Difference between revisions of "ABCD2Concepts"
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|A flag indicating that the accession is grown outdoors in the botanical garden. | |A flag indicating that the accession is grown outdoors in the botanical garden. | ||
| + | |- | ||
| + | |HybridFlag | ||
| + | | x | ||
| + | |Indicates the type of hybrid (if appropriate), according to | ||
| + | * no hybrid: <empty> | ||
| + | * named hybrid: x | ||
| + | * graft chimaera: + | ||
| + | * any other type of hybrid: "hybrid" | ||
| + | gardens4science providers should also see the notes below. | ||
|- | |- | ||
|IPEN | |IPEN | ||
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|} | |} | ||
| − | '''Note for | + | '''Note for gardens4Science data providers:''' |
| + | # Whether or not a given record will be visible in the public view of the [http://gardens4science.biocase.org gardens4science data portal] (that is, without being logged in) is determined by the value of the ''DonorCategory'' field: Records "O = other" will be visible only for logged-in curators; if the field is filled with "I = individual" or empty, the record will also show up for unregistered users. | ||
| + | # Use ''HybridFlag'' in addition to the correct [https://www.bgci.org/files/Databases/itf2.pdf nomenclature of hybrid or graft chimera names] in ''fullScientificName'' (e.g. ''xDisoselenicereus fulgidus (Hook.f.) E.Meier''; ''Epiphyllum x floribundum Kimnach''; ''+Crataegomespilus potsdamiensis''; ''Echinopsis hybrid''). The https://terms.tdwg.org/wiki/abcd2:TaxonIdentified-HybridFlag-@insertionpoint does not need to be mapped/filled and can be ignored (value will be taken from ''fullScientificName''). | ||
===SpecimenUnit/Accessions=== | ===SpecimenUnit/Accessions=== | ||
Latest revision as of 16:17, 5 February 2021
This page provides an overview of the most commonly used ABCD elements with short explanations and sample values. If you're looking for a complete list of ABCD elements, please refer to the full documentation at the ABCD Wiki.
Mandatory fields are marked with an asterisk. If you don't provide them, the element - and potentially non-mandatory sibling/parental elements - will be removed from the ABCD document.
Contents
Metadata
Metadata describe the dataset as whole - as opposed to individual specimens/observations.
General metadata
| Group | Element | Example | Remark |
|---|---|---|---|
| ContentContact* | Name* | John Doe | Contact information for the curator of the dataset. |
| Address | Botanic Garden and Botanical Museum Berlin. Königin-Luise-Str. 6-8; 14195 Berlin, Germany | ||
| john.doe@acme.com | |||
| Phone | +49 30 838 99999 | ||
| TechnicalContact* | Name* | John Doe | Contact information of the person that is responsible for the BioCASe installation - in most cases, this will be the IT department. |
| Address | Botanic Garden and Botanical Museum Berlin. Königin-Luise-Str. 6-8; 14195 Berlin, Germany | ||
| john.doe@acme.com | |||
| Phone | +49 30 838 99999 | ||
| Metadata | IconURI | http://ww3.bgbm.org/providerResources/BGBM.jpg | Link to an image that represents the dataset. |
| Metadata/RevisionData* | DateCreated | 2018-07-19 | Date when the dataset has been first published (DateCreated) and of the last changes/additions/removals (DateModified). |
| DateModified* | 2018-09-27 | ||
| Metadata/Version | DateIssued | 2018-09-27 | If you keep track of dataset versions, the info can be specified in this section. |
| Major* | 3 | ||
| Minor | 1 | ||
| Metadata/Description/Representation* | Title* | Herbarium Berolinense | Short description of the dataset (preferrably in english), consisting of a title, a 2-3 sentences long description and an optional URL. |
| @language* | en | ||
| Description | The herbarium of the Botanic Garden and Botanical Museum Berlin-Dahlem (herbarium acronym: B) is ... | ||
| URL | https://www.bgbm.org/en/herbarium | ||
| Metadata/Owners/Owner | Addresses/Address | Botanic Garden and Botanical Museum Berlin. Königin-Luise-Str. 6-8; 14195 Berlin, Germany | Institution that owns the dataset. |
| EmailAddresses/EmailAddress | john.doe@acme.com | ||
| TelephoneNumbers/TelephoneNumber | +49 30 838 99999 | ||
| URIs/URL | https://www.bgbm.org | ||
| LogoURI | http://ww3.bgbm.org/providerResources/BGBM.jpg | ||
| Organisation/Name/Representation/Text* | Botanic Garden and Botanical Museum Berlin-Dahlem | ||
| Organisation/Name/Representation/Abbrevation | BGBM |
IPR Statements
The section Metadata/IPRStatements contains several sub-sections that allow to provide IPR (intellectual property rights) statements. Each sub-section contains the mandatory element Text for the statement and the optional elements Details and URI for delivering more details and/or a link to a web page mit more information. The seven sections are as follows:
| Section | Example | Remark |
|---|---|---|
| Acknowledgements | The project was funded by the German Federal Ministry of Education and Research (BMBF) | A free text acknowledging support for the dataset (e.g. grant money, help, permission to reuse published material, etc.). |
| Citation | Röpert D. (ed.) 2000+ [continuously updated]: Digital specimen images at the Herbarium Berolinense. - Published at http://ww2.bgbm.org/herbarium/default.cfm [accessed dd Mmm yyyy]. | Citation guidline for using the data in publications. |
| Disclaimer | No responsibility is accepted for the accuracy of the information in this database. | A disclaimer statement for the dataset (e. g. concerning responsibility for data quality or legal implications). |
| License | Creative Commons 1.0 Public Domain Dedication waiver | The license for using the data; we suggest one of the Creative Commons licenses that can be found at here. |
| TermsOfUse | Textual metadata on specimens from the Herbarium Berolinense (B) are released under the Creative Commons 1.0 Public Domain Dedication waiver. | Terms for using the published data. |
Note: If you publish your data to GBIF, you are required to specify a license in the License node with the language attribute and the elements Text and URI. The latter should contain a link to a well-defined license, for example https://creativecommons.org/publicdomain/zero/1.0/. More details on GBIF licensing can be found here.
Specimen Data
In ACBD terminology, a single specimen/observation is called a Unit; for each specimen, one Units/Unit will be created. Below you'll find the most commonly used ABCD elements in this sub-tree.
General unit data
| ABCD element | Example | Remark |
|---|---|---|
| SourceID* | Herbarium Berolinense | The name or code of the data source. |
| SourceInstitutionID* | B | The unique identifier (code or name) of the institution holding the original data source. |
| UnitID* | B -W 08738 -01 0 | A unique identifier for the unit record within the data source. |
| UnitGUID | http://herbarium.bgbm.org/object/BW08738010 | A globally unique identifier for the unit record. |
| CollectorsFieldNumber | 765/10 | The original number assigned to the unit by the collector or observer. |
| RecordBasis | LivingSpecimen | An indication of what the unit record describes; needs to comply with a controlled vocabulary. |
| KindOfUnit | Seed; (whole) plant | Part(s), physical state, or class of materials represented by this specimen. |
| Sex | Male | Sex of the unit. |
| RecordURI | http://herbarium.bgbm.org/object/BW08738010 | The web address of the page where more information on this particular unit record can be found. |
| Notes | Specimen examined in a review of the genera of the tribe Eupatorieae, R. M. King & H. Robinson 1968-1969 | A free text description of the unit. Any notes that do not fit elsewhere. |
| DateLastEdited | 2009-030-7 | The date of the creation of or last change to this unit record. |
| LastEditor | John Doe | The name or other indication of the person or team that created or last edited this record. |
Gathering event
The Gathering subsection of ABCD covers all details about the gathering site and the gathering agents. All the follwing groups and elements are located in Units/Unit/Gathering.
| Group | Element | Example | Remark |
|---|---|---|---|
| Agents | GatheringAgentsText | Scholz, Sipman | A free text representation or concatenated version of those responsible for collecting or recording. In case of a gathering team, it is advised not to provide a concatenated text of the collectors, but individual gathering agents (see below). |
| GatheringAgent/AgentText | Sipman | Name of an individual gathering agent. The element GatheringAgent is repeatable, so it can be provided several times in case of a gathering team. | |
| Altitude | MeasurementOrFactText | 1500-1600m | Use this element if you have the altitude stored as a free text, that is as a single, concatenated text. If the boundaries of a range are stored as separate values in your database, use the MeasurementOrFactAtomised elements below. |
| MeasurementOrFactAtomised/LowerValue* | 1500 | The lower or only value of the gathering site altitude. | |
| MeasurementOrFactAtomised/UpperValue | 1600 | The upper value for the measured gathering site altitude, if there is a range. | |
| MeasurementOrFactAtomised/UnitOfMeasurement | m | The unit of measurement used to measure the gathering site altitude. | |
| Country | ISO3166Code | US | ISO code of the country where the voucher was collected/observed. |
| Name* | United States of America | Name of the gathering country. | |
| DateTime | DateText | August 2012 | Date when voucher was collected if it doesn't conform to a specific date format and is stored just as a freet text. |
| ISODateTimeBegin | 2012-08-17 | Gathering date in ISO format. If you want to provide a time span, this will be the start of the time span. | |
| ISODateTimeEnd | 2012-08-19 | End datetime (in ISO format) if the gathering covers a time span. | |
| LocalityText | Landkreis Neustrelitz, Feldberger Seengebiet, Carwitz, ca. 1 km SW von Carwitz. | The original gathering locality data as appearing on a label or in an original entry, as a text string. This field should be transcribed verbatim from the specimen label. | |
| NamedArea | AreaName | Europe | Any geographic term that is neither a country (use Country element) nor the exact locality description (use LocalityText). |
| AreaClass | Continent | Type of geographic term provided in AreaName | |
| Biotope | Text | Amongst rocks and stones, calcareous soil and screes | Gathering site biotope description. |
| - | AreaDetail | A free text description of further details pertaining to the observation, sampling, or collection locality which which did not fit into the one of the other elements. | |
| SiteCoordinateSets/ SiteCoordinates/ CoordinatesLatLong | ../CoordinateMethod | Inferred map reference | Method of coordinates determination (GPS vs. inferred from description). |
| LatitudeDecimal | 52.49179 | Latitude in decimal degrees. | |
| LongitudeDecimal | 13.23589 | Longitude in decimal degreed. | |
| CoordinatesText | 52°30' N 13°23' E | An alternative concatenated text representation of the lat/lon coordinates if they can't be provided as separate lat/lon values. | |
| SpatialDatum | WGS 84 | A mathematical surface on which the mapping and coordinate system used for the geocodes of the gathering site are based. | |
| CoordinateErrorDistanceInMeters | 500 | An estimate of how tightly the collecting locality was specified, expressed as a distance in meters corresponding to a radius around the lat/long coordinates. | |
| AccuracyStatement | Coordinates rounded to 2 decimal places. | A free text statement of the degree of accuracy of the latitude and longitude coordinates. | |
| CoordinateErrorMethod | Maximum error defined by dimensions of original ordinance survey map. | Verbatim statement of how the Coordinate Error was determined. | |
| - | Notes | Further text relating to the gathering event that does not fit one of the specified elements. |
Identification history
Most specimen databases record the complete determination or identification history of a single specimen. ABCD allows to provide this complete history; each determination becomes an Identifications/Identification subtree.
| Group | Subgroup | Element | Example | Remark |
|---|---|---|---|---|
| - | - | PreferredFlag | 1 | The currently preferred determination should be marked with 1 or True, historic determinations with 0 or False. |
| Date | - | DateText/ISODateTimeBegin | 2018-08-17 | Date of the unit identification event. If in ISO format, use ISODateTimeBegin, DateText otherwise. |
| Identifiers | - | IdentifiersText | Humboldt & Bonpland | Text indicating the person, person team, or organisation that made the identification. If it is a team, individual Identifier subtrees should be provided, if possible (see below). |
| Identifier/PersonName | FullName | Humboldt | Person that made the identification. | |
| Result/TaxonIdentified | HigherTaxa/HigherTaxon | HigherTaxonName* | Asteraceae | Name of the higher taxon. Please have a look at the BioCASE Wiki for how to prepare your database for the repeatable elements |
| HigherTaxonRank | familia | Rame of the higher taxon. | ||
| ScientificName | FullScientificNameString* | Aaronsohnia factorovskyi Warb. & Eig. var. factorovskyi | Complete name of the taxon including Authors (and years for animals). | |
| ScientificName/NameAtomised/Botanical | GenusOrMonomial | Aaronsohnia | ABCD has several container for NameAtomised, it depens on your sampes which one to choose (Botanical or Zoology etc.) | |
| FirstEpithet | factorovskyi | |||
| InfraspecificEpithet | factorovskyi | |||
| Rank | var. | |||
| AuthorTeam | Warb. & Eig. | |||
| - | NameComments | Free text comments related to the name identified for the unit. | ||
| References/Reference | - | TitleCitation | Ralfs, J: The British Desmidieae, London 1848 | A reference (e.g. an article or monograph) that was used as the base for the identifier's taxon identification (e.g. by means of providing a key or a description of the taxon). |
| CitationDetail | p. 22 + 226, 35 pl. | |||
| - | - | Notes | Invalid publication as: Echinella rotata Greville in W.J. Hooker 1833: British Flora Vol II, pp. 432, London, p.398 | Supplementary remarks about the unit identification. |
Botanical Garden Unit
| ABCD element | Example | Remark |
|---|---|---|
| AccessionStatus | C | The current status of the accession in the garden. Possible values are
|
| Cultivation | Allows for cultivation information to be passed as free text in order to help the receiving garden care for the transferred accession or to record the garden's experience made with this accession. | |
| DonorCategory | E | A code to indicate the type of the immediate donor from which the accession was obtained. This may not necessarily be the original collector of wild material. One or more of the following characters: E, G, B, R, S, U, H, M, N, I, O, U. For a description of these values, please refer to https://www.bgci.org/files/Databases/itf2.pdf, section E.5 (donor type flag). Gardens4Science data providers should also see the note below. |
| Hardiness | 1 | A flag indicating that the accession is grown outdoors in the botanical garden. |
| HybridFlag | x | Indicates the type of hybrid (if appropriate), according to
gardens4science providers should also see the notes below. |
| IPEN | XX-0-HEID-3253 | A unique number given to plant materials accessioned in conformance with the rules of the International Plant Exchange Network. |
| LocationInGarden | MD4 | The current location of the living plant in the botanical garden. |
| Perennation | A code to indicate the means of perennation. | |
| PlantingDate | 2007-07-07 | The date in ISO format the plant was planted at its current location in the botanical garden. |
Note for gardens4Science data providers:
- Whether or not a given record will be visible in the public view of the gardens4science data portal (that is, without being logged in) is determined by the value of the DonorCategory field: Records "O = other" will be visible only for logged-in curators; if the field is filled with "I = individual" or empty, the record will also show up for unregistered users.
- Use HybridFlag in addition to the correct nomenclature of hybrid or graft chimera names in fullScientificName (e.g. xDisoselenicereus fulgidus (Hook.f.) E.Meier; Epiphyllum x floribundum Kimnach; +Crataegomespilus potsdamiensis; Echinopsis hybrid). The https://terms.tdwg.org/wiki/abcd2:TaxonIdentified-HybridFlag-@insertionpoint does not need to be mapped/filled and can be ignored (value will be taken from fullScientificName).
SpecimenUnit/Accessions
| ABCD element | Example | Remark |
|---|---|---|
| AccessionCatalogue | Identifier of an accessions catalogue or numbering scheme | |
| AccessionDate | 2007-07-07 | Date on which the accession was recorded |
| AccessionNumber | 001010680 | Institutional number applied to an accession and recorded in the accessions register. |
Multimedia
For providing links to associated images, videos and sounds, the sub-tree MultimediaObjects can be used. Each ABCD unit can have multiple multimedia objects, each represented by its own MultimediaObject with the following elements:
| ABCD element | Example | Remark |
|---|---|---|
| FileURI* | http://ww2.bgbm.org/herbarium/images/B/-W/14/61/B_-W_14616%20-00%200.jpg | The Universal Resource Identifier (URI) of the underlying multimedia file. |
| ProductURI | http://ww2.bgbm.org/herbarium/view_biocase.cfm?SpecimenPK=726 | The Universal Resource Identifier of an electronic source of a multimedia object including HTML, Javascript or similar means delivering rendered output. |
| Comment | Image of herbarium specimen E00732880 by Specimen Digitisation Pipeline. | Short description of the multimedia object. |
| Format | image/jpeg | A code or descriptive term for the file or object format. |
| FileSize | 2365 | The size in Kb of the file referred to by the URI or filename for the multimedia object. |
| Creator | Paris, Museum National d'Histoire Naturelle, OD | The identifier (e.g. name or other id) of personnel who has taken the image. |
| CreatedDate | 2012-07-07 | The date the multimedia object was created. |
| ID | 22658 | Identifier for the multimedia object relating to or forming the unit. This may be a filename. |
| IPR | Intellectual Property Rights relating specifically to the multimedia object. This subtree has the same elements as Metadata/IPRStatements. Fore more details, see the respective remarks. |
