GGBN Wiki - User contributions [en]

Data Privacy

2015-12-08T14:11:51Z

Patricia Kelbert:

<div id="wikinote">
*If the opportunity for the input of personal or business data (email addresses, name, addresses) is given, the input of these data takes place voluntarily. The use and payment of all offered services are permitted - if and so far technically possible and reasonable - without specification of any personal data or under specification of anonymized data or an alias.
*GGBN servers are maintained by the Freie Universität Berlin, Botanic Garden and Botanical Museum Berlin-Dahlem and underlie German and European law. See [[Imprint]] for more information.
*GGBN.org uses open source products only.</div>

'''The following components within the GGBN platform include the opportunity to input personal or business data:'''

=GGBN Data Portal=
Login with username and password is required to order samples. GGBN records business data (your email address, name and institutional address). If you don't want to input your business data you must contact the institutions via email.

The GGBN Portal Software is developed as open source software by the team of the Botanic Garden and Botanical Museum Berlin-Dahlem. More information can be found soon at http://wiki.bgbm.org/gps

Documents shared via GGBN Data Portal are open access documents or documents without copyright license only.

=GGBN Registry=
Login with username and password is required to create or update institutional metadata such as name of institution, address, metadata about its collection. GGBN Registry uses the Natural Collection Toolkit.

=GGBN Conference System=
Login with username and password is required to register for the GGBN conference. GGBN records business data (your email address, name and institutional address as well as your abstract and title of presentation). If you don't want to input your business data you must contact GGBN via email (conference@ggbn.org). The conference system uses the [https://pkp.sfu.ca/ocs/ Open Conference System] as software.

=GGBN Wiki=
Login is restricted to the GGBN general secretariat and GGBN technical secretariat only. GGBN records username and password. The GGBN wiki uses [https://www.mediawiki.org MediaWiki] as software. All changes made by registered users are logged.

=Web Analytics=
Like most website operators, ggbn.org collects non-personally-identifying information of the sort that web browsers and servers typically make available, such as the browser type, language preference, referring site, and the date and time of each visitor request. GGBN.org’s purpose in collecting non-personally identifying information is to better understand how GGBN.org’s visitors use its website. From time to time, GGBN may release non-personally-identifying information in the aggregate, e.g., by publishing a report on trends in the usage of its website.

GGBN.org also collects potentially personally-identifying information like Internet Protocol (IP) addresses. Piwik.org does not use such information to identify its visitors, however, and does not disclose such information, other than under the same circumstances that it uses and discloses personally-identifying information, as described below.

GGBN uses [http://www.piwik.org Piwik] for analyzing its website visits.

<div id="wikinote">Note: You can opt-out tracking here: http://data.ggbn.org/ggbn_portal/site/cookies</div>

=Maps=
GGBN.org uses [http://www.openstreetmap.org OpenStreetMap] to display all of its maps.

Collection Data Form

2015-11-20T09:25:09Z

Patricia Kelbert:

The most time consuming part always is data cleaning. We developed a powerful little helper for standardised data recording in the field, lab or office. The Collection Data Form (CDF) is an EXCEL file and contains several Macros for data handling and label printing.

Please feel free to download the new Version 1.11. You have to unpack the zip-file, which includes all required files. Some of our partners have included the CDF in their own workflows. It's an easy way to import lot of standardised data into specimen databases.

<div id="wikinote">New users should read the instructions for enabling Macros in EXCEL.</div>

=Customised views=
When you open the Collection Data form you will see some buttons in the top left corner. By hitting the buttons you can switch between the views. You can even create your own customised view. Just enter an "x" in first row of the columns that you want to see.

=Label printing=
So far label printing is done for Botanists, since size of labels for zoological samples are much more divers.

=Download=
[http://www.dnabank-network.org/downloads/collectiondataform_V1.11.zip Version 1.11]
<br>
[http://www.dnabank-network.org/downloads/collectiondataform_V1.10.zip Version 1.10]<br>
Version 1.7, outdated

Collection Data Form

2015-11-20T09:24:52Z

Patricia Kelbert: /* Download */

The most time consuming part always is data cleaning. We developed a powerful little helper for standardised data recording in the field, lab or office. The Collection Data Form (CDF) is an EXCEL file and contains several Macros for data handling and label printing.

Please feel free to download the new Version 1.7. You have to unpack the zip-file, which includes all required files. Some of our partners have included the CDF in their own workflows. It's an easy way to import lot of standardised data into specimen databases.

<div id="wikinote">New users should read the instructions for enabling Macros in EXCEL.</div>

=Customised views=
When you open the Collection Data form you will see some buttons in the top left corner. By hitting the buttons you can switch between the views. You can even create your own customised view. Just enter an "x" in first row of the columns that you want to see.

=Label printing=
So far label printing is done for Botanists, since size of labels for zoological samples are much more divers.

=Download=
[http://www.dnabank-network.org/downloads/collectiondataform_V1.11.zip Version 1.11]
<br>
[http://www.dnabank-network.org/downloads/collectiondataform_V1.10.zip Version 1.10]<br>
Version 1.7, outdated

Collection Data Form

2015-11-20T09:23:15Z

Patricia Kelbert: /* Download */

The most time consuming part always is data cleaning. We developed a powerful little helper for standardised data recording in the field, lab or office. The Collection Data Form (CDF) is an EXCEL file and contains several Macros for data handling and label printing.

Please feel free to download the new Version 1.7. You have to unpack the zip-file, which includes all required files. Some of our partners have included the CDF in their own workflows. It's an easy way to import lot of standardised data into specimen databases.

<div id="wikinote">New users should read the instructions for enabling Macros in EXCEL.</div>

=Customised views=
When you open the Collection Data form you will see some buttons in the top left corner. By hitting the buttons you can switch between the views. You can even create your own customised view. Just enter an "x" in first row of the columns that you want to see.

=Label printing=
So far label printing is done for Botanists, since size of labels for zoological samples are much more divers.

=Download=
[http://www.dnabank-network.org/downloads/collectiondataform_V1.7.zip Version 1.11]
<br>
[http://www.dnabank-network.org/downloads/collectiondataform_V1.7.zip Version 1.7, outdated]

How to search for material

2015-11-11T15:14:49Z

Patricia Kelbert: /* 4: indexation with SOLR */

<div id="wikinote"> '''This page is currently under construction (Nov 2015)!''' </div>

In general you can use three options to search our data portal:

1. Browse Taxonomy
2. Search by Fields
3. Search by Citation

=Browse Taxonomy [http://data.ggbn.org/CoL.php]=
[[File:Navi-Browse Taxonomy.JPG|thumb|100px]]
The GGBN/DNA Bank Network's Data Portal makes currently use of the Catalogue of Life (CoL) as its main taxonomic backbone. We match family and genus of original records provided by our partners with the CoL annual checklist (version 2009). Selecting [XXX "Browse Taxonomy"] leads you to our Taxonomic Backbone site (figure below).

This site gives you an overview on how many samples and taxa are online available for certain higher taxa and genera (taxa and sample counts bracketed). By clicking on "Show DNA samples" you will be redirected to a query that gives you all records for selected taxon.

Furthermore you can click on the little plus icon to see the next level of taxa.

[[File:CoL-Start1.JPG|500px]]

=Search by Fields [http://data.ggbn.org/Query.php]=
[[File:Navi-Data Portal.JPG|thumb|100px]]
The main query form for the data portal can be found at "Search & Preorder". Here you can choose a lot of criteria to filter your results. The upper part contains parameters related to the underlying voucher and collection event and the lower part contains facts about the DNA samples. If you select for example a certain DNA bank you can browse it's whole DNA and tissue collection.

The NCBI Taxonomy ID is often used by the microorganismic community. Right now search does not include synonyms, but will do in the future. Many records are provided with multiple determinations (their determination history). We index all determinations and you can search for all of them. Suggestion lists will help you when entering Family name or Species name.

Furthermore we filter collection year as well as Seas and Oceans out of the raw data. Seas/Oceans and Countries are matched with an existing list, so that also countries like "England" will be recognized as United Kingdom for instance.

We also index related Sequence Accession Numbers (BOLD and GenBank/EMBL/DDBJ) to be available for search.

==Dependent parameters==
Some parameters are related to each other, e.g. if you select a Continent or an Ocean, the list of Countries or Seas respectively will be reduced to those belonging to the selected Continent/Ocean.
The same happens for Family name and Species name/Taxonomy ID. If you select a Family name, the list of suggested Species names and Taxonomy IDs is reduced to the relevant ones.

[[File:Queryform.JPG|600px]]

==Getting results==
After clicking on "Search" you will receive a hitlist with 50 records per page. The column heading contain small arrows. Clicking on such an arrow will arrange the results in the new order. The green arrow marks the current order (in the figure ordered by Species name from A to Z). The hitlist contains the species name, the country where the specimen/sample was collected, the DNA number as well as the specimen/voucher number. Clicking on the small magnifier or the species name will give you the record details.

<div id="wikinote">Some samples doesn't have a DNA number. This means that DNA was not extracted yet but can be ordered on-demand.</div>

[[File:Hitlist-portal.JPG|600px]]

==Retrieving details==
The single record details page is a synoptic virtual dataset combined from at least 2 different sources (DNA sample and voucher). The upper part contains information on the physical DNA sample as well as links to published sequences and papers. The lower part contains the underlying specimen information, sometimes associated vouchers are also listed (e.g. duplum in another collection, cultivated/captivated individuals). GGBN encourages its partners to provide digital images of the vouchers as well. Due to several reasons (e.g. size of the organism) this can not always be realized easily.

[[File:RecordDetail.jpg|600px]]

==Pre-order samples==
Login is required for pre-ordering samples. When you are logged in you can select the required samples (checkboxes on the right) and click on "Add selected DNA/Tissue samples to shopping cart" on top right.
Some samples are blocked for the ordering process and marked with a big red X.
[[File:Hitlist-portal-shop.JPG|600px]]
===Shopping Cart===
After putting samples into the shopping cart on top of the website appears the message "Your shopping cart contains xy samples". Clicking on "Show details" will open you shopping cart and will guide you through the pre-ordering process.
[[File:ShoppingCart1.JPG|600px]]

The Shopping cart gives you an overview of your selected DNA/tissue samples. Here you can delete samples from your cart or by clicking on the taxon name see the record details again. Click on "Continue Pre-Order (->Step 2/3)" to continue.
[[File:ShoppingCart2.JPG|600px]]

The next steps orders the samples by institutions/DNA banks. In the example below you see that the selected samples are deposited at BGBM and DSMZ. You can check your invoice and delivery address and add some notes if you want. When clicking on "Finish Pre-Order (->Step 3/3) your pre-order will be forwarded to the DNA bank(s) in authority of requested samples. Every DNA bank only receives its relevant order information. Subsequently a confirmation email will be send to you by the DNA bank(s) in question. An offer including binding prices will than be made within a separate email.

[[File:ShoppingCart3.jpg|600px]]

=Search by Citation [http://library.ggbn.org]=
The prototype of the GGBN Document Library contains more than 4400 papers citing either DNA and Tissue samples or vouchers that are provided via the GGBN/DNA Bank Network Data Portal. Therefore a lot of non-molecular papers can be found here. The publications are provided in citation format with every voucher and DNA record. You can search for a DNA or Specimen Number, a certain DNA Bank, publication years or free text within citations.
[[File:Library1.JPG|600px]]

The resulting hitlist contains 50 records per page and is ordered by publication year (from lower to upper). By clicking on a DNA number you will directed to the record details.
[[File:Library2.JPG|600px]]

=Technical informations=
==1: harvesting and indexing==
Data is harvested and indexed using B-HIT (http://wiki.bgbm.org/bhit/). B-HIT is a harvesting and indexing toolkit, based on the GBIF-HIT software.<BR>
[[File:bhit.png|500px]]

The records(or units) can be harvested from providers having either a BioCASe or an IPT installation. For BioCASe providers, the schema ABCD 2.06, ABCD 2.1, ABCDDNA, ABCDGGBN and ABCDEFG are supported (single records or ABCD Archives). For IPT providers, DarwinCore Archives are supported. Elements that are indexed are listed under http://wiki.bgbm.org/bhit/index.php/Indexed_fields.

==2: data quality==
Data quality tests are done using B-HIT. Country names are translated in English, ISO codes are compared to the country names, coordinates are validated and checked again both ISO code and country name. In case of incomplete data, the tool is looking into the namedareas and localities and tries to extract some information regarding the country or the water body.

Scientific names are parsed using the GBIF Name Parser (http://www.gbif.org/developer/species#parser) and custom regular expressions.

==3: backbone==
Every single name is compared to the GBIF Backbone, the Catalog of Life Backbone, and the NCBI Backbone. Higher taxa, synonyms and accepted taxa are retrieved, using the GBIF Checklistbank webservice (http://api.gbif.org/v1/species).

The "Prokaryotic Nomenclature Up-to-Date API" (http://bacdive.dsmz.de/api/pnu/) is used for bacterial names.

==4: indexation with SOLR==
SOLR is used to indexed all fields that are searchable in the portal. It makes it possible to perform fast searches (case-sensitive or case-insensitive), search within several fields simulteanously for a value etc.

How to search for material

2015-11-11T10:21:26Z

Patricia Kelbert: /* Technical informations */

How to search for material

2015-11-11T09:36:17Z

Patricia Kelbert: /* Third step: backbone */

<div id="wikinote"> '''This page is currently under construction (Nov 2015)!''' </div>

In general you can use three options to search our data portal:

1. Browse Taxonomy
2. Search by Fields
3. Search by Citation

=Browse Taxonomy [http://data.ggbn.org/CoL.php]=
[[File:Navi-Browse Taxonomy.JPG|thumb|100px]]
The GGBN/DNA Bank Network's Data Portal makes currently use of the Catalogue of Life (CoL) as its main taxonomic backbone. We match family and genus of original records provided by our partners with the CoL annual checklist (version 2009). Selecting [XXX "Browse Taxonomy"] leads you to our Taxonomic Backbone site (figure below).

This site gives you an overview on how many samples and taxa are online available for certain higher taxa and genera (taxa and sample counts bracketed). By clicking on "Show DNA samples" you will be redirected to a query that gives you all records for selected taxon.

Furthermore you can click on the little plus icon to see the next level of taxa.

[[File:CoL-Start1.JPG|500px]]

=Search by Fields [http://data.ggbn.org/Query.php]=
[[File:Navi-Data Portal.JPG|thumb|100px]]
The main query form for the data portal can be found at "Search & Preorder". Here you can choose a lot of criteria to filter your results. The upper part contains parameters related to the underlying voucher and collection event and the lower part contains facts about the DNA samples. If you select for example a certain DNA bank you can browse it's whole DNA and tissue collection.

The NCBI Taxonomy ID is often used by the microorganismic community. Right now search does not include synonyms, but will do in the future. Many records are provided with multiple determinations (their determination history). We index all determinations and you can search for all of them. Suggestion lists will help you when entering Family name or Species name.

Furthermore we filter collection year as well as Seas and Oceans out of the raw data. Seas/Oceans and Countries are matched with an existing list, so that also countries like "England" will be recognized as United Kingdom for instance.

We also index related Sequence Accession Numbers (BOLD and GenBank/EMBL/DDBJ) to be available for search.

==Dependent parameters==
Some parameters are related to each other, e.g. if you select a Continent or an Ocean, the list of Countries or Seas respectively will be reduced to those belonging to the selected Continent/Ocean.
The same happens for Family name and Species name/Taxonomy ID. If you select a Family name, the list of suggested Species names and Taxonomy IDs is reduced to the relevant ones.

[[File:Queryform.JPG|600px]]

==Getting results==
After clicking on "Search" you will receive a hitlist with 50 records per page. The column heading contain small arrows. Clicking on such an arrow will arrange the results in the new order. The green arrow marks the current order (in the figure ordered by Species name from A to Z). The hitlist contains the species name, the country where the specimen/sample was collected, the DNA number as well as the specimen/voucher number. Clicking on the small magnifier or the species name will give you the record details.

<div id="wikinote">Some samples doesn't have a DNA number. This means that DNA was not extracted yet but can be ordered on-demand.</div>

[[File:Hitlist-portal.JPG|600px]]

==Retrieving details==
The single record details page is a synoptic virtual dataset combined from at least 2 different sources (DNA sample and voucher). The upper part contains information on the physical DNA sample as well as links to published sequences and papers. The lower part contains the underlying specimen information, sometimes associated vouchers are also listed (e.g. duplum in another collection, cultivated/captivated individuals). GGBN encourages its partners to provide digital images of the vouchers as well. Due to several reasons (e.g. size of the organism) this can not always be realized easily.

[[File:RecordDetail.jpg|600px]]

==Pre-order samples==
Login is required for pre-ordering samples. When you are logged in you can select the required samples (checkboxes on the right) and click on "Add selected DNA/Tissue samples to shopping cart" on top right.
Some samples are blocked for the ordering process and marked with a big red X.
[[File:Hitlist-portal-shop.JPG|600px]]
===Shopping Cart===
After putting samples into the shopping cart on top of the website appears the message "Your shopping cart contains xy samples". Clicking on "Show details" will open you shopping cart and will guide you through the pre-ordering process.
[[File:ShoppingCart1.JPG|600px]]

The Shopping cart gives you an overview of your selected DNA/tissue samples. Here you can delete samples from your cart or by clicking on the taxon name see the record details again. Click on "Continue Pre-Order (->Step 2/3)" to continue.
[[File:ShoppingCart2.JPG|600px]]

The next steps orders the samples by institutions/DNA banks. In the example below you see that the selected samples are deposited at BGBM and DSMZ. You can check your invoice and delivery address and add some notes if you want. When clicking on "Finish Pre-Order (->Step 3/3) your pre-order will be forwarded to the DNA bank(s) in authority of requested samples. Every DNA bank only receives its relevant order information. Subsequently a confirmation email will be send to you by the DNA bank(s) in question. An offer including binding prices will than be made within a separate email.

[[File:ShoppingCart3.jpg|600px]]

=Search by Citation [http://library.ggbn.org]=
The prototype of the GGBN Document Library contains more than 4400 papers citing either DNA and Tissue samples or vouchers that are provided via the GGBN/DNA Bank Network Data Portal. Therefore a lot of non-molecular papers can be found here. The publications are provided in citation format with every voucher and DNA record. You can search for a DNA or Specimen Number, a certain DNA Bank, publication years or free text within citations.
[[File:Library1.JPG|600px]]

The resulting hitlist contains 50 records per page and is ordered by publication year (from lower to upper). By clicking on a DNA number you will directed to the record details.
[[File:Library2.JPG|600px]]

=Technical informations=
==First step: harvesting and indexing==
Data is harvested and indexed using B-HIT (http://wiki.bgbm.org/bhit/). B-HIT is a harvesting and indexing toolkit, based on the GBIF-HIT software.<BR>
[[File:bhit.png|500px]]

The records(or units) can be harvested from providers having either a BioCASe or an IPT installation. For BioCASe providers, the schema ABCD 2.06, ABCD 2.1, ABCDDNA, ABCDGGBN and ABCDEFG are supported (single records or ABCD Archives). For IPT providers, DarwinCore Archives are supported. Elements that are indexed are listed under http://wiki.bgbm.org/bhit/index.php/Indexed_fields.

==Second step: data quality==
Data quality tests are done using B-HIT. Country names are translated in English, ISO codes are compared to the country names, coordinates are validated and checked again both ISO code and country name. In case of incomplete data, the tool is looking into the namedareas and localities and tries to extract some information regarding the country or the water body.

Scientific names are parsed using the GBIF Name Parser (http://www.gbif.org/developer/species#parser) and custom regular expressions.

==Third step: backbone==
Every single name is compared to the GBIF Backbone, the Catalog of Life Backbone, and the NCBI Backbone. Higher taxa, synonyms and accepted taxa are retrieved, using the GBIF Checklistbank webservice (http://api.gbif.org/v1/species).

The "Prokaryotic Nomenclature Up-to-Date API" (http://bacdive.dsmz.de/api/pnu/) is used for bacterial names.

How to search for material

2015-11-11T09:35:54Z

Patricia Kelbert: /* Third step: backbone */

<div id="wikinote"> '''This page is currently under construction (Nov 2015)!''' </div>

In general you can use three options to search our data portal:

1. Browse Taxonomy
2. Search by Fields
3. Search by Citation

=Browse Taxonomy [http://data.ggbn.org/CoL.php]=
[[File:Navi-Browse Taxonomy.JPG|thumb|100px]]
The GGBN/DNA Bank Network's Data Portal makes currently use of the Catalogue of Life (CoL) as its main taxonomic backbone. We match family and genus of original records provided by our partners with the CoL annual checklist (version 2009). Selecting [XXX "Browse Taxonomy"] leads you to our Taxonomic Backbone site (figure below).

This site gives you an overview on how many samples and taxa are online available for certain higher taxa and genera (taxa and sample counts bracketed). By clicking on "Show DNA samples" you will be redirected to a query that gives you all records for selected taxon.

Furthermore you can click on the little plus icon to see the next level of taxa.

[[File:CoL-Start1.JPG|500px]]

=Search by Fields [http://data.ggbn.org/Query.php]=
[[File:Navi-Data Portal.JPG|thumb|100px]]
The main query form for the data portal can be found at "Search & Preorder". Here you can choose a lot of criteria to filter your results. The upper part contains parameters related to the underlying voucher and collection event and the lower part contains facts about the DNA samples. If you select for example a certain DNA bank you can browse it's whole DNA and tissue collection.

The NCBI Taxonomy ID is often used by the microorganismic community. Right now search does not include synonyms, but will do in the future. Many records are provided with multiple determinations (their determination history). We index all determinations and you can search for all of them. Suggestion lists will help you when entering Family name or Species name.

Furthermore we filter collection year as well as Seas and Oceans out of the raw data. Seas/Oceans and Countries are matched with an existing list, so that also countries like "England" will be recognized as United Kingdom for instance.

We also index related Sequence Accession Numbers (BOLD and GenBank/EMBL/DDBJ) to be available for search.

==Dependent parameters==
Some parameters are related to each other, e.g. if you select a Continent or an Ocean, the list of Countries or Seas respectively will be reduced to those belonging to the selected Continent/Ocean.
The same happens for Family name and Species name/Taxonomy ID. If you select a Family name, the list of suggested Species names and Taxonomy IDs is reduced to the relevant ones.

[[File:Queryform.JPG|600px]]

==Getting results==
After clicking on "Search" you will receive a hitlist with 50 records per page. The column heading contain small arrows. Clicking on such an arrow will arrange the results in the new order. The green arrow marks the current order (in the figure ordered by Species name from A to Z). The hitlist contains the species name, the country where the specimen/sample was collected, the DNA number as well as the specimen/voucher number. Clicking on the small magnifier or the species name will give you the record details.

<div id="wikinote">Some samples doesn't have a DNA number. This means that DNA was not extracted yet but can be ordered on-demand.</div>

[[File:Hitlist-portal.JPG|600px]]

==Retrieving details==
The single record details page is a synoptic virtual dataset combined from at least 2 different sources (DNA sample and voucher). The upper part contains information on the physical DNA sample as well as links to published sequences and papers. The lower part contains the underlying specimen information, sometimes associated vouchers are also listed (e.g. duplum in another collection, cultivated/captivated individuals). GGBN encourages its partners to provide digital images of the vouchers as well. Due to several reasons (e.g. size of the organism) this can not always be realized easily.

[[File:RecordDetail.jpg|600px]]

==Pre-order samples==
Login is required for pre-ordering samples. When you are logged in you can select the required samples (checkboxes on the right) and click on "Add selected DNA/Tissue samples to shopping cart" on top right.
Some samples are blocked for the ordering process and marked with a big red X.
[[File:Hitlist-portal-shop.JPG|600px]]
===Shopping Cart===
After putting samples into the shopping cart on top of the website appears the message "Your shopping cart contains xy samples". Clicking on "Show details" will open you shopping cart and will guide you through the pre-ordering process.
[[File:ShoppingCart1.JPG|600px]]

The Shopping cart gives you an overview of your selected DNA/tissue samples. Here you can delete samples from your cart or by clicking on the taxon name see the record details again. Click on "Continue Pre-Order (->Step 2/3)" to continue.
[[File:ShoppingCart2.JPG|600px]]

The next steps orders the samples by institutions/DNA banks. In the example below you see that the selected samples are deposited at BGBM and DSMZ. You can check your invoice and delivery address and add some notes if you want. When clicking on "Finish Pre-Order (->Step 3/3) your pre-order will be forwarded to the DNA bank(s) in authority of requested samples. Every DNA bank only receives its relevant order information. Subsequently a confirmation email will be send to you by the DNA bank(s) in question. An offer including binding prices will than be made within a separate email.

[[File:ShoppingCart3.jpg|600px]]

=Search by Citation [http://library.ggbn.org]=
The prototype of the GGBN Document Library contains more than 4400 papers citing either DNA and Tissue samples or vouchers that are provided via the GGBN/DNA Bank Network Data Portal. Therefore a lot of non-molecular papers can be found here. The publications are provided in citation format with every voucher and DNA record. You can search for a DNA or Specimen Number, a certain DNA Bank, publication years or free text within citations.
[[File:Library1.JPG|600px]]

The resulting hitlist contains 50 records per page and is ordered by publication year (from lower to upper). By clicking on a DNA number you will directed to the record details.
[[File:Library2.JPG|600px]]

=Technical informations=
==First step: harvesting and indexing==
Data is harvested and indexed using B-HIT (http://wiki.bgbm.org/bhit/). B-HIT is a harvesting and indexing toolkit, based on the GBIF-HIT software.<BR>
[[File:bhit.png|500px]]

The records(or units) can be harvested from providers having either a BioCASe or an IPT installation. For BioCASe providers, the schema ABCD 2.06, ABCD 2.1, ABCDDNA, ABCDGGBN and ABCDEFG are supported (single records or ABCD Archives). For IPT providers, DarwinCore Archives are supported. Elements that are indexed are listed under http://wiki.bgbm.org/bhit/index.php/Indexed_fields.

==Second step: data quality==
Data quality tests are done using B-HIT. Country names are translated in English, ISO codes are compared to the country names, coordinates are validated and checked again both ISO code and country name. In case of incomplete data, the tool is looking into the namedareas and localities and tries to extract some information regarding the country or the water body.

Scientific names are parsed using the GBIF Name Parser (http://www.gbif.org/developer/species#parser) and custom regular expressions.

==Third step: backbone==
Every single name is compared to the GBIF Backbone, the Catalog of Life Backbone, and the NCBI Backbone. Higher taxa, synonyms and accepted taxa are retrieved, using the GBIF Checklistbank webservice (http://api.gbif.org/v1/species).
The Prokaryotic Nomenclature Up-to-Date API (http://bacdive.dsmz.de/api/pnu/) is used for bacterial names.

How to search for material

2015-11-11T09:32:40Z

Patricia Kelbert: /* Technical informations */

<div id="wikinote"> '''This page is currently under construction (Nov 2015)!''' </div>

In general you can use three options to search our data portal:

1. Browse Taxonomy
2. Search by Fields
3. Search by Citation

=Browse Taxonomy [http://data.ggbn.org/CoL.php]=
[[File:Navi-Browse Taxonomy.JPG|thumb|100px]]
The GGBN/DNA Bank Network's Data Portal makes currently use of the Catalogue of Life (CoL) as its main taxonomic backbone. We match family and genus of original records provided by our partners with the CoL annual checklist (version 2009). Selecting [XXX "Browse Taxonomy"] leads you to our Taxonomic Backbone site (figure below).

This site gives you an overview on how many samples and taxa are online available for certain higher taxa and genera (taxa and sample counts bracketed). By clicking on "Show DNA samples" you will be redirected to a query that gives you all records for selected taxon.

Furthermore you can click on the little plus icon to see the next level of taxa.

[[File:CoL-Start1.JPG|500px]]

=Search by Fields [http://data.ggbn.org/Query.php]=
[[File:Navi-Data Portal.JPG|thumb|100px]]
The main query form for the data portal can be found at "Search & Preorder". Here you can choose a lot of criteria to filter your results. The upper part contains parameters related to the underlying voucher and collection event and the lower part contains facts about the DNA samples. If you select for example a certain DNA bank you can browse it's whole DNA and tissue collection.

The NCBI Taxonomy ID is often used by the microorganismic community. Right now search does not include synonyms, but will do in the future. Many records are provided with multiple determinations (their determination history). We index all determinations and you can search for all of them. Suggestion lists will help you when entering Family name or Species name.

Furthermore we filter collection year as well as Seas and Oceans out of the raw data. Seas/Oceans and Countries are matched with an existing list, so that also countries like "England" will be recognized as United Kingdom for instance.

We also index related Sequence Accession Numbers (BOLD and GenBank/EMBL/DDBJ) to be available for search.

==Dependent parameters==
Some parameters are related to each other, e.g. if you select a Continent or an Ocean, the list of Countries or Seas respectively will be reduced to those belonging to the selected Continent/Ocean.
The same happens for Family name and Species name/Taxonomy ID. If you select a Family name, the list of suggested Species names and Taxonomy IDs is reduced to the relevant ones.

[[File:Queryform.JPG|600px]]

==Getting results==
After clicking on "Search" you will receive a hitlist with 50 records per page. The column heading contain small arrows. Clicking on such an arrow will arrange the results in the new order. The green arrow marks the current order (in the figure ordered by Species name from A to Z). The hitlist contains the species name, the country where the specimen/sample was collected, the DNA number as well as the specimen/voucher number. Clicking on the small magnifier or the species name will give you the record details.

<div id="wikinote">Some samples doesn't have a DNA number. This means that DNA was not extracted yet but can be ordered on-demand.</div>

[[File:Hitlist-portal.JPG|600px]]

==Retrieving details==
The single record details page is a synoptic virtual dataset combined from at least 2 different sources (DNA sample and voucher). The upper part contains information on the physical DNA sample as well as links to published sequences and papers. The lower part contains the underlying specimen information, sometimes associated vouchers are also listed (e.g. duplum in another collection, cultivated/captivated individuals). GGBN encourages its partners to provide digital images of the vouchers as well. Due to several reasons (e.g. size of the organism) this can not always be realized easily.

[[File:RecordDetail.jpg|600px]]

==Pre-order samples==
Login is required for pre-ordering samples. When you are logged in you can select the required samples (checkboxes on the right) and click on "Add selected DNA/Tissue samples to shopping cart" on top right.
Some samples are blocked for the ordering process and marked with a big red X.
[[File:Hitlist-portal-shop.JPG|600px]]
===Shopping Cart===
After putting samples into the shopping cart on top of the website appears the message "Your shopping cart contains xy samples". Clicking on "Show details" will open you shopping cart and will guide you through the pre-ordering process.
[[File:ShoppingCart1.JPG|600px]]

The Shopping cart gives you an overview of your selected DNA/tissue samples. Here you can delete samples from your cart or by clicking on the taxon name see the record details again. Click on "Continue Pre-Order (->Step 2/3)" to continue.
[[File:ShoppingCart2.JPG|600px]]

The next steps orders the samples by institutions/DNA banks. In the example below you see that the selected samples are deposited at BGBM and DSMZ. You can check your invoice and delivery address and add some notes if you want. When clicking on "Finish Pre-Order (->Step 3/3) your pre-order will be forwarded to the DNA bank(s) in authority of requested samples. Every DNA bank only receives its relevant order information. Subsequently a confirmation email will be send to you by the DNA bank(s) in question. An offer including binding prices will than be made within a separate email.

[[File:ShoppingCart3.jpg|600px]]

=Search by Citation [http://library.ggbn.org]=
The prototype of the GGBN Document Library contains more than 4400 papers citing either DNA and Tissue samples or vouchers that are provided via the GGBN/DNA Bank Network Data Portal. Therefore a lot of non-molecular papers can be found here. The publications are provided in citation format with every voucher and DNA record. You can search for a DNA or Specimen Number, a certain DNA Bank, publication years or free text within citations.
[[File:Library1.JPG|600px]]

The resulting hitlist contains 50 records per page and is ordered by publication year (from lower to upper). By clicking on a DNA number you will directed to the record details.
[[File:Library2.JPG|600px]]

=Technical informations=
==First step: harvesting and indexing==
Data is harvested and indexed using B-HIT (http://wiki.bgbm.org/bhit/). B-HIT is a harvesting and indexing toolkit, based on the GBIF-HIT software.<BR>
[[File:bhit.png|500px]]

The records(or units) can be harvested from providers having either a BioCASe or an IPT installation. For BioCASe providers, the schema ABCD 2.06, ABCD 2.1, ABCDDNA, ABCDGGBN and ABCDEFG are supported (single records or ABCD Archives). For IPT providers, DarwinCore Archives are supported. Elements that are indexed are listed under http://wiki.bgbm.org/bhit/index.php/Indexed_fields.

==Second step: data quality==
Data quality tests are done using B-HIT. Country names are translated in English, ISO codes are compared to the country names, coordinates are validated and checked again both ISO code and country name. In case of incomplete data, the tool is looking into the namedareas and localities and tries to extract some information regarding the country or the water body.

Scientific names are parsed using the GBIF Name Parser (http://www.gbif.org/developer/species#parser) and custom regular expressions.

==Third step: backbone==
Every single name is compared to the GBIF Backbone, the Catalog of Life Backbone, and the NCBI Backbone. Higher taxa, synonyms and accepted taxa are retrieved.

How to search for material

2015-11-11T09:26:56Z

Patricia Kelbert: /* Technical informations */

<div id="wikinote"> '''This page is currently under construction (Nov 2015)!''' </div>

In general you can use three options to search our data portal:

1. Browse Taxonomy
2. Search by Fields
3. Search by Citation

=Browse Taxonomy [http://data.ggbn.org/CoL.php]=
[[File:Navi-Browse Taxonomy.JPG|thumb|100px]]
The GGBN/DNA Bank Network's Data Portal makes currently use of the Catalogue of Life (CoL) as its main taxonomic backbone. We match family and genus of original records provided by our partners with the CoL annual checklist (version 2009). Selecting [XXX "Browse Taxonomy"] leads you to our Taxonomic Backbone site (figure below).

This site gives you an overview on how many samples and taxa are online available for certain higher taxa and genera (taxa and sample counts bracketed). By clicking on "Show DNA samples" you will be redirected to a query that gives you all records for selected taxon.

Furthermore you can click on the little plus icon to see the next level of taxa.

[[File:CoL-Start1.JPG|500px]]

=Search by Fields [http://data.ggbn.org/Query.php]=
[[File:Navi-Data Portal.JPG|thumb|100px]]
The main query form for the data portal can be found at "Search & Preorder". Here you can choose a lot of criteria to filter your results. The upper part contains parameters related to the underlying voucher and collection event and the lower part contains facts about the DNA samples. If you select for example a certain DNA bank you can browse it's whole DNA and tissue collection.

The NCBI Taxonomy ID is often used by the microorganismic community. Right now search does not include synonyms, but will do in the future. Many records are provided with multiple determinations (their determination history). We index all determinations and you can search for all of them. Suggestion lists will help you when entering Family name or Species name.

Furthermore we filter collection year as well as Seas and Oceans out of the raw data. Seas/Oceans and Countries are matched with an existing list, so that also countries like "England" will be recognized as United Kingdom for instance.

We also index related Sequence Accession Numbers (BOLD and GenBank/EMBL/DDBJ) to be available for search.

==Dependent parameters==
Some parameters are related to each other, e.g. if you select a Continent or an Ocean, the list of Countries or Seas respectively will be reduced to those belonging to the selected Continent/Ocean.
The same happens for Family name and Species name/Taxonomy ID. If you select a Family name, the list of suggested Species names and Taxonomy IDs is reduced to the relevant ones.

[[File:Queryform.JPG|600px]]

==Getting results==
After clicking on "Search" you will receive a hitlist with 50 records per page. The column heading contain small arrows. Clicking on such an arrow will arrange the results in the new order. The green arrow marks the current order (in the figure ordered by Species name from A to Z). The hitlist contains the species name, the country where the specimen/sample was collected, the DNA number as well as the specimen/voucher number. Clicking on the small magnifier or the species name will give you the record details.

<div id="wikinote">Some samples doesn't have a DNA number. This means that DNA was not extracted yet but can be ordered on-demand.</div>

[[File:Hitlist-portal.JPG|600px]]

==Retrieving details==
The single record details page is a synoptic virtual dataset combined from at least 2 different sources (DNA sample and voucher). The upper part contains information on the physical DNA sample as well as links to published sequences and papers. The lower part contains the underlying specimen information, sometimes associated vouchers are also listed (e.g. duplum in another collection, cultivated/captivated individuals). GGBN encourages its partners to provide digital images of the vouchers as well. Due to several reasons (e.g. size of the organism) this can not always be realized easily.

[[File:RecordDetail.jpg|600px]]

==Pre-order samples==
Login is required for pre-ordering samples. When you are logged in you can select the required samples (checkboxes on the right) and click on "Add selected DNA/Tissue samples to shopping cart" on top right.
Some samples are blocked for the ordering process and marked with a big red X.
[[File:Hitlist-portal-shop.JPG|600px]]
===Shopping Cart===
After putting samples into the shopping cart on top of the website appears the message "Your shopping cart contains xy samples". Clicking on "Show details" will open you shopping cart and will guide you through the pre-ordering process.
[[File:ShoppingCart1.JPG|600px]]

The Shopping cart gives you an overview of your selected DNA/tissue samples. Here you can delete samples from your cart or by clicking on the taxon name see the record details again. Click on "Continue Pre-Order (->Step 2/3)" to continue.
[[File:ShoppingCart2.JPG|600px]]

The next steps orders the samples by institutions/DNA banks. In the example below you see that the selected samples are deposited at BGBM and DSMZ. You can check your invoice and delivery address and add some notes if you want. When clicking on "Finish Pre-Order (->Step 3/3) your pre-order will be forwarded to the DNA bank(s) in authority of requested samples. Every DNA bank only receives its relevant order information. Subsequently a confirmation email will be send to you by the DNA bank(s) in question. An offer including binding prices will than be made within a separate email.

[[File:ShoppingCart3.jpg|600px]]

=Search by Citation [http://library.ggbn.org]=
The prototype of the GGBN Document Library contains more than 4400 papers citing either DNA and Tissue samples or vouchers that are provided via the GGBN/DNA Bank Network Data Portal. Therefore a lot of non-molecular papers can be found here. The publications are provided in citation format with every voucher and DNA record. You can search for a DNA or Specimen Number, a certain DNA Bank, publication years or free text within citations.
[[File:Library1.JPG|600px]]

The resulting hitlist contains 50 records per page and is ordered by publication year (from lower to upper). By clicking on a DNA number you will directed to the record details.
[[File:Library2.JPG|600px]]

=Technical informations=
Data is harvested and indexed using B-HIT (http://wiki.bgbm.org/bhit/). B-HIT is a harvesting and indexing toolkit, based on the GBIF-HIT software.<BR>
[[File:bhit.png|500px]]

The records(or units) can be harvested from providers having either a BioCASe or an IPT installation. For BioCASe providers, the schema ABCD 2.06, ABCD 2.1, ABCDDNA, ABCDGGBN and ABCDEFG are supported (single records or ABCD Archives). For IPT providers, DarwinCore Archives are supported. Elements that are indexed are listed under http://wiki.bgbm.org/bhit/index.php/Indexed_fields.

How to search for material

2015-11-11T09:25:59Z

Patricia Kelbert: /* Technical informations */

<div id="wikinote"> '''This page is currently under construction (Nov 2015)!''' </div>

In general you can use three options to search our data portal:

1. Browse Taxonomy
2. Search by Fields
3. Search by Citation

=Browse Taxonomy [http://data.ggbn.org/CoL.php]=
[[File:Navi-Browse Taxonomy.JPG|thumb|100px]]
The GGBN/DNA Bank Network's Data Portal makes currently use of the Catalogue of Life (CoL) as its main taxonomic backbone. We match family and genus of original records provided by our partners with the CoL annual checklist (version 2009). Selecting [XXX "Browse Taxonomy"] leads you to our Taxonomic Backbone site (figure below).

This site gives you an overview on how many samples and taxa are online available for certain higher taxa and genera (taxa and sample counts bracketed). By clicking on "Show DNA samples" you will be redirected to a query that gives you all records for selected taxon.

Furthermore you can click on the little plus icon to see the next level of taxa.

[[File:CoL-Start1.JPG|500px]]

=Search by Fields [http://data.ggbn.org/Query.php]=
[[File:Navi-Data Portal.JPG|thumb|100px]]
The main query form for the data portal can be found at "Search & Preorder". Here you can choose a lot of criteria to filter your results. The upper part contains parameters related to the underlying voucher and collection event and the lower part contains facts about the DNA samples. If you select for example a certain DNA bank you can browse it's whole DNA and tissue collection.

The NCBI Taxonomy ID is often used by the microorganismic community. Right now search does not include synonyms, but will do in the future. Many records are provided with multiple determinations (their determination history). We index all determinations and you can search for all of them. Suggestion lists will help you when entering Family name or Species name.

Furthermore we filter collection year as well as Seas and Oceans out of the raw data. Seas/Oceans and Countries are matched with an existing list, so that also countries like "England" will be recognized as United Kingdom for instance.

We also index related Sequence Accession Numbers (BOLD and GenBank/EMBL/DDBJ) to be available for search.

==Dependent parameters==
Some parameters are related to each other, e.g. if you select a Continent or an Ocean, the list of Countries or Seas respectively will be reduced to those belonging to the selected Continent/Ocean.
The same happens for Family name and Species name/Taxonomy ID. If you select a Family name, the list of suggested Species names and Taxonomy IDs is reduced to the relevant ones.

[[File:Queryform.JPG|600px]]

==Getting results==
After clicking on "Search" you will receive a hitlist with 50 records per page. The column heading contain small arrows. Clicking on such an arrow will arrange the results in the new order. The green arrow marks the current order (in the figure ordered by Species name from A to Z). The hitlist contains the species name, the country where the specimen/sample was collected, the DNA number as well as the specimen/voucher number. Clicking on the small magnifier or the species name will give you the record details.

<div id="wikinote">Some samples doesn't have a DNA number. This means that DNA was not extracted yet but can be ordered on-demand.</div>

[[File:Hitlist-portal.JPG|600px]]

==Retrieving details==
The single record details page is a synoptic virtual dataset combined from at least 2 different sources (DNA sample and voucher). The upper part contains information on the physical DNA sample as well as links to published sequences and papers. The lower part contains the underlying specimen information, sometimes associated vouchers are also listed (e.g. duplum in another collection, cultivated/captivated individuals). GGBN encourages its partners to provide digital images of the vouchers as well. Due to several reasons (e.g. size of the organism) this can not always be realized easily.

[[File:RecordDetail.jpg|600px]]

==Pre-order samples==
Login is required for pre-ordering samples. When you are logged in you can select the required samples (checkboxes on the right) and click on "Add selected DNA/Tissue samples to shopping cart" on top right.
Some samples are blocked for the ordering process and marked with a big red X.
[[File:Hitlist-portal-shop.JPG|600px]]
===Shopping Cart===
After putting samples into the shopping cart on top of the website appears the message "Your shopping cart contains xy samples". Clicking on "Show details" will open you shopping cart and will guide you through the pre-ordering process.
[[File:ShoppingCart1.JPG|600px]]

The Shopping cart gives you an overview of your selected DNA/tissue samples. Here you can delete samples from your cart or by clicking on the taxon name see the record details again. Click on "Continue Pre-Order (->Step 2/3)" to continue.
[[File:ShoppingCart2.JPG|600px]]

The next steps orders the samples by institutions/DNA banks. In the example below you see that the selected samples are deposited at BGBM and DSMZ. You can check your invoice and delivery address and add some notes if you want. When clicking on "Finish Pre-Order (->Step 3/3) your pre-order will be forwarded to the DNA bank(s) in authority of requested samples. Every DNA bank only receives its relevant order information. Subsequently a confirmation email will be send to you by the DNA bank(s) in question. An offer including binding prices will than be made within a separate email.

[[File:ShoppingCart3.jpg|600px]]

=Search by Citation [http://library.ggbn.org]=
The prototype of the GGBN Document Library contains more than 4400 papers citing either DNA and Tissue samples or vouchers that are provided via the GGBN/DNA Bank Network Data Portal. Therefore a lot of non-molecular papers can be found here. The publications are provided in citation format with every voucher and DNA record. You can search for a DNA or Specimen Number, a certain DNA Bank, publication years or free text within citations.
[[File:Library1.JPG|600px]]

The resulting hitlist contains 50 records per page and is ordered by publication year (from lower to upper). By clicking on a DNA number you will directed to the record details.
[[File:Library2.JPG|600px]]

=Technical informations=
Data is harvested and indexed using B-HIT (http://wiki.bgbm.org/bhit/). B-HIT is a harvesting and indexing toolkit, based on the GBIF-HIT software.<BR>
[[File:bhit.png|500px]]

The records(or units) can be harvested from providers having either a BioCASe or an IPT installation. For BioCASe providers, the schema ABCD 2.06, ABCD 2.1, ABCDDNA, ABCDGGBN and ABCDEFG are supported (single records or ABCD Archives). For IPT providers, DarwinCore Archives are supported.

File:Bhit.png

2015-11-11T09:22:52Z

Patricia Kelbert:

How to search for material

2015-11-11T09:22:21Z

Patricia Kelbert: /* Technical informations */

<div id="wikinote"> '''This page is currently under construction (Nov 2015)!''' </div>

In general you can use three options to search our data portal:

1. Browse Taxonomy
2. Search by Fields
3. Search by Citation

=Browse Taxonomy [http://data.ggbn.org/CoL.php]=
[[File:Navi-Browse Taxonomy.JPG|thumb|100px]]
The GGBN/DNA Bank Network's Data Portal makes currently use of the Catalogue of Life (CoL) as its main taxonomic backbone. We match family and genus of original records provided by our partners with the CoL annual checklist (version 2009). Selecting [XXX "Browse Taxonomy"] leads you to our Taxonomic Backbone site (figure below).

This site gives you an overview on how many samples and taxa are online available for certain higher taxa and genera (taxa and sample counts bracketed). By clicking on "Show DNA samples" you will be redirected to a query that gives you all records for selected taxon.

Furthermore you can click on the little plus icon to see the next level of taxa.

[[File:CoL-Start1.JPG|500px]]

=Search by Fields [http://data.ggbn.org/Query.php]=
[[File:Navi-Data Portal.JPG|thumb|100px]]
The main query form for the data portal can be found at "Search & Preorder". Here you can choose a lot of criteria to filter your results. The upper part contains parameters related to the underlying voucher and collection event and the lower part contains facts about the DNA samples. If you select for example a certain DNA bank you can browse it's whole DNA and tissue collection.

The NCBI Taxonomy ID is often used by the microorganismic community. Right now search does not include synonyms, but will do in the future. Many records are provided with multiple determinations (their determination history). We index all determinations and you can search for all of them. Suggestion lists will help you when entering Family name or Species name.

Furthermore we filter collection year as well as Seas and Oceans out of the raw data. Seas/Oceans and Countries are matched with an existing list, so that also countries like "England" will be recognized as United Kingdom for instance.

We also index related Sequence Accession Numbers (BOLD and GenBank/EMBL/DDBJ) to be available for search.

==Dependent parameters==
Some parameters are related to each other, e.g. if you select a Continent or an Ocean, the list of Countries or Seas respectively will be reduced to those belonging to the selected Continent/Ocean.
The same happens for Family name and Species name/Taxonomy ID. If you select a Family name, the list of suggested Species names and Taxonomy IDs is reduced to the relevant ones.

[[File:Queryform.JPG|600px]]

==Getting results==
After clicking on "Search" you will receive a hitlist with 50 records per page. The column heading contain small arrows. Clicking on such an arrow will arrange the results in the new order. The green arrow marks the current order (in the figure ordered by Species name from A to Z). The hitlist contains the species name, the country where the specimen/sample was collected, the DNA number as well as the specimen/voucher number. Clicking on the small magnifier or the species name will give you the record details.

<div id="wikinote">Some samples doesn't have a DNA number. This means that DNA was not extracted yet but can be ordered on-demand.</div>

[[File:Hitlist-portal.JPG|600px]]

==Retrieving details==
The single record details page is a synoptic virtual dataset combined from at least 2 different sources (DNA sample and voucher). The upper part contains information on the physical DNA sample as well as links to published sequences and papers. The lower part contains the underlying specimen information, sometimes associated vouchers are also listed (e.g. duplum in another collection, cultivated/captivated individuals). GGBN encourages its partners to provide digital images of the vouchers as well. Due to several reasons (e.g. size of the organism) this can not always be realized easily.

[[File:RecordDetail.jpg|600px]]

==Pre-order samples==
Login is required for pre-ordering samples. When you are logged in you can select the required samples (checkboxes on the right) and click on "Add selected DNA/Tissue samples to shopping cart" on top right.
Some samples are blocked for the ordering process and marked with a big red X.
[[File:Hitlist-portal-shop.JPG|600px]]
===Shopping Cart===
After putting samples into the shopping cart on top of the website appears the message "Your shopping cart contains xy samples". Clicking on "Show details" will open you shopping cart and will guide you through the pre-ordering process.
[[File:ShoppingCart1.JPG|600px]]

The Shopping cart gives you an overview of your selected DNA/tissue samples. Here you can delete samples from your cart or by clicking on the taxon name see the record details again. Click on "Continue Pre-Order (->Step 2/3)" to continue.
[[File:ShoppingCart2.JPG|600px]]

The next steps orders the samples by institutions/DNA banks. In the example below you see that the selected samples are deposited at BGBM and DSMZ. You can check your invoice and delivery address and add some notes if you want. When clicking on "Finish Pre-Order (->Step 3/3) your pre-order will be forwarded to the DNA bank(s) in authority of requested samples. Every DNA bank only receives its relevant order information. Subsequently a confirmation email will be send to you by the DNA bank(s) in question. An offer including binding prices will than be made within a separate email.

[[File:ShoppingCart3.jpg|600px]]

=Search by Citation [http://library.ggbn.org]=
The prototype of the GGBN Document Library contains more than 4400 papers citing either DNA and Tissue samples or vouchers that are provided via the GGBN/DNA Bank Network Data Portal. Therefore a lot of non-molecular papers can be found here. The publications are provided in citation format with every voucher and DNA record. You can search for a DNA or Specimen Number, a certain DNA Bank, publication years or free text within citations.
[[File:Library1.JPG|600px]]

The resulting hitlist contains 50 records per page and is ordered by publication year (from lower to upper). By clicking on a DNA number you will directed to the record details.
[[File:Library2.JPG|600px]]

=Technical informations=
Data is harvested and indexed using B-HIT (http://wiki.bgbm.org/bhit/). B-HIT is a harvesting and indexing toolkit, based on the GBIF-HIT software.
[[File:bhit.png]]

How to search for material

2015-11-11T08:52:33Z

Patricia Kelbert:

Main Page

2015-11-04T14:19:17Z

Patricia Kelbert:

<big>'''Welcome to the DNA Bank Network Wiki!'''</big>

These wiki sites lead you through installing and using the open source software "DNA Module". Furthermore you will find information about the project and how to join the DNA Bank Network.

=The DNA Module=
* Manage your DNA collection and customer requests with an open source software
* Set references to voucher specimens by using GBIF infrastructure
* Get original specimen data from GBIF providers instead of copies
* Set links to NCBI, EMBL, DDBJ, or BOLD
* Set references to publications
* Use the Specimen Tool for specimen data that are not available via GBIF
* Share your DNA data with others
* Find out more about the [[DNA Module]] and the [[Specimen Tool]]
[[File:Start1.jpg|thumb|650px|The DNA Module can interact with every GBIF compliant database]]

=The Network=
* Administer your data locally
* Share your data with the world
* Join the DNA Bank Network with your DNA Bank
* Join GBIF with your specimen and observation records
* Let other scientists find and order your DNA samples via a central platform
* Help us to bridge the gap between natural history collections and sequence portals
* Find out more about how to [[Join the Network]]
[[File:Start2.jpg|thumb|650px|The data architecture of the DNA Bank Network holds the potential to become an international platform of biological DNA banks to bridge the gap between natural history collections and molecular sequence databases.]]

=ABCDDNA and BioCASE=
* Use this powerful team for exchange and transfer of DNA and sequence data
* Use the main schema ABCD for providing specimen and observations records to GBIF
* Use BioCASE for your own network purposes
* More than 30 Mio. records are presently provided to GBIF with BioCASE and ABCD
* Find out more about the pros of [[ABCDDNA]] and [http://wiki.bgbm.org/bps/index.php/Main_Page BioCASE]
[[File:Start3.jpg|thumb|650px|ABCDDNA and BioCASE - a powerful team for biodiversity data exchange]]

Main Page

2015-11-04T14:18:34Z

Patricia Kelbert:

<big>'''Welcome to the DNA Bank Network Wiki!'''</big>

These wiki sites lead you through installing and using of the open source software "DNA Module". Furthermore you will find information about the project and how to join the DNA Bank Network.

=The DNA Module=
* Manage your DNA collection and customer requests with an open source software
* Set references to voucher specimens by using GBIF infrastructure
* Get original specimen data from GBIF providers instead of copies
* Set links to NCBI, EMBL, DDBJ, or BOLD
* Set references to publications
* Use the Specimen Tool for specimen data that are not available via GBIF
* Share your DNA data with others
* Find out more about the [[DNA Module]] and the [[Specimen Tool]]
[[File:Start1.jpg|thumb|650px|The DNA Module can interact with every GBIF compliant database]]

=The Network=
* Administer your data locally
* Share your data with the world
* Join the DNA Bank Network with your DNA Bank
* Join GBIF with your specimen and observation records
* Let other scientists find and order your DNA samples via a central platform
* Help us to bridge the gap between natural history collections and sequence portals
* Find out more about how to [[Join the Network]]
[[File:Start2.jpg|thumb|650px|The data architecture of the DNA Bank Network holds the potential to become an international platform of biological DNA banks to bridge the gap between natural history collections and molecular sequence databases.]]

=ABCDDNA and BioCASE=
* Use this powerful team for exchange and transfer of DNA and sequence data
* Use the main schema ABCD for providing specimen and observations records to GBIF
* Use BioCASE for your own network purposes
* More than 30 Mio. records are presently provided to GBIF with BioCASE and ABCD
* Find out more about the pros of [[ABCDDNA]] and [http://wiki.bgbm.org/bps/index.php/Main_Page BioCASE]
[[File:Start3.jpg|thumb|650px|ABCDDNA and BioCASE - a powerful team for biodiversity data exchange]]

Main Page

2015-11-04T14:17:53Z

Patricia Kelbert:

<big>'''Welcome to the DNA Bank Network Wiki!'''</big>

These wiki sites lead you through installing and use of the open source software "DNA Module". Furthermore you will find information about the project and how to join the DNA Bank Network.

=The DNA Module=
* Manage your DNA collection and customer requests with an open source software
* Set references to voucher specimens by using GBIF infrastructure
* Get original specimen data from GBIF providers instead of copies
* Set links to NCBI, EMBL, DDBJ, or BOLD
* Set references to publications
* Use the Specimen Tool for specimen data that are not available via GBIF
* Share your DNA data with others
* Find out more about the [[DNA Module]] and the [[Specimen Tool]]
[[File:Start1.jpg|thumb|650px|The DNA Module can interact with every GBIF compliant database]]

=The Network=
* Administer your data locally
* Share your data with the world
* Join the DNA Bank Network with your DNA Bank
* Join GBIF with your specimen and observation records
* Let other scientists find and order your DNA samples via a central platform
* Help us to bridge the gap between natural history collections and sequence portals
* Find out more about how to [[Join the Network]]
[[File:Start2.jpg|thumb|650px|The data architecture of the DNA Bank Network holds the potential to become an international platform of biological DNA banks to bridge the gap between natural history collections and molecular sequence databases.]]

=ABCDDNA and BioCASE=
* Use this powerful team for exchange and transfer of DNA and sequence data
* Use the main schema ABCD for providing specimen and observations records to GBIF
* Use BioCASE for your own network purposes
* More than 30 Mio. records are presently provided to GBIF with BioCASE and ABCD
* Find out more about the pros of [[ABCDDNA]] and [http://wiki.bgbm.org/bps/index.php/Main_Page BioCASE]
[[File:Start3.jpg|thumb|650px|ABCDDNA and BioCASE - a powerful team for biodiversity data exchange]]