]docutils.nodesdocument)}( rawsourcechildren]hsection)}(hhh](htitle)}(h Introductionh]hText Introduction}(hhparenthhhsourceNlineNuba attributes}(ids]classes]names]dupnames]backrefs]utagnamehhh hhhY/var/lib/jenkins/jobs/Metacat_stable/workspace/metacat/docs/user/metacat/source/intro.rsthKubh paragraph)}(hXMetacat is a repository for data and metadata (descriptions of data) that helps scientists find, understand and effectively use the data sets they manage or that have been created by others. Thousands of data sets are currently documented in a standardized way and stored in Metacat systems, providing the scientific community with a broad range of science data that--because the data are well and consistently described--can be easily searched, compared, merged, or used in other ways.h]hXMetacat is a repository for data and metadata (descriptions of data) that helps scientists find, understand and effectively use the data sets they manage or that have been created by others. Thousands of data sets are currently documented in a standardized way and stored in Metacat systems, providing the scientific community with a broad range of science data that–because the data are well and consistently described–can be easily searched, compared, merged, or used in other ways.}(hh/hh-hhhNhNubah}(h]h!]h#]h%]h']uh)h+hh*hKhh hhubh,)}(hX1Not only is the Metacat repository a reliable place to store metadata and data (the database is replicated over a secure connection so that every record is stored on multiple machines and no data is ever lost to technical failures), it provides a user-friendly interface for information entry and retrieval. Scientists can search the repository via the Web using a customizable search form. Searches return results based on user-specified criteria, such as desired geographic coverage, taxonomic coverage, and/or keywords that appear in places such as the data set's title or owner's name. Users need only click a linked search result to open the corresponding data-set documentation in a browser window and discover whom to contact to obtain the data themselves (or how to immediately download the data via the Web).h]hX5Not only is the Metacat repository a reliable place to store metadata and data (the database is replicated over a secure connection so that every record is stored on multiple machines and no data is ever lost to technical failures), it provides a user-friendly interface for information entry and retrieval. Scientists can search the repository via the Web using a customizable search form. Searches return results based on user-specified criteria, such as desired geographic coverage, taxonomic coverage, and/or keywords that appear in places such as the data set’s title or owner’s name. Users need only click a linked search result to open the corresponding data-set documentation in a browser window and discover whom to contact to obtain the data themselves (or how to immediately download the data via the Web).}(hh=hh;hhhNhNubah}(h]h!]h#]h%]h']uh)h+hh*hK hh hhubh,)}(hXMetacat's user-friendly Registry application allows data providers to enter data set documentation into Metacat using a Web form. When the form is submitted, Metacat compiles the provided documentation into the required format and saves it. Information providers need never work directly with the XML_ format in which the metadata are stored or with the database records themselves. In addition, the Metacat application can easily be extended to provide a customized data-entry interface that suits the particular requirements of each project. Metacat users can also choose to enter metadata using the Morpho application, which provides data entry wizards that guide information providers through the process of documenting each data set.h](hX+Metacat’s user-friendly Registry application allows data providers to enter data set documentation into Metacat using a Web form. When the form is submitted, Metacat compiles the provided documentation into the required format and saves it. Information providers need never work directly with the }(hX)Metacat's user-friendly Registry application allows data providers to enter data set documentation into Metacat using a Web form. When the form is submitted, Metacat compiles the provided documentation into the required format and saves it. Information providers need never work directly with the hhIhhhNhNubh reference)}(hXML_h]hXML}(hhhhTubah}(h]h!]h#]h%]h']nameXMLrefuri http://en.wikipedia.org/wiki/XMLuh)hRhhIresolvedKubhX format in which the metadata are stored or with the database records themselves. In addition, the Metacat application can easily be extended to provide a customized data-entry interface that suits the particular requirements of each project. Metacat users can also choose to enter metadata using the Morpho application, which provides data entry wizards that guide information providers through the process of documenting each data set.}(hX format in which the metadata are stored or with the database records themselves. In addition, the Metacat application can easily be extended to provide a customized data-entry interface that suits the particular requirements of each project. Metacat users can also choose to enter metadata using the Morpho application, which provides data entry wizards that guide information providers through the process of documenting each data set.hhIhhhNhNubeh}(h]h!]h#]h%]h']uh)h+hh*hKhh hhubh,)}(hX|The metadata stored in Metacat includes all of the information needed to understand what the described data are and how to use them: a descriptive data set title; an abstract; the temporal, spatial, and taxonomic coverage of the data; the data collection methods; distribution information; and contact information. Each information provider decides who has access to this information (the public, or just specified users), and whether or not to upload the data set itself with the data documentation. Information providers can also edit the metadata or delete it from the repository, again using Metacat's straightforward Web interface.h]hX~The metadata stored in Metacat includes all of the information needed to understand what the described data are and how to use them: a descriptive data set title; an abstract; the temporal, spatial, and taxonomic coverage of the data; the data collection methods; distribution information; and contact information. Each information provider decides who has access to this information (the public, or just specified users), and whether or not to upload the data set itself with the data documentation. Information providers can also edit the metadata or delete it from the repository, again using Metacat’s straightforward Web interface.}(hhthhrhhhNhNubah}(h]h!]h#]h%]h']uh)h+hh*hK#hh hhubh,)}(hXMetacat is a `Java servlet`_ application that runs on Linux and Mac OS platforms in conjunction with a database, such as PostgreSQL_, a Web server, and a Solr server. The Metacat application stores data in an XML_ format using `Ecological Metadata Language`_ (EML) or other metadata standards such as `ISO 19139`_ or the `FGDC Biological Data Profile`_. For more information about Metacat or for examples of projects currently using Metacat, please see http://knb.ecoinformatics.org.h](h Metacat is a }(h Metacat is a hhhhhNhNubhS)}(h`Java servlet`_h]h Java servlet}(hhhhubah}(h]h!]h#]h%]h']name Java servlethd)http://en.wikipedia.org/wiki/Java_Servletuh)hRhhhfKubh^ application that runs on Linux and Mac OS platforms in conjunction with a database, such as }(h^ application that runs on Linux and Mac OS platforms in conjunction with a database, such as hhhhhNhNubhS)}(h PostgreSQL_h]h PostgreSQL}(hhhhubah}(h]h!]h#]h%]h']name PostgreSQLhdhttp://www.postgresql.org/uh)hRhhhfKubhM, a Web server, and a Solr server. The Metacat application stores data in an }(hM, a Web server, and a Solr server. The Metacat application stores data in an hhhhhNhNubhS)}(hXML_h]hXML}(hhhhubah}(h]h!]h#]h%]h']nameXMLhdheuh)hRhhhfKubh format using }(h format using hhhhhNhNubhS)}(h`Ecological Metadata Language`_h]hEcological Metadata Language}(hhhhubah}(h]h!]h#]h%]h']nameEcological Metadata Languagehd*http://knb.ecoinformatics.org/software/emluh)hRhhhfKubh+ (EML) or other metadata standards such as }(h+ (EML) or other metadata standards such as hhhhhNhNubhS)}(h `ISO 19139`_h]h ISO 19139}(hhhhubah}(h]h!]h#]h%]h']name ISO 19139hd-http://marinemetadata.org/references/iso19139uh)hRhhhfKubh or the }(h or the hhhhhNhNubhS)}(h`FGDC Biological Data Profile`_h]hFGDC Biological Data Profile}(hhhhubah}(h]h!]h#]h%]h']nameFGDC Biological Data ProfilehdShttp://www.fgdc.gov/standards/projects/FGDC-standards-projects/metadata/biometadatauh)hRhhhfKubhe. For more information about Metacat or for examples of projects currently using Metacat, please see }(he. For more information about Metacat or for examples of projects currently using Metacat, please see hhhhhNhNubhS)}(hhttp://knb.ecoinformatics.orgh]hhttp://knb.ecoinformatics.org}(hhhj ubah}(h]h!]h#]h%]h']refurijuh)hRhhubh.}(h.hhhhhNhNubeh}(h]h!]h#]h%]h']uh)h+hh*hK-hh hhubhtarget)}(h).. _XML: http://en.wikipedia.org/wiki/XMLh]h}(h]xmlah!]h#]xmlah%]h']hdheuh)j&hK6hh hhhh* referencedKubj')}(h;.. _Java servlet: http://en.wikipedia.org/wiki/Java_Servleth]h}(h] java-servletah!]h#] java servletah%]h']hdhuh)j&hK8hh hhhh*j4Kubj')}(h*.. _PostgreSQL: http://www.postgresql.org/h]h}(h] postgresqlah!]h#] postgresqlah%]h']hdhuh)j&hK:hh hhhh*j4Kubj')}(h".. _Oracle: http://www.oracle.com/h]h}(h]oracleah!]h#]oracleah%]h']hdhttp://www.oracle.com/uh)j&hKhh hhhh*j4Kubj')}(h<.. _ISO 19139: http://marinemetadata.org/references/iso19139h]h}(h] iso-19139ah!]h#] iso 19139ah%]h']hdhuh)j&hK@hh hhhh*j4Kubj')}(hu.. _FGDC Biological Data Profile: http://www.fgdc.gov/standards/projects/FGDC-standards-projects/metadata/biometadatah]h}(h]fgdc-biological-data-profileah!]h#]fgdc biological data profileah%]h']hdjuh)j&hKBhh hhhh*j4Kubh )}(hhh](h)}(hWhat's in this Guideh]hWhat’s in this Guide}(hjhjhhhNhNubah}(h]h!]h#]h%]h']uh)hhj~hhhh*hKEubh,)}(hXOThis Administrator's guide includes information for installing, configuring, managing and extending Metacat for Ubuntu and other Linux variants. Metacat can run on MacOS but it needs users' customized installation. Chapter Four contains instructions for downloading and installing Metacat and the applications required to run the software on Linux platform. Chapter Five covers how to configure Metacat, both for new and upgraded installations. Chapter Seven details the ways in which you can customize the Metacat interface so users can access and submit information easily: using Metacat's generic web-interface (the Registry), creating your own HTML forms, and creating your own desktop client (like Morpho). Chapter Eight discusses how to work with Metacat's embedded Geoserver. Chapter Nine describes how to set up the Metacat's replication service, which permits Metacat servers to share data with each other, effectively backing up metadata and data files. Chapter Ten looks at the Metacat Harvester, a program that automates the retrieval of EML documents from one or more sites and their subsequent upload (insert or update) to Metacat. Chapter Eight discusses logging, Chapter Twelve contains instructions for creating a site map, which makes individual metadata entries available via Web searches. Metacat's `Java API`_ is available for developers.h](hX3This Administrator’s guide includes information for installing, configuring, managing and extending Metacat for Ubuntu and other Linux variants. Metacat can run on MacOS but it needs users’ customized installation. Chapter Four contains instructions for downloading and installing Metacat and the applications required to run the software on Linux platform. Chapter Five covers how to configure Metacat, both for new and upgraded installations. Chapter Seven details the ways in which you can customize the Metacat interface so users can access and submit information easily: using Metacat’s generic web-interface (the Registry), creating your own HTML forms, and creating your own desktop client (like Morpho). Chapter Eight discusses how to work with Metacat’s embedded Geoserver. Chapter Nine describes how to set up the Metacat’s replication service, which permits Metacat servers to share data with each other, effectively backing up metadata and data files. Chapter Ten looks at the Metacat Harvester, a program that automates the retrieval of EML documents from one or more sites and their subsequent upload (insert or update) to Metacat. Chapter Eight discusses logging, Chapter Twelve contains instructions for creating a site map, which makes individual metadata entries available via Web searches. Metacat’s }(hX'This Administrator's guide includes information for installing, configuring, managing and extending Metacat for Ubuntu and other Linux variants. Metacat can run on MacOS but it needs users' customized installation. Chapter Four contains instructions for downloading and installing Metacat and the applications required to run the software on Linux platform. Chapter Five covers how to configure Metacat, both for new and upgraded installations. Chapter Seven details the ways in which you can customize the Metacat interface so users can access and submit information easily: using Metacat's generic web-interface (the Registry), creating your own HTML forms, and creating your own desktop client (like Morpho). Chapter Eight discusses how to work with Metacat's embedded Geoserver. Chapter Nine describes how to set up the Metacat's replication service, which permits Metacat servers to share data with each other, effectively backing up metadata and data files. Chapter Ten looks at the Metacat Harvester, a program that automates the retrieval of EML documents from one or more sites and their subsequent upload (insert or update) to Metacat. Chapter Eight discusses logging, Chapter Twelve contains instructions for creating a site map, which makes individual metadata entries available via Web searches. Metacat's hjhhhNhNubhS)}(h `Java API`_h]hJava API}(hhhjubah}(h]h!]h#]h%]h']nameJava APIhd./api/index.htmluh)hRhjhfKubh is available for developers.}(h is available for developers.hjhhhNhNubeh}(h]h!]h#]h%]h']uh)h+hh*hKFhj~hhubj')}(h.. _Java API: ./api/index.htmlh]h}(h]java-apiah!]h#]java apiah%]h']hdjuh)j&hKYhj~hhhh*j4Kubeh}(h]what-s-in-this-guideah!]h#]what's in this guideah%]h']uh)h hh hhhh*hKEubh )}(hhh](h)}(hMetacat Featuresh]hMetacat Features}(hjhjhhhNhNubah}(h]h!]h#]h%]h']uh)hhjhhhh*hK\ubh,)}(hMetacat is a repository for data and metadata (documentation about data), that helps scientists find, understand and effectively use the data sets they manage or that have been created by others. Specifically,h]hMetacat is a repository for data and metadata (documentation about data), that helps scientists find, understand and effectively use the data sets they manage or that have been created by others. Specifically,}(hjhjhhhNhNubah}(h]h!]h#]h%]h']uh)h+hh*hK]hjhhubh bullet_list)}(hhh](h list_item)}(htMetacat is an open source web application, which can run on Linux and MacOS operating systems and is written in Javah]h,)}(hjh]htMetacat is an open source web application, which can run on Linux and MacOS operating systems and is written in Java}(hjhjubah}(h]h!]h#]h%]h']uh)h+hh*hKahjubah}(h]h!]h#]h%]h']uh)jhjhhhh*hNubj)}(hCMetacat's Web interface facilitates the input and retrieval of datah]h,)}(hjh]hEMetacat’s Web interface facilitates the input and retrieval of data}(hjhj ubah}(h]h!]h#]h%]h']uh)h+hh*hKbhjubah}(h]h!]h#]h%]h']uh)jhjhhhh*hNubj)}(hwMetacat's optional mapping functionality enables you to query and visualize the geographic coverage of stored data setsh]h,)}(hjh]hyMetacat’s optional mapping functionality enables you to query and visualize the geographic coverage of stored data sets}(hjhj ubah}(h]h!]h#]h%]h']uh)h+hh*hKchjubah}(h]h!]h#]h%]h']uh)jhjhhhh*hNubj)}(huMetacat's replication feature ensures that all Metacat data and metadata is stored safely on multiple Metacat serversh]h,)}(hj5h]hwMetacat’s replication feature ensures that all Metacat data and metadata is stored safely on multiple Metacat servers}(hj5hj7ubah}(h]h!]h#]h%]h']uh)h+hh*hKdhj3ubah}(h]h!]h#]h%]h']uh)jhjhhhh*hNubj)}(hThe Metacat interface can be easily extended and customized via Web forms, themes, and/or user-developed client tools in Java and other languagesh]h,)}(hjLh]hThe Metacat interface can be easily extended and customized via Web forms, themes, and/or user-developed client tools in Java and other languages}(hjLhjNubah}(h]h!]h#]h%]h']uh)h+hh*hKehjJubah}(h]h!]h#]h%]h']uh)jhjhhhh*hNubj)}(hjThe Metacat harvester automates the process of retrieving and storing EML documents from one or more sitesh]h,)}(hjch]hjThe Metacat harvester automates the process of retrieving and storing EML documents from one or more sites}(hjchjeubah}(h]h!]h#]h%]h']uh)h+hh*hKfhjaubah}(h]h!]h#]h%]h']uh)jhjhhhh*hNubj)}(hjMetacat can be customized to use Life Sciences Identifiers (LSIDs), uniquely identifying every data recordh]h,)}(hjzh]hjMetacat can be customized to use Life Sciences Identifiers (LSIDs), uniquely identifying every data record}(hjzhj|ubah}(h]h!]h#]h%]h']uh)h+hh*hKghjxubah}(h]h!]h#]h%]h']uh)jhjhhhh*hNubj)}(hrMetacat has a built-in logging system for tracking events such as document insertions, updates, deletes, and readsh]h,)}(hjh]hrMetacat has a built-in logging system for tracking events such as document insertions, updates, deletes, and reads}(hjhjubah}(h]h!]h#]h%]h']uh)h+hh*hKhhjubah}(h]h!]h#]h%]h']uh)jhjhhhh*hNubj)}(hGThe appearance of Metacat's Web interface can be customized via themes.h]h,)}(hjh]hIThe appearance of Metacat’s Web interface can be customized via themes.}(hjhjubah}(h]h!]h#]h%]h']uh)h+hh*hKihjubah}(h]h!]h#]h%]h']uh)jhjhhhh*hNubj)}(hMetacat fully supports the DataONE Member Node interface, allowing Metacat deployments to easily participate in the DataONE federation h]h,)}(hMetacat fully supports the DataONE Member Node interface, allowing Metacat deployments to easily participate in the DataONE federationh]hMetacat fully supports the DataONE Member Node interface, allowing Metacat deployments to easily participate in the DataONE federation}(hjhjubah}(h]h!]h#]h%]h']uh)h+hh*hKjhjubah}(h]h!]h#]h%]h']uh)jhjhhhh*hNubeh}(h]h!]h#]h%]h']bullet*uh)jhh*hKahjhhubhfigure)}(hhh](himage)}(h.. figure:: images/screenshots/image007.png Metacat's default home page. 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