A citable source for a CoL data provider
+Abstract base class of all entities that we track creation and last modified for.
| key | -integer | -- | yes | -primary key - |
- |||
| datasetKey | -integer | -- | yes | -key to the dataset this source belongs to - |
- |||
| title | -string | -- | yes | -Full name of the source. Defaults to dataset title. - |
- |||
| alias | -string | -- | yes | -Short alias for the source to show in trees etc. - |
- |||
| description | -string | -- | no | -Free text describing the source supporting markdown formatting - |
- |||
| organisation | -string | -- | no | -Organisation which has compiled or is owning the source - |
- |||
| contactPerson | -string | +created | +datetime | no | -Contact person of the source + | datetime the dataset was registered in the Clearinghouse |
|
| authorsAndEditors | -string[] | +createdBy | +integer | no | -Optional author(s) and editor(s) of the source + | key of the user that created the object initially |
|
| version | -string | +modified | +datetime | no | -Latest version number of the source used in the Catalogue of Life + | datetime the object was last changed |
|
| released | -date-only | +modifiedBy | +integer | no | -Latest release date of the source used in the Catalogue of Life + | key of the user that last modified the object |
Metadata about the source dataset, e.g. a GSD
+ + +| Name | +Type | +Pattern | +Required | +Description | +|||
|---|---|---|---|---|---|---|---|
| homepage | -string | +created | +datetime | no | -Homepage URL of the source + | datetime the dataset was registered in the Clearinghouse |
|
| group | -string | +createdBy | +integer | no | -taxonomic group in english language - |
- ||
| coverage | -DatasetType | -nomenclator, taxonomic, national, personal, other | -yes | -global vs regional sources + | key of the user that created the object initially |
||
| citation | -string | +modified | +datetime | no | -full bibliographic citation to be used + | datetime the object was last changed |
|
| livingSpeciesCount | -integer | -- | no | -- | |||
| livingInfraspecificCount | -integer | -- | no | -- | |||
| extinctSpeciesCount | -integer | -- | no | -- | |||
| extinctInfraspecificCount | -integer | -- | no | -- | |||
| synonymsCount | -integer | -- | no | -- | |||
| vernacularsCount | -integer | -- | no | -- | |||
| namesCount | +modifiedBy | integer | no | -- | |||
| created | -datetime | -- | yes | -datetime the source was registered in the Clearinghouse + | key of the user that last modified the object |
Metadata about the source dataset, e.g. a GSD
- - -| Name | -Type | -Pattern | -Required | -Description | -||||
|---|---|---|---|---|---|---|---|---|
| key | integer | - | yes | +no | Primary key for the source dataset |
|||
| type | DatasetType | -nomenclator, taxonomic, national, personal, other | +nomenclatural, taxonomic, article, personal, otu, thematic, other | yes | coarse classification of datasets + |
+ |||
| origin | +DatasetOriginType | +external, uploaded, managed | +yes | +Where does the data of the dataset origin from. If external a dataAccess url should be given. |
||||
| dataFormat | enum | -dwca, tcs, xls, other | +dwca, acef, tcs", coldp, proxy | no | data format |
@@ -626,16 +529,6 @@ bacterial, botanical, cultivated, viral, zoological, unknown | no | a default nomenclatural code to be used when importing - |
-
| catalogue | -CatalogueType | -scrutinized, provisional | -yes | -If the dataset participates in any of the 2 catalouge assemblies this is indicated here. -All scrutinized sources will also be included as provisional ones. -Dataset used to build the provisional catalogue will be trusted and insert their names into the names index. |
||||
| created | -datetime | -- | yes | -datetime the dataset was registered in the Clearinghouse - |
- ||||
| modified | -datetime | +locked | +boolean | no | -datetime the data from this dataset was last changed in the Clearinghouse + | Indicates if a dataset is immutable and it’s data cannot be changed. |
||
| Description | ||||||||
| created | +datetime | ++ | no | +datetime the dataset was registered in the Clearinghouse + |
+ ||||
| createdBy | +integer | ++ | no | +key of the user that created the object initially + |
+ ||||
| modified | +datetime | ++ | no | +datetime the object was last changed + |
+ ||||
| modifiedBy | +integer | ++ | no | +key of the user that last modified the object + |
+ ||||
| key | integer | @@ -1055,7 +972,7 @@|||||||
| subject | -NameRef | +SimpleName | yes | the name usage this decision is about @@ -1087,34 +1004,50 @@Decision | ||||
| name | +Name | ++ | no | +the new scientific name object + |
+ ||||
| extinct | +boolean | ++ | no | +the new extinct flag + |
+ ||||
| temporalRangeStart | string | no | -the new scientific name + | the new temporalRangeStart |
||||
| authorship | +temporalRangeEnd | string | no | -the new authorship + | the new temporalRangeEnd |
|||
| created | -datetime | +lifezones | +LifezoneType[] | - | yes | -datetime the decision was created + | no | +the new lifezones |
| deleted | -datetime | +note | +string | no | -datetime the decision was deleted + | editorial notes |
datetime the dataset was registered in the Clearinghouse
+key of the user that created the object initially
+datetime the object was last changed
+key of the user that last modified the object
+Key to the source dataset this record belongs to
+datetime the dataset was registered in the Clearinghouse
key of the user that created the object initially
+datetime the object was last changed
+key of the user that last modified the object
+Key to the source dataset this record belongs to
+The total number of records available.
-A reference to a name based on ids and the name itself
- - -| Name | -Type | -Pattern | -Required | -Description | -
|---|---|---|---|---|
| id | -string | -- | yes | -the names id within its dataset - |
-
| indexNameId | -string | -- | no | -the name id from the matching name index record - |
-
| name | -string | -- | yes | -the literal name - |
-
| authorship | -string | -- | no | -the literal, full authorship - |
-
| rank | -RankType | -domain, superkingdom, kingdom, subkingdom, infrakingdom, superphylum, phylum, subphylum, infraphylum, superclass, class, subclass, infraclass, parvclass, superlegion, legion, sublegion, infralegion, supercohort, cohort, subcohort, infracohort, magnorder, superorder, grandorder, order, suborder, infraorder, parvorder, superfamily, family, subfamily, infrafamily, supertribe, tribe, subtribe, infratribe, suprageneric name, genus, subgenus, infragenus, supersection, section, subsection, superseries, series, subseries, infrageneric name, species aggregate, species, infraspecific name, grex, subspecies, cultivar group, convariety, infrasubspecific name, proles, natio, aberration, morph, variety, subvariety, form, subform, pathovar, biovar, chemovar, morphovar, phagovar, serovar, chemoform, forma specialis, cultivar, strain, other, unranked | -no | -the rank |
datetime the dataset was registered in the Clearinghouse
+key of the user that created the object initially
+datetime the object was last changed
+key of the user that last modified the object
+An ordered taxonomic rank enumeration with the most frequently used values. See: https://api.catalogue.life/vocab/rank
- -{
@@ -2730,6 +2697,38 @@ Reference
Description
+
+ created
+ datetime
+ no
+ datetime the dataset was registered in the Clearinghouse
+
+
+ createdBy
+ integer
+ no
+ key of the user that created the object initially
+
+
+ modified
+ datetime
+ no
+ datetime the object was last changed
+
+
+ modifiedBy
+ integer
+ no
+ key of the user that last modified the object
+
datasetKey
integer
@@ -2931,6 +2930,38 @@ Sector
Description
+
+ created
+ datetime
+ no
+ datetime the dataset was registered in the Clearinghouse
+
+
+ createdBy
+ integer
+ no
+ key of the user that created the object initially
+
+
+ modified
+ datetime
+ no
+ datetime the object was last changed
+
+
+ modifiedBy
+ integer
+ no
+ key of the user that last modified the object
+
key
integer
@@ -2940,96 +2971,66 @@ Sector
- colSourceKey
+ datasetKey
integer
yes
- key to the ColSource this sector originates from
+ key to the catalogue dataset this sector is attached to
- root
- NameRef
+ target
+ SimpleName
yes
- A reference to the single root taxon from the col source for this sector. Can even be a species, but usually some higher taxon.
+ attachement point in the catalogue
- exclude
- NameRef[]
+ subjectDatasetKey
+ integer
yes
- Optional list of taxa within the descendants of root to exclude from this sector definition
+ key to the source dataset this sector is attached to
- attachment
- NameRef
+ subject
+ SimpleName
yes
- The attachment point in the CoL tree, i.e. the CoL parent taxon for the sector root
+ root taxon of the sector in the source dataset
- suppress
- NameRef[]
- mode
+ SectorMode
+ attach, union, merge
yes
- Optional list of CoL tree taxa that should be suppressed when this sector is attached.
-E.g. the CoL management classification might define an alternative taxonomy that uses
-different taxa which are covered by this sector already.
+ The mode a sector is attached to the catalogue.
- created
- datetime
- code
+ NomCodeType
+ bacterial, botanical, cultivated, viral, zoological, unknown
yes
- datetime the sector was created
+ The nomenclatural code to apply to all names in this sector
- deleted
- datetime
+ note
+ string
no
- datetime the sector was deleted
+ yes
+ Editorial notes
- Serial
+ SectorImport
- {
- "key": 432561,
- "datasetKey": 15,
- "bph": "460.06",
- "tl2": "11.084",
- "call": "QK1.J55",
- "oclc": 1754397,
- "bhl": 68922,
- "firstYear": 1799,
- "lastYear": 1804,
- "csl": {
- "call-number": "QK1.J55",
- "type":"journal",
- "title":"Journal für die Botanik",
- "title-short":"J. Bot. (Schrader)",
- "editor":[{"family":"Schrader","given":"H. A."}],
- "publisher-place": "Göttingen"
- }
-}
-
- A journal or other serial used as a container for references.
-A serial is a publication in any medium issued under the same title in a succession of discrete parts,
-usually numbered (or dated) and appearing at regular or irregular intervals with no predetermined conclusion.
-Serial publications include print periodicals and newspapers, electronic magazines and journals, annuals (reports, yearbooks, etc.),
-proceedings and transactions, and numbered monographic series cataloged separately.
-When serials split, merge, or are absorbed, a title change may occur.
-A specific serial title is identified by a unique International Standard Serials Number (ISSN) and key title,
-assigned and maintained by the International Serials Data System (ISDS), a network of national serials data centers.
-Serials and annuals are listed in Ulrich’s International Periodicals Directory published annually by ProQuest and in The Serials Directory published by EBSCO.
+ A sector import into assembly.
@@ -3046,94 +3047,135 @@ Serial
integer
yes
- Key to the source dataset this record belongs to
+ the dataset ID
- aliases
- string[]
+ attempt
+ integer
+ yes
+ the number of import attempts
+
+
+ state
+ ImportState
+ waiting, preparing, copying, deleting, relinking, indexing, finished, canceled, failed
+ yes
+ the state of the import
+
+
+ started
+ datetime
+ yes
+ the date and time the import started
+
+
+ finished
+ datetime
no
- Alternative titles known for the serial
+ the date and time the import finished
- bph
- string
+ nameCount
+ integer
no
- BPH Online identifier. Botanic periodicals published between 1665 and the present.
+ the number of names imported
- call
- string
+ taxonCount
+ integer
no
- library of congress classification number
+ the number of taxa imported
- tl2
- string
+ synonymCount
+ integer
no
- TL2 number
+ the number of synonyms imported
- oclc
+ referenceCount
integer
no
- OCLC number
+ the number of references imported
- bhl
+ distributionCount
integer
no
- BHL title number
+ the number of distribution records imported
- firstYear
+ mediaCount
integer
no
- First year the serial was published
+ the number of media records imported
- lastYear
+ vernacularCount
integer
no
- Last year the serial was published. Empty for current journals
+ the number of common names imported
- csl
- object
+ type
+ string
yes
- Serial metadata as CSL-JSON, see CSL JSON schema
+ the type of sector sync
- notes
- string
+ sectorKey
+ integer
no
- Notes about the serial
+ yes
+ the sector ID
+
+
+ ignoredUsageCount
+ integer
+ yes
+ The number of ignored scientific name usages, which could be explicitly blocked by a decision or
+implicitly excluded (e.g., hybrid formulas, placeholders, no_names, etc).
+
+
+ usagesCount
+ integer
+ yes
+ the number of scientific name usages
- SectorImport
+ SectorResultSet
- A sector import into assembly.
+ A paging resultset for Sectors.
@@ -3146,132 +3188,167 @@ SectorImport
- datasetKey
- integer
+ result
+ object[]
yes
- the dataset ID
+ Result page
- attempt
+ offset
integer
yes
- the number of import attempts
+ The offset applied during request. Can be less than requested if the limit is reached.
- state
- ImportState
- waiting, preparing, copying, deleting, relinking, indexing, finished, canceled, failed
+ limit
+ integer
+ yes
- the state of the import
+ The maximum number of records returned. Can be less than requested if the limit is reached.
- started
- datetime
+ total
+ integer
yes
- the date and time the import started
+ The total number of records available.
+
+ Serial
+
+ {
+ "key": 432561,
+ "datasetKey": 15,
+ "bph": "460.06",
+ "tl2": "11.084",
+ "call": "QK1.J55",
+ "oclc": 1754397,
+ "bhl": 68922,
+ "firstYear": 1799,
+ "lastYear": 1804,
+ "csl": {
+ "call-number": "QK1.J55",
+ "type":"journal",
+ "title":"Journal für die Botanik",
+ "title-short":"J. Bot. (Schrader)",
+ "editor":[{"family":"Schrader","given":"H. A."}],
+ "publisher-place": "Göttingen"
+ }
+}
+
+
+ A journal or other serial used as a container for references.
+A serial is a publication in any medium issued under the same title in a succession of discrete parts,
+usually numbered (or dated) and appearing at regular or irregular intervals with no predetermined conclusion.
+Serial publications include print periodicals and newspapers, electronic magazines and journals, annuals (reports, yearbooks, etc.),
+proceedings and transactions, and numbered monographic series cataloged separately.
+When serials split, merge, or are absorbed, a title change may occur.
+A specific serial title is identified by a unique International Standard Serials Number (ISSN) and key title,
+assigned and maintained by the International Serials Data System (ISDS), a network of national serials data centers.
+Serials and annuals are listed in Ulrich’s International Periodicals Directory published annually by ProQuest and in The Serials Directory published by EBSCO.
+
+
+
+
+ Name
+ Type
+ Pattern
+ Required
+ Description
+
+
- finished
- datetime
+ datasetKey
+ integer
no
- the date and time the import finished
+ yes
+ Key to the source dataset this record belongs to
- nameCount
- integer
+ aliases
+ string[]
no
- the number of names imported
+ Alternative titles known for the serial
- taxonCount
- integer
+ bph
+ string
no
- the number of taxa imported
+ BPH Online identifier. Botanic periodicals published between 1665 and the present.
- synonymCount
- integer
+ call
+ string
no
- the number of synonyms imported
+ library of congress classification number
- referenceCount
- integer
+ tl2
+ string
no
- the number of references imported
+ TL2 number
- distributionCount
+ oclc
integer
no
- the number of distribution records imported
+ OCLC number
- mediaCount
+ bhl
integer
no
- the number of media records imported
+ BHL title number
- vernacularCount
+ firstYear
integer
no
- the number of common names imported
-
-
- type
- string
- yes
- the type of sector sync
+ First year the serial was published
- sectorKey
+ lastYear
integer
yes
- the sector ID
+ no
+ Last year the serial was published. Empty for current journals
- ignoredUsageCount
- integer
+ csl
+ object
yes
- The number of ignored scientific name usages, which could be explicitly blocked by a decision or
-implicitly excluded (e.g., hybrid formulas, placeholders, no_names, etc).
+ Serial metadata as CSL-JSON, see CSL JSON schema
- usagesCount
- integer
+ notes
+ string
yes
- the number of scientific name usages
+ no
+ Notes about the serial
@@ -3355,9 +3432,17 @@ SimpleName
- rank
- Rank
+ authorship
+ string
no
+ the scientific name authorship
+
+
+ rank
+ RankType
+ domain, superkingdom, kingdom, subkingdom, infrakingdom, superphylum, phylum, subphylum, infraphylum, superclass, class, subclass, infraclass, parvclass, superlegion, legion, sublegion, infralegion, supercohort, cohort, subcohort, infracohort, magnorder, superorder, grandorder, order, suborder, infraorder, parvorder, superfamily, family, subfamily, infrafamily, supertribe, tribe, subtribe, infratribe, suprageneric name, genus, subgenus, infragenus, supersection, section, subsection, superseries, series, subseries, infrageneric name, species aggregate, species, infraspecific name, grex, subspecies, cultivar group, convariety, infrasubspecific name, proles, natio, aberration, morph, variety, subvariety, form, subform, pathovar, biovar, chemovar, morphovar, phagovar, serovar, chemoform, forma specialis, cultivar, strain, other, unranked
yes
the taxonomic rank
SimpleName
code
NomCodeType
bacterial, botanical, cultivated, viral, zoological, unknown
- yes
+ no
the nomenclatural code
@@ -3383,7 +3468,7 @@ SimpleName
string
no
- the parent
+ the scientific name of the parent
SpeciesEstimate
Description
+
+ created
+ datetime
+ no
+ datetime the dataset was registered in the Clearinghouse
+
+
+ createdBy
+ integer
+ no
+ key of the user that created the object initially
+
+
+ modified
+ datetime
+ no
+ datetime the object was last changed
+
+
+ modifiedBy
+ integer
+ no
+ key of the user that last modified the object
+
key
integer
@@ -3553,6 +3670,38 @@ Taxon
Description
+
+ created
+ datetime
+ no
+ datetime the dataset was registered in the Clearinghouse
+
+
+ createdBy
+ integer
+ no
+ key of the user that created the object initially
+
+
+ modified
+ datetime
+ no
+ datetime the object was last changed
+
+
+ modifiedBy
+ integer
+ no
+ key of the user that last modified the object
+
datasetKey
integer
@@ -4060,19 +4209,19 @@ VernacularName
Vocabularies
- CatalogueType
+ DatasetOriginType
- Enumeration: scrutinized, provisional
+ Enumeration: external, uploaded, managed
- Assembled catalogues in the CoL See https://api.catalogue.life/vocab/catalogue for the latest full list.
+ Enumeration of the origin of a dataset. See https://api.catalogue.life/vocab/datasetorigin
DatasetType
- Enumeration: nomenclator, taxonomic, national, personal, other
+ Enumeration: nomenclatural, taxonomic, article, personal, otu, thematic, other
Enumeration of kind of datasets See https://api.catalogue.life/vocab/datasettype for the latest full list.
@@ -4335,7 +4484,7 @@ OriginType
Enumeration: source, denormed classification, verbatim parent, verbatim accepted, verbatim basionym, proparte, autonym, implicit name, missing accepted, basionym placeholder, ex author synonym, name matching, other
- Enumeration of the kind of matches possible. See https://api.catalogue.life/vocab/origin
+ Enumeration of the how a record came to existance during an import into the Clearinghouse. See https://api.catalogue.life/vocab/origin
@@ -4366,6 +4515,15 @@ ReferenceTopicType
+ SectorMode
+
+
+ Enumeration: attach, union, merge
+
+ The mode a sector is attached to the catalogue. See: https://api.catalogue.life/vocab/sector$mode
+
+
+
TaxonomicStatus
@@ -4462,7 +4620,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{"gbifSync":true,"importer":false}
@@ -4518,7 +4676,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: text/plain
@@ -4549,7 +4707,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: text/plain
@@ -4580,7 +4738,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: text/plain
@@ -4611,7 +4769,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: text/plain
@@ -4648,7 +4806,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json-assembly-idle
{
@@ -4662,7 +4820,7 @@ Response 200
Content: any
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json-assembly-running
{
@@ -4710,7 +4868,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -4786,7 +4944,7 @@ Response 400
HTTP/1.1 400 Bad Request
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json-dataset-not-imported-yet
{
@@ -4799,7 +4957,7 @@ Response 400
Content: any
HTTP/1.1 400 Bad Request
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json-dataset-still-importing
{
@@ -4812,7 +4970,7 @@ Response 400
Content: any
HTTP/1.1 400 Bad Request
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json-sector-does-not-exist
{
@@ -4825,7 +4983,7 @@ Response 400
Content: any
HTTP/1.1 400 Bad Request
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json-only-draft-catalogue
{
@@ -4886,7 +5044,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -4912,7 +5070,7 @@ Response 404
HTTP/1.1 404 Not Found
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -4950,7 +5108,7 @@ Response 201
HTTP/1.1 201 Created
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: text/plain
3031
@@ -4961,7 +5119,7 @@ Response 400
HTTP/1.1 400 Bad Request
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -4991,7 +5149,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: text/plain
@@ -5030,7 +5188,7 @@ Response 400
HTTP/1.1 400 Bad Request
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -5045,7 +5203,7 @@ Response 404
HTTP/1.1 404 Not Found
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -5103,7 +5261,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -6345,7 +6503,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -6379,17 +6537,7 @@ Response 200
Host: api.catalogue.life
Content-Type: application/json
- # Request body for an uploaded dataset
-{
- "title": "Example uploaded dataset",
- "license": "cc0",
- "type": "taxonomic",
- "origin": "uploaded",
- "dataFormat": "coldp"
-}
-
-# Request body for an externally hosted dataset
-{
+ {
"title": "Example externally hosted dataset",
"license": "cc0",
"type": "nomenclatural",
@@ -6408,7 +6556,7 @@ POST http://api.catalogue.life/dataset
Body
application/json
- Content: any
+ Content: Dataset
@@ -6416,7 +6564,7 @@ Response 201
HTTP/1.1 201 Created
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
2051
@@ -6469,7 +6617,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -7057,7 +7205,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
# import attempt processing
@@ -7264,7 +7412,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -7299,7 +7447,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -7334,7 +7482,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: image/bmp
@@ -7342,7 +7490,7 @@ Response 200
Content: any
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: image/gif
@@ -7350,7 +7498,7 @@ Response 200
Content: any
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: image/jpg
@@ -7358,7 +7506,7 @@ Response 200
Content: any
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: image/png
@@ -7366,7 +7514,7 @@ Response 200
Content: any
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: image/psd
@@ -7374,7 +7522,7 @@ Response 200
Content: any
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: image/tiff
@@ -7384,7 +7532,7 @@ Response 404
HTTP/1.1 404 Not Found
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -7432,7 +7580,7 @@ Response 400
HTTP/1.1 400 Bad Request
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -7507,7 +7655,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
@@ -7559,7 +7707,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -7618,7 +7766,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
[{
@@ -7704,7 +7852,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -7772,7 +7920,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
[{
@@ -7820,7 +7968,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -7880,7 +8028,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: text/plain
@@ -7950,7 +8098,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
@@ -8002,7 +8150,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -8106,7 +8254,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
@@ -8158,7 +8306,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -8220,7 +8368,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -8290,7 +8438,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
[{
@@ -8382,7 +8530,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
@@ -8413,7 +8561,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
[
@@ -8625,7 +8773,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -8685,7 +8833,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: text/plain
Animalia [kingdom]
@@ -8730,7 +8878,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: text/plain
--- /home/col/bin/dev/metrics/dataset/2050/tree/1.txt 2019-10-09 21:43:18.083256660 +0000
@@ -8749,7 +8897,7 @@ Response 404
HTTP/1.1 404 Not Found
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -8824,7 +8972,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
@@ -8876,7 +9024,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -8993,6 +9141,24 @@ Parameters
yes
if true only show decisions which cannot be linked to a source name usage
+
+
+ offset
+ integer
+ no
+ The requested number of offset records. Defaults to zero
+
+
+ limit
+ integer
+ no
+ The requested number of maximum records to be returned. Defaults to 10 and can be no more than 1000.
@@ -9002,7 +9168,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -9070,7 +9236,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
6
@@ -9081,7 +9247,7 @@ Response 200
/estimate
- Returns species estimates
+ Species estimates are linked to a target taxon of a managed catalogue.
@@ -9092,7 +9258,7 @@ /estimate
GET http://api.catalogue.life/estimate
- List of species estimates with optional filters.
+ Page through species estimates with optional filters.
@@ -9160,6 +9326,24 @@ Parameters
yes
if true only show estimates which cannot be linked to their target name usage
+
+ offset
+ integer
+ no
+ The requested number of offset records. Defaults to zero
+
+
+ limit
+ integer
+ no
+ The requested number of maximum records to be returned. Defaults to 10 and can be no more than 1000.
@@ -9169,7 +9353,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -9248,7 +9432,7 @@ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -9364,7 +9548,8 @@ Response 404
/sector
-
+ Sectors are taxonomic groups that are represented by a subtree with a single root taxon. They link a subject (the root taxon in a source dataset) to a target (the attachment point) in a managed catalogue.
+
@@ -9374,26 +9559,145 @@ /sector
GET http://api.catalogue.life/sector
- List of taxonomic sectors in the CoL.
-queryParameters:
-sourceKey:
-description: Filter by CoL source.
+ Page through sectors with optional filters.
+ Parameters
+
+
+ Name
+ Type
+ Pattern
+ Required
+ Default
+ Description
+
+
+
+ id
+ string
+ yes
+ The subjects taxon id
+
+
+ datasetKey
+ integer
+ yes
+ The catalogue dataset the sector is attached to
+
+
+ subjectDatasetKey
+ integer
+ yes
+ The source dataset the subject belongs to
+
+
+ userKey
+ integer
+ yes
+ The user that last modified the sector
+
+
+ rank
+ RankType
+ domain, superkingdom, kingdom, subkingdom, infrakingdom, superphylum, phylum, subphylum, infraphylum, superclass, class, subclass, infraclass, parvclass, superlegion, legion, sublegion, infralegion, supercohort, cohort, subcohort, infracohort, magnorder, superorder, grandorder, order, suborder, infraorder, parvorder, superfamily, family, subfamily, infrafamily, supertribe, tribe, subtribe, infratribe, suprageneric name, genus, subgenus, infragenus, supersection, section, subsection, superseries, series, subseries, infrageneric name, species aggregate, species, infraspecific name, grex, subspecies, cultivar group, convariety, infrasubspecific name, proles, natio, aberration, morph, variety, subvariety, form, subform, pathovar, biovar, chemovar, morphovar, phagovar, serovar, chemoform, forma specialis, cultivar, strain, other, unranked
+ yes
+ The rank of the subject
+
+
+ mode
+ SectorMode
+ attach, union, merge
+ yes
+ The sector mode, e.g. ATTACH
+
+
+ broken
+ boolean
+ yes
+ if true only show decisions which cannot be linked to a source name usage
+
+
+ offset
+ integer
+ no
+ The requested number of offset records. Defaults to zero
+
+
+ limit
+ integer
+ no
+ The requested number of maximum records to be returned. Defaults to 10 and can be no more than 1000.
+
+
Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
+Content-Type: application/json
+
+
+ application/json
+ Content: SectorResultSet
+
+
+POST //sector HTTP/1.1
+Host: api.catalogue.life
+Content-Type: application/json
+
+
+
+ POST http://api.catalogue.life/sector
+
+
+
+ Body
+ application/json
+ Content: Sector
+
+
+
+ Response 201
+
+
+HTTP/1.1 201 Created
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
+ 2051
application/json
- Content: Sector[]
+ Content: integer
/importer
@@ -9413,7 +9717,7 @@ GET http://api.catalogue.life/importer
- Parameters
+ Parameters
Name
@@ -9472,11 +9776,11 @@ Parameters
- Response 200
+ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
@@ -9501,17 +9805,17 @@ POST http://api.catalogue.life/importer
- Body
+ Body
application/json
Content: ImportRequest
- Response 201
+ Response 201
HTTP/1.1 201 Created
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -9547,11 +9851,11 @@ GET http://api.catalogue.life/importer/{key
- Response 200
+ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
# inserting import
@@ -9681,11 +9985,11 @@ Response 200
application/json
Content: any
- Response 404
+ Response 404
HTTP/1.1 404 Not Found
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -9710,7 +10014,7 @@ POST http://api.catalogue.life/importer/{ke
- Body
+ Body
application/octet-stream
Content: any
application/zip
@@ -9720,11 +10024,11 @@ Body
- Response 201
+ Response 201
HTTP/1.1 201 Created
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -9754,7 +10058,7 @@ DELETE http://api.catalogue.life/importer/{
- Response 204
+ Response 204
@@ -9781,7 +10085,7 @@ GET http://api.catalogue.life/nameusage/sea
- Parameters
+ Parameters
Name
@@ -9921,11 +10225,11 @@ Parameters
- Response 200
+ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -10195,7 +10499,7 @@ GET http://api.catalogue.life/nameusage/sug
- Parameters
+ Parameters
Name
@@ -10245,11 +10549,11 @@ Parameters
- Response 200
+ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
@@ -10275,7 +10579,7 @@ GET http://api.catalogue.life/name/matching
- Parameters
+ Parameters
Name
@@ -10334,11 +10638,11 @@ Parameters
- Response 200
+ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -10392,7 +10696,7 @@ GET http://api.catalogue.life/parser/nameParameters
+ Parameters
Name
@@ -10415,11 +10719,11 @@ Parameters
- Response 200
+ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
[{
@@ -10494,7 +10798,7 @@ POST http://api.catalogue.life/parser/name<
- Body
+ Body
application/json
Content: any
multipart/form-data
@@ -10504,11 +10808,11 @@ Body
- Response 200
+ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
[{
@@ -10596,11 +10900,11 @@ GET http://api.catalogue.life/user/{userKey
- Response 200
+ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -10614,11 +10918,11 @@ Response 200
application/json
Content: any
- Response 404
+ Response 404
HTTP/1.1 404 Not Found
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -10650,11 +10954,11 @@ GET http://api.catalogue.life/user/me
- Response 200
+ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
{
@@ -10696,11 +11000,11 @@ GET http://api.catalogue.life/user/loginResponse 200
+ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: text/plain
eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJzY290Y2guaW8iLCJleHAiOjEzMDA4MTkzODAsIm5hbWUiOiJDaHJpcyBTZXZpbGxlamEiLCJhZG1pbiI6dHJ1ZX0.03f329983b86f7d9a9f5fef85305880101d5e302afafa20154d094b229f75773
@@ -10731,7 +11035,7 @@ PUT http://api.catalogue.life/user/settings
- Body
+ Body
application/json
Content: any
@@ -10758,11 +11062,11 @@ GET http://api.catalogue.life/version
- Response 200
+ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: text/plain
"70d8d5b 2019-10-09T14:26:15+0000"
@@ -10792,11 +11096,11 @@ GET http://api.catalogue.life/vocab
- Response 200
+ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
["continent","country","areastandard","cslreftype","nametype","origin","language","frequency","rank","nomacttype","coverage","nomstatus","dataformat","importstate","issue","gazetteer","cslvariable","typestatus","lifezone","distributionstatus","taxonomicstatus","kingdom","datasettype","license","nomcode","namepart"]
@@ -10825,11 +11129,11 @@ GET http://api.catalogue.life/vocab/{name}<
- Response 200
+ Response 200
HTTP/1.1 200 OK
-Date: Thursday, November 28, 2019 at 5:20:36 PM Central European Standard Time
+Date: Thursday, November 28, 2019 at 10:52:04 PM Central European Standard Time
Content-Type: application/json
["domain","superkingdom","kingdom","subkingdom","infrakingdom","superphylum","phylum","subphylum","infraphylum","superclass","class","subclass","infraclass","parvclass","superlegion","legion","sublegion","infralegion","supercohort","cohort","subcohort","infracohort","magnorder","superorder","grandorder","order","suborder","infraorder","parvorder","superfamily","family","subfamily","infrafamily","supertribe","tribe","subtribe","infratribe","suprageneric name","genus","subgenus","infragenus","supersection","section","subsection","superseries","series","subseries","infrageneric name","species aggregate","species","infraspecific name","grex","subspecies","cultivar group","convariety","infrasubspecific name","proles","natio","aberration","morph","variety","subvariety","form","subform","pathovar","biovar","chemovar","morphovar","phagovar","serovar","chemoform","forma specialis","cultivar","strain","other","unranked"]
diff --git a/docs/api/api.raml b/docs/api/api.raml
index 7690404..1d26cea 100644
--- a/docs/api/api.raml
+++ b/docs/api/api.raml
@@ -41,6 +41,7 @@ types: !include inc/types.raml
/dataset: !include inc/dataset.raml
/decision:
get:
+ is: paged
description: |
List of editorial decisions with optional filters.
queryParameters:
@@ -117,11 +118,12 @@ types: !include inc/types.raml
description: the decision key
example: '6'
/estimate:
- displayName: Gets species estimates
- description: Returns species estimates
+ displayName: Species estimates
+ description: Species estimates are linked to a target taxon of a managed catalogue.
get:
+ is: paged
description: |
- List of species estimates with optional filters.
+ Page through species estimates with optional filters.
queryParameters:
datasetKey:
type: integer
@@ -226,17 +228,53 @@ types: !include inc/types.raml
type: integer
description: species estimate key
/sector:
+ displayName: Taxonomic sectors
+ description: >
+ Sectors are taxonomic groups that are represented by a subtree with a single root taxon.
+ They link a subject (the root taxon in a source dataset)
+ to a target (the attachment point) in a managed catalogue.
get:
+ is: paged
description: |
- List of taxonomic sectors in the CoL.
- queryParameters:
- sourceKey:
- description: Filter by CoL source.
+ Page through sectors with optional filters.
+ queryParameters:
+ id:
+ type: string
+ description: The subjects taxon id
+ datasetKey:
+ type: integer
+ description: The catalogue dataset the sector is attached to
+ subjectDatasetKey:
+ type: integer
+ description: The source dataset the subject belongs to
+ userKey:
+ type: integer
+ description: The user that last modified the sector
+ rank:
+ type: RankType
+ description: The rank of the subject
+ mode:
+ type: SectorMode
+ description: The sector mode, e.g. ATTACH
+ broken:
+ type: boolean
+ description: if true only show decisions which cannot be linked to a source name usage
responses:
200:
body:
application/json:
- type: Sector[]
+ type: SectorResultSet
+ post:
+ body:
+ application/json:
+ type: Sector
+ responses:
+ 201:
+ body:
+ application/json:
+ description: the new sectors key
+ type: integer
+ example: 2051
/importer:
get:
description: Retrieve import metrics sorted chronologically descending.
diff --git a/docs/api/inc/dataset.raml b/docs/api/inc/dataset.raml
index 10d090f..71f5b22 100644
--- a/docs/api/inc/dataset.raml
+++ b/docs/api/inc/dataset.raml
@@ -33,17 +33,8 @@
description: Creates a new dataset specified through the JSON request body and returns the database key of the new dataset.
body:
application/json:
+ type: Dataset
example: |
- # Request body for an uploaded dataset
- {
- "title": "Example uploaded dataset",
- "license": "cc0",
- "type": "taxonomic",
- "origin": "uploaded",
- "dataFormat": "coldp"
- }
-
- # Request body for an externally hosted dataset
{
"title": "Example externally hosted dataset",
"license": "cc0",
diff --git a/docs/api/inc/types.raml b/docs/api/inc/types.raml
index ca68f90..23afb67 100644
--- a/docs/api/inc/types.raml
+++ b/docs/api/inc/types.raml
@@ -64,102 +64,40 @@ BackgroundProcesses:
description: whether the importer scheduler is enabled
description: |
Static class of background processes
-CatalogueType:
- type: string
- enum: ["scrutinized", "provisional"]
- description: >
- Assembled catalogues in the CoL
- See https://api.catalogue.life/vocab/catalogue for the latest full list.
-ColSource:
+DataEntity:
type: object
- description: |
- A citable source for a CoL data provider
+ description: Abstract base class of all entities that we track creation and last modified for.
properties:
- key:
- type: integer
- description: primary key
- datasetKey:
- type: integer
- description: key to the dataset this source belongs to
- title:
- type: string
- description: Full name of the source. Defaults to dataset title.
- alias:
- type: string
- description: Short alias for the source to show in trees etc.
- description:
- type: string
- description: Free text describing the source supporting markdown formatting
- required: false
- organisation:
- type: string
- description: Organisation which has compiled or is owning the source
- required: false
- contactPerson:
- type: string
- description: Contact person of the source
- required: false
- authorsAndEditors:
- type: string[]
- description: Optional author(s) and editor(s) of the source
- required: false
- version:
- type: string
- description: Latest version number of the source used in the Catalogue of Life
- required: false
- released:
- type: date-only
- description: Latest release date of the source used in the Catalogue of Life
- required: false
- homepage:
- type: string
- description: Homepage URL of the source
- required: false
- group:
- type: string
- description: taxonomic group in english language
- required: false
- coverage:
- type: DatasetType
- description: global vs regional sources
- citation:
- type: string
- description: full bibliographic citation to be used
- required: false
- livingSpeciesCount:
- type: integer
- required: false
- livingInfraspecificCount:
- type: integer
- required: false
- extinctSpeciesCount:
- type: integer
- required: false
- extinctInfraspecificCount:
- type: integer
+ created:
+ type: datetime
+ description: datetime the dataset was registered in the Clearinghouse
required: false
- synonymsCount:
+ createdBy:
type: integer
+ description: key of the user that created the object initially
required: false
- vernacularsCount:
- type: integer
+ modified:
+ type: datetime
+ description: datetime the object was last changed
required: false
- namesCount:
+ modifiedBy:
type: integer
+ description: key of the user that last modified the object
required: false
- created:
- type: datetime
- description: datetime the source was registered in the Clearinghouse
Dataset:
- type: object
+ type: DataEntity
description: Metadata about the source dataset, e.g. a GSD
properties:
key:
type: integer
description: Primary key for the source dataset
+ required: false
type:
type: DatasetType
description: coarse classification of datasets
+ origin:
+ type: DatasetOriginType
+ description: Where does the data of the dataset origin from. If external a dataAccess url should be given.
title:
type: string
description: Full name of the source dataset
@@ -208,7 +146,7 @@ Dataset:
required: false
dataFormat:
type: string
- enum: ["dwca", "tcs", "xls", "other"]
+ enum: ["dwca", "acef", tcs", "coldp", "proxy"]
description: data format
required: false
dataAccess:
@@ -222,22 +160,13 @@ Dataset:
type: NomCodeType
description: a default nomenclatural code to be used when importing
required: false
- catalogue:
- type: CatalogueType
- description: |
- If the dataset participates in any of the 2 catalouge assemblies this is indicated here.
- All scrutinized sources will also be included as provisional ones.
- Dataset used to build the provisional catalogue will be trusted and insert their names into the names index.
notes:
type: string
description: any notes
required: false
- created:
- type: datetime
- description: datetime the dataset was registered in the Clearinghouse
- modified:
- type: datetime
- description: datetime the data from this dataset was last changed in the Clearinghouse
+ locked:
+ type: boolean
+ description: Indicates if a dataset is immutable and it's data cannot be changed.
required: false
deleted:
type: datetime
@@ -400,14 +329,20 @@ DatasetObject:
type: integer
description: Key to the source dataset this record belongs to
required: true
+DatasetOriginType:
+ type: string
+ enum: ["external", "uploaded", "managed"]
+ description: >
+ Enumeration of the origin of a dataset.
+ See https://api.catalogue.life/vocab/datasetorigin
DatasetType:
type: string
- enum: ["nomenclator","taxonomic","national","personal","other"]
+ enum: ["nomenclatural","taxonomic","article","personal","otu","thematic","other"]
description: >
Enumeration of kind of datasets
See https://api.catalogue.life/vocab/datasettype for the latest full list.
Decision:
- type: object
+ type: DataEntity
properties:
key:
type: integer
@@ -416,7 +351,7 @@ Decision:
type: integer
description: the catalogue the decision applies to
subject:
- type: NameRef
+ type: SimpleName
description: the name usage this decision is about
subjectDatasetKey:
type: integer
@@ -429,19 +364,28 @@ Decision:
description: the new status
required: false
name:
+ type: Name
+ description: the new scientific name object
+ required: false
+ extinct:
+ type: boolean
+ description: the new extinct flag
+ required: false
+ temporalRangeStart:
type: string
- description: the new scientific name
+ description: the new temporalRangeStart
required: false
- authorship:
+ temporalRangeEnd:
type: string
- description: the new authorship
+ description: the new temporalRangeEnd
required: false
- created:
- type: datetime
- description: datetime the decision was created
- deleted:
- type: datetime
- description: datetime the decision was deleted
+ lifezones:
+ type: LifezoneType[]
+ description: the new lifezones
+ required: false
+ note:
+ type: string
+ description: editorial notes
required: false
DecisionMode:
type: string
@@ -458,7 +402,7 @@ DecisionResultSet:
type: Decision[]
description: the resulting Decisions
Distribution:
- type: DatasetObject
+ type: [ DataEntity, DatasetObject ]
description: An area distribution record
properties:
area:
@@ -496,6 +440,11 @@ Error:
"status": 404,
"message": "Name 467324, version 7 not found"
}
+EstimateType:
+ type: string
+ enum: [DESCRIBED_SPECIES_LIVING, DESCRIBED_SPECIES_EXTINCT, ESTIMATED_SPECIES]
+ description: >
+ An enumeration of species estimate types
FrequencyType:
type: string
enum: ["never", "once", "daily", "weekly", "monthly", "yearly"]
@@ -616,6 +565,28 @@ IssueType:
Not all flagged issues are highlighting data problems. Some simply flag the fact that data was modified during imports,
for example "vernacular name transliterated" is added then a latin transliteration of a vernacular name was automatically generated.
See https://api.catalogue.life/vocab/issue for the latest full list.
+KingdomType:
+ type: string
+ enum: ["Animalia","Archaea","Bacteria","Chromista","Fungi","Plantae","Protozoa","Viruses"]
+ description: >
+ Enumeration of all kingdoms recognized in the Catalogue of Life.
+ See https://api.catalogue.life/vocab/kingdom
+LicenseType:
+ type: string
+ enum: ["cc0","cc by","cc by nc","unspecified"]
+ description: >
+ Enumeration of Creative Commons license types supported by the Clearinghouse.
+ See https://api.catalogue.life/vocab/license
+LifezoneType:
+ type: string
+ enum: ["brackish", "freshwater", "marine", "terrestrial"]
+ description: >
+ Coarse classification of the environment an organism lives in.
+ See https://api.catalogue.life/vocab/lifezone
+MatchType:
+ type: string
+ enum: ["exact", "variant", "inserted", "ambiguous", "none"]
+ description: Enumeration of the kind of matches possible.
NomCode:
type: string
enum: ["ICNP", "ICN", "ICNCP", "ICVCN", "ICZN"]
@@ -690,171 +661,8 @@ NomenclaturalStatusType:
unevaluated
: if the name status has not been evaluated yet
-
-NameType:
- type: string
- enum: ["scientific", "virus", "hybrid-formula", "cultivar", "otu", "placeholder", "none"]
- description: >
- Classification of names, mostly based on their syntactic structure.
- See https://api.catalogue.life/vocab/nametype
-NameRelationType:
- type: string
- enum: ["spelling correction","basionym","based on","replacement name","conserved","later homonym","superfluous","homotypic"]
- description: >
- Coarse classification of nomenclatural name relations.
- See https://api.catalogue.life/vocab/nomreltype
-
- spelling correction
- : The current name is a spelling correction, called emendation in zoology, of the related name having the same type.
- Intentional changes in the original spelling of an available name, whether justified or unjustified.
- The binomial authority remains unchanged.
- Valid emendations include changes made to correct:
- a) typographical errors in the original work describing the species,
- b) errors in transliteration from non-Latin languages,
- c) names that included diacritics, hyphens
- d) endings of species to match the gender of the generic name, particularly when the combination has been changed
-
- For example, Hieronima and Hyeronima are orthographical variants of Hieronyma.
- One of the spellings must be treated as the correct one. In this case, the spelling Hieronyma has been conserved
- and is to be used as the correct spelling.
-
- Botany (Article 61).: An inadvertent use of one of the other spellings has no consequences:
- the name is to be treated as if it were correctly spelled.
-
- Zoology (Art. 32-33 ): Orthographical variants in the formal sense do not exist;
- a misspelling or orthographic error is treated as a lapsus, a form of inadvertent error.
- The first reviser is allowed to choose one variant for mandatory further use, but in other ways,
- these errors generally have no further formal standing.
-
- basionym
- : The current name has a basionym and therefore is either
- a recombination (combinatio nova, comb. nov.) of the name pointed to
- (and the name pointed to is not, itself, a recombination),
- or a change in rank (status novus, stat. nov.).
-
- based on
- : The current name is the validation of a name that was not fully published before.
- Covers the use of ex in botanical author strings.
-
- ICN Art. 46.4: e.g. if this name object represents G. tomentosum Nutt. ex Seem.
- then the related name should be G. tomentosum Nutt.
-
- replacement name
- : Current name is replacement for the related name.
- Also called 'Nomen Novum' or 'avowed substitute'
- ICN: Article 7.3
- ICZN: Article 60.3.
-
- conserved
- : The current name or spelling is conserved / protected against the related name
- or the related name is suppressed / rejected in favor of the current name.
-
- A spelling which has been conserved relates two homotypic names, otherwise
- the related names should be based on different types.
-
- Based on an individual publication but more often
- due to actions of the ICZN or ICBN exercising its Plenary Powers.
-
- ICN: Conservation is covered under Article 14 and Appendix II and Appendix III (this name is nomina conservanda).
- ICZN: Reversal of precedence under Article 23.9 (this name is nomen protectum and the target name is nomen oblitum)
- or suppression via plenary power Article 81.
-
- later homonym
- : Current name has same spelling as related name
- but was published later and has priority over it (unless conserved or sanctioned)
- and is based on a different type. Called a junior homonym in zoology.
- This includes botanical parahomonyms which differ slightly in spelling
- but are similar enough that they are likely to be confused (Art 53.3).
- The zoological code has a set of spelling variations (article 58) that are considered to be identical.
- When acts of conservation or suppression have occurred then the terms 'Conserved Later Homonym'and 'Rejected Earlier Homonym' should be used.
- Two identical and homotypic names (isonyms) should be indicated with the superfluous relation type.
- ICN: Article 53
- ICZN: Chapter 12, Article 52.
-
- superfluous
- : Current name was superfluous at its time of publication,
- i. e. it was based on the same type as the related, previously published name (ICN article 52).
- The current, superfluous name is available but illegitimate.
- Includes the special case of isonyms which are identical names.
-
- homotypic
- : A relation indicating two homotypic names, i.e. objective or nomenclatural synonymy, but not further specifying why.
-LicenseType:
- type: string
- enum: ["cc0","cc by","cc by nc","unspecified"]
- description: >
- Enumeration of Creative Commons license types supported by the Clearinghouse.
- See https://api.catalogue.life/vocab/license
-LifezoneType:
- type: string
- enum: ["brackish", "freshwater", "marine", "terrestrial"]
- description: >
- Coarse classification of the environment an organism lives in.
- See https://api.catalogue.life/vocab/lifezone
-ReferenceTopicType:
- type: string
- enum: ["nomen", "taxon", "vernacular", "distribution"]
- description: >
- Enumeration of types of CoL relevant information that is treated in a publication
- See https://api.catalogue.life/vocab/gazetteer
-TaxonomicStatus:
- type: string
- enum: [ACCEPTED, PROVISIONALLY_ACCEPTED, SYNONYM, AMBIGUOUS_SYNONYM, MISAPPLIED]
- description: >
- The taxonomic status of an accepted taxon.
- For synonyms only a nomenclatural status is allowed.
-TaxonomicStatusType:
- type: string
- enum: ["accepted", "doubtful", "ambiguous synonym"]
- description: >
- Taxonomic status enumeration for both accepted taxa and synonyms.
- See https://api.catalogue.life/vocab/taxonomicstatus
-KingdomType:
- type: string
- enum: ["Animalia","Archaea","Bacteria","Chromista","Fungi","Plantae","Protozoa","Viruses"]
- description: >
- Enumeration of all kingdoms recognized in the Catalogue of Life.
- See https://api.catalogue.life/vocab/kingdom
-MatchType:
- type: string
- enum: ["exact", "variant", "inserted", "ambiguous", "none"]
- description: Enumeration of the kind of matches possible.
-OriginType:
- type: string
- enum: ["source", "denormed classification", "verbatim parent", "verbatim accepted","verbatim basionym",
- "proparte","autonym","implicit name","missing accepted","basionym placeholder","ex author synonym","name matching","other"]
- description: >
- Enumeration of the kind of matches possible.
- See https://api.catalogue.life/vocab/origin
-ResultSet:
- type: object
- description: >
- A paging resultset without the actual type specific result payload.
- properties:
- result:
- type: object[]
- description: Result page
- offset:
- type: integer
- description: >
- The offset applied during request.
- Can be less than requested if the limit is reached.
- limit:
- type: integer
- description: >
- The maximum number of records returned.
- Can be less than requested if the limit is reached.
- total:
- type: integer
- description: >
- The total number of records available.
-EstimateType:
- type: string
- enum: [DESCRIBED_SPECIES_LIVING, DESCRIBED_SPECIES_EXTINCT, ESTIMATED_SPECIES]
- description: >
- An enumeration of species estimate types
Name:
- type: VerbatimIdObject
+ type: [ DataEntity, VerbatimIdObject ]
description: |
A scientific name.
CoL deals and categorizes the following types of names:
@@ -1099,31 +907,8 @@ NameResultSet:
A paging resultset for Names.
properties:
result:
- type: Name[]
- description: the resulting names
-NameRef:
- type: object
- description: >
- A reference to a name based on ids and the name itself
- properties:
- id:
- type: string
- description: the names id within its dataset
- indexNameId:
- type: string
- description: the name id from the matching name index record
- required: false
- name:
- type: string
- description: the literal name
- authorship:
- type: string
- description: the literal, full authorship
- required: false
- rank:
- type: RankType
- description: the rank
- required: false
+ type: Name[]
+ description: the resulting names
NameRelation:
type: VerbatimKeyObject
description: A published act which affects the nomenclatural status of a scientific name or the typification of a nominal taxon.
@@ -1463,6 +1248,101 @@ NameSuggestResponse:
suggestions:
type: NameSuggestion[]
description: A list of suggestions matching the search phrase
+NameType:
+ type: string
+ enum: ["scientific", "virus", "hybrid-formula", "cultivar", "otu", "placeholder", "none"]
+ description: >
+ Classification of names, mostly based on their syntactic structure.
+ See https://api.catalogue.life/vocab/nametype
+NameRelationType:
+ type: string
+ enum: ["spelling correction","basionym","based on","replacement name","conserved","later homonym","superfluous","homotypic"]
+ description: >
+ Coarse classification of nomenclatural name relations.
+ See https://api.catalogue.life/vocab/nomreltype
+
+ spelling correction
+ : The current name is a spelling correction, called emendation in zoology, of the related name having the same type.
+ Intentional changes in the original spelling of an available name, whether justified or unjustified.
+ The binomial authority remains unchanged.
+ Valid emendations include changes made to correct:
+ a) typographical errors in the original work describing the species,
+ b) errors in transliteration from non-Latin languages,
+ c) names that included diacritics, hyphens
+ d) endings of species to match the gender of the generic name, particularly when the combination has been changed
+
+ For example, Hieronima and Hyeronima are orthographical variants of Hieronyma.
+ One of the spellings must be treated as the correct one. In this case, the spelling Hieronyma has been conserved
+ and is to be used as the correct spelling.
+
+ Botany (Article 61).: An inadvertent use of one of the other spellings has no consequences:
+ the name is to be treated as if it were correctly spelled.
+
+ Zoology (Art. 32-33 ): Orthographical variants in the formal sense do not exist;
+ a misspelling or orthographic error is treated as a lapsus, a form of inadvertent error.
+ The first reviser is allowed to choose one variant for mandatory further use, but in other ways,
+ these errors generally have no further formal standing.
+
+ basionym
+ : The current name has a basionym and therefore is either
+ a recombination (combinatio nova, comb. nov.) of the name pointed to
+ (and the name pointed to is not, itself, a recombination),
+ or a change in rank (status novus, stat. nov.).
+
+ based on
+ : The current name is the validation of a name that was not fully published before.
+ Covers the use of ex in botanical author strings.
+
+ ICN Art. 46.4: e.g. if this name object represents G. tomentosum Nutt. ex Seem.
+ then the related name should be G. tomentosum Nutt.
+
+ replacement name
+ : Current name is replacement for the related name.
+ Also called 'Nomen Novum' or 'avowed substitute'
+ ICN: Article 7.3
+ ICZN: Article 60.3.
+
+ conserved
+ : The current name or spelling is conserved / protected against the related name
+ or the related name is suppressed / rejected in favor of the current name.
+
+ A spelling which has been conserved relates two homotypic names, otherwise
+ the related names should be based on different types.
+
+ Based on an individual publication but more often
+ due to actions of the ICZN or ICBN exercising its Plenary Powers.
+
+ ICN: Conservation is covered under Article 14 and Appendix II and Appendix III (this name is nomina conservanda).
+ ICZN: Reversal of precedence under Article 23.9 (this name is nomen protectum and the target name is nomen oblitum)
+ or suppression via plenary power Article 81.
+
+ later homonym
+ : Current name has same spelling as related name
+ but was published later and has priority over it (unless conserved or sanctioned)
+ and is based on a different type. Called a junior homonym in zoology.
+ This includes botanical parahomonyms which differ slightly in spelling
+ but are similar enough that they are likely to be confused (Art 53.3).
+ The zoological code has a set of spelling variations (article 58) that are considered to be identical.
+ When acts of conservation or suppression have occurred then the terms 'Conserved Later Homonym'and 'Rejected Earlier Homonym' should be used.
+ Two identical and homotypic names (isonyms) should be indicated with the superfluous relation type.
+ ICN: Article 53
+ ICZN: Chapter 12, Article 52.
+
+ superfluous
+ : Current name was superfluous at its time of publication,
+ i. e. it was based on the same type as the related, previously published name (ICN article 52).
+ The current, superfluous name is available but illegitimate.
+ Includes the special case of isonyms which are identical names.
+
+ homotypic
+ : A relation indicating two homotypic names, i.e. objective or nomenclatural synonymy, but not further specifying why.
+OriginType:
+ type: string
+ enum: ["source", "denormed classification", "verbatim parent", "verbatim accepted","verbatim basionym",
+ "proparte","autonym","implicit name","missing accepted","basionym placeholder","ex author synonym","name matching","other"]
+ description: >
+ Enumeration of the how a record came to existance during an import into the Clearinghouse.
+ See https://api.catalogue.life/vocab/origin
Page:
description: |
A page used for requesting or responding to a pageable service.
@@ -1486,14 +1366,56 @@ Page:
limit:
type: integer
description: the number of records to display
-Rank:
+ReferenceTopicType:
+ type: string
+ enum: ["nomen", "taxon", "vernacular", "distribution"]
+ description: >
+ Enumeration of types of CoL relevant information that is treated in a publication
+ See https://api.catalogue.life/vocab/gazetteer
+ResultSet:
+ type: object
description: >
- An ordered taxonomic rank enumeration with the most frequently used values.
- See: https://api.catalogue.life/vocab/rank
+ A paging resultset without the actual type specific result payload.
+ properties:
+ result:
+ type: object[]
+ description: Result page
+ offset:
+ type: integer
+ description: >
+ The offset applied during request.
+ Can be less than requested if the limit is reached.
+ limit:
+ type: integer
+ description: >
+ The maximum number of records returned.
+ Can be less than requested if the limit is reached.
+ total:
+ type: integer
+ description: >
+ The total number of records available.
+RankType:
type: string
- enum: []
+ enum: ["domain","superkingdom","kingdom","subkingdom","infrakingdom","superphylum","phylum","subphylum","infraphylum","superclass","class","subclass","infraclass","parvclass","superlegion","legion","sublegion","infralegion","supercohort","cohort","subcohort","infracohort","magnorder","superorder","grandorder","order","suborder","infraorder","parvorder","superfamily","family","subfamily","infrafamily","supertribe","tribe","subtribe","infratribe","suprageneric name","genus","subgenus","infragenus","supersection","section","subsection","superseries","series","subseries","infrageneric name","species aggregate","species","infraspecific name","grex","subspecies","cultivar group","convariety","infrasubspecific name","proles","natio","aberration","morph","variety","subvariety","form","subform","pathovar","biovar","chemovar","morphovar","phagovar","serovar","chemoform","forma specialis","cultivar","strain","other","unranked"]
+ description: >
+ Enumeration of all possible rank values across all codes.
+ See https://api.catalogue.life/vocab/rank for the complete list in use
+
+ There is the need to deal with old ranks not accepted anymore.
+ The list given is intended to be interoperable between name providers for bacteria, viruses, fungi, plants, and animals.
+ The enumeration attempts to strike a balance between listing all possible rank terms, and remaining comprehensible.
+ Not included in the list are the botanical "notho-" ranks, which are used to designate hybrids (nothospecies, nothogenus) as this information is handled by the Name.notho property already.
+
+ Sources:
+
+ - [GBIF](https://github.com/gbif/gbif-api/blob/master/src/main/java/org/gbif/api/vocabulary/Rank.java)
+ - [TCS](https://github.com/tdwg/tcs/blob/master/TCS101/v101.xsd#L860)
+ - [TaxCat2](http://mansfeld.ipk-gatersleben.de/apex/f?p=185:78:::NO::P77_TAXCAT,P77_DB_CHECKBOX1,77_TAXCAT2RAD,77_SHOWRAD:%25,,0,s_All)
+ - [NOMEN](https://raw.githubusercontent.com/SpeciesFileGroup/nomen/master/src/ontology/nomen.owl)
+
+ TODO: extract all values from sources
Reference:
- type: VerbatimIdObject
+ type: [ DataEntity, VerbatimIdObject ]
description: |
A (literature) reference mostly given in [CSL-JSON](https://github.com/citation-style-language/schema#csl-json-schema).
A reference can be linked to a serial, e.g. a journal, that defines the content for the CSL container attributes.
@@ -1560,38 +1482,77 @@ ResultPage:
description: the size of the results
required: false
Sector:
- type: object
+ type: DataEntity
description: |
A taxonomic sector in the Catalogue of Life
properties:
key:
type: integer
description: primary key
- colSourceKey:
+ datasetKey:
+ type: integer
+ description: key to the catalogue dataset this sector is attached to
+ target:
+ type: SimpleName
+ description: attachement point in the catalogue
+ subjectDatasetKey:
+ type: integer
+ description: key to the source dataset this sector is attached to
+ subject:
+ type: SimpleName
+ description: root taxon of the sector in the source dataset
+ mode:
+ type: SectorMode
+ description: The mode a sector is attached to the catalogue.
+ code:
+ type: NomCodeType
+ description: The nomenclatural code to apply to all names in this sector
+ note:
+ type: string
+ description: Editorial notes
+SectorImport:
+ type: ImportMetrics
+ description: |
+ A sector import into assembly.
+ properties:
+ attempt:
+ type: integer
+ description: the number of attempts
+ state:
+ type: string
+ enum: ["waiting", "preparing", "copying", "deleting", "relinking", "indexing", "finished", "canceled", "failed"]
+ description: the current status of the sector sync
+ taxonCount:
+ type: integer
+ description: the number of taxa in the sector sync
+ type:
+ type: string
+ description: the type of sector sync
+ sectorKey:
+ type: integer
+ description: the sector ID
+ ignoredUsageCount:
type: integer
- description: key to the ColSource this sector originates from
- root:
- type: NameRef
- description: A reference to the single root taxon from the col source for this sector. Can even be a species, but usually some higher taxon.
- exclude:
- type: NameRef[]
- description: Optional list of taxa within the descendants of root to exclude from this sector definition
- attachment:
- type: NameRef
- description: The attachment point in the CoL tree, i.e. the CoL parent taxon for the sector root
- suppress:
- type: NameRef[]
description: |
- Optional list of CoL tree taxa that should be suppressed when this sector is attached.
- E.g. the CoL management classification might define an alternative taxonomy that uses
- different taxa which are covered by this sector already.
- created:
- type: datetime
- description: datetime the sector was created
- deleted:
- type: datetime
- description: datetime the sector was deleted
- required: false
+ The number of ignored scientific name usages, which could be explicitly blocked by a decision or
+ implicitly excluded (e.g., hybrid formulas, placeholders, no_names, etc).
+ usagesCount:
+ type: integer
+ description: the number of scientific name usages
+SectorMode:
+ description: >
+ The mode a sector is attached to the catalogue.
+ See: https://api.catalogue.life/vocab/sector$mode
+ type: string
+ enum: [attach, union, merge]
+SectorResultSet:
+ type: ResultSet
+ description: >
+ A paging resultset for Sectors.
+ properties:
+ result:
+ type: Sector[]
+ description: the resulting sectors
Serial:
type: DatasetObject
description: |
@@ -1670,35 +1631,6 @@ Serial:
"publisher-place": "Göttingen"
}
}
-SectorImport:
- type: ImportMetrics
- description: |
- A sector import into assembly.
- properties:
- attempt:
- type: integer
- description: the number of attempts
- state:
- type: string
- enum: ["waiting", "preparing", "copying", "deleting", "relinking", "indexing", "finished", "canceled", "failed"]
- description: the current status of the sector sync
- taxonCount:
- type: integer
- description: the number of taxa in the sector sync
- type:
- type: string
- description: the type of sector sync
- sectorKey:
- type: integer
- description: the sector ID
- ignoredUsageCount:
- type: integer
- description: |
- The number of ignored scientific name usages, which could be explicitly blocked by a decision or
- implicitly excluded (e.g., hybrid formulas, placeholders, no_names, etc).
- usagesCount:
- type: integer
- description: the number of scientific name usages
SerialResultSet:
type: ResultSet
description: >
@@ -1720,22 +1652,27 @@ SimpleName:
name:
type: string
description: the scientific name
+ authorship:
+ type: string
+ description: the scientific name authorship
+ required: false
rank:
- type: Rank
+ type: RankType
description: the taxonomic rank
code:
type: NomCodeType
description: the nomenclatural code
+ required: false
status:
type: TaxonomicStatus
description: the taxonomic status
required: false
parent:
type: string
- description: the parent
+ description: the scientific name of the parent
required: false
SpeciesEstimate:
- type: object
+ type: DataEntity
description: >
A class representing species estimates.
properties:
@@ -1771,7 +1708,7 @@ SpeciesEstimateResultSet:
type: SpeciesEstimate[]
description: the resulting SpeciesEstimates
Taxon:
- type: VerbatimIdObject
+ type: [ DataEntity, VerbatimIdObject ]
description: >
A taxon concept, i.e. an accepted name. Not used for synonyms.
properties:
@@ -1912,6 +1849,18 @@ TaxonInfo:
}
]
}
+TaxonomicStatus:
+ type: string
+ enum: [ACCEPTED, PROVISIONALLY_ACCEPTED, SYNONYM, AMBIGUOUS_SYNONYM, MISAPPLIED]
+ description: >
+ The taxonomic status of an accepted taxon.
+ For synonyms only a nomenclatural status is allowed.
+TaxonomicStatusType:
+ type: string
+ enum: ["accepted", "doubtful", "ambiguous synonym"]
+ description: >
+ Taxonomic status enumeration for both accepted taxa and synonyms.
+ See https://api.catalogue.life/vocab/taxonomicstatus
TaxonResultSet:
type: ResultSet
description: >
@@ -2027,24 +1976,4 @@ VernacularName:
description: the country given as 2 letter ISO codes
referenceIds:
type: string[]
- description: Links to references supporting the vernacular name record
-RankType:
- type: string
- enum: ["domain","superkingdom","kingdom","subkingdom","infrakingdom","superphylum","phylum","subphylum","infraphylum","superclass","class","subclass","infraclass","parvclass","superlegion","legion","sublegion","infralegion","supercohort","cohort","subcohort","infracohort","magnorder","superorder","grandorder","order","suborder","infraorder","parvorder","superfamily","family","subfamily","infrafamily","supertribe","tribe","subtribe","infratribe","suprageneric name","genus","subgenus","infragenus","supersection","section","subsection","superseries","series","subseries","infrageneric name","species aggregate","species","infraspecific name","grex","subspecies","cultivar group","convariety","infrasubspecific name","proles","natio","aberration","morph","variety","subvariety","form","subform","pathovar","biovar","chemovar","morphovar","phagovar","serovar","chemoform","forma specialis","cultivar","strain","other","unranked"]
- description: >
- Enumeration of all possible rank values across all codes.
- See https://api.catalogue.life/vocab/rank for the complete list in use
-
- There is the need to deal with old ranks not accepted anymore.
- The list given is intended to be interoperable between name providers for bacteria, viruses, fungi, plants, and animals.
- The enumeration attempts to strike a balance between listing all possible rank terms, and remaining comprehensible.
- Not included in the list are the botanical "notho-" ranks, which are used to designate hybrids (nothospecies, nothogenus) as this information is handled by the Name.notho property already.
-
- Sources:
-
- - [GBIF](https://github.com/gbif/gbif-api/blob/master/src/main/java/org/gbif/api/vocabulary/Rank.java)
- - [TCS](https://github.com/tdwg/tcs/blob/master/TCS101/v101.xsd#L860)
- - [TaxCat2](http://mansfeld.ipk-gatersleben.de/apex/f?p=185:78:::NO::P77_TAXCAT,P77_DB_CHECKBOX1,77_TAXCAT2RAD,77_SHOWRAD:%25,,0,s_All)
- - [NOMEN](https://raw.githubusercontent.com/SpeciesFileGroup/nomen/master/src/ontology/nomen.owl)
-
- TODO: extract all values from sources
\ No newline at end of file
+ description: Links to references supporting the vernacular name record
\ No newline at end of file