Mandatory and recommended fields for sharing data with GGBN
From GGBN Wiki
Contents
Introduction
ABCD and ABCDDNA contain hundreds of elements. Some are mandatory. Further information about ABCDDNA and a complete Mapping example can be found here in the Wiki. The curator of the DNA Bank has to define the Metadata of the DNA Bank data first.
We have to differ between elements that are required to build a valid xml file, elements that are required for the DNA Bank Network, and further elements that are not essential. The following table contains only those elements required for providing your DNA data via the web portal of the DNA Bank Network.
Red labelling means required for building a valid xml file.
Asterisk (*) means mandatory for the DNA Bank Network.
Metadata of your DNA bank
| Group | Element | Remarks | Example |
|---|---|---|---|
| ContentContact | *Address | Complete Address of the responsible person | Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Koenigin-Luise-Str. 6-8, 14195 Berlin, Germany |
| ContentContact | valid email address; will be used by the web portal for sending you annotations etc. | please use @ instead of masquerades like "[at]" | |
| ContentContact | *Name | Person, person team responsible for curation of your DNA Bank | Dr. Birgit Gemeinholzer |
| Description/Representation | *Details | Short text to describe the focus and number of samples in your DNA collection. It must include the following phrase: The DNA bank is part of the DNA Bank Network which was established in spring 2007. The network was initiated by GBIF Germany and provides a technically optimized DNA collection service facility for all biological research accessible via one central web portal. The network promotes deposition of well documented reference DNA samples after project completion or data publication from scientists of other universities and institutions. | The DNA bank of the Botanic Garden and Botanical Museum Berlin-Dahlem holds currently a collection of 8200 plant DNA and tissue samples growing constantly. Its core collection focuses on the flora of the Berlin and Brandenburg but it also preserves DNA from the Alps, the Mediterranean and the Altai Mountains. |
| Description/Representation | *@language | language of description | should be "en" as literal |
| Description/Representation | *Title | Short title that describes your DNA collection | DNA Bank of the Herbarium Berolinense |
| IPRStatements/Citation | *Text | Droege, G., Zetzsche, H. & Gemeinholzer, B. (Ed.) 2008 - (continuously updated): DNA samples of the DNA bank at the BGBM (Botanic Garden and Botanical Museum Berlin-Dahlem). | |
| IPRStatements/Citation | *@language | language of citation | should be "en" as literal |
| IPRStatements/Copyright | *Text | The copyright for any material created by the DNA bank of the BGBM is reserved. The duplication or use of information and data such as texts or images is only permitted with the indication of the source or with prior approval by the BGBM. | |
| IPRStatements/Copyright | *@language | language of copyright | should be "en" as literal |
| IPRStatements/TermsOfUse | *Text | The use of the data is allowed only for non-profit scientific use and for non-profit nature conservation purpose. The data bases or part of it may only be used or copied by the written permission from the legal owner. | |
| IPRStatements/TermsOfUse | @language | language of the terms of use | should be "en" as literal |
| IconURI | *complete url path to the logo of your institution | ||
| Owner | *Address | Complete Address of the institution that owns the DNA bank samples and data | |
| Owner/Representation | *Text | name of your institution | Botanic Garden an Botanical Museum Berlin-Dahlem (Freie Universität Berlin) |
| Owner | *URL | path to website of your institution | http://www.bgbm.org |
| RevisionData | DateModified | date of last modification of your data | |
| TechnicalContact | *Address | Complete Address of the responsible person | Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Koenigin-Luise-Str. 6-8, 14195 Berlin, Germany |
| TechnicalContact | valid email address; will be used by the web portal for sending you annotations etc. | please use @ instead of masquerades like "[at]" | |
| TechnicalContact | *Name | Person, person team responsible for technical issues of your database | Gabriele Droege |
| Unit | *RecordBasis | this value must be part of the ABCD vocabulary | must be "OtherSpecimen" |
| Unit | *KindOfUnit | the type of DNA | e.g. gDNA |
Related Specimen Data
The voucher identifier
All specimen voucher information must be available via a GBIF compliant database! Both DiGIR and BioCASe specimen providers are possibe!
| Group | Element | Remarks | Example |
|---|---|---|---|
| Associations/UnitAssociation | *AssociatedUnitID | the UnitID or CatalogueNumber used for GBIF | e.g. the barcode number of your specimens |
| Associations/UnitAssociation | *AssociatedUnitSourceInstitutionID | the SourceInstitutionID or InstitutionCode used for GBIF | e.g. the acronym of your institution |
| Associations/UnitAssociation | *AssociatedUnitSourceID | 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 | *Comment | the wrapper url of the voucher record | e.g. "http://nhb-acsmith2.si.edu/emuwebvzbirdsweb/webservices/digir.php" |
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. Please note that DiGIR/DarwinCore is not able to deal with more than one determination! In opposite ABCD has many repeatable elements and can handle multiple determinations. For the DNA Bank Network we try to get all available information into the portal. So if you use DiGIR for your specimens you might think about switching to ABCD and BioCASe instead. It's the same with Multimedia urls. DarwinCore can provide only one url, ABCD provides as much urls as required.
| 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
In ABCD you have two ways of providing multimedia items, MultimediaObject mean for example digital scans of a herbarium sheet or a photograph of the living specimen. In the gathering container there is SiteImages which means images/sounds etc. of the place where the specimen has been collected. For the DNA mapping we need the image urls of the voucher only (they will be indexed) but if you want to provide also the SiteImages you are very welcome!
| Group | Element | Remarks | Example |
|---|---|---|---|
| MultiMediaObject | *FileURI | the complete path to your image; you can provide as much multimedia items as you want! |
DNA sample data
The DNA extension contains much more elements than presently in use. When we developed the schema we wanted to propose a standard for exchange of molecular data in general. The following fields are the most common in use, but feel free to map more!
| Group | Element | Remarks | Example |
|---|---|---|---|
| DNA/Amplification | AmplificationDate | date of amplification; if unknown or general without content you don't have to map it | should be ISO format yyyy-mm-dd |
| DNA/Amplification | *GeneticLocus | COX1 | |
| DNA/Amplification | *GenBankNumber | the accession number of NCBI/EMBL/DDBJ or the process ID of BOLD; this is a repeatable element, you can provide as much as you want | e.g. AJ45567 |
| DNA/Amplification | *GenBankNumber-URI | complete link to the accession number of NCBI/EMBL/DDBJ or the process ID of BOLD | |
| DNA/Amplification | ReferenceCitation | molecular publication related to this DNA sample | Citation format, free text |
| DNA/Amplification | ReferenceURI | if available link to online version | |
| DNA | *BlockedUntil | in case the DNA sample is blocked until a specific date it's nevertheless searchable but customers cannot order it | ISO format |
| DNA | *Concentration | map only if filled with content; concentration of the DNA | 65,34 |
| DNA | *@Unit | unit of the concentration | µg/ml |
| DNA | *ExtractionDate | date of DNA extraction | if unknown type "unknown" |
| DNA | *ExtractionMethod | extraction kit or protocoll | if unknown type "unknown" |
| DNA | *ExtractionStaff | extraction staff | if unknown type "unknown" |
| DNA | *Preservation | preservation of the tissue | if unknown type "unknown" |
| DNA | ProvidedBy | if someone provided the samples | |
| DNA | PurificationMethod | purification kit or protocoll | |
| DNA | Quality | quality of the sample | high, medium, low |
| DNA | *QualityCheckDate | date when quality parameters has been measured, e.g. Nanodrop etc. | ISO format |
| DNA | *RatioOfAbsorbance260_230 | map only if filled with conten | 1,2 |
| DNA | *RatioOfAbsorbance260_280 | map only if filled with conten | 1,8 |
| DNA | Tissue | type of tissue used for DNA extraction | e.g. leaf, blood, leg |
| Unit | Notes | Notes for the customer |
