Difference between revisions of "ABCD2Concepts"
From BioCASe Provider Software
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| − | == | + | ==Specimen Data== |
| + | In ACBD terminology, a specimen is called a ''Unit''. For each specimen, one ''Units/Unit'' will be created. | ||
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===The sample identifiers=== | ===The sample identifiers=== | ||
We use identifier the same way as GBIF does. In addition to the traditional triple ID (see below) you can also provide the GUID. '''Please note that UnitID should be unique in one database!''' Mostly the extraction number is used for it. | We use identifier the same way as GBIF does. In addition to the traditional triple ID (see below) you can also provide the GUID. '''Please note that UnitID should be unique in one database!''' Mostly the extraction number is used for it. | ||
Revision as of 14:45, 27 September 2018
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) | |
| 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. | |
| 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.
The sample identifiers
We use identifier the same way as GBIF does. In addition to the traditional triple ID (see below) you can also provide the GUID. Please note that UnitID should be unique in one database! Mostly the extraction number is used for it.
| Group | Element | Remarks | Example |
|---|---|---|---|
| Unit | *SourceID | short description of relevant collection | should be "DNA Bank" or "tissue collection" |
| Unit | *SourceInstitutionID | short name/abbreviation of relevant institution | BGBM |
| Unit | *UnitID | DNA extraction number or tissue number | DNA 123 |
| Unit | UnitGUID | sample record GUID | f6c7fd5a-2f04-4dcb-ba38-0230bf196d30 |
GGBN terms
The following fields are highly recommended, some are mandatory (marked with *), but feel free to map more!
Please have a look at the GGBN Data Standard documentation where all GGBN terms are described in detail. The table below is just listing the most important ones. Since the Nagoya Protocol has come into force we higly recommend to map the Permit fields. They will become mandatory for providing data to GGBN at the end of 2020. Until then all core members must have implemented the required fields in their databases.
| Group | Element | Remarks | Example |
|---|---|---|---|
| *RecordBasis | The specific nature of the data record, controlled vocabulary! | "PreservedSpecimen", "MaterialSample", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation"; for Tissue or DNA samples use "MaterialSample" | |
| *materialSampleType | Classification of kind of physical sample in addition to BasisOfRecord/RecordBasis and Preparation Type | "tissue", "DNA", "specimen" | |
| SpecimenUnit/Preparation | *preparationType | description of type of material, free text | or DNA: gDNA, eDNA, aDNA; for tissues/specimens: leaf, muscle, leg, blood |
| SpecimenUnit/Preparation | *preparationDate | date of DNA extraction | if unknown type "unknown" |
| SpecimenUnit/Preparation | *preparatioMaterials | extraction kit or protocoll | if unknown type "unknown" |
| SpecimenUnit/Preparation | *preparedBy | extraction staff | if unknown type "unknown" |
| SpecimenUnit/Preservation | preservation | preservation of the tissue or DNA | if unknown type "unknown" |
| SpecimenUnit/Loan/Permit | *permitStatus | Information about the presence, absence or other basic status of permits associated with the sample(s), controlled vocabulary! | Permit available, Permit not required, Permit not available, Unknown Material collected after 2014-10-12 cannot be in "Unknown" permit status! |
| SpecimenUnit/Loan/Permit | *permitStatusQualifier | Description of why a certain permit was not required or why Permit Status is unknown | "no national requirement for a permit at date of access", "officially authorized illegal holder", "collected on private land", "pre-Nagoya" |
| SpecimenUnit/Loan/Permit | *permitType | A permit is a document that allows someone to take an action that otherwise would not be allowed, controlled vocabulary! | Collecting Permit, Import Permit, Export Permit, Intellectual Property Rights, Copyright, Patent, Data use, Phytosanitary, Salvage, Exemption Permit, Material Transfer Agreement, Internationally Recognized Certificate of Compliance, Contract, Memorandum of Understanding, Memorandum of Cooperation, Veterinary Certificate, Human Pathogens, Genetically Modified Organism, Other |
| SpecimenUnit/Loan/Permit | *permitText | The text of a permit related to the gathering/shipping or further details | |
| GGBN/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 |
| GGBN/Amplification | marker | COX1 | |
| GGBN/Amplification | geneticAccessionNumber | 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 |
| GGBN/Amplification | genBankNumber-URI | complete link to the accession number of NCBI/EMBL/DDBJ or the process ID of BOLD | |
| SpecimenUnit | blockedUntil | in case the sample is blocked until a specific date it's nevertheless searchable but customers cannot order it | ISO format |
| SpecimenUnit | blocked | sample is blocked (e.g. because it is consumed), but data are still available | Yes/No |
| GGBN | concentration | concentration of the DNA | 65,34 |
| GGBN | @unit | unit of the concentration | µg/ml |
| GGBN | ratioOfAbsorbance260_230 | map only if filled with content | 1,2 |
| GGBN | ratioOfAbsorbance260_280 | map only if filled with content | 1,8 |
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 |
