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Add specimen and taxon circumscription #75

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merged 14 commits into from
Mar 9, 2021
+10,340 −1,173
Merged

Add specimen and taxon circumscription #75

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9aa93a1
First stab at incorporating Fisher et al 2007.
gaurav Feb 16, 2021
e9594e6
Improved error display for failed conversion.
gaurav Feb 25, 2021
5f14db4
First stab at adding specimen-related terms to the JSON Schema.
gaurav Feb 25, 2021
862065e
Updated occurrence information in Fisher et al 2007.
gaurav Feb 25, 2021
48a6d0c
Updated Fisher et al expected ontologies.
gaurav Feb 25, 2021
657d6d8
Regenerated Fisher et al 2007 expected JSON-LD and NQ.
gaurav Mar 2, 2021
c1fcd85
Added genus-level taxon concept to Exodictyon.
gaurav Mar 3, 2021
023e12f
Removed `dwc:` prefix from `nameAccordingTo` and `basisOfRecord`.
gaurav Mar 3, 2021
5bf8f6e
Fixed JSON Schema validation issues.
gaurav Mar 3, 2021
c63bcfb
Rewrote algorithm for generating phylorefs with external specifiers.
gaurav Mar 3, 2021
673af47
Regenerated expected files.
gaurav Mar 3, 2021
27c304e
Removed redundant code for generating phylorefs with external specifers.
gaurav Mar 3, 2021
16f6c50
Added test file to make sure multiple external specifiers work.
gaurav Mar 4, 2021
7354c6f
Removed label as a required field in a taxonomic name.
gaurav Mar 4, 2021
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Removed dwc: prefix from nameAccordingTo and basisOfRecord.
@gaurav
gaurav committed Mar 3, 2021
commit 023e12f077005ddcd81b4e8d4fd6dfc2715c1627
1 change: 1 addition & 0 deletions docs/context/development/phyx.json
View file
Original file line number Diff line number Diff line change
@@ -88,6 +88,7 @@
"@type": "xsd:string"
},

"basisOfRecord": "dwc:basisOfRecord",
"occurrenceID": "dwc:occurrenceID",
"catalogNumber": "dwc:catalogNumber",
"collectionCode": "dwc:collectionCode",
4 changes: 2 additions & 2 deletions docs/context/development/schema.json
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Original file line number Diff line number Diff line change
@@ -181,12 +181,12 @@
"minLength": 1,
"description": "A label for this taxonomic unit."
},
"dwc:nameAccordingTo": {
"nameAccordingTo": {
"type": "string",
"minLength": 1,
"description": "For a taxon concept, provides the source in which the specific taxon concept circumscription is defined or implied (i.e. the 'sensu' or 'sec' of the name)."
},
"dwc:basisOfRecord": {
"basisOfRecord": {
"type": "string",
"minLength": 1,
"description": "The basis of record for this specimen."
4 changes: 2 additions & 2 deletions test/examples/correct/fisher_et_al_2007.json
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Original file line number Diff line number Diff line change
@@ -40,7 +40,7 @@
"label": "Exodictyon Cardot, Rev. Bryol. Lichénol. 26: 6. (1899), excl. parte, emend Ellis in Lindbergia 11: 16 (1985)",
"nameComplete": "Exodictyon"
},
"dwc:nameAccordingTo": "Ellis in Lindbergia 11: 16 (1985)"
"nameAccordingTo": "Ellis in Lindbergia 11: 16 (1985)"
},
{
"label": "Wall 2527, Fiji (UC)",
@@ -94,7 +94,7 @@
"externalSpecifiers": [
{
"@type": "http://rs.tdwg.org/dwc/terms/Occurrence",
"dwc:basisOfRecord": "PreservedSpecimen",
"basisOfRecord": "PreservedSpecimen",
"institutionCode": "UC",
"catalogNumber": "Wall 2527, Fiji",
"label": "Wall 2527, Fiji (uc)"