AgriOcean DSpace

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AgriOcean DSpace

AgriOcean DSpace (AOD) is a joint initiative of the United Nations agencies of FAO and UNESCO-IOC/IODE to provide a customized version of DSpace 1.7.1 (JSPUI version), an open source, digital repository software. Its main objective is to make scientific literature in the field of oceanography, agriculture and related sciences available in digital form. AgriOcean DSpace is set-up for the digital repository communities of AGRIS (FAO) and Odin (UNESCO-IOC), but can be downloaded and used by any research institution interested.

Usage and deployment (if publicly accessible)

Downloadable application: https://code.google.com/p/agriocean/downloads/list

VM deployed at the INFN MyCloud service: http://212.189.145.249

Example Usage Scenario

Our users

Elizabeth is a librarian at the Ministry of Agriculture in Peru. She is responsible for cataloguing and exposing online metadata and records of documents generated and archived by the ministry. She has IT support, there is fine bandwidth and IT infrastructure at her institution to set up a repository on AgriOcean DSpace, and she intends to expose high quality metadata and to use AGROVOC terms for subject indexing.

Carlos is the IT person in the Ministry and his responsibilities involve managing the IT infrastructure for the Ministry. Elizabeth tells Carlos of her interest in repository software and he is overwhelmed with work. Because of policy issues he cannot even authorize AgriOcean DSpace team to do a remote installation on the Ministry servers.

INAHINA participates in the OceanDocs Network Repository, which seeks to share scientific and scholarly research in oceanography. OceanDocs has a platform to support the existing institutional members to publish open access research outputs on the web, and established to use widely used application profiles and metadata formats to facilitate easy exchange of information amongst service providers and other initiatives. AgriOcean DSpace is the document management tool used by OceanDocs.

UNESCO/IOC receives the request from INAHINA which needs to set up an institutional repository but does not have the infrastructure to do so. The institution considers that (i) they could join OceanDocs using AgriOcean DSpace and its capabilities to expose metadata – in xml (AGRIS AP, MODS) and Ris-based formats (Endnote); (ii) that AgriOcean DSpace can be harvested by important service providers like AGRIS, VOA3R; (iii) the possibility to use vocabularies like ASFA and AGROVOC. This institution chooses to be part of the OceanDocs repository and use the AgriOcean DSpace software.

Dirk is the IT person in OceanDocs and ensures that the platform is up and running, and requires a stable infrastructure to facilitate the community-focused integrated service for the retrieval of relevant open content and data.

The information manager at INAHINA is keen to participate in the OceanDocs Network tool. He intends to use AGROVOC terms in describing his resources and seeks to use a repository that is visible and hence an interest to participate in OceanDocs. He also intends to support the implementation of additional services by exposing his content in a stable network, such as aggregating related content and the use of social network for his researchers. Researcher A is affiliated with INAHINA participating in the OceanDocs Network and would wish to expose his research output and also would want to formulate his information needs requests.

Before agINFRA

Scenario A

AgriOcean DSpace is installed on a server in the Ministry of Agriculture network. While Elizabeth has managed to install AgriOcean DSpace by following the guidelines provided, she however, feels inadequate to configure the installation on the Linux server. In order to install the AgriOcean DSpace for the Linux environment, Tracy ask Carlos to install AgriOcean DSpace and he need to do the following procedure

  • Download the following requisite software:
    • Oracle Java JDK 6 or later
    • Apache Tomcat 5.5 or later; he needs to ensure that Apache Tomcat has enough memory to run DSpace, and also uses UTF-8 as its default coding for international character support. Tomcat should be properly configured to support searching and browsing of multi-byte UTF-8 correctly.
    • PostgreSQL 8.4 or higher, there is also a need to download pgAdmin III client for Postgresql
  • Download the AgriOcean DSpace 1.1 Linux Application file on Google Code (AODSetup-1-1_Linux_Beta.7z)
  • Install the software by ensuring that the installing the Postgresql database, Tomcat Server and ensuring that they configure they follow the provided AOD configuration path.
  • Final setup steps and launch the browser and run the installation at http://localhost:8080/dspace

Carlos the IT person is also asked to adapt the AgriOcean DSpace interface meet Elizabeth’s needs. Carlos notes that this will take a great portion of his time and also he has a list of other support requests from different departments. He schedules Elizabeth’s implementation to some other time.

Scenario B

OceanDocs has different partners and it needs a stable infrastructure to guarantee a good service for participating institutions. Since OceanDocs intends to be a service for various providers in the network, INAHINA requests to use the repository tool that will enable them to expose their metadata to the OceanDocs network. The information person at INAHINA, is in a situation similar to Elizabeth, described above, and requires assistance in migration data, using the tool and customizing his communities and collections that will meet not only his document management needs but also that will enable his participation in OAAR Network.

Alternatively, Dirk should be able to provide technical expertise in mapping INAHINA‘s repository, which he cannot do as he has other OceanDocs platform related issues to address. He is not in a position to help him performing the required tasks, but can only advise him on what technical issues are required to participate in the OceanDocs common repository and platform services. Dirk is faced with his own challenges of ensuring that the OceanDocs platform infrastructure can accommodate all participating repositories. Meanwhile, Researcher A, is registered within the OceanDocs platform, and he currently finds the platform very slow in harvesting records he needs from the service.

agINFRA powered version

Elizabeth is aware that AgriOcean DSpace can be downloaded, but has limited technical knowledge to do so, and compounding her problem is lack of support by Carlos in installing the software for her. Unbeknownst to her, Carlos is has limited resources and does not have proper server infrastructure to host her repository.

Elizabeth is informed of the possibility of having an agINFRA-hosted version of AgriOcean DSpace, and decides to try it. The agINFRA homepage provides information about AgriOcean DSpace and an option to set up on a virtual machine, operating on Cloud resources. After completing a request form with her particular needs, her request is approved and an install button is activated for her to click. After clicking this button after a short time she is informed that her newly installed repository is ready. She receives an short manual as an administrator to configure and set up her communities and collections. She discovers that this tools comes with ability to index with AGROVOC and ASFA terms (also with an option to add other ontologies and vocabularies); and also that it is already operating on the Cloud and that after uploading her content she can simply click publish button, and the repository becomes visible.

APIs

Example 1. Listing all the collections (sets) available in an AOD instance


Parameter verb
Value ListSets
Example Request http://www.oceandocs.org/odin-oai/request?verb=ListSets
Example Response <OAI-PMH xmlns="http://www.openarchives.org/OAI/2.0/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/ http://www.openarchives.org/OAI/2.0/OAI-PMH.xsd"> <responseDate>2013-11-21T09:14:57Z</responseDate> <request verb="ListSets">http://www.oceandocs.org/odin-oai/request</request> <ListSets> <set> <setSpec>hdl_1834_159</setSpec> <setName>01. Bulletin Scientifique de l'IMROP</setName> </set> <set> <setSpec>hdl_1834_160</setSpec> <setName>02. Documents Techniques de l'IMROP</setName> </set> <set> <setSpec>hdl_1834_172</setSpec> <setName>03. Bulletin Statistique</setName> </set> <set> <setSpec>hdl_1834_175</setSpec> <setName>04. Rapports Techniques</setName> </set> <set> <setSpec>hdl_1834_171</setSpec> <setName>05. Rapports de Projets</setName> </set> <set> <setSpec>hdl_1834_161</setSpec> <setName>06. Thèses</setName> </set> <set> <setSpec>hdl_1834_174</setSpec> <setName>07. Actes de Conférence</setName> </set> <set> <setSpec>hdl_1834_173</setSpec> <setName>08. La Lettre de l’IMROP</setName> </set> <set> <setSpec>hdl_1834_206</setSpec> <setName>09. Livres</setName> </set> <set> <setSpec>hdl_1834_4642</setSpec> <setName>10. Congresos de Ciencias del Mar</setName> </set> <set> <setSpec>hdl_1834_162</setSpec> <setName>10. Rapports de Programmation</setName> </set> <set> <setSpec>hdl_1834_207</setSpec> <setName>11. Divers</setName> </set> <set> <setSpec>hdl_1834_1408</setSpec> <setName>1. Acta oceanográfica del Pacífico</setName> </set> <set> <setSpec>hdl_1834_3230</setSpec> <setName>1. Anales del Instituto de la Patagonia</setName> </set> <set> <setSpec>hdl_1834_167</setSpec> <setName>1. Articles</setName> </set> <set> <setSpec>hdl_1834_141</setSpec> <setName>1. Articles</setName> </set> <set> <setSpec>hdl_1834_1366</setSpec> <setName>1. Articles - Artículos</setName> </set> <set> <setSpec>hdl_1834_1362</setSpec> <setName>1. Artículos</setName> </set> <set> <setSpec>hdl_1834_2487</setSpec> <setName>1. Articulos científicos</setName> </set> <set> <setSpec>hdl_1834_1916</setSpec> <setName>1. Artículos científicos</setName> </set> <set> <setSpec>hdl_1834_3220</setSpec> <setName>1. Boletín Antártico Chileno</setName> </set> <set> <setSpec>hdl_1834_2873</setSpec> <setName>1. Boletín Científico y Técnico</setName> </set> <set> <setSpec>hdl_1834_156</setSpec> <setName>1. Bulletin de l'INSTM-Salammbô</setName> </set> <set> <setSpec>hdl_1834_4644</setSpec> <setName>1. Ciencia y Tecnología de los Alimentos</setName> </set> <set> <setSpec>hdl_1834_3534</setSpec> <setName>1. Contribución Científica CADIC</setName> </set> <set> <setSpec>hdl_1834_1398</setSpec> <setName>1. Documentos científicos</setName> </set> <set> <setSpec>hdl_1834_98</setSpec> <setName>1. Document Scientifique du CRODT</setName> </set> <set> <setSpec>hdl_1834_2524</setSpec> <setName>1. GEOHAB Report Series</setName> </set> <set> <setSpec>hdl_1834_3681</setSpec> <setName>1. IBMP Serie Publicaciones</setName> </set> <set> <setSpec>hdl_1834_4541</setSpec> <setName>1. IMR Publication</setName> </set> <set> <setSpec>hdl_1834_2548</setSpec> <setName>1. Informes técnicos</setName> </set> <set> <setSpec>hdl_1834_4009</setSpec> <setName>1. Investigaciones</setName> </set> <set> <setSpec>hdl_1834_1511</setSpec> <setName>1. IODE Session Summary Reports</setName> </set> <set> <setSpec>hdl_1834_1414</setSpec> <setName>1. Mitteilungen aus dem Instituto Colombo-Alemán</setName> </set> <set> <setSpec>hdl_1834_1373</setSpec> <setName>1. Publicaciones técnicas</setName> </set> <set> <setSpec>hdl_1834_1395</setSpec> <setName>1. Publications</setName> </set> <set> <setSpec>hdl_1834_4863</setSpec> <setName>1. Publications du CRBST</setName> </set> <set> <setSpec>hdl_1834_4850</setSpec> <setName>1. Publications du CRO</setName> </set> <set> <setSpec>hdl_1834_4869</setSpec> <setName>1. Publications du IRSH</setName> </set> <set> <setSpec>hdl_1834_4859</setSpec> <setName>1. Publications of CCG</setName> </set> <set> <setSpec>hdl_1834_4855</setSpec> <setName>1. Publications of IRAD</setName> </set> <set> <setSpec>hdl_1834_5147</setSpec> <setName>1. Publicatons of INIP</setName> </set> <set> <setSpec>hdl_1834_1376</setSpec> <setName>1. Revista Cubana de Investigaciones Pesqueras</setName> </set> <set> <setSpec>hdl_1834_1388</setSpec> <setName>1. Revista de Ciencias Marinas</setName> </set> <set> <setSpec>hdl_1834_4518</setSpec> <setName>1. Revista de Investigaciones Marinas (CIM-UH)</setName> </set> <set> <setSpec>hdl_1834_1357</setSpec> <setName>1. Revista de Investigación y Desarrollo Pesquero</setName> </set> <set> <setSpec>hdl_1834_2931</setSpec> <setName> 1. Revista Investigaciones Marinas (desde 2008 LAJAR) </setName> </set> <set> <setSpec>hdl_1834_1436</setSpec> <setName>1. Serie Oceanológica</setName> </set> <set> <setSpec>hdl_1834_2834</setSpec> <setName>1. Tesis de Licenciatura en Ciencias Biológicas</setName> </set> <set> <setSpec>hdl_1834_3536</setSpec> <setName> 1. Tesis de Maestría en Ciencias con Especialidad en Recursos Marinos </setName> </set> <set> <setSpec>hdl_1834_3410</setSpec> <setName>1. Tesis de Maestría y Doctorado</setName> </set> <set> <setSpec>hdl_1834_3913</setSpec> <setName>1. Tesis de Pregrado</setName> </set> <set> <setSpec>hdl_1834_4554</setSpec> <setName>1. Tesis de pregrado Biología Marina (UACh)</setName> </set> <set> <setSpec>hdl_1834_1383</setSpec> <setName>1. Tesis En Ciencias Marinas</setName> </set> <set> <setSpec>hdl_1834_163</setSpec> <setName>1. Thèses</setName> </set> <set> <setSpec>hdl_1834_1941</setSpec> <setName> 2. Anales del Instituto de Investigaciones Marinas de Punta Betín </setName> </set> <set> <setSpec>hdl_1834_1437</setSpec> <setName>2. Archives du CRODT</setName> </set> <set> <setSpec>hdl_1834_164</setSpec> <setName>2. Articles</setName> </set> <set> <setSpec>hdl_1834_1374</setSpec> <setName>2. Artículos</setName> </set> <set> <setSpec>hdl_1834_4010</setSpec> <setName>2. Artículos de Tesis de Grado - CENAIM</setName> </set> <set> <setSpec>hdl_1834_139</setSpec> <setName>2. Autres Articles</setName> </set> <set> <setSpec>hdl_1834_2549</setSpec> <setName>2. Boletines informativos</setName> </set> <set> <setSpec>hdl_1834_2874</setSpec> <setName>2. Boletín Especial</setName> </set> <set> <setSpec>hdl_1834_1396</setSpec> <setName>2. Caribbean Marine Studies</setName> </set> <set> <setSpec>hdl_1834_170</setSpec> <setName>2. Conference Paper</setName> </set> <set> <setSpec>hdl_1834_1367</setSpec> <setName>2. Conference papers - Presentaciones</setName> </set> <set> <setSpec>hdl_1834_1399</setSpec> <setName>2. Documentos técnicos</setName> </set> <set> <setSpec>hdl_1834_3762</setSpec> <setName>2. GEOHAB Working Documents</setName> </set> <set> <setSpec>hdl_1834_4542</setSpec> <setName>2. IMR Articles</setName> </set> <set> <setSpec>hdl_1834_1409</setSpec> <setName>2. Informes Científicos</setName> </set> <set> <setSpec>hdl_1834_3682</setSpec> <setName>2. Informe Técnico IBMP</setName> </set> <set> <setSpec>hdl_1834_1358</setSpec> <setName>2. INIDEP Informe Técnico</setName> </set> <set> <setSpec>hdl_1834_1512</setSpec> <setName>2. IODE Session Working Documents</setName> </set> <set> <setSpec>hdl_1834_2940</setSpec> <setName> 2. Latin American Journal of Aquatic Research - LAJAR (formerly Investigaciones Marinas) </setName> </set> <set> <setSpec>hdl_1834_1363</setSpec> <setName>2. Presentaciones a congresos</setName> </set> <set> <setSpec>hdl_1834_1384</setSpec> <setName>2. Reportes</setName> </set> <set> <setSpec>hdl_1834_142</setSpec> <setName>2. Reports</setName> </set> <set> <setSpec>hdl_1834_3391</setSpec> <setName>2. Tesis</setName> </set> […] </ListSets> </OAI-PMH>

Example 2. List of metadata records for a specific metadata set and collection


Parameters verb, set, metadataPrefix
Values ListRecords, the setSpec of the chosen set, the metadataPrefix of the chosen metadata format
Example Request http://www.oceandocs.org/odin-oai/request?verb=ListRecords&metadataPrefix=agris
Example Response (shortened) <OAI-PMH xmlns="http://www.openarchives.org/OAI/2.0/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/ http://www.openarchives.org/OAI/2.0/OAI-PMH.xsd"> <responseDate>2013-11-21T09:20:36Z</responseDate> <request verb="ListRecords" metadataPrefix="agris">http://www.oceandocs.org/odin-oai/request</request> <ListRecords> <record> <header> <identifier>oai:http://www.oceandocs.org:1834/14</identifier> <datestamp>2008-11-27T10:09:20Z</datestamp> <setSpec>hdl_1834_103</setSpec> </header> <metadata> <ags:resources xmlns:ags="http://purl.org/agmes/1.1/" xmlns:dcterms="http://purl.org/dc/terms/"xmlns:agls="http://www.naa.gov.au/recordkeeping/gov_online/agls/1.2" xmlns:dc="http://purl.org/dc/elements/1.1/"> <ags:resource ags:ARN="BE1996700014"> <dc:title xml:lang="en">Outline of tuna fishery in Madagascar</dc:title> <dc:title xml:lang="fr">Aperçu sur la Pêche Thonière à Madagascar</dc:title> <dc:creator> <ags:creatorPersonal>Gilbert, F.</ags:creatorPersonal> <ags:creatorConference> 6th Expert Consultation on Indian Ocean Tunas - IOTC, Colombo, Sri Lanka - 1996 </ags:creatorConference> </dc:creator> <dc:date> <dcterms:dateIssued>1996</dcterms:dateIssued> </dc:date> <dc:description> <dcterms:abstract xml:lang="en"> Following a brief history of the tuna fisheries in Madagascar, an account is given of the current situation, providing also details of various fishing agreements and protocols passed by Madagascar during the period 1986-1994. Tuna catches in the Madagascan EEZ since 1988 are listed and financial costs of tuna activities are outlined. </dcterms:abstract> <ags:descriptionNotes>Status: Published</ags:descriptionNotes> </dc:description> <dc:identifier scheme="dcterms:URI">http://hdl.handle.net/1834/14</dc:identifier> <dc:type>Proceedings Paper</dc:type> <dc:format> <dcterms:medium>application/pdf</dcterms:medium> <dcterms:extent>p. 22-25</dcterms:extent> </dc:format> <dc:language scheme="ags:ISO639-1">en</dc:language> <ags:citation> <ags:citationTitle> IOTC Proceedings, 6th Expert Consultation on Indian Ocean Tunas </ags:citationTitle> </ags:citation> </ags:resource> </ags:resources> </metadata> </record> <record> <header> <identifier>oai:http://www.oceandocs.org:1834/15</identifier> <datestamp>2012-02-23T10:13:19Z</datestamp> <setSpec>hdl_1834_103</setSpec> <setSpec>hdl_1834_1021</setSpec> </header> <metadata> <ags:resources xmlns:ags="http://purl.org/agmes/1.1/" xmlns:dcterms="http://purl.org/dc/terms/"xmlns:agls="http://www.naa.gov.au/recordkeeping/gov_online/agls/1.2" xmlns:dc="http://purl.org/dc/elements/1.1/"> <ags:resource ags:ARN="BE1996700015"> <dc:title xml:lang="en">Country report -- Mauritius</dc:title> <dc:creator> <ags:creatorPersonal>Munbodh, M.</ags:creatorPersonal> <ags:creatorConference> 6th Expert Consultation on Indian Ocean Tunas - IOTC, Colombo, Sri Lanka - 2005 </ags:creatorConference> </dc:creator> <dc:date> <dcterms:dateIssued>1996</dcterms:dateIssued> </dc:date> <dc:subject> <ags:subjectThesaurus scheme="ags:AGROVOC" xml:lang="en">Tuna</ags:subjectThesaurus> <ags:subjectThesaurus scheme="ags:AGROVOC" xml:lang="en">Fishery production</ags:subjectThesaurus> <ags:subjectThesaurus scheme="ags:AGROVOC" xml:lang="en">Canning</ags:subjectThesaurus> <ags:subjectThesaurus scheme="ags:AGROVOC" xml:lang="en">fishery economics</ags:subjectThesaurus> <ags:subjectThesaurus scheme="ags:ASFAT" xml:lang="en">Tuna fisheries</ags:subjectThesaurus> <ags:subjectThesaurus scheme="ags:ASFAT" xml:lang="en">Fishery industry</ags:subjectThesaurus> <ags:subjectThesaurus scheme="ags:ASFAT" xml:lang="en">Canning</ags:subjectThesaurus> <ags:subjectThesaurus scheme="ags:ASFAT" xml:lang="en">Fishery regulations</ags:subjectThesaurus> <ags:subjectThesaurus scheme="ags:ASFAT" xml:lang="en">Fishery development</ags:subjectThesaurus> </dc:subject> <dc:description> <dcterms:abstract xml:lang="en"> A brief account is given of the current situation regarding the tuna fishery industry in the Mauritius. A handline fishery from 13 motherships exploits the banks of the Mascarenes Ridge and the Chagos Archipelago and a purse seine fishery has developed since 1979 under a joint venture enterprise. Tuna canning operations and tuna transhipment are outlined and details provided of fishing agreements and licensing of fishing vessels. Measures which will expand benefits from tuna resources are listed. </dcterms:abstract> <ags:descriptionNotes> Research Group: Fishery Survey of Indian, Botawala Chambers, Sir P.M. Road, Bombay 400 001, India </ags:descriptionNotes> <ags:descriptionNotes>Status: Published</ags:descriptionNotes> <ags:descriptionNotes>Status: Non-Refereed</ags:descriptionNotes> </dc:description> <dc:identifier scheme="dcterms:URI">http://hdl.handle.net/1834/15</dc:identifier> <dc:type>Proceedings Paper</dc:type> <dc:format> <dcterms:medium>application/pdf</dcterms:medium> <dcterms:extent>p. 38-39</dcterms:extent> </dc:format> <dc:language scheme="ags:ISO639-1">en</dc:language> <dc:coverage> <dcterms:spatial>Mascarene Is., Mauritius</dcterms:spatial> </dc:coverage> <ags:citation> <ags:citationTitle> IOCT Proceedings , 6th Expert Consultation on Indian Ocean Tunas </ags:citationTitle> </ags:citation> </ags:resource> </ags:resources> </metadata> </record> […] <resumptionToken expirationDate="2013-11-21T10:20:41Z"> 0001-01-01T00:00:00Z/9999-12-31T23:59:59Z//agris/100 </resumptionToken> </ListRecords> </OAI-PMH>
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