ABCD2Concepts
From BioCASe Provider Software
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.
General metadata
| Group | Element | Example | Remarks |
|---|---|---|---|
| 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 99999999 | ||
| 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 99999999 | ||
| 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 99999999 | ||
| 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. |
Specimen Data
In ACBD terminology, a specimen 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 | 1055 | The original number assigned to the unit by the collector or observer. |
| RecordBasis | PreservedSpecimen | An indication of what the unit record describes; needs to comply with a coontrolled vocabulary. |
| KindOfUnit | 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. |
Related Specimen Data
All specimen voucher information must be available via a GBIF compliant database! Both Darwin Core-Archive and BioCASE specimen providers are possibe! To provide the underlying specimen data you can use your existing GBIF dataset mapping.
File:Relationships.jpg
In the database and the mapping the child record should refer to its mother record in opposite to the real world example
The voucher identifiers
| Group | Element | Remarks | Example |
|---|---|---|---|
| Associations/UnitAssociation | *UnitID | the UnitID or CatalogueNumber used for GBIF | e.g. the barcode number of your specimens |
| Associations/UnitAssociation | *SourceInstitutionID | the SourceInstitutionID or InstitutionCode used for GBIF | e.g. the acronym of your institution |
| Associations/UnitAssociation | *SourceName | the SourceID or CollectionCode used for GBIF | e.g. the name of the collection where the specimen belongs to, e.g. "Birds" |
| Associations/UnitAssociation | *AssociationType | the Relation between the DNA and the voucher | e.g. "DNA and voucher from same individual" |
| Associations/UnitAssociation | *DatasetAccessPoint | the wrapper url of the voucher record | e.g. "http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=Herbar" |
Gathering event of the voucher
All elements marked with * will be indexed and must be mapped! Mapping these gathering facts twice (one for the specimen database and one for the DNA mapping) is required because of indexing and later search purposes.
| Group | Element | Remarks | Example |
|---|---|---|---|
| *CollectorsFieldNumber | the number the collector gave to the specimen in the field, often used in Botany but not in Zoology; map it if you have content | e.g. 765/10 | |
| Gathering/Agents/GatheringAgent | *FullName | the Collector or Collector Team | e.g. Scholz & Sipman |
| Gathering/Altitude | *LowerValue | if you have both the lower and upper value in different columns map both field, if not map LowerValue only | e.g. 100 |
| Gathering/Altitude | UpperValue | e.g. 200 | |
| Gathering/Altitude | *Unit | e.g. m | |
| Gathering/Country | *ISO3166Code | ISO code of the country where the voucher was collected | e.g. US |
| Gathering/Country | *Name | english Name of the country | e.g. United States of America |
| Gathering/DateTime | *DateText | date when voucher was collected, if you have content yuo can also use ISO format | e.g. 21. April 1951 |
| Gathering/Locality | *LocalityText | e.g. 5km NO Berlin | |
| Gathering/NamedArea | AreaName | name of continent | e.g. Europe |
| Gathering/NamedArea | @language | language of the name of continent | e.g. "en" |
| Gathering/SiteCoordinates | *LatitudeDecimal | e.g. -15,88876 | |
| Gathering/SiteCoordinates | *LongitudeDecimal | e.g. 72,88876 |
Identification history of the voucher
Mostly specimen databases record the complete determination or identification history of a single specimen. For GGBN we try to get all available information into the portal.
| Group | Element | Remarks | Example |
|---|---|---|---|
| Identification | *PreferredFlag | mark the presently preferred Identification | e.g. true, false, 0, 1 |
| Identification/HigherTaxon | *HigherTaxonName | the name of the higher taxon, please have a look at the BioCASE Wiki for how to prepare your database for the repeatable elements | e.g. Asteraceae, Animalia |
| Identification/HigherTaxon | *HigherTaxonRank | the rank of the taxon in english or latin | e.g. familia, regnum, phylum |
| Identification/ScientificName | *FullScientificName | the complete name of the taxon including Authors (and years for animals) | e.g. Aaronsohnia factorovskyi Warb. & Eig. var. factorovskyi |
| Identification/ScientificName/NameAtomised | *FirstEpithet | Please note: ABCD has several container for NameAtomised, it depens on your sampes which one to choose (Botanical or Zoology etc.) | e.g. factorovskyi |
| Identification/ScientificName/NameAtomised | *GenusOrMonomial | e.g. Aaronsohnia | |
| Identification/ScientificName/NameAtomised | *InfraspecificEpithet | Please note: ABCD has several container for NameAtomised, it depens on your sampes which one to choose (Botanical or Zoology etc.) | e.g. factorovskyi |
| Identification/ScientificName/NameAtomised | *Rank | Please note: ABCD has several container for NameAtomised, it depens on your sampes which one to choose (Botanical or Zoology etc.) | e.g. var. |
Multimedia items of the voucher
These should be mapped in the specimen mapping, not the DNA mapping.
| Category | Element | Discription | Comment |
|---|---|---|---|
| Metadata | Title | ||
| IPR | |||
| TechnicalContact | |||
| Unit | UnitID |
