation",
"columnInsertIndex": 2,
"baseColumnName": "phylumSuggested",
"expression": "grel:if(value==cells[\"phylum\"].value,'1','0').toString()",
"onError": "set-to-blank"
},
{
"op": "core/column-move",
"description": "Move column phylum to position 2",
"columnName": "phylum",
"index": 2
},
{
"op": "core/column-addition",
"description": "Create column A at index 2 based on column callAPIworms",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"newColumnName": "kingdomSuggested",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('kingdom')",
"onError": "set-to-blank"
},
{
"op": "core/column-addition",
"description": "Create column kingdomValidation at index 2 based on column suggestedKingdom",
"engineConfig": {
"mode": "row-based",
"facets": []
},
"newColumnName": "kingdomValidation",
"columnInsertIndex": 2,
"baseColumnName": "kingdomSuggested",
"expression": "grel:if(value==cells[\"kingdom\"].value,'1','0').toString()",
"onError": "set-to-blank"
},
{
"op": "core/column-move",
"description": "Move column kingdom to position 2",
"columnName": "kingdom",
"index": 2
},
{
"op": "core/column-addition",
"description": "Create column suggestedTaxonomicStatus at index 2 based on column callAPIworms",
"engineConfig": {
"mode": "row-based",
"facets": []
},
"newColumnName": "taxonomicStatusSuggested",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('status')",
"onError": "set-to-blank"
},
{
"op": "core/column-addition",
"description": "Create column A at index 2 based on column callAPIworms",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"newColumnName": "taxonRankSuggested",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('rank')",
"onError": "set-to-blank"
},
{
"op": "core/column-addition",
"description": "Create column A at index 2 based on column callAPIworms",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"newColumnName": "scientificNameAuthorshipSuggested",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('authority')",
"onError": "set-to-blank"
},
{
"op": "core/column-addition",
"description": "Create column authorshipValidation at index 2 based on column suggstedAuthorship",
"engineConfig": {
"mode": "row-based",
"facets": []
},
"newColumnName": "scientificNameAuthorshipValidation",
"columnInsertIndex":2,
"baseColumnName": "scientificNameAuthorshipSuggested",
"expression": "grel:if(value==cells[\"scientificNameAuthorship\"].value,'1','0').toString()",
"onError": "set-to-blank"
},
{
"op": "core/column-move",
"description": "Move column scientificNameAuthorship to position 2",
"columnName": "scientificNameAuthorship",
"index": 2
},
{
"op": "core/column-addition",
"description": "Create column acceptedScientificName(species) at index 2 based on column callAPIworms",
"engineConfig": {
"mode": "row-based",
"facets": []
},
"newColumnName": "acceptedScientificName",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('valid_name')",
"onError": "set-to-blank"
},
{
"op": "core/column-move",
"description": "Move column scientificName to position 2",
"columnName": "scientificName",
"index": 2
},
{
"op": "core/column-addition",
"description": "Create column scientificNameIDSuggested at index 2 based on column callAPIworms",
"engineConfig": {
"mode": "row-based",
"facets": []
},
"newColumnName": "scientificNameIDSuggested",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('lsid')",
"onError": "set-to-blank"
},
{
"op": "core/column-addition",
"description": "Create column authorshipValidation at index 2 based on column scientificNameIDSuggested",
"engineConfig": {
"mode": "row-based",
"facets": []
},
"newColumnName": "scientificNameIDValidation",
"columnInsertIndex":2,
"baseColumnName": "scientificNameIDSuggested",
"expression": "grel:if(value==cells[\"scientificNameID\"].value,'1','0').toString()",
"onError": "set-to-blank"
},
{
"op": "core/column-move",
"description": "Move column scientificNameID to position 2",
"columnName": "scientificNameID",
"index": 2
},
{
"op": "core/column-addition",
"description": "Create column A at index 2 based on column callAPIworms",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"newColumnName": "taxonMatchType",
"columnInsertIndex": 2,
"baseColumnName": "callAPIworms",
"expression": "grel:value.parseJson().get('match_type')",
"onError": "set-to-blank"
}
]