The recommended exchange format for data to and from the CoL Clearinghouse is a tabular text format with a fixed set of files and columns.
The format is a single ZIP archive that bundles various delimited text files described below together with a metadata.yaml file providing basic metadata about the entire dataset. Each file holds records for the same class of things shown in this diagram:
The ColDP format was developed to overcome limitations existing in currently used formats for sharing taxonomic information, namely Darwin Core Archives and the Catalogue of Life submission format also known as ACEF (Annual Checklist Exchange Format). Darwin Core Archives and ACEF could still be used for exchanging data to and from the Catalogue of Life clearinghouse, but the COLDP format will support the most features. The following table provides an overview of different features supported in each of the 3 formats:
| Feature | ACEF | DwC-A | ColDP |
|---|---|---|---|
| Linnean classification (KPCOFG) | x | x | x |
| Extended Linnean classification (subranks) | - | - | x |
| Flexible Parent-child classification | - | x | x |
| Unrestricted ranks | - | x | x |
| Higher taxon details | - | x | x |
| Infraspecific taxa | x | x | x |
| Nested infraspecific taxa | - | x | x |
| Basionyms | - | x | x |
| Synonyms | x | x | x |
| Synonyms for higher taxa | - | x | x |
| Name identifier | - | x | x |
| Nomenclatural status | x | x | x |
| Fossils/extinction flags | x | x | x |
| Name & taxon separation | - | - | x |
| Structured references | x | - | x |
| Nomenclatural relations | - | - | x |
| Type species | - | x | x |
| Type specimen | - | x | * |
| Taxon concepts | - | x | x |
| Taxon concept relations | - | x | * |
| Vernacular names | x | x | x |
| Structured distributions | x | x | x |
| Taxon descriptions | - | x | x |
| Multimedia metadata | - | x | x |
x= supported-= not supported*= not yet supported but expected soon
The filename for an entity in the above diagram is a case insensitive version of the class name, any number of ignored hyphens or underscores and a known tabular text suffix. The suffix specifies one of the two supported tabular flavours, comma separated or tab separated files:
csv: a comma separated, optionally quoted CSV file as per RFC 4180tsv,tabortxt: indicates a tab seperated file without quoting
Valid examples are Taxon.tsv or vernacular-name.csv
It is recommended to place all data files in a subfolder called data, but having them on the root level is allowed.
All files should be encoded in UTF-8.
- metadata.yaml
- Name
- NameRel
- Taxon
- Synonym
- Reference
- Reference JSON-CSL
- Reference BIBTEX
- Description
- Distribution
- Media
- VernacularName
A YAML file with metadata about the entire dataset should be included. The file consists mostly of key value pairs, see the comments in metadata.yaml for all available keys. Additional entries to the YAML file is allowed to express non standard properties.
All data files should contain a header row that specifies the name of the columns as given below. In the absence of a header row it is expected that all columns exist in the exact order given below. With headers given it is allowed to share additional columns which are not part of the standard as listed below.
See NAMES.md for examples and rationales.
Unique name identifier that is referred to elsewhere via nameID.
Required scientific name excluding the authorship
Authorship of the scientificName
type: rank enum
The rank of the name preferrably given in case insensitive english. The recommended vocabulary is included in rank_enum.
The genus part of a bi/trinomial
The infrageneric epithet in case of bi/trinomials. In zoological names often the subgenus.
The specific epithet in case of bi/trinomials.
The infraspecific epithet in case of bi/trinomials.
The name of the cultivar for name governed by the cultivar code.
An optional, unrestricted, lose phrase appended to the name which is not covered by the existing attributes with strict semantics. Can be used for bacterial strain names or temporary placeholder names for unpublished species.
A referenceID pointing to the Reference table indicating the original publication of the name in its given combination
The exact page number within the referenced reference that the original publication of the name in its given combination starts.
The effective year the name was published.
type: code enum
The nomenclatural code the name falls under.
type: boolean If true indicates an original name, i.e. a protonym/basionym. False for all subsequent combinations.
type: code enum
The broad nomenclatural status of the name. For the exact status note, e.g. nomen nudum, the remarks field should additionally be used
A link to a webpage provided by the source depicting the name.
Additional nomenclatural remarks about the name. Often indicating its status or relevant rules in the code.
A directed nomenclatural name relation. See NAMES.md#name-relations for examples.
The name this relation originates from.
The name this relation relates to.
type: enum
The kind of directed relation.
The reference or nomenclatural act where this nomenclatural relation was established.
Remarks about the relation.
An accepted name with a taxonomic classification given either as a parent-child relation or as a flat, denormalized record.
Unique taxon identifier that is referred to elsewhere via taxonID.
The direct parent in the classification. This is the preferred way of exchanging a hierarchy and takes precedence over any classification given in the denormalized fields.
Pointer to the accepted name referring to an existing Name.ID within this data package.
A comma concatenated list of reference IDs supporting the taxonomic concept. Each ID must refer to an existing Reference.ID within this data package.
type: boolean
A flag indicating that the taxon is only provisionally accepted and should be handled with care.
The latest scrutinizer who reviewed the taxonomic concept. In case of multiple scrutinizers concatenate their names with a semicolon.
An identifier for the latest scrutinizer who reviewed the taxonomic concept. Recommended are ORCID identifier which can be used inside DOI metadata of the CoL. In case of multiple scrutinizers concatenate the ORCIDs with a semicolon in the same order as the scrutinizers above.
type: ISO8601 date
The date when the taxonomic concept was last reviewed.
type: boolean
Nullable flag indicating that the taxon is extinct (true) or extant (false). This includes species that died out very recently.
type: enum
Earliest appearance of the taxon in the geological time scale. Recommended values are geochronological names from the official International Commission on Stratigraphy (ICS).
type: enum
Latest appearance of the taxon in the geological time scale. Recommended values are geochronological names from the official International Commission on Stratigraphy (ICS).
type: enum[] A comma delimited list of lifezones this taxon is known to exist in.
A link to a webpage provided by the source depicting the taxon.
Any further taxonomic remarks.
The species binomial the taxon is classified in. If parentID is given this field is ignored.
The (botanical) section the taxon is classified in. Considered a botanical rank below subgenus, not a zoological above family. If parentID is given this field is ignored.
The subgenus the taxon is classified in. If parentID is given this field is ignored.
The genus the taxon is classified in. If parentID is given this field is ignored.
The subtribe the taxon is classified in. If parentID is given this field is ignored.
The tribe the taxon is classified in. If parentID is given this field is ignored.
The subfamily the taxon is classified in. If parentID is given this field is ignored.
The family the taxon is classified in. If parentID is given this field is ignored.
The superfamily the taxon is classified in. If parentID is given this field is ignored.
The suborder the taxon is classified in. If parentID is given this field is ignored.
The order the taxon is classified in. If parentID is given this field is ignored.
The subclass the taxon is classified in. If parentID is given this field is ignored.
The class the taxon is classified in. If parentID is given this field is ignored.
The subphylum the taxon is classified in. If parentID is given this field is ignored.
The phylum the taxon is classified in. If parentID is given this field is ignored.
The kingdom the taxon is classified in. If parentID is given this field is ignored.
A synonymous name for a taxon. Note that the same name can be linked to mulitple taxa by having several Synonym records to model pro parte synonyms.
Pointer to the synonymous name referring to an existing Name.ID within this data package.
Pointer to the taxon that this synonym is used for. For pro parte synonyms with multiple accepted names several synonym records sharing the same name but having different taxonIDs should be created. Refers to an existing Taxon.ID within this data package.
type: enum
The kind of synonym. One of synonym, ambiguous synonym or misapplied.
A comma concatenated list of reference IDs supporting the synonym status of the name. Each ID must refer to an existing Reference.ID within this data package.
Taxonomic remarks
Structured bibliographic references with a unique id to refer to from other entities. References can be given in 3 ways of different degree of atomization that are not mutually exclusive. The main reference file contains a full citation and 4 Dublin Core based properties that are also used in ACEF.
The local identifier for the reference as used in publishedIn and other fields.
Full bibliographic citation as one single string as an alternative to the rest of the more structured fields. If individual fields are given the full citation can be ignored.
The author(s) of the work. If multiple authors use a style that can safely be parsed. Recommended is to list authors by comma and prefix their surname with initials. If a comma is used to separate surname, firstname please use a semicolon to delimit individual authors.
The title of the work. In case of journal articles the article title, not the journal itself.
The year of the publication.
The title of the journal or book the work was published in. The source should exclude volume, edition, pages and other specifics.
All details to locate the work within the source, sometimes also referred to as collation. That can include journal volume, edition, pages, pointer to illustrations or anything else.
The DOI of the reference
A URL link to the reference
Additional comments about the reference.
In addition to the main reference file a reference.json file can be added to provide a JSON array of highly structured references
in the CSL-JSON format, e.g. as provided by CrossRef:
curl --location --silent --header "Accept: application/vnd.citationstyles.csl+json" https://doi.org/10.1126/science.169.3946.635
The id field in each record of the array must correspond to a Reference record with the same ID in the CSV file.
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"publisher":"Oxford University Press (OUP)",
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"content-type":"unspecified",
"content-version":"vor",
"intended-application":"similarity-checking"
}
],
"deposited":{
"date-parts":[
[
2017,
8,
25
]
],
"date-time":"2017-08-25T02:23:14Z",
"timestamp":1503627794000
},
"score":1.0,
"subtitle":[
],
"short-title":[
],
"issued":{
"date-parts":[
[
2016
]
]
},
"references-count":46,
"alternative-id":[
"10.1093\/database\/baw125"
],
"URL":"http:\/\/dx.doi.org\/10.1093\/database\/baw125",
"relation":{
"cites":[
]
},
"ISSN":[
"1758-0463"
],
"container-title-short":"Database"
},
{
"indexed":{
"date-parts":[
[
2019,
2,
16
]
],
"date-time":"2019-02-16T05:39:49Z",
"timestamp":1550295589144
},
"reference-count":0,
"publisher":"American Association for the Advancement of Science (AAAS)",
"issue":"3946",
"content-domain":{
"domain":[
],
"crossmark-restriction":false
},
"published-print":{
"date-parts":[
[
1970,
8,
14
]
]
},
"DOI":"10.1126\/science.169.3946.635",
"type":"article-journal",
"created":{
"date-parts":[
[
2006,
10,
5
]
],
"date-time":"2006-10-05T12:56:56Z",
"timestamp":1160053016000
},
"page":"635-641",
"source":"Crossref",
"is-referenced-by-count":61,
"title":"The Structure of Ordinary Water: New data and interpretations are yielding new insights into this fascinating substance",
"prefix":"10.1126",
"volume":"169",
"author":[
{
"given":"H. S.",
"family":"Frank",
"sequence":"first",
"affiliation":[
]
}
],
"member":"221",
"container-title":"Science",
"original-title":[
],
"language":"en",
"link":[
{
"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1126\/science.169.3946.635",
"content-type":"unspecified",
"content-version":"vor",
"intended-application":"similarity-checking"
}
],
"deposited":{
"date-parts":[
[
2016,
12,
23
]
],
"date-time":"2016-12-23T19:54:07Z",
"timestamp":1482522847000
},
"score":1.0,
"subtitle":[
],
"short-title":[
],
"issued":{
"date-parts":[
[
1970,
8,
14
]
]
},
"references-count":0,
"journal-issue":{
"published-print":{
"date-parts":[
[
1970,
8,
14
]
]
},
"issue":"3946"
},
"URL":"http:\/\/dx.doi.org\/10.1126\/science.169.3946.635",
"relation":{
},
"ISSN":[
"0036-8075",
"1095-9203"
],
"container-title-short":"Science"
}
]
Alternatively to CSL-JSON a BibTex file reference.bib can be given to provide highly structured citations.
The id field following the curly opening bracket must correspond to a record ID from the reference.csv file.
@article{Droege_2016,
title={The Global Genome Biodiversity Network (GGBN) Data Standard specification},
volume={2016},
ISSN={1758-0463},
url={http://dx.doi.org/10.1093/database/baw125},
DOI={10.1093/database/baw125},
journal={Database},
publisher={Oxford University Press (OUP)},
author={Droege, G. and Barker, K. and Seberg, O. and Coddington, J. and Benson, E. and Berendsohn, W. G. and Bunk, B. and Butler, C. and Cawsey, E. M. and Deck, J. and et al.},
year={2016},
pages={baw125}
}
@article{Frank_1970,
title = {The Structure of Ordinary Water: New data and interpretations are yielding new insights into this fascinating substance},
volume = {169},
ISSN = {1095-9203},
url = {http://dx.doi.org/10.1126/science.169.3946.635},
DOI = {10.1126/science.169.3946.635},
number = {3946},
journal = {Science},
publisher = {American Association for the Advancement of Science (AAAS)},
author = {Frank, H. S.},
year = {1970},
month = {Aug},
pages = {635–641}
}
Pointer to the taxon referring to an existing Taxon.ID within this data package.
The category the description text is about. Ideally derived from a shared, controlled vocabulary such as TDWG SPM InfoItems or GBIF Description Types.
type: enum The format the description text is given in. One of plain text, markdown or html.
A descriptive, human readable text about the given category in the declared format.
ISO 3 letter code
Pointer to the reference that is the source of this description. Refers to an existing Reference.ID within this data package.
A structured distribution record for a taxon in a given area.
Pointer to the taxon referring to an existing Taxon.ID within this data package.
The geographic area this distribution record is about.
type: enum
The geographic gazetteer the area is defined in.
type: enum Distribution status.
Pointer to the reference that supports this distribution. Refers to an existing Reference.ID within this data package.
Multimedia items for a taxon such as an image, audio or video.
Pointer to the taxon referring to an existing Taxon.ID within this data package.
The URL that resolves to the media item itself, not a webpage that depicts it.
The MIME-type of the media item the url identifies.
Preferrably the full type/subtype combination, e.g image/jpeg, but the primary type alone is sufficient (image, video, audio).
Optional title for the item.
type: ISO8601 date Date the media item was recorded.
Author of the media item.
type: license
Optional webpage from the source this media item is shown on.
A vernacular or common name for a taxon.
Pointer to the taxon referring to an existing Taxon.ID within this data package.
The vernacular name in the original script.
An optional transliteration of the verncular name into the latin script.
Language of the vernacular name given as an ISO 639 3 letter code.
Country this vernacular name is used in given as an ISO 3166 2 letter code.
Optional area desribing the geographic use of the vernacular name in free text within the given country
Optional life stage of the organism this vernacular name is restricted to.
type: enum
Optional sex of the organism this vernacular name is restricted to.
Pointer to the reference that supports this vernacular name. Refers to an existing Reference.ID within this data package.