Difference between revisions of "Mandatory and recommended fields for sharing data with GGBN"

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(→‎Metadata of your DNA bank)
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=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.
 +
 +
<div id="wikinote">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.<br/>
 +
'''Red labelling means required for building a valid xml file.<br/>
 +
Asterisk (*) means mandatory for the DNA Bank Network.<br/>'''
 +
All metadata information should be in English! Please map a many fields as possible, the better your data in GBIF and the DNA Bank Network the better for other scientists and at the end for yourself!</div>
 +
 
=Metadata of your DNA bank=
 
=Metadata of your DNA bank=
 
{| border="1" width="60%"
 
{| border="1" width="60%"
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|-
 
|-
 
|ContentContact
 
|ContentContact
−
|Address
+
|*Address
 
|Complete Address of the responsible person
 
|Complete Address of the responsible person
 
|Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Koenigin-Luise-Str. 6-8, 14195 Berlin, Germany
 
|Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Koenigin-Luise-Str. 6-8, 14195 Berlin, Germany
 
|-
 
|-
 
|ContentContact
 
|ContentContact
−
|Email
+
|*Email
 
|valid email address; will be used by the web portal for sending you annotations etc.
 
|valid email address; will be used by the web portal for sending you annotations etc.
 
|please use @ instead of masquerades like "[at]"
 
|please use @ instead of masquerades like "[at]"
 
|-
 
|-
 
|ContentContact
 
|ContentContact
−
|<span style="color:red">Name</span>
+
|*<span style="color:red">Name</span>
 
|Person, person team responsible for curation of your DNA Bank
 
|Person, person team responsible for curation of your DNA Bank
 
|Dr. Birgit Gemeinholzer
 
|Dr. Birgit Gemeinholzer
 
|-
 
|-
 
|Description/Representation
 
|Description/Representation
−
|Details
+
|*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.''
 
|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.
 
|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
 
|Description/Representation
−
|<span style="color:red">@language</span>
+
|*<span style="color:red">@language</span>
 
|language of description
 
|language of description
 
|should be "en" as literal
 
|should be "en" as literal
 
|-
 
|-
 
|Description/Representation
 
|Description/Representation
−
|<span style="color:red">Title</span>
+
|*<span style="color:red">Title</span>
 
|Short title that describes your DNA collection
 
|Short title that describes your DNA collection
 
|DNA Bank of the Herbarium Berolinense
 
|DNA Bank of the Herbarium Berolinense
 
|-
 
|-
 
|IPRStatements/Citation
 
|IPRStatements/Citation
−
|Text
+
|*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).
 
|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
 
|IPRStatements/Citation
−
|<span style="color:red">@language</span>
+
|*<span style="color:red">@language</span>
 
|language of citation
 
|language of citation
 
|should be "en" as literal
 
|should be "en" as literal
 
|-
 
|-
 
|IPRStatements/Copyright
 
|IPRStatements/Copyright
−
|Text
+
|*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.
 
|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
 
|IPRStatements/Copyright
−
|<span style="color:red">@language</span>
+
|*<span style="color:red">@language</span>
 
|language of copyright
 
|language of copyright
 
|should be "en" as literal
 
|should be "en" as literal
 
|-
 
|-
 
|IPRStatements/TermsOfUse
 
|IPRStatements/TermsOfUse
−
|Text
+
|*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.
 
|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.
Line 68: Line 76:
 
|
 
|
 
|IconURI
 
|IconURI
−
|complete url path to the logo of your institution
+
|*complete url path to the logo of your institution
 
|
 
|
 
|-
 
|-
 
|Owner
 
|Owner
−
|Address
+
|*Address
 
|Complete Address of the institution that owns the DNA bank samples and data
 
|Complete Address of the institution that owns the DNA bank samples and data
 
|
 
|
 
|-
 
|-
 
|Owner/Representation
 
|Owner/Representation
−
|Text
+
|*Text
 
|name of your institution
 
|name of your institution
 
|Botanic Garden an Botanical Museum Berlin-Dahlem (Freie Universität Berlin)
 
|Botanic Garden an Botanical Museum Berlin-Dahlem (Freie Universität Berlin)
 
|-
 
|-
 
|Owner
 
|Owner
−
|URL
+
|*URL
 
|path to website of your institution
 
|path to website of your institution
 
|http://www.bgbm.org
 
|http://www.bgbm.org
Line 92: Line 100:
 
|-
 
|-
 
|TechnicalContact
 
|TechnicalContact
−
|Address
+
|*Address
 
|Complete Address of the responsible person
 
|Complete Address of the responsible person
 
|Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Koenigin-Luise-Str. 6-8, 14195 Berlin, Germany
 
|Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Koenigin-Luise-Str. 6-8, 14195 Berlin, Germany
 
|-
 
|-
 
|TechnichalContact
 
|TechnichalContact
−
|Email
+
|*Email
 
|valid email address; will be used by the web portal for sending you annotations etc.
 
|valid email address; will be used by the web portal for sending you annotations etc.
 
|please use @ instead of masquerades like "[at]"
 
|please use @ instead of masquerades like "[at]"
 
|-
 
|-
 
|TechnicalContact
 
|TechnicalContact
−
|<span style="color:red">Name</span>
+
|*<span style="color:red">Name</span>
 
|Person, person team responsible for technical issues of your database
 
|Person, person team responsible for technical issues of your database
 
|Gabriele Droege
 
|Gabriele Droege
 
|-
 
|-
 
|
 
|
−
|RecordBasis
+
|*RecordBasis
 
|this value must be part of the ABCD vocabulary
 
|this value must be part of the ABCD vocabulary
 
|must be "OtherSpecimen"
 
|must be "OtherSpecimen"
 
|-
 
|-
 
|
 
|
−
|<span style="color:red">SourceID</span>
+
|*<span style="color:red">SourceID</span>
 
|short description of relevant collection
 
|short description of relevant collection
 
|should be "DNA Bank"
 
|should be "DNA Bank"
 
|-
 
|-
 
|
 
|
−
|<span style="color:red">SourceInstitutionID</span>
+
|*<span style="color:red">SourceInstitutionID</span>
 
|short name/abbreviation of relevant institution
 
|short name/abbreviation of relevant institution
 
|BGBM
 
|BGBM
 +
|}
 +
 +
=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!'''
 +
 +
{| border="1" width="60%"
 +
! width="120px" | 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 and Identification of the voucher=
 +
{| border="1" width="60%"
 +
! width="120px" | 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
 +
|*UppaerValue
 +
|
 +
|e.g. 200
 +
|-
 +
|Gathering/Altitude
 +
|*Unit
 +
|
 +
|e.g. m
 
|}
 
|}

Revision as of 19:48, 9 February 2012

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.

All metadata information should be in English! Please map a many fields as possible, the better your data in GBIF and the DNA Bank Network the better for other scientists and at the end for yourself!

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 *Email 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
TechnichalContact *Email 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
*RecordBasis this value must be part of the ABCD vocabulary must be "OtherSpecimen"
*SourceID short description of relevant collection should be "DNA Bank"
*SourceInstitutionID short name/abbreviation of relevant institution BGBM

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 and Identification of the voucher

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 *UppaerValue e.g. 200
Gathering/Altitude *Unit e.g. m
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