Home

Data Portal Technical Description

1. 3 670 records 2 762 records Number of records from BGCI http www bgci org BGCI accessed on 2007 07 06 Data use gudelines 14 records TODO Number of records from SINGER http singer grinfo net SINGER was accessed on 2007 07 23 Terms of use Not found in the SINGER dataset No georeferences records available from the SINGER data index TODO Number of records from EURISCO http eurisco ecpgr org EURISCO was accessed on 2007 07 23 Terms of use 172 records 68 records TODO Search information provided from FAO portals ECOLEX Conus CARIS Search FAOLEX for legal legislation on Allium schoenoprasum Data use agreement Search EcoPort for more information on Allium schoenoprasum Data use agreement Search ECOLEX for more information on Allium schoenoprasum Data use agreement Search AGRIS CARIS for more information on Allium schoenoprasum Search information from other sources Google Species ILDIS wTROPICOS flickr eere Search Google for Allium schoenoprasum Search Google Images for Allium schoenoprasum Search Species2000 for Allium schoenoprasum Species2000 is part of Catalogue of Life Search Wikispecies for Allium schoenoprasum Wikispecies is an open free wiki directory of species Search ILDIS for more information about Allium schoenoprasum International Legume Database amp Information Service Search TROPICOS Missouri Botanical Ga
2. Final Report for the CWR Global Portal http cwrint grinfo net Prepared by Dag Terje Filip Endresen Nordic Genetic Resource Center NORDGEN Bioversity International Email dag endresen nordgen org d endresen cgiar org Germplasm Data Portal Technical Description Last updated February 19 2008 Page 1 Home About CWR Data Feedback Help Site map Search Welcome to the Crop Wild Relative Global Portal Project Partners This portal provides access to information and data resources important for the conservation and utilization of crop wild relatives CWR It was created within the UNEP GEF supported project in situ conservation of crop wild relatives through External Datasets enhanced information management and field application The development of the portal is ongoing and new resources are being added as they become available National Inventories Data sharing and use agreements Portal technical specifications Latest Images CWR Links Search the CWR Portal web site CWR Data aci A selection ofthe latest images added to the CWR Image Archive Please contact us if you want to contribute images of Crop Wild Relatives a he Latest News Stories CWR Portal 2007 01 01 The CWR Portal is developed by Bioversity International as a generic web application written in PHP and with a generic ADODB database connection to the PostgreSQL database system Some of the routine operations have also been coded fo
3. 10 18 51 El webpages amp cwr portal inc 6KB INCFie 2007 10 08 21 10 8 3 svn amp 4 cwr portal terms of use inc 10KB INCFile 2007 10 08 21 10 x bioversity amp j cwris inc 3KB INCFie 2007 09 30 08 37 ED chm g data sharing inc 2KB INCFile 2007 11 08 10 17 E cr amp 4 external datasets inc 5KB INCFile 2007 10 10 13 59 z default help inc 2KB INCFie 2007 09 10 19 17 eapgren amp import datasets inc 5KB INCFile 2007 09 24 14 15 2 op A INFO TXT 1KB TextDocument 2007 09 10 19 17 sesto A info_activities inc 3KB INC File 2007 09 30 06 55 PA sgsv amp 4 info_global_initiatives inc 4KB INCFile 2007 09 14 11 09 amp links inc 6KB INCFile 2007 10 10 13 59 amp national inventories inc 5KB INCFile 2007 11 08 10 17 amp j project history inc 3KB INCFile 2007 09 14 14 48 G project partners inc 8KB INCFile 2007 11 08 10 17 amp site map inc 5KB INCFile 2007 11 08 10 17 G site search inc 4KB INC File 2007 11 08 10 17 PA temp txt 2KB TextDocument 2007 03 17 12 37 G todo inc 3KB INC File 2007 09 30 06 55 amp j use_cases inc 3KB INC File 2007 09 10 18 51 amp welcome inc 13KB INCFile 2007 11 08 10 17 amp j welcome bak inc 2KB INCFile 2007 07 01 23 17 Figure 9 information web pages are loaded from the data portal webpages scope directory requested by the REQUEST page GET attribute Sub applications The data portal comes with a set of sub applications you may chose to use for your portal
4. Ine E ode co S 24 An example of the service request style asking for all occurrence records of the species Allium porrum with geospatial origin attributes reported geo referenced LeCOrds DBIS oes eei RR tas oe eae const esu cM E eu 25 Datasets provided as a simple file io eio et pecie reet ede on nas Pep t een bass 29 Import of external datasets ttr tote rie a a V EEDI VR E DA OPERE pENN 30 Step 1 download dataset file from online source URL eese 32 Step 2 un compress the source dataset file if needed zip tar gz bz2 32 Step 3 Convert the un compressed dataset file to tab separated text 32 Step 4 recode the tab text dataset file to Unicode if needed 32 Step 5 transform the tab delimited dataset file to SQL INSERT script 33 Step 6 IMPORT dataset to the database eruit etre thei voce esse n PLE AN b reped 33 Import of external reference datasets examples from the CWR Global Portal 34 WIEWS Institute E P 34 BGC Garden aud BGCLPIABS is eei ene ert aperiunt ege b dope inem es ee 34 IUCN Red List ee roi pactio Gata average eee d a doces Erde 35 WDPA World Database on Protected Areas eeeeeeee emen 35 BURISUGO cscs aot ects ches aou det date deumque eR rU D Ud 35 SINGER diesem eas acne daa ad tae hectare ULT E Pa E aU 36 Germplasm Data Portal Technical D
5. TREE OE 8 INFO pod 9 Example how is the display of the welcome home page implemented 12 Object primary keys as URL GET attributes zuo pie deed 13 Getting started with a new data portal implementation sese 13 The Iayout elerne nts ao aevo a en Er asian aes ve pio de i Qe HE PE PER S QURE 13 HTME HEAD ue cocto tbtin eat dotum dme cua uM duced lU widen UN E UE 14 CSS Cascading Style See o Sais sate ae PR eme vo steal ee case useage 15 Page TNE TIS diere coa n ot terius actu ete edet losa tea ena d efie tases 15 Page content frame ee iesu siae Dre QURE E Es UI QUERER accu arene CUERO ANN E E 16 Information pasese en beendet editi eU E ct dado de 17 Sub AP PIC AL OMS aeran devia aleae uM Sfc saat ncc SUE cat M don da EE Ud 17 Data harvest routines and methods eerie tete ia eoe tes elated 18 Datasets provided as a XML web service BioCASE eee 19 Dataset s provided as a REST XML web service GBIPF eese 23 The GBIF data portal offer REST web service interfaces for taxon occurrence records occurrence density dataset metadata data provider metadata and data network metadata level data An example of the occurrence record REST service TOUUESESLVIe osos mide eaae eas st E enfe bi et See 24 An example of the service request style asking for all occurrence records of the species Allium porrum oie o Greer e v Que Een qe e daa East v epos
6. data file from a stable URL The dataset imported to the CWR Global Portal was manually extracted from the ESRI shape files of protected areas provided online from the UNEP WCMC WDPA web site The WDPA dataset ESRI shapefiles require the user to manually accept the data license during download and can thus not be automated From the WDPA dataset in ESRI shapefile format the descriptive text data on the protected areas was extracted in dBase format and converted to tab delimited text manually The process to extract data from the dBase file format can be done using an external application like e g dbf http berg systeme de dbf html http pkgsrc se wip dbf or the dbf2psql ftp ftp ngb se pub linux db application Using MS Excel may cause problems with the 65 536 record limit You are recommended to use the ESRI shapefiles for set 2 and set 4 only point data and without polygon data as these contains a unique list of all the protected areas To update this dataset save a refreshed tab delimited list of protected areas as data portal files data import unep wdpa wdpa protected area txt and execute step 5 and 6 text2psql pl and sql2db pl Note that you will need to make a new data use license with UNEP WCMC before you do this Note also that the current data use license for the WDPA dataset in the CWR Global Portal is time limited EURISCO Germplasm Data Portal Technical Description Last updated February 19 2008 Page 35 The EURISC
7. datasets on biodiversity based on the standards developed and maintained by TDWG Biodiversity Information Standards The GBIF data portal provides a public web service interface to the harvested and indexed distributed datasets The GBIF data portal web service interface supports SOAP and REST type interaction REST Representational State Transfer is an architectural style which in practice means that the online web resource is called from a standard URL where each of the parts of the URL divided by the slash represent one state Each of these URL parts can roughly be compared to the XML markup tags of a SOAP XML service request A REST style service basically means that each unique URL is a representation of some object And that you can get the contents of that object using an HTTP GET The GBIF data portal offer REST web service interfaces for taxon occurrence records occurrence density dataset metadata data provider metadata and data network metadata level data An example of the occurrence record REST service request style http data gbif org ws rest occurrence action parameter list An example of the service request style asking for all occurrence records of the species Allium porrum http data gbif org ws rest occurrence count scientificname Allium porrum Germplasm Data Portal Technical Description Last updated February 19 2008 Page 24 9 GBIF occurrence web service response Request de
8. described Edit NGBIF data last updated Details DM Edit DM gbif occurrences Column NOT described Not described Edit IF Georeferenced reci Details DM Edit DM gbif records Column NOT described Not described Edit GBlecords Details DM Edit DM Figure 34 start the data dictionary description by a description of the database table step 1 Update column description for taxon metadata bgci dtm BGCI data last updated Timestamp when the metadata value from the BGCI external reference dataset was last updated Remarks An asterix marks the required fields Register description Return to the table detail page Figure 35 next describe the individual columns using the Edit DM links from the table description detail page You may also consider updating the column description from the Edit link as well Work is in progress for a new improved data dictionary model based on this concept Germplasm Data Portal Technical Description Last updated February 19 2008 Page 42 Frequently asked questions May I install my own local implementation of the germplasm data portal The germplasm data portal is open source free to use for any purpose and GPL2 licensed You are thus most welcome to implement the complete data portal application or take parts of it You are free to distribute the application and or the source code further But if you wish to distribute a modifi
9. descriptors data model describes the raw data structure including tables and columns this is the previous primitive data dictionary tables descriptors columns coded values Table details Table name taxon metadata criptive name Taxon level metadata cription caption Taxon species unit level summary metadata from the external reference datasets on CWR resources Columns 32 Records 1846 Update table description View Columns BACK to the list of tables Database table fields descriptors for taxon metadata Column name Descriptive column name Data Model bgci dtm Column NOT described Not described Edit Details DM Edit DM bgci id Column NOT described Not described Edit Details DM Edit DM bgci records Column NOT described Not described Edit Details DM Edit DM credtm Column NOT described Not described Edit Details DM Edit DM creusr Column NOT described Not described Edit Not Described Details DM Edit DM eurisco id Column NOT described Not described Edit EURISCO ID Details DM Edit DM eurisco occurrences Column NOT described Not described Edit EURISCO Georeferenced records Details DM Edit DM eurisco records Column NOT described Not described Edit EURISCO records Details DM Edit DM full scientific name Column NOT described Not described Edit Not Described Details DM Edit DM gbif dtm Column NOT described Not
10. gz and tar formats are supported e convert the un compressed dataset file to tab separated text o if the dataset file is of the comma separated values CSV spreadsheet format convert to tab separated text o if the dataset file is of the Excel spreadsheet format gt convert to tab separated text o if the dataset file is of the dBase database table format gt convert to tab separated text e convert the tab separated text version of the dataset to a SQL INSERT script e import the SQL INSERT version of the downloaded dataset to the portal database e some datasets are also post processed after import to the database e calculation of taxon and country level summary metadata Germplasm Data Portal Technical Description Last updated February 19 2008 Page 30 An overview of the steps to access download convert and import an external reference dataset to the germplasm data portal is also visualized in Figure 24 As input configuration to the import dataset sub application of the data portal you will need to give a short acronym for your dataset to be used as the default folder name and file name below If the source dataset is published by the dataset provider from a online URL you need to describe this to the configuration file If your source dataset file is not available from a stable URL you may need to download the file and save it to the correct folder manually You will need to give the character encoding of the source dataset fi
11. hispida 162 2162 25 25 2007 10 11 16 26 33 142 Acalypha lanceolata 1145 134 2222 2007 10 11 16 26 33 143 Acalypha racemosa 41541 1818 2007 10 11 16 26 34 fiss Acalypha supera 252 0 p00r1 1162634 146 Acanthophyllum gypsophylloides 0 o 2007 10 11 162634 145 Acanthophyllum paniculatum 0 0 0071011162635 147 Acanthophyllum tadshikistanicum 0 o 007 1011 16 26 35 148 Achyranthes aspera 788 gt 788 432 2432 2007 10 11 16 26 36 149 Achyranthes bidentata 169 gt 169 45 245 2007 10 11 16 26 37 151 Adenanthera bicolor 0 0 2007 10 11 16 26 37 Figure 21 the function in the previous figure Figure 20 to refresh the cached summary number of species occurrences from the GBIF web service can be invoked from the germplasm data portal web interface Germplasm Data Portal Technical Description Last updated February 19 2008 Page 28 Gi f data portal A svn File Folder 2008 02 19 14 04 amp O svn gA default phps 5KB PHPS File 2007 09 18 10 33 i z applications Vg functions phps 15KB PHPS File 2007 09 10 18 51 amp C3 svn llimport baci garden phps 5KB PHPSFile 2007 11 05 08 03 amp Eg perhaps to use gl import baci plants phps 5KB PHPSFile 2007 11 05 08 03 adodb Vzl import dataset file phps 31KB PHPS File 2007 11 11 19 28 BioCaseTester gll import_eapgren phps 6KB PHPS File 2007 11 05 08 03 D contacts Z impor
12. import_gbif amp data_unit taxon amp taxon_name spe cies_name and index php app import_dataset amp inc import_gbif amp data_unit country amp country_name country_name The link is displayed for logged in users from the corresponding species and country metadata page Datasets provided as a simple file Many relevant and interesting datasets of importance to genetic resources management are still only available as simple files We are still a long way from seeing a wider implementation of standard web services for even half of the relevant source datasets Many of these datasets are maintained and updated using local database systems and local data models and then regularly exported and provided as a simple file In the best cases this regularly updated simple file is published from a stable URL available either from the HTTP or the FTP protocol In other cases the simple file needs to be extracted Germplasm Data Portal Technical Description Last updated February 19 2008 Page 29 from a manual user interaction with an online information system often protected by a data disclaimer or a data use license the user will need to manually accept And yet another data exchange alternative is when the simple file is provided by personal interaction e g email attachment or manually uploaded to the data portal web site with a web form file upload or a FTP file upload The simple file may also be provided as a variety of file formats The XM
13. search form 1 Allium Search Simple keyword search Total 26 hits or records record 1 to 25 displayed gt gt Next page A Letterbar Allium 2936 840 7561 Allium aflatunense 46 3 6 3 Allium altaicum 244 11 5 37 Allium altissimum 13 0 2 1 Allium ampeloprasum 3098 1684 10 240 Allium atroviolaceum 107 13 1 16 r Allium chinense 42 4 1 3 r Allium galanthum TT 1 1 11 r Allium giganteum 85 14 4 8 r Allium hookeri 4 0 2 r Allium karataviense 85 5 5 8 r Allium lineare 70 12 2 6 r Allium Innniciienis RA 1n 10 Details Taxon Figure 25 search interface simple keyword search for taxon level metadata from the indexed external datasets on CWR resources Germplasm Data Portal Technical Description Last updated February 19 2008 Page 36 Allium schoenoprasum Taxon summary data Family Full scientific name Genus Species Taxonomical reference IUCN The World Consenscion Unies IUCN status A GBIF Records Georeferenced BGCI BGCI Records Countries X SINGER Records Georeferenced Countries a EURISCO Records Georeferenced Countries Alliaceae Allium schoenoprasum L Allium schoenoprasum 1753 Sp PI 301 The 2006 IUCN Red List of Threatened Species Accessed on 2007 07 09 Data use guidelines Not found in the IUCN Red List NE Not Evaluated Number of records from GBIF http data gbif org Accessed on 2007 07 20 Data use guidelines
14. txt dataset_file_type csv dataset_encoding utf8 text file name institute wiews txt sql file name institute wiews sgql import table institute wiews Figure 23 the configuration attributes for the import dataset sub applications showing the attributes for the WIEWS Institute as example The import dataset configuration file is located in the directory of the sub application itself data portal applications import dataset import dataset acronym phps The web interface for the dataset import is invoked by the GET attribute inccimport dataset acronym e g http servername net index php app import dataset amp inc import wiews institute You may execute ALL the import dataset steps from one single link or execute individual steps from the data portal web interface All steps can be completed manually following the instructions below or added to an automatic server routine from the Germplasm Data Portal Technical Description Last updated February 19 2008 Page 31 crontab The sub routines for each step are implemented with the Perl scripting language Some supporting external software need to be installed on your server as described below Step 1 download dataset file from online source URL This step will download the source dataset using the attribute source url from the dataset configuration file You may of course download the source dataset file manually and save the file to the directo
15. 08 Page 11 Example how is the display of the welcome home page implemented Most users will first see the home page This is the standard default if no further feature request is called The public portal web root is mounted from data_portal html and the page index php will be loaded data portal html index php This page index php does nothing but include the script data portal page elements main phps The data portal page elements main phps creates the html page itself loading the html head and lt body gt tags The page icon the page top banner and menus are loaded from this main phps html index php main phps Jsettings phps page_elements settings phps page_elements cwr settings phps init_adodb phps Jlibraries adodb tohtml inc php libraries adodb toexport inc php libraries adodb adodb inc php hinit db phps page_elements functions phps page_elements cwr html_head phps Jpage elements cwr page menu O phps page_elements cwr page_banner phps page_elements cwr page_menu_1 phps page_elements cwr page_menu_2 phps page_elements page_content phps webpages cwr welcome inc page_elements cwr page_menu_left phps page_elements cwr page_foot phps Figure 3 chain or sequence of scripts to display the welcome home page I have used the tab indent to indicate from which scripts the individual scripts are included For example you will see that the data_portal html index php it
16. 2008 02 19 14 04 D sesto page menu O phps 3KB PHPS File 2007 11 05 08 03 ED sgsv IA page_menu_1 phps 4KB PHPS File 2007 12 10 12 55 8 E tools _menu_2 phps 2KB PHPSFie 2007 10 26 22 59 amp webpages Wz page menu lef phps 4KB PHPSFie 2008 02 19 14 04 settings phps 1K8 PHPSFie 2007 12 10 12 55 Figure 4 file directory showing the content of the data portal page elments folder f data portal A C svn File Folder 2007 11 09 11 07 B svn Blhtmi head phps 4KB PHPSFile 2007 10 04 21 10 amp applications Walhtmi_head_bak phps 2KB PHPSFie 2007 03 21 14 12 E fies W page_banner phps 2KB PHPSFile 2007 09 10 18 51 E html I page foot phps 10KB PHPSFie 2007 10 26 22 59 8 ez libraries Wlpage_menu_O phps 3KB PHPSFie 2007 09 10 18 51 El page elements i page menu i phps SKB PHPSFie 2007 10 08 21 10 amp 3 svn W page_menu_2 phps 3KB PHPSFie 2007 09 10 18 51 x bioversity Mz page menu leftphps 13KB PHPSFile 2007 10 10 14 26 ED chm Mg settings phps 1KB PHPSFile 2007 09 10 18 51 i onr z default GD eapgren oc e sesto sgsv E tools amp G webpages O files Figure 5 file directory showing the content of the data portal page elments cwr folder HTML HEAD The HTML HEAD is defined from the data portal page elements scope html head phps script Here the HTML META tags are defined The default page shows an example on how to define most of the relevant Germplasm Data Portal Techn
17. L data format is not very common for simple files In the best cases the simple file is provided as tab delimited data values with line breaks between individual data records The comma separated values CSV format is also common The benefit of this format is that quote marks can be used to wrap more complex data values which again can also be a source of error when mistakes including un escaped quotes inside the wrapped data value and missing closing quote marks are transmitted The proprietary spreadsheet format of the Microsoft Excel files is also popular as well as even simply sharing a complete Microsoft Access database file The dBase file format is yet another common file format which at least have a published open file format protocol Another challenge with interpretation and extract of data from datasets provided as simple files is that these are often provided as compressed files Most common is the ZIP format file zip and the GZ and BZ2 format file gz file tar gz file tar bz2 GZ compressed files is often a compression of a TAR ball used to combine several files and or directories in one file The methods and routines of the data portal to access interpret and index datasets provided as a simple file attempts to meet all these challenges mentioned above Import of external datasets e if dataset is online gt wget online dataset source file e if dataset file is compressed gt un compress and save file to the portal zip
18. O dataset is maintained by Bioversity International on behalf of ECPGR The EURISCO database is available as a BioCASE web service and shared with GBIF The current metadata for the EURISCO dataset was manually extracted directly from a copy of the original EURISCO database as maintained at Bioversity The Perl script update metadata pl eurisco may be used to update the CWR taxon level and country level metadata The recommended extension of indexing the EURISCO dataset would be to use the BioCASE or the TAPIR PyWrapper3 web service interface SINGER The SINGER dataset is maintained by Bioversity International on behalf of the CGIAR SINGER The SINGER database is available as a BioCASE web service and shared with GBIF The current metadata for the SINGER dataset was manually extracted directly from a copy of the original SINGER database as maintained at Bioversity The Perl script update metadata pl singer may be used to update the CWR taxon level and country level metadata The recommended extension of indexing the SINGER dataset would be to use the BioCASE or the TAPIR PyWrapper3 web service interface Taxon and country unit level summary metadata The external datasets for the CWR Global Portal is summarized from individual taxon and a country unit level search interface see Figure 25 with taxon see Figure 26 and country pages Taxon metadata Search taxon metadata by keyword You will find more search options with the advanced
19. Wiis cOBce pb ore ot e rr eh IR PORE D Mes bt olere RO Ae 42 Germplasm Data Portal Technical Description Last updated February 19 2008 Page 7 Introduction The germplasm data portal is developed by Bioversity International and the Nordic Genetic Resource Center NORDGEN as a generic web application written in PHP version 5 and with a generic ADODB database connection to the PostgreSQL database system PostgreSQL version 8 Some of the routines and methods have also been coded using the Perl scripting language The portal web application has been successfully tested with the Apache web server version 2 for the Apple Mac OSX Linux and Windows XP operating system environment The portal web application is based on the SESTO genebank system developed by NORDGEN The CWR Global Portal is actually only one layout skin of the very same portal application as used for the Svalbard Global Seed Vault data portal the Generation Challenge Program Central Registry and the ECPGR ECCDB databases hosted from NORDGEN with more Source code The data portal source code is available from the Subversion code repository hosted by NORDGEN http wwwdev ngb se WebS VN listing php repnamezdata portal Source code directory and file structure e data portal EJ E E E EH EJ EJ svn 2 applications files html f libraries page elements tools webpages LJ svn applications fil
20. ataset was last accessed by the CWR global portal on 2007 05 21 Data use guidelines WDPA 1 042 protected areas in Italy reported in WDPA of UNEP WCMC Germplasm Data Portal Technical Description Last updated February 19 2008 Page 38 Search information from FAO Number of institutes with reported PGR activity in Italy from WIEWS WIEWS Accessed on 2007 03 15 Data use elines es in Italy have PGR activity reported in WIEWS p T Search FAOLEX for legal legislation on Italy EX Data use agreement D arch EcoPort for more information on Italy a ata use agreement ECOLEX Search ECOLEX for more information Data use agreement GfRacris caris Searc SRIS CA for more information on Italy These links to update the metadata is displayed ONLY for logged in users Figure 28 example of a country level metadata detail page for Italy Manual update of taxon and country unit level metadata You may want to quickly update the taxon or country unit level summary metadata for a specific unit or perhaps you want to update the summary metadata without importing a new external reference dataset If you know PostgreSQL you may update the database table holding the summary metadata directly using the database prompt as displayed in Figure 29 Figure 29 example of using the PostgreSQL database prompt to update table data Germplasm Data Portal Technical Description Last updated February 19 2008 Page 39 The CWR Global Po
21. ave been registered Figure 8 the page middle content frame wrapps the data portal content from a sub application or from a information web page Germplasm Data Portal Technical Description Last updated February 19 2008 Page 16 Information pages If the data portal is called from a URL with a GET attribute page REQUESTPT page the data portal will look for a information web page file located in the data portal webpages scope folder with file extension inc or phps Figure 9 If such a file is not located the data portal webpages directory will be searched to include the default generic information page If no file is located an error message will explain this to the user Add the information web pages you wish to use in your portal implementation to the data_portal webpages lt scope gt directory and link to them using the internal link lt a href index php page LINK TEXT a Ba e data portal LJj svn File Folder 2007 11 09 11 07 B svn amp about inc 7KB INC File 2007 11 08 10 17 z applications amp citation inc 2KB INCFie 2007 11 08 10 17 amp f files amp contact us inc 2KB INCFie 2007 11 08 10 17 E html BA contact us bk phps 20KB PHPS File 2007 10 08 21 10 E libraries E cwr data section inc 7KB INC File 2007 11 08 10 17 G page elements A cwr definition inc 3KB INCFile 2007 09 10 18 51 amp f tools cwr gris inc 7KB INCFile 2007 09
22. back File Folder 2007 11 08 10 17 germplasm File Folder 2007 03 17 12 37 images File Folder 2007 10 29 12 08 import_dataset File Folder 2007 11 05 08 03 literature File Folder 2007 09 10 18 51 login File Folder 2007 11 08 10 17 news File Folder 2007 11 08 10 17 fj ontology File Folder 2007 09 30 06 55 z taxon metadata File Folder 2007 10 10 13 59 Gawebgis File Folder 2007 09 10 18 51 amp INFO TXT 1KB TextDocument 2007 09 10 18 51 vi shared_functions phps 16KB PHPSFile 2007 09 10 18 51 Figure 10 portal content sub applications are loaded from the data portal applications directory requested by the REQUEST app GET attribute See the user manual for more information of how to use the individual sub applications Data harvest routines and methods The data portal is designed to publish and integrate distributed datasets not to maintain original source datasets The target distributed source datasets can be provided as a set of simple file s or as a more mature web service The data portal was originally designed to access scan and index XML data output from the GBIF type BioCASE PyWrapper database wrapper web service Many relevant and important datasets on genetic resources and related biodiversity data types are not yet available as XML data from web services Many datasets are still either provided as an online file or as a file provided in by personal contact or as uploaded to the portal web site The portal appl
23. be invoked from the germplasm data portal web interface eee peer eerte ae nee Ie HaT EP FRI E Ce edge 28 Figure 22 the function Figure 19 to refresh the count of occurrence records for a species from the GBIF REST web service can be invoked from a PHP script data portal applications import datasets import gbif taxon phps This script can be executed from the command line or added to the crontab for a scheduled automatic refresh may require some minor update of the current version of the deque T P 29 Figure 23 the configuration attributes for the import dataset sub applications showing the attributes for the WIEWS Institute as example eene 31 Figure 24 a summary flow of the steps to access download convert and import an external reference dataset to the germplasm data portal sess 33 Figure 25 search interface simple keyword search for taxon level metadata from the indexed external datasets on CWR resources 0 0 cece cece eeeeesceeecnseceeeeeeeeeeeeeaees 36 Figure 26 example of a taxon level metadata detail page for Allium schoenoprasum 37 Figure 27 search interface advanced search for country level metadata from the indexed external datasets on CWR resources 0 0 eee cece eeeeesceseceeeceeteeeeeseeeeeaees 38 Figure 28 example of a country level metadata detail page for Italy 39 F
24. but could be a serious security problem for a production version of the data portal Add the following lines to the httpd conf of your Apache web server Alias portal path to the data portal folder html Directory path to the data portal html Options Indexes AllowOverride None Order allow deny Allow from all Directory The path to the data portal could for example be usr local data portal The httpd conf configuration could also be added to the extension folder e g usr local apache2 conf extra data portal conf You will find an example file to copy here in the tools httpd conf d folder FILES in the ROOT directory main phps The main phps starts by reading the settings phps init db phps and init adodb phps scripts inside the lpage elements folder See INFO TXT inside this folder for more information Then main phps will continue with building the HTML tags for html head and body Inside the body the content is collected from the sub folder page element settings phps The settings script in the ROOT directory is included in main phps before the settings from the page element sub folder page elements settings phps Here some generic System parameters are set or calculated from the web server environment variables init adodb phps This script is used to include
25. c default example elements Start by creating a subfolder in the page elements directory with the same folder name as your chosen scope acronym see Figure 5 Next copy the default scripts you wish to modify from the page elements directory to your new scope directory If the data portal application does not find the individual page element scripts in your scope folder the default script will be loaded Contrary if the scope specific script is successfully located the default page element script will not be loaded there can only be one top menu page banner etc Germplasm Data Portal Technical Description Last updated February 19 2008 Page 13 amp G data portal X C3 svn File Folder 2008 02 19 14 04 amp C3 svn bioversity File Folder 2007 09 10 18 51 G applications achm File Folder 2007 11 11 23 44 8 i files fcr File Folder 2007 11 14 18 47 E i html default File Folder 2007 11 05 08 03 ie libraries Qeaparen File Folder 2007 11 05 08 03 page elements decpor File Folder 2008 02 19 14 04 amp O svn Gian File Folder 2007 09 10 18 51 bioversity B sesto File Folder 2007 12 10 12 55 ED chm BD sgsv File Folder 2008 02 19 14 04 3 cw igi html head phps 4KB PHPSFie 2008 02 19 14 04 Ez default amp INFO TXT 2KB TextDocument 2008 02 19 14 45 f eapgren Walpage_banner phps 2KB PHPSFie 2007 10 26 22 59 D ecpor Wz page content phps 6KB PHPSFie 2008 02 19 14 04 2 o iz page foot phps 6KB PHPSFie
26. cord for INSTCODE CHE082 The Swiss Agency for Development and Cooperation Due to problems to parse this record it will unfortunately be excluded during the dataset import An exception for this record is hard coded in the csv2txt pl Perl script The WIEWS Institute dataset will successfully be imported from a fully automatic procedure BGCI Garden and BGCI Plants The dataset from the Botanical Gardens Conservation International BGCI is not yet made available from a stable online URL The dataset imported to the CWR Global portal will be shared through personal communication with BGCI and made available as an email attachment The provided source dataset files are bgci garden csv bgci plants csv and bgci plant to garden csv The BGCI datset is provided as semi colon separated values partly wrapped in double quote marks CR LR are used to separate records Windows style line breaks For many of the records the values from multiple columns directly after the plantid seems to be wrapped inside the same double quote marks For this reason the quote marks are ignored as defining the wrapping of data values for the bgci plants dataset A significant number of records do not contain data and also ignored Exceptions for data records difficult to parse are hard coded in Germplasm Data Portal Technical Description Last updated February 19 2008 Page 34 csv2txt pl and in text2psgl pl The BGCI dataset as last provided will i
27. ect Jn situ conservation of crop wild relatives through enhanced information management and field application The development of the portal is ongoing and new resources are being added as they become available The germplasm data portal is a generic data portal application for integration and online publication distributed datasets based on the SESTO genebank information system developed by the Nordic Genetic Resource Center NORDGEN previously called Nordic Gene Bank NGB The generic data portal application is also based on the GCP Central Repository and the Germplasm Clearing House Mechanism CHM both developed by Bioversity International Germplasm Data Portal Technical Description Last updated February 19 2008 Page 2 Germplasm Data Portal Germplasm Data Portal A generic data portal application for distributed datasets Technical description of the germplasm data portal application Dag Terje Filip Endresen Document last updated February 19 2008 Germplasm Data Portal Technical Description Last updated February 19 2008 Page 3 Index hun 4 List of Deut ES e m etetuevesie lectio Soo etn alisteod bt nios tae the Do aso co rebat io Eve oer in feque uit s 5 EnttOOWCUOl eor ai fn acs wa E E E E A sgl a E eal E ERA 8 Source COUG aei S esta eei E EAR NT AEE tui uic EAI TERE TAa 8 Source code directory and file structure ioo code Ideen ee Eie den INR PAREN RIS E
28. ed through the portal source code E g the CSS for the CWR is in a sub folder named cwr data portal html css cwr style css the images of the CWR image archive is saved to a sub folder named cwr data portal html image archive cwr etc INFO TXT All or most of the directories of the source code contains a file INFO TXT with more detailed information about the files you find at each directory level Below you see the INFO TXT file of the data portal ROOT directory as an example Source code ROOT directory All content for the data portal is included from the html index php page The html index php page does little itself than open the main phps script in the ROOT directory described here Th main phps script starts by reading the settings phps init adodb phps and init db phps scripts inside the ROOT directory folder settings phps init adodb phps init db phps Germplasm Data Portal Technical Description Last updated February 19 2008 Page 9 The index php inside the ROOT directory is only a dummy page and should normally not be available from the web tree When the data portal is properly installed only the html folder will be mounted in the public web tree Note that if the complete data portal directory itself is unzipped or copied into the web tree then all the settings and configuration may be publicly readable This may be useful during development
29. ed version please contact the Nordic Gene bank or Bioversity International Will the data portal work with Tomcat The data portal is not a Java application and will not work with Apache Tomcat If you wish to serve both PHP applications and Java applications from your online web server you will need to install both Apache Httpd and Apache Tomcat or analogue web application servers You may serve Java applications through the Apache Httpd with a connector plug in for the Apache Tomcat server I do not believe it is as easy to serve PHP applications from a similar approach through the Apache Tomcat web server Does the germplasm portal follow the W3C guidelines The data portal attempts to follow the W3C Web Accessibility Guidelines WCAGIO http www w3c org TR 2000 NOTE WCAG10 TECHS 20001106 The data portal attempts to implement a separation of content and layout using the CSS cascading style sheet definitions for generation of the layout Software used by or useful to the data portal Apache web server httpd server http httpd apache org PHP Hypertext Preprocessor script programming language http www php net PostgreSQL database server http www postgresql org ADOdb Database Abstraction Library for PHP http adodb sourceforge net Perl programming language http www perl org Subversion version control system Code Repository alternative to CVS http subversion tigris org Recode character set con
30. erenne NGB13332 Details Pisum sativum ssp sativum NGB12196 Lolium multiflorum NGB15422 Nordic Gene Bank Details Brassica oleracea var capitata f alba NGB13555 Nordic Gene Bank Details Export search results to Excel Brassica rapa ssp oleifera Nordic Gene Bank Nordic Gene Bank Nordic Gene Bank Figure 16 the CHM portal also comes with a search interface to the CHM database index Dataset s provided as a REST XML web service GBIF The Global Biodiversity Information Facility GBIF support the implementation of tools to establish a distributed global network of biodiversity information resources based on the standards developed and maintained by TDWG Biodiversity Information Standards The GBIF data portal http data gbif org harvest data records from this network of distributed biodiversity data providers and index a selected number of descriptors including the scientific name geospatial origin record identifier catalog number holding institute etc The GBIF data index can be explored from the excellent data search portal but more important to the germplasm data portal is the web service interface of the GBIF data index http data gbif org tutorial services Germplasm Data Portal Technical Description Last updated February 19 2008 Page 23 Biodiversity Information Standards Figure 17 the Global Biodiversity Information Facility GBIF maintains a data portal of global distributed
31. es html libraries G page_elements E tools webpages amp CREDITS STT 2KB I functions phps 28 KB index php 13KB G INFO TXT 4KB liglinit adodb phps 2 KB lili init db phps 5KB j INSTALL TXT 5KB G LICENSE TXT 26KB I main phps 8KB I settings phps 5KB test php 1KB GI VERSION TXT 1KB File Folder File Folder File Folder File Folder File Folder File Folder File Folder File Folder Text Document PHPS File PHP Script Text Document PHPS File PHPS File Text Document Text Document PHPS File PHPS File PHP Script Text Document Figure 2 file directory showing the data portal root directory Germplasm Data Portal Technical Description Last updated February 19 2008 2008 02 19 14 04 2008 02 19 14 00 2008 02 19 14 00 2008 02 19 14 04 2007 03 17 12 37 2008 02 19 14 04 2007 08 24 17 42 2008 02 19 14 00 2008 02 19 14 04 2008 02 19 14 04 2008 02 19 14 04 2007 10 26 11 06 2008 02 19 14 04 2008 02 19 14 04 2007 10 26 11 06 2007 03 17 12 37 2008 02 19 14 04 2008 02 19 14 04 2008 02 19 14 04 2007 03 17 12 37 Page 8 The data portal source code is easily installed simply by extracting the source code directories and files to a folder on your local server or a desktop laptop workstation with the Apache web server and PHPS installed Apache httpd http httpd apache org PHP http www php net You may extract the data portal source code to any folder you want as the application use a relative pa
32. escription Last updated February 19 2008 Page 4 Taxon and country unit level summary metadata eese 36 Manual update of taxon and country unit level metadata eese 39 Data dicllDHdly oec doses eb Wah da use Sets aa De dodo ets cf ess ec n Sac haa eat cag 41 Frequently asked quesos eec ata top ree t ras or Ple Ha Ee EE Pe AR PUER QU VERS AN ARN SES TEE PARUYN 43 Software used by or useful to the data portal sese 43 Relerencessoo xoa sudare euh dui aed SUA RAE d ELE 44 List of figures Figure 1 screenshot of the CWR CropWild Relative Global Portal http csvrint ermfo Net 2226 rerit tad p p beca 2 Figure 2 file directory showing the data portal root directory sess 8 Figure 3 chain or sequence of scripts to display the welcome home page 12 Figure 4 file directory showing the content of the data portal page elments folder 14 Figure 5 file directory showing the content of the data portal page elments cwr foldet a ptt ertt n Etat ipt wee pudasunacse vas A sueta fled d TL AERD 14 Figure 6 page application menu level 1 page menu 1 phps sseess 15 Figure 7 left side menu page_menu_left phps aor opt a eiii ine eae 16 Figure 8 the page middle content frame wrapps the data portal content from a sub application or from a information web page sese 16 Figure 9 i
33. esponse from the harvested BioCASE end point when there are more records available than the requested number of records per page or the maximum allowed records per page the remote BioCASE DSA is configured to allow 21 Figure 15 step 4 is the preview of the harvested XML data extracting selected data values and the import of these values to the CHM database index 22 Figure 16 the CHM portal also comes with a search interface to the CHM database I D RET ET RUNE 29 Germplasm Data Portal Technical Description Last updated February 19 2008 Page 5 Figure 17 the Global Biodiversity Information Facility GBIF maintains a data portal of global distributed datasets on biodiversity based on the standards developed and maintained by TDWG Biodiversity Information Standards 24 Figure 18 example of GBIF response format http data gbif org ws rest occurrence count scientificname Allium porrum 25 Figure 19 example of GBIF response format http data gbif org ws rest occurrence count scientificname A llium porrum amp geor eferencedonlystrue amp stylesheet oci o eite itd tune tug oit e Cae cH 26 Figure 20 this is the PHP code to access the GBIF data portal REST web service Irae eandem ie Nd eu deu e 27 Figure 21 the function in the previous figure Figure 19 to refresh the cached summary number of species occurrences from the GBIF web service can
34. file formats can be added as needed You may of course manually convert the dataset file to tab separated text and save to the data portal files data import data acronym directory Step 4 recode the tab text dataset file to Unicode if needed The recommended implementation of the data portal is for the Unicode utf 8 encoding You may of course define your database also with other encoding schemas The data portal ill by default transform the source dataset file to the utf 8 character encoding The Perl script data portal tools bin text recode pl is used for this operation ad will require the external application recode http www gnu org software recode to be installed at the server You may perhaps prefer to use the iconv API http en wikipedia org wiki Iconv for the recoding of the dataset character encoding You may of course recode the tab delimited text file manually for example using iconv Germplasm Data Portal Technical Description Last updated February 19 2008 Page 32 and save the recoded file under the same file name data portal files data import data acronym data acronym txt Step 5 transform the tab delimited dataset file to SQL INSERT script The data portal may automatically transform tab delimited text data values to a SQL INSERT script Records are expected to be separated by a line break and data values by the tab character The first row of the file is expected to hold the column fie
35. horizontal menus for your portal implementation For example the CWR implementation have blank top menu page menu O phps and second level application menu page menu 2 phps see Figure 6 Home About CWR Data Feedback Help Site map ES Search Figure 6 page application menu level 1 page_menu_1 phps The left side menu items see Figure 7 is defined in the same way by a bullet list and transformed by the CSS layout definitions for portlet_left portlet_title and portlet content Germplasm Data Portal Technical Description Last updated February 19 2008 Page 15 Project Partners National Inventories External Datasets Data sharing and use agreements Portal technical specifications CWR Links Search the CWR Portal web site Figure 7 left side menu page menu left phps Page content frame The page content frame itself is defined by the CSS definition for content of the div id content gt element on the main phps script Everything INSIDE this content div block frame is included from the page elements page content phps script The content of the middle page frame can be either a page from the data_portal webpages folder requested by the REQUEST page GET attribute or a sub application request from the REQUEST app GET attribute see Figure 8 Welcome to the Crop Wild Relative Global Portal This portal provides access to information and data resources important for
36. ical Description Last updated February 19 2008 Page 14 Dublin Core definitions The html head phps is also where you define the link to the CSS style definitions you wish to use CSS Cascading Style Sheet As mentioned the CSS style to be linked is defined in the HTML HEAD script It is recommended that you keep the link to the generic data portal html css style css You may define your own CSS style from the data portal html css scope style css to override the generic style definitions You may name your style sheet files as you wish as long as you provide the link to them from the page elements scope html head phps script The portal application output is written as XHTML and with the aim of keeping all presentation layout definitions in the separate CSS file style css Page menus The top menu of the page is defined by the script page elements scope page menu O phps The two page application menus are defined by the page elements scope page menu 1 phps and the page elements scope page menu 2 phps The menus are defined as a basic HTML bullet list The CSS definition for nav1 and nav is used to transform the list to the horizontal menu as displayed ul li menu item 1 li li menu item 2 lt li gt lt ul gt Add or remove list items to reflect the menu items you wish to have displayed You may leave your scope version of the menu blank no bullet list to remove individual
37. ication was thus extended for easier import and indexing of also files of a defined data model and following one of the supported file formats Germplasm Data Portal Technical Description Last updated February 19 2008 Page 18 e Web services e Simple files Datasets provided as a XML web service BioCASE The original data portal as derived from the GCP Central Registry application the Germplasm Clearing House Mechanism CHM http chm grinfo net The CHM portal was developed during January to March 2006 Figure 11 SINGER EURISCO ECPGR GBIF NGB Bioversity Germplasm Data Portal PROTOTYPE Genetic Diversity Why is T biodiversity What is the Germplasm Data Portal important Should the Germplasm Data Portal form a consortium of genebanks and What is genetic z z diversity other institutes involved in the conservation of germplasm Why conserve germplasm Germplasm Databases Global germplasm index Germplasm Clearing House Mechanism about CHM Sections under development Data Standards Schema Data HARVEST Data IMPORT Germplasm Data Contact institutes persons CHM Data Model Welcome to the Germplasm Data Portal Should the GDP provide an index of global accession level passport data GBIF style index Should the GDP provide a forum for collaborative development of standards and tools to access global information on germplasm TDWG style consortium Shou
38. igure 29 example of using the PostgreSQL database prompt to update table data 39 Figure 30 here is the link to the edit country metadata form This link is ONLY displayed for logged in Users dorsi ovt onset bens Esto netus Ve feo tire e MER S EPA PE ETE re sides 40 Figure 31 this is the edit form for country level metadata You would normally update these data points from the semi automatic update routines for external datasets For example the GBIF summary metadata is very easy to update per unit as well as for more units from the link located directly next to the link to this form from the taxon and country level metadata detail pages sese 40 Figure 32 example of descriptive column names and mouse over column tip as defined from the data dictionary for a data unit list view eee 41 Figure 33 example of descriptive column names from the data dictionary for a data unit ur V1 AI EUER 41 Figure 34 start the data dictionary description by a description of the database table step ID E E gn Riese EE E E E 42 Figure 35 next describe the individual columns using the Edit DM links from the table description detail page You may also consider updating the column description Germplasm Data Portal Technical Description Last updated February 19 2008 Page 6 from the Edit link as well Work is in progress for a new improved data dictionary inodel base dom
39. implementation Add a link to the sub applications you wish to use with the internal link lt a href index php page LINK TEXT lt a gt from one of the navigation menus You may of course add your own sub applications to the data portal applications directory Figure 10 and call them the same way with the REQUEST app GET attribute value equal to the sub application folder name Please do not include any html head Germplasm Data Portal Technical Description Last updated February 19 2008 Page 17 or body HTML tags You should also remember to create the main phps script data portal applications sub application name main phps to start the new sub application data portal LJ svn File Folder 2007 11 09 11 07 B C3 svn M3 perhaps to use File Folder 2007 05 29 14 34 G applications Qadodb File Folder 2007 03 17 12 37 E files I BioCaseTester File Folder 2007 03 17 12 37 E fe html G contacts File Folder 2007 11 08 10 17 amp libraries fa country ni File Folder 2007 09 10 18 51 amp ez page elements aQdata_harvest File Folder 2007 03 17 12 37 amp tools a data_import File Folder 2007 09 10 19 17 amp webpages G data_model File Folder 2007 11 05 08 03 G data_providers File Folder 2007 03 17 12 37 G data_schema File Folder 2007 03 17 12 37 a data_unit File Folder 2007 11 09 11 07 f dummy File Folder 2007 03 17 12 37 events File Folder 2007 03 17 12 37 f feed
40. l Portal The data portal as implemented for the CWR Global Portal is prepared for automatic import of a number of external reference datasets A few details for each of these datasets will be described here as examples Other implementations of the germplasm data portal application than the CWR Global Portal may use the very same configuration to import these external reference datasets if this is useful WIEWS Institute The WIEWS institute table holds the Institute code used as the standard identifier for institutes with activities relevant to the Genetic Resources community The dataset is maintained by FAO Food and Agriculture Organization of the United Nations The dataset is available from the stable online URL http apps3 fao org wiews export zip and have been so for years The WIEWS institute dataset is provided as utf 8 and zip compressed The un compressed dataset file is export txt and provided as comma separated values where all the data values are wrapped in double quote marks The WIEWS institute dataset file use simple carriage returns CR v 0x0D Mac OS 9 style line break to separate the records The carriage return characters are converted to line feed LF n 0x0a UNIX style line break with the Perl script data portal tools bin text line break pl At the time of writing this technical manual the WIEWS institute dataset includes a CR LF Windows style line break inside of the data value for URL in the re
41. ld be a useful extension of this step 1 Data schema List data schema schema elements concepts Data schema xsd Schema title Version Schema full name Published ABCD ABCD 1 20 Details List concepts ABCD 2 06 Details List concepts Darwin Core 2 Darwin Core 2 v1 2 Details List concepts GCP Passport GCP Passport 1 02 Details List concepts GCP Passport GCP Passport 1 03 Details List concepts GCP Passport GCP Passport 1 04 Details List concepts Germplasm CHM Germplasm CHM 1 0 Details List concepts Multi Crop Passport Multi Crop Passport Details List concepts Figure 13 step 2 is the list of supported global data standards including their mapping to the implemented CHM data model of the CHM database index Germplasm Data Portal Technical Description Last updated February 19 2008 Page 20 Data harvest BioCASE web service entry point Data Provider Nordic inventory of plant germplasm v More information about the selected data provider here Data Schema to harvest Data schema http www ipgri org schemas gcp passport 1 04 GCP Passport 1 04 J Revie resh the list of supported schema live he More information about the selected data schema h Data Harvest Filter condition Filter concept Genus v Filter value Horde Additional settings Number of records HarvestALL records No limit M Records per page Limit of 1000 records per
42. ld names The Perl script data portal tools bin text2psql pl is used for this operation If you want to create the SQL INSERT script manually please save the file as data portal files data import data acronym data acronym sql Step 6 IMPORT dataset to the database This step will import the data from the SQL INSERT script to the database The Perl script data portal tools bin sqlI2db pl is used for this operation This script will start by deleting DROP of the previous table with the dataset acronym name before the table is recreated and loaded with the new data values The sql2db pl script is developed for the PostgreSQL database system only You may of course perform this step manually using for example the command psql d lt database gt f SQL INSERT file name gt Download source file wget dataset pl Source file Unzip source file if zipped unzip gunzip Dataset file Convert to tab text xls2tx pl pl esv2txt pl Tab text file hi Convert to SQL data text2psql pl SQL data file Import SQL data to the database sql2db pl Database Update metadata update_metadata pl Figure 24 a summary flow of the steps to access download convert and import an external reference dataset to the germplasm data portal Germplasm Data Portal Technical Description Last updated February 19 2008 Page 33 Import of external reference datasets examples from the CWR Globa
43. ld the GDP provide tools to access global information on germplasm data harvest desktop software for download Suggested activities outputs Global unique IDs and a system to resolve metadata from the GUID LSID Taxonomic name service synonyms resolution of taxon concepts etc Inventory of germplasm collecting missions Inventory of collecting events collecting number location time collecting mission Inventory of commercial cultivars breeding company names release year Inventory of breeding events cultivars landraces Global index of conserved germplasm accessions fixed release of a index download version every month every 6 month Inventory of donor events Inventory of regeneration events Inventory of germplasm distribution events Inventory of institutes and persons complement and collaborate with the WIEWS db NB many of these activities need close collaboration with WIEWS to avoid dupplication of efforts Figure 11 the first version of the data portal was the Germplasm Clearing House Mechanism designed to access scan and index XML data from BioCASE database wrapper web service end points The steps of the CHM portal are implemented as sub applications and available to other implementations of the data portal like the CWR SGSV EAPGREN etc The steps of indexing remote and distributed BioCASE end points includes 1 Figure 12 a list of the Germplasm Data Portal Technical Descri
44. le If no character encoding is given the data portal will attempt to guess the encoding If you source dataset file is compressed as a zip or a gz gz tar gz tar bz2 the data portal will sense this using the file extension and un compress the file Other compression formats are not yet supported and you will need to un compress the file manually You may want to give the file type If the un compressed source dataset file has the correct file extension you may leave the file type o be decided by the extension The data portal supports tab delimited files tab txt MS Excel spreadsheet xls and comma separated values csv XML data and dBase files are partially supported but this will be developed further Other file types will give an error message and you will need to convert them to tab delimited text manually The list of supported file types will be extended You will need to give the directory path to the folder on your server where you want the temporary files to be placed during the import dataset routines The directory data_portal files data_import lt dataset_acronym gt will be used as the default NB Make sure the web server have write permission to this folder if you wish to use this routine dataset_acronym institute_wiews source_url http apps3 fao org wiews export zip source_file_name export zip import_path usr local data_portal files data_import institute_wiews dataset_file_name export
45. mport successfully if new dataset files are saved as data portal files data 1mport bgci bgci garden csv and data portal files data 1import bgci bgci plants csv The import data sub application includes an automatic routine to update the taxon level and country level CWR metadata For this purpose the data portal tools bin update metadata pl is used You may of course execute this Perl script manually or add to you crontab as update metadata pl bgci garden and update metadata pl bgci plants IUCN Red List The IUCN Red List dataset is not yet online from a stable URL The dataset imported to the CWR Global portal was manually extracted from the IUCN web portal http www iucnredlist org and downloaded as comma separated values where only the data values for scientific name are wrapped in double quote marks Line feed characters n LF 0x0A UNIX style line breaks are used to separate data records The import data sub application automatic routine to update the taxon level and country level CWR metadata uses the data_portal tools bin update_metadata pl Perl script To execute this Perl script manually or add to you crontab use the command update metadata pl iucn redlist Note that the data model of the exported IUCN red list dataset may change in later version so attention is advised WDPA World Database on Protected Areas The World Database on Protected Areas WDPA is not yet available as a standard
46. nformation web pages are loaded from the data_portal webpages lt scope gt directory requested by the _REQUEST page GET attribute 17 Figure 10 portal content sub applications are loaded from the data portal applications directory requested by the _REQUEST app GET attribute 18 Figure 11 the first version of the data portal was the Germplasm Clearing House Mechanism designed to access scan and index XML data from BioCASE database wrapper web service end potis esteri eotn rueda RR QR cea Rv soshacavevbecetenpoanae 19 Figure 12 step 1 of the CHM is a list of data provider BioCASE service end points All the BioCASE DSA URLs are registered to provide the starting point for a data harvest session A normal UDDI with a standard WSDL style discovery would be a useful extension fithis step T et tee contes Eri Atrides Eure eerte viae eu bor ape vectus 20 Figure 13 step 2 is the list of supported global data standards including their mapping to the implemented CHM data model of the CHM database index 20 Figure 14 step 3 is the interface to formulate the data request request xml according to the BioCASE protocol The data harvest methods are developed as a PHP library and can be started either directly from the web interface or from the UNIX prompt command line or the crontab The data harvest includes paging of the XML data r
47. on This acronym is named scope in the context of the portal scripts and used as the directory folder name for specific content and configuration for your new implementation The concept of this scope is such that multiple portal implementations can live in these scope acronym directory folders sharing the same base portal source code The default scope acronym can for example be defined from the data portal settings phps configuration script in a similar manner as the presented examples for the CWR SGSV and EAPGREN implementations This is only the default scope whereas the scope can thus be swapped by the user simply giving the URL GET attribute _REQUEST scope You may of course deactivate this behavior in for example the generic data portal settings phps configuration file if you do not wish to support user initiated scope swaps The layout elements The layout elements are located in the ROOT sub folder page elements data portal page elements see Figure 4 Here you will find the script defining the HTML page wrapper including the HTML META tags data portal page elements html head phps the page banner data portal page elements page banner phps and the page menus data portal page elements page menu O phps menu l phps menu 2 phps menu left phps as well as the page footer data portal page elements page foot phps Directly in this page elements directory you will find the generi
48. page An asterix marks the required fields Please login for permissions to start data harvest Figure 14 step 3 is the interface to formulate the data request request xml according to the BioCASE protocol The data harvest methods are developed as a PHP library and can be started either directly from the web interface or from the UNIX prompt command line or the crontab The data harvest includes paging of the XML data response from the harvested BioCASE end point when there are more records available than the requested number of records per page or the maximum allowed records per page the remote BioCASE DSA is configured to allow Germplasm Data Portal Technical Description Last updated February 19 2008 Page 21 Data import BioCASE web service entry point Data provider http biocase grinfo net pywrapper cgi dsa SINGER Preview of the harvested records this page Records preview 10 records v Total 500 records harvestec Data import no data import preview data only v Harvest settings for previous data harvest instance was BioCASE URL http 192 168 181 162 pywrapper cgi dsa SINGER Schema http www ipgri org schemas gcp_pass 1 02 Max number of records per page 100 Max number pages Harvest results for previous data harvest instance was Last data harvest 2006 03 21 16 43 06 Harvest duration was 9 519 seconds Total records 500 CIATBEAN G1 Be
49. ption Last updated February 19 2008 Page 19 discovery URLs of the data provider services 2 Figure 13 a list of the supported global data standards used by these data providers to publish the relevant datasets including a mapping of these standards to the data model of the CHM index 3 Figure 14 methods to formulate the data request query as specified by the BioCASE protocol request xml and harvest the XML data from the selected BioCASE provider service 4 Figure 15 methods to preview the harvested XML data and extract data values to be imported to the CHM database index Figure 16 Data providers BioCASE data provider entry points URL DSA BIOCASE URL Data Source Data provider N A AVRDC http ww3 bgbm org biocase http www plant dlo nl bioc Details ss http gene3 Details gt http CIP Details http genebank iit IITA s X http genebank iita IITA s http genebank iita IITA http genebank iit IITA NA http ebank iita IITA _YAM http IITA SINGER http IPGRI MGIS http bioca IPGRI INIBAP IPGRI INIBAP ICIS http biocase IRRI IRRI Iva http LUBI NGB NGB http NGB NGB grin http 198 77 USDA GRIN USDA GRIN Figure 12 step 1 of the CHM is a list of data provider BioCASE service end points All the BioCASE DSA URLs are registered to provide the starting point for a data harvest session A normal UDDI with a standard WSDL style discovery wou
50. r the Perl scripting language The portal web application have been successfully tested with the Apache web server for the Apple Mac Linux and Windows operating system environment CWR Project 2004 01 01 The crop wild relatives global portal has been established within the framework of the UNEP GEF supported project In situ conservation of crop wild relatives through enhanced information management and field application lead by Bioversity International and implemented from 2004 to 2009 Funds for the development of the global portal were also received from the German Federal Ministry for Economic Cooperation and Development BMZ View all News items A total of 2 news stories have been registered Page last modified 2007 11 07 23 27 52 0100 Wed 07 Nov 2007 Currenttime is 2007 11 09 13 42 07 Contact Feedback CWR Portal terms of use Terms of use external datasets Citation You are not logged in Login here e UNEP ce hovem IPGRI and INIBAP operate under the name Bioversity International Bioversity International Headquarters Via dei Tre Denari 472a 00057 Maccarese Rome Italy Tel 39 066118 1 Fax 39 0661979661 Figure 1 screenshot of the CWR CropWild Relative Global Portal http cwrint grinfo net The CWR global portal provides access to information and data resources important for the conservation and utilization of crop wild relatives CWR It was created within the UNEP GEF supported proj
51. rden for more information about Allium schoenoprasum Search flickr for pictures of Allium schoenoprasum Search picsearch for pictures of Allium schoenoprasum Edit Taxon Metadata Update GBIF taxon metadata These links to update the metadata is displayed ONLY for logged in users Figure 26 example of a taxon level metadata detail page for Allium schoenoprasum Germplasm Data Portal Technical Description Last updated February 19 2008 Page 37 Country metadata Search form Your search criteria was Country name contains it Clearfilter Go Add search criteria S mans E Add columns to the list rT a Display 25 hits per page Total 19 hits or records record 1 to 19 displayed B E E H l K L M Lid S Uu Letterbar o Ememsame _ County 1502 Connon namo GEIF records BGC planis recorde EURISCO records SINGER recorde British Indian Ocean Territory Asia Details Country British Virgin Islands J North America cem 6 Details Country Eritrea ERI Africa 1939 13 38 Details Country France Metropolitan FXX Details Country Haiti HTI North America 21501 3 236 Details Country Holy See Vatican City VAT Europe 6604 2 Details Country Italy ITA Europe 330506 4377 24905 2809 Details Country Kuwait KWT Asia 1094 3 Details Country Lithuania LTU Europe 7358 2750 2487 15 Details Country Mauritania MNT Afrina AANE 24 440 F natailel F niintel Figure 27 search in
52. rtal also has an edit interface for such manual update of taxon and country level metadata CU Data use agreement ECO LEX Search ECOLEX for more information Data use agreement ud AGRIS CARIS for more information on Italy Edit Country Metadata Update GBIF country metadata These links to update the metadata is displayed ONLY for logged in users Figure 30 here is the link to the edit country metadata form This link is ONLY displayed for logged in users Country level metadata Search the CWR Country metadata by keyword GO Or use the Advanced search form Update Country Metadata for Italy GBIF dataset GBIF Records 330506 oreferenced Records 2008 01 30 22 10 07 BGCI dataset BGCI Records 4377 BGCI gardens 104 _ BGCI last accessed 2007 07 06 00 00 00 EURISCO dataset EURISCO Records 24905 EURISCO Georeferenced Records 1454 EURISCO last accessed 2007 07 23 00 00 00 SINGER dataset SINGER Records 2809 SINGER Georeferenced Records 525 SINGER last accessed 2007 07 23 00 00 00 NI dataset NI Records NI Georeferenced Records NI last accessed WPDA dataset WDPA Areas 1042 WDPA last accessed 2007 05 21 00 00 00 An asterix marks the required fields Register country metadata Figure 31 this is the edit form for country level metadata You would normally update these data points from the semi automatic update routines for external da
53. ry data portal files data import dataset acronym of your data portal installation directory The data portal web interface will provide you with information of the last time the source file was downloaded file date as well as the file size E g Source dataset file export zip was last modified on November 01 2007 12 22 15 0 6493 MByte The data portal web interface will also describe the manual download link and the full path to the directory where you are expected to save the file Step 2 un compress the source dataset file if needed zip tar gz bz2 This step will un compress the source dataset file if the file have the file extension zip gz tar gz or tar bz2 Other compression formats like the rar is not yet supported You may of course un compress the source dataset file manually and save the un compressed file to data_portal files data_import lt dataset_acronym gt Step 3 Convert the un compressed dataset file to tab separated text The routine to convert the dataset to the appropriate SQL INSERT script expects tab separated text input The data portal comes with support for automatic conversion of MS Excel spreadsheet xls and comma separated values csv to tab separated text data portal tools bin xls2txt pI data portal tools bin csv2txt pl XML data and dBase files are partially supported but this will be developed further Support for the conversion of additional
54. s GBIF data last updatel Web Mapping visualization BGCI plants records 14 CWR Ontology Baci dtm 2008 02 12 18 04 33 EURISCO ID Import Dataset EURISCO records 172 EURI CO Georeferenced records 68 Data dictionary SINGER ID Explore the Data Model SINGER records 0 Browse CWR Data Units SINGER Georeferenced records 0 CWR NI Records NI Georeferenced records TaxonID PRIMARY KEY 208 Taxon GUID Allium schoenoprasum L Allium schoenoprasum Full scientific nanje species Remarks Figure 33 example of descriptive column names from the data dictionary for a data unit detail view Germplasm Data Portal Technical Description Last updated February 19 2008 Page 41 Taxon level metadata Country level metadata Contact institutes persons Image Archive News stories Literature about CWR resources Web Mapping visualization A Explore the Data Model CWR Ontology Import Dataset Data dictionary Browse CWR Data Units Data dictionary The data dictionary provides description and definitions of database tables and columns as well as coded data values db tables describes the tables in the database db columns describes the column fields or attributes ofthe tables db values describes coded column values including their decoding data objects is an abstractions of db tables db tables are data objects data descriptors is an abstractions ofthe db columns db columns are
55. self only is responsible for include of the data_portal main phps while this script data_portal main phps is responsible for including most of the other scripts Only the data_portal init_adodb phps and the data_portal page_elements page_content phps actually include script elements themselves Most interesting is the page_content phps as this script acts as a content wrapper When the portal receives the GET _REQUESTT app or _REQUEST page feature request the corresponding webpage or sub application will be loaded Most of the sub applications will initiate an independent chain sequence of included scripts from its own main phps application wrapper This way the sub applications can easily be moved to another content wrapper Germplasm Data Portal Technical Description Last updated February 19 2008 Page 12 like for example sometimes even another format than the HTML web page environment Object primary keys as URL GET attributes The portal will also respond when no app or page GET attribute is transmitted if a data object key is transmitted as a URL GET attribute For example REQUESTY taxon id REQUEST taxon name _REQUEST country_id _REQUESTT institute_id REQUEST person id REQUEST image id etc Getting started with a new data portal implementation To create a new data portal implementation you need to choose an acronym for your portal implementati
56. t gbif header gt lt gbif statements gt This document contains data shared through the GBIF Network see http data gbif org for more information All usage of these data must be in accordance with the GBIF Data Use Agreement see http www_ gbif org DataProviders Agreements DUA lt gbif statements gt lt gbif help gt http data_gbif_ org ws rest occurrence help lt gbif help gt lt gbif request gt count lt gbif request gt lt gbif parameter name service value occurrence gt lt gbif parameter name coordinatestatus value true gt lt gbif parameter name scientificname value Allum porrum gt lt gbif parameter name request value count gt lt gbif parameter name stylesheet value gt lt gbif summary total Matched 90 gt lt gbif header gt lt gbif gbifResponse gt Figure 19 example of GBIF response format http data gbif org ws rest occurrence count scientificname A llium porrum amp georeferencedonly t rue amp stylesheet It is the XML mark up tag attribute totalMatched of the mark up tag named obif summary we are interested in for the germplasm data portal In the example for Allium porrum only geo referenced records we find this attribute to report 90 such occurrence records indexed by the GBIF data portal Figure 20 show the PHP source code implementation of the germplasm data portal to access and extract the total count of occurrence records for a given species and or a coun
57. t_eurisco phps 5KB PHPS File 2007 11 05 08 03 country ni ZA import gbif phps 5KB PHPSFile 2007 11 11 23 44 f data dictionary import gbif country phps 7KB PHPSFile 2008 02 19 14 00 E eg data harvest 7KB PHPSFie 2008 02 19 14 00 G data import Vll import iucn redist phps 5KB PHPSFile 2007 11 11 19 28 f data model V import singer phps 6KB PHPSFie 2007 11 05 08 03 G data providers YA import wdpa phps 6KB PHPSFile 2007 11 05 08 03 data schema 4 import_wiews_institute phps 4KB PHPS File 2007 11 05 08 03 w data unit P INFO TXT 1KB TextDocument 2007 07 04 07 33 dummy 42 main phps 2KB PHPSFile 2007 11 05 08 03 E events Vgl navigation arrows phps 3KB PHPSFile 2007 09 25 07 39 z feedback g page top phps 3KB PHPSFile 2007 09 25 07 18 2 germplasm 7 E images E import dataset f literature ED login B news ontology ED seedstore ED taxon metadata G webgis Figure 22 the function Figure 20 to refresh the count of occurrence records for a species from the GBIF REST web service can be invoked from a PHP script data portal applications import datasets import gbif taxon phps This script can be executed from the command line or added to the crontab for a scheduled automatic refresh may require some minor update of the current version of the script Update of the summary metadata on the taxon and country unit level may also be updated for an individual species or country from the URL index php app import_dataset amp inc
58. ta vulgaris L coLoo3 erar Bean collection CIATBEAN G10071 Beta vulgaris L coLoo3 erar Bean collection CIATBEAN G10072 Beta vulgaris L coLoo3 caT Bean collection CIATBEAN G10073 Beta vulgaris L coLoo3 eir Bean collection IPGRI CIATBEAN G10074 Beta vulgaris L coLoo3 cia Bean collection CIATBEAN G10075 Beta vulgaris L coLoo3 eir Bean collection CIATBEAN G10077 Beta vulgaris L coLoo3 caT Bean collection CIATBEAN G10078 Beta vulgaris L coLoo3 L o 1 jJ Preview of 10 records from the last harvested data Figure 15 step 4 is the preview of the harvested XML data extracting selected data values and the import of these values to the CHM database index Germplasm Data Portal Technical Description Last updated February 19 2008 Page 22 Harvested and Indexed Germplasm Data default search form simple search form Search form Your search criteria was No search criteria given All files in the registry displayed Add search criteria v Fa Caer Add columns to the list J Display 10 hits per page Go Total hits 8212 record 1 to 10 displayed 9 Next page Ur Beta vulgaris L CIATBEAN G1 COLO003 Beta vulgaris L CIATBEAN G10 COLO003 Details CIATBEAN G100 COL003 Details Nordic Gene Bank sen Details Details Beta vulgaris L NGB13106 Lactuca sativa NGB4102 Poa pratensis NGB2439 Lolium p
59. tails service occurrence scientificname Allium porrum request count Number of records matched 1467 For help with this web service see http data gbif org ws rest occurrence help Figure 18 example of GBIF response format http data gbif org ws rest occurrence count scientificname Allium porrum An example of the service request style asking for all occurrence records of the species Allium porrum with geospatial origin attributes reported geo referenced records only http data gbif org ws rest occurrence count scientificname Allium porrum amp georeference donly true amp stylesheet Germplasm Data Portal Technical Description Last updated February 19 2008 Page 25 gbif gbifResponse xsi schemaLocation http portal gbif org ws response gbif http data gbif org ws rest occurrence schema http purl org dc elements 1 1 http data gbif org schema dc xsd http purl org dc terms http data gbif org schema dcterms xsd http www w3 org 1999 02 22 rdf syntax nsz http data gbif org schema rdf xsd http www w3 org 2002 07 owt http data gbif org schema owl xsd http rs tdwg org ontology voc Common http data gbif org schema tcom xsd http rs tdwg org ontology voc TaxonOccurrence http data gbif org schema TaxonOccurrence xsd http rs tdwg org ontology voc TaxonConcept http data gbif org schema TaxonConcept xsd http rs tdwg org ontology voc TaxonNames http data gbif org schema TaxonName xsd l
60. tasets For example the GBIF summary metadata is very easy to update per unit as well as for more units from the link located directly next to the link to this form from the taxon and country level metadata detail pages Germplasm Data Portal Technical Description Last updated February 19 2008 Page 40 Data dictionary Data displayed in the data portal may have a more descriptive column names or data labels than the basic database table column name if defined in the data dictionary see Figure 32 and Figure 33 The logged in users will find a link to the data dictionary from the left menu or from the site map to define data dictionary descriptions see Figure 34 and Figure 35 Taxonname IUCN status GBIF records GBIF Georeferenced records BGCI pl Abelmoschus angulosus Abelmoschus ficulneus Abelmoschus moschatus 437 Abutilon 469 Abutilon avicennae 750 Number of records indexed by the GBIF data portal 193 172 1 Figure 32 example of descriptive column names and mouse over column tip as defined from the data dictionary for a data unit list view Taxon metadata CWR Data LEE Taxon metadata details Taxon level metadata TaXn name Allium schoenoprasum INCN ID IUCN s atus GBIF TaxonConceptKey GBIF recois 3670 s 2762 2008 02 12 17 42 30 Country level metadata Contact institutes persons Image Archive News stories GB Georeferenced record Literature about CWR resource
61. terface advanced search for country level metadata from the indexed external datasets on CWR resources Country summary data Italy Continent name Europe Country ISO 3 Code ITA Country ISO 2 Code IT Number of total records from GBIF http data gbif org on Last accessed on 2008 01 30 Data use guidelines GBIF Records 330 506 records not limited to CWR taxa Number of plant records from BGCI http www bgci org 1 BGCI accessed on 2007 07 06 Data use gudelines BGC plants 4 377 plant records not limited to CWR taxa BGCI gardens 104 Number of records from SINGER http singer grinfo net Accessed on 2007 07 23 Terms of use SINGER 2 809 accessions not limited to CWR taxa Georeferenced 525 accessions in SINGER are georeferenced Number of ex situ accessions from EURISCO http eurisco ecpgr org Accessed on 2007 07 23 Terms of use EURISCO 24 905 accessions not limited to CWR taxa Georeferenced 1 454 accessions in EURISCO are georeferenced Number of protected areas in Italy from the World Database of Protected Areas WDPA The Italy map om the CIA World abo WDPA is a joint venture of UNEP and the IUCN produced by UNEP WCMC and the IUCN WCPA UNEP WCMc working with governments and collaborating NGOs It is updated continuously providing the most current data on protected areas worldwide The following link gives you access to this database http www unep wcmc org wdpa The WDPA d
62. th to refer to internal scripts see Figure 2 Second you will need to mount the data_portal html directory to the public web tree www of your web server You may mount the html folder anywhere you want in your public web tree as the data portal use relative internal URLs to reference internal resources Only the html directory should be mounted not the entire data portal directory folder If you mount the entire data portal directory the data portal will still work as normal but you will also publish online all the source code including your configuration files with usernames and passwords with more The data portal is divided in modules inspired by the cascading style sheet type logic The execution of the portal PHP scripts starts at the higher directory level and follow the path down the directories to child directories for more specific features or functionality For example general configuration settings are provided at the higher directory level data portal settings phps more specific settings are included for the layout page elements data portal page elements settings phps with even more specific layout settings for the CWR portal implementation in a sub folder with the same name as the implementation scope data portal page elements cwr settings php The same pattern of a subfolder for specific implementations for a particular data portal implementation like the CWR SGSV SESTO EAPGREN ECPGR ECCDB etc is repeat
63. the ADODB database abstraction library init db phps This script is used for configuration of the database connection for the ADODB database abstraction library included in the init adodb phps script SUB DIRECTORIES of the data portal ROOT applications Germplasm Data Portal Technical Description Last updated February 19 2008 Page 10 The applications sub folder is for the sub applications inside the page content framed box These sub applications are included by the _REQUEST app parameter from the URL The application with the directory name equal to the value of the REQUEST app will be loaded The data portal will start by looking for the script main phps in this directory and give an error message if the directory is missing or if the directory does not have this script main phps webpages Simple information web pages are included from the _REQUEST page parameter from the URL A web page with the extension inc or phps after the value of REQUEST page will be displayed If no such page an error message will inform the user of this problem The data portal will look fr this page inc or page phps in the data portal webpages directory files The files folder in the ROOT directory is for data files Here the data backup files for the database tables are saved The data harvest and data import ro
64. the conservation and utilization of crop wild relatives CWR It was created within the UNEP GEF supported project in situ conservation of crop wild relatives through enhanced information management and field application The development of the portal is ongoing and new resources are being added as they become available Latest Images a LH dao ih d A selection of the latest images added to the CWR Image Archive Please contact us if you want to contribute images of Crop Wild Relatives Latest News Stories CWR Portal 2007 01 01 The CWR Portal is developed by Bioversity International as a generic web application written in PHP and with a generic ADODB database connection to the PostgreSQL database system Some of the routine operations have also been coded for the Perl scripting language The portal web application have been successfully tested with the Apache web server for the Apple Mac Linux and Windows operating system environment CWR Project 2004 01 01 The crop wild relatives global portal has been established within the framework of the UNEP GEF supported project In situ conservation of crop wild relatives through enhanced information management and field application lead by Bioversity International and implemented from 2004 to 2009 Funds for the development of the global portal were also received from the German Federal Ministry for Economic Cooperation and Development BMZ View all News items A total of 2 news stories h
65. try of origin with the filer condition for geo referenced records only on and off The germplasm data portal administrator may invoke the refreshing of the GBIF occurrence count from the web interface Figure 21 The function can also be called from the command line or added to the crontab UNIX like systems for a scheduled automatic refresh of the taxon level summery number of GBIF occurrence records Figure 22 Germplasm Data Portal Technical Description Last updated February 19 2008 Page 26 function gbif count occurrences taxon name country_iso2 georeferenced only false function gbif count occurrences Connect to the GBIF Data Portal and calculate summary species level or country level record count INPUT Species name Country ISO 2 Code Georeferenced only true false jj totalMatched init variable if country_iso2 country_iso2 strtoupper country_iso2 endif rest url http data gbif org ws rest occurrence count rest url stylesheet switch off stylesheet browser formatting if taxon_name rest_url amp scientificname urlencode taxon_name endif if country_iso2 rest_url amp originisocountrycode strtoupper country_iso2 endif rest url amp georeferencedonly georeferenced_only switch for georeferenced ONLY on off file_content file_get_contents rest_url Read the GBIF Data Portal web service response as REST URL xml ne
66. utines also save files here The web server will need write permissions for this folder as well as to the relevant sub folders html This folder is mounted in the web tree of the web server Files Scripts and sub directories will be published online from your data portal implementation libraries Code libraries are included here This folder should be used much more Most of the functionalities of the sub applications in the lapplications folder should be rewritten as PHP classes and moved here I hope to find the opportunity to do this as the data portal will be significantly more robust with more functionality in PHP classes than in crude phps scripts Later versions of PHP version 6 may require that more functionality is done as object oriented classes page elements All the layout elements are included from this sub folder The page banner the page menus as well as some of the scope specific configuration files for database settings etc tools This sub folder includes some supporting tools and script You will find a number of scripts coded in Perl or the bash shell Scripting language with more in tools bin You will also find some useful SQL scripts in the tools sql folder READ MORE about the individual sub folders from the INFO TXT located inside each folder Germplasm Data Portal Technical Description Last updated February 19 20
67. version library The open source recode library is used for import of non UNICODE external datasets http directory fsf org recode html Germplasm Data Portal Technical Description Last updated February 19 2008 Page 43 CONV character set conversion library The open source iconv library is an alternative to recode used for import of non UNICODE external datasets http www gnu org software libiconv documentation libiconv iconv 1 html e GNU Weet http www gnu org software wget e ImageMagick convert The command line tool convert from the ImageMagick is used by the Simple Image Archive http www imagemagick org script convert php References e CWR Global Portal http cwrint grinfo net CWR Global Portal User Manual http cwrint grinfo net files cwr CWR Portal Search Manual pdf SESTO genebank information system http www nordgen org sesto GCP Central Repository http gcpcr grinfo net Germplasm Clearing House Mechanism CHM http chm grinfo net REST web service style http en wikipedia org wiki Representational State Transfer e W3C Web Accessibility Guidelines WCAGI0 http www w3c org TR 2000 NOTE WCAG10 TECHS 20001106 e SGSV Portal Svalbard Global Seed Vault data portal http www nordgen org sgsv Germplasm Data Portal Technical Description Last updated February 19 2008 Page 44
68. w SimpleXMLElement file_content xml registerXPathNamespace gbif http portal gbif org ws response gbif Register namespace result xml gt xpath gbif summary 1 foreach result as data_node foreach data_node gt attributes as key gt value if key totalMatched totalMatched string value end if key totalMatched end foreach data node attribute end foreach result data node echo lt xmp gt n file content xmp hr gt n DEBUG return totalMatched j Figure 20 this is the PHP code to access the GBIF data portal REST web service interface Germplasm Data Portal Technical Description Last updated February 19 2008 Page 27 Total hits 1846 record 1to 20 displayed gt gt Next page o raon O 770734 CE Provious updats 33 Abelmoschusanguosus 252 0 2007 10 11 16 26 27 134 Abelmoschus ficulneus 5555 3 3 2007 10 11 162627 135 Abelmoschus moschatus 433 2433 134 5134 2007 10 11 16 26 28 5 uio 388 388 122 122 2007 10 11 162629 137 Abutilon avicennae 51455124 151 2007 10 11 16 26 29 136 Abutilon theophrasti 1994 1994 1616 5 1616 2007 10 11 16 26 30 138Acalypha amentacea 215215 3030 2007 10 11 16 26 31 139 Acalypha ciliata 54 554 10 10 2007 10 11 16 26 32 140 Acalyphafruticosa 79579 15 15 2007 10 11 16 26 32 i41 Acalypha

Data Portal Technical Description

Contents

Download Pdf Manuals

Related Search

Related Contents