2008-12-03 SBIS 2008 Data exchange alternatives

Biodiversity Data Provider Software
Hands-on exercises with TAPIR
Stockholm Biodiversity Informatics Symposium 2008 (SBIS2008)
Dag Terje Filip Endresen, Nordic Genetic Resources Center (Sweden) / Bioversity International (Italy)

Fallacies of Distributed Computing
The network is reliable.
Latency is zero.
Bandwidth is infinite.
The network is secure.
Topology doesn't change.
There is one administrator.
Transport cost is zero.
The network is homogeneous.
This list of fallacies came about at Sun Microsystems around 1994.
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TAPIR
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Cartoon by Sasha Kopf (Creative Commons)

TAPIR
TAPIR - TDWG Access Protocol for Information Retrieval.
During the 2004 TDWG meeting in Christchurch, NZ, work started on a unified protocol and named TAPIR.
TAPIR is based on the protocol from the two data provider software, BioCASE and DiGIR.
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Provider software, wrappers
DiGIR (2002, not active)
http://digir.sourceforge.net
BioCASE (2003, PyWrapper)
http://www.biocase.org
PyWrapper3 (2006, not active)
http://trac.pywrapper.org/
TapirLink (2007)
http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirLink
GBIF Provider Toolkit (2009)
http://code.google.com/p/gbif-providertoolkit
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BioCASE 2.5.ORC
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The BioCASE provider software is a product of the EU funded BioCASE project (2001-2004).
Developed at BGBM in Berlin.
Last updated in April 2008, with support for Python version 2.5 and less required external
Implement the BioCASE provider to share data as ABCD 2.06.

1. Make sure you have Python 2.5 installed
(command line: python –v)
2.Download the latest provider software from
3. Uncompress the BioCASE provider software to a folder on your system [provider_software_2.5.0RC.tar.gz]
(tar –xzvf provider_...tar.gz)
4. Run setup.py, (python setup.py)
5. Configure your web server to mount biocase/www as
http://localhost/biocase/
Hint: You will find an example for httpd.conf as the last terminal output from running setup.py
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BioCASE 2.5.ORC

BioCASE 2.5.ORC
6. Visit the library test page:
http://localhost/biocase/utilities/testlibs.cgi
6a. Download latest 4 Suite
from http://4suite.org/
Uncompress and install
[4Suite-XML-1.0.2.tar.bz2]
6b. Install additional python
libraries, including the desired
database driver. For each
python package:
(python setup.py install)
6c. Graphviz is useful to
visualize the database
table structure.
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BioCASE 2.5.ORC
7. Configuration

Add datasource (dsa)
Database connection
Database table structure
Mapping of data model to standard schema

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BioCASE 2.5.ORC
8. Query Form
The manual query form is illustrative for understanding exactly how the wrapper software works! http://localhost/biocase/utilities/queryforms/qf_manual.cgi?dsa=sesto
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PyWrapper3
Home:http://trac.pywrapper.org/
Primary developers: Markus Döring, Javier de la Torre
14/07/2008 - Development stalled
We are sorry to inform you that development of the TAPIR branch of PyWrapper has been stalled. The latest 3.1 alpha version is not stable and not recommended for production! (Message from the home page)

PyWrapper 3.0.0 (Latest stable version, requires Python 2.4)
PyWrapper 3.1.0 alpha (development version, works with Python 2.5)

PyWrapper is tested and verified to work fine with Windows, Mac OS X and Linux.
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Required configuration
Web server: Any CGI compliant web server: Apache, IIS etc. (The built in CherryPy web server can also be used).
Database: Major databases are supported, including MySQL, Oracle, SQLServer, Sybase, Access, PostgreSQL. Theoretically any database with a Python library should work.
Python PyWrapper is developed with the Python programming language. (The latest version from the SVN code repository works with Python version 2.5)
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Apache, MySQL and Python are open source software, free to use - even for commercial products.

Installation
http://trac.pywrapper.org/pywrapper/wiki/InstallationGuide
1. Download the latest PyWrapper3 installer.
Use SVN export or checkout for Python 2.5 support
2. Uncompress to a folder of your choice.
Example: “/usr/local/pywrapper3/”
Example: “C:pywrapper”
Local installation: If you have a Subversion client installed, you may use the automatic installer. (Local Python and libraries are installed to your pywrapper folder)
promt$ svn export svn://svn.pywrapper.org:80/pywrapper/trunk pywrapper
promt$ cd pywrapper/tools
promt$ /bin/shinstall.sh
This will require that you have a bash shell, and probably that you have a Unix line system like e.g. FreeBSD, Linux or Mac OS X…
3. Execute: pywrapper/setup.py
Example: promt$ python setup.py (Mac OS X, Linux)
On Windows locate setup.py and double-click
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Start standalone server
Execute start_server.py(default port is 8080)
promt$ cdwebapp/
promt$ ./start_server.py 8088(example to start on port 8088)
On a Windows system you may do this in a MS-DOS window (or double-click the file - if you accept the default port).
Some messages will pass across your screen. Please be patient, this could take a minute. Wait for the message “start server …” and find find PyWrapper at:
http://localhost:8088/pywrapper
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Configuration
After successful installation, you will need to configure your data provider. Follow the instructions from the PyWrapper documentation web page to configure.
Data sources. If you provide more datasets or several databases they will be configured as individual data sources (dsa).
Database connection. For PyWrapper to access your database.
Database structure. Define the relevant database tables, the primary keys and foreign keys.
Data model. Map your database model to the standard represented by the XML Schemas you choose.
http://trac.pywrapper.org/pywrapper/wiki/Documentation
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Screen examples
PyWrapper comes with a graphical web based configuration tool
For more information and more screen dumps from the configuration of PyWrapper, see:
http://circa.gbif.net/Public/irc/gbif/nodes/library?l=/meetings/2007_10_amsterdam/tapir_pywrapper3/_EN_1.0_&a=i
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TapirLink 0.6.1
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TapirLink 0.6.1
Home: http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirLink
Primary developers: Renato De Giovanni, Dave Vieglais
Download: http://sourceforge.net/project/showfiles.php?group_id=38190
Uncompress PHP source code
Eg: /usr/local/tapir/tapirlink
Mount admin and www directory for your web server.
Example: Apache “httpd.conf”
Alias /tapirlink "/usr/local/tapir/tapirlink/www”
Alias /tapirlink-admin "/usr/local/tapir/tapirlink/admin"
<Location /tapirlink>
Order allow,deny
Allow from all
</Location>
<Location /tapirlink-admin>
Order allow,deny
Allow from all
</Location>
Read permissions on all directories
Write on cache, config, log, statistics
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TapirLink 0.6.1
Start by adding a new resource http://localhost/tapirlink-admin/
Step 1: Describe your new resource
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TapirLink 0.6.1
Step 2: Data source, database connection
Step 3: Table structure
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TapirLink 0.6.1
Step 4: Filter
Step 5: Select mapping standards to use
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TapirLink 0.6.1
Step 5b: Mapping data schema (ABCD 2.06)
etc…
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TapirLink 0.6.1
Step 5c: Mapping data concepts (Darwin Core)
etc…
Step 5d: Remember that DwC have an extension for geospatial descriptors
etc…
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TapirLink 0.6.1
Step 6: Settings
New resource successfully configured
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TapirLink 0.6.1
Test resource with client form:
http://localhost/tapirlink/tapir_client.php
The XML Client form is very illustrative for understanding exactly how the wrapper software works!
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Service interface
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Example of a service request
All exchanged data is formatted with XML tags.
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Example of a service response
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...

Example TAPIR service request
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Example TAPIR service response
singer:/sourcename
singer:/taxonomy/genus
singer:/taxonomy/species
singer:/taxonomy/subspecies
singer:/holding/ID
singer:/holding/name
singer:/origin/collecting/countrysource
singer:/origin/collecting/countrysourceID
singer:/status/biologicalstatus
singer:/status/biologicalstatusID
...
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Example TAPIR service SEARCH request
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Example TAPIR service Search response
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Example of OAI-PMH service request
OAI-PMH requests are expressed as HTTP requests.
OAI-PMH requests must be submitted using either the HTTP GET or POST methods.
http://an.oa.org/OAI-script?verb=GetRecord
&identifier=oai:arXiv.org:hep-th/9901001
&metadataPrefix=oai_dc
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Example of OAI-PMH service RESPONSE
OAI-PMH responses are formatted as HTTP responses.
With The Content-Type as text/xml.
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OAI-PMH PROTOCOL, metadata formats
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Request types (verb):
Identify
ListMetadataFormats
ListSets
GetRecord
ListIdentifiers
ListRecords
For purposes of interoperability, the metadataPrefix `oai_dc’ is reserved for Dublin Core.
Communities adopt own metadataPrefixesfor own metadata fomats. Relevant formats/schemas for Biodiversity Informatics are Darwin Core and ABCD.

Why sharing data?
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[http://data.gbif.org/]
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[http://data.gbif.org/datasets/resource/1487]

GBIF PGR Network 2
[http://data.gbif.org/datasets/network/2]
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Distributed network
The image is from the BioCASE web site

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Decentralized network
GBIF
(Global Biodiversity
Information Facility)
ALIS
(Accession Level
Information System)
USER
Svalbard Global Seed Vault
(Safe Backup)
(USDA ARS
National
Germplasm
Repositories...)
Web
Services
USDA GRIN (USA)
SINGER
(CGIAR)
(CGIAR
International
Future Harvest
gene banks...)
EURISCO
(Europe)
MCPD
IHAR
(Poland)
WUR CGN
(Netherlands)
NordGen
(Northern Europe)
IPK Gatersleben
(Germany)
(Other European
gene banks...)

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Crop Wild Relatives
LKA
ARM
BOL
National Datasets
are shared with
the central
CWR data index.
The national
datasets as well as
access to other International
datasets are provided from the CWR data portal.
MDG
EURISCO
UZB
http://www.cropwildrelatives.org
SINGER

Data portal example
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http://wwwdev.ngb.se/portal/index.php?scope=demo

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Outlook
The compatibility of data standards between PGR and biodiversity collections made it possible to integrate the worldwide germplasm collections into the biodiversity community.
Using GBIF technology (and contributing to its development), the PGR community can easily establish specific PGR networks without duplicating GBIF's work.
Use of GBIF technology and integration of PGR collection data into GBIF allows PGR users to simultaneously search PGR collections and other biodiversity collections, and to get access to the data (and possibly the material) of relevant biodiversity collections.
The establishment of new data portals on a specific crop, a regional thematic network or similar subset of the total global biodiversity datasets; can be done with rather few efforts! This requires only that all the relevant datasets are provided by GBIF compatible web services (like the BioCASE PyWrapper).

Participation and the sharing of your institute datasets with global and national biodiversity projects
is important for your public and scientific visibility,
promoting the use (usefulness) of your data
and ultimately for the continued funding of your institutional activities.
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Special thanks to
Bioversity International
[http://www.bioversityinternational.org]
GBIF, Global Biodiversity Information Facility [http://www.gbif.org]
BioCASE, The Biological Collection Access Service for Europe.
[http://www.biocase.org]
TDWG, Biodiversity Information Standards [http://www.tdwg.org]
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Special thanks to
BioCASE and PyWrapper3 software
Markus Döring
Javier de la Torre
DiGIR and TapirLink software
Renato de Giovanni
Dave Vieglais
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Thank you for listening!
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