€cdocutils.nodes document q)q}q(U nametypesq}q(XxmlqˆX iso 19139qˆXwhat's in this guideqNX postgresqlq ˆX introductionq NXmetacat featuresq NXjava apiq ˆXfgdc biological data profileq ˆX java servletqˆXoracleqˆXecological metadata languageqˆuUsubstitution_defsq}qUparse_messagesq]qUcurrent_sourceqNU decorationqNUautofootnote_startqKUnameidsq}q(hUxmlqhU iso-19139qhUwhat-s-in-this-guideqh U postgresqlqh U introductionqh Umetacat-featuresqh Ujava-apiq h Ufgdc-biological-data-profileq!hU java-servletq"hUoracleq#hUecological-metadata-languageq$uUchildrenq%]q&cdocutils.nodes section q')q(}q)(U rawsourceq*UUparentq+hUsourceq,X_/var/lib/jenkins/jobs/Metacat_stable/workspace/METACAT_2_8_2/docs/user/metacat/source/intro.rstq-Utagnameq.Usectionq/U attributesq0}q1(Udupnamesq2]Uclassesq3]Ubackrefsq4]Uidsq5]q6haUnamesq7]q8h auUlineq9KUdocumentq:hh%]q;(cdocutils.nodes title q<)q=}q>(h*X Introductionq?h+h(h,h-h.Utitleq@h0}qA(h2]h3]h4]h5]h7]uh9Kh:hh%]qBcdocutils.nodes Text qCX IntroductionqD…qE}qF(h*h?h+h=ubaubcdocutils.nodes paragraph qG)qH}qI(h*XæMetacat 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.qJh+h(h,h-h.U paragraphqKh0}qL(h2]h3]h4]h5]h7]uh9Kh:hh%]qMhCXæMetacat 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.qN…qO}qP(h*hJh+hHubaubhG)qQ}qR(h*X1Not 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).qSh+h(h,h-h.hKh0}qT(h2]h3]h4]h5]h7]uh9K h:hh%]qUhCX1Not 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).qV…qW}qX(h*hSh+hQubaubhG)qY}qZ(h*XâMetacat'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+h(h,h-h.hKh0}q[(h2]h3]h4]h5]h7]uh9Kh:hh%]q\(hCX)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 q]…q^}q_(h*X)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 h+hYubcdocutils.nodes reference q`)qa}qb(h*XXML_UresolvedqcKh+hYh.U referenceqdh0}qe(UnameXXMLUrefuriqfX http://en.wikipedia.org/wiki/XMLqgh5]h4]h2]h3]h7]uh%]qhhCXXMLqi…qj}qk(h*Uh+haubaubhCXµ 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.ql…qm}qn(h*Xµ 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+hYubeubhG)qo}qp(h*X|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.qqh+h(h,h-h.hKh0}qr(h2]h3]h4]h5]h7]uh9K#h:hh%]qshCX|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.qt…qu}qv(h*hqh+houbaubhG)qw}qx(h*XëMetacat is a `Java servlet`_ application that runs on Linux, Mac OS, and Windows platforms in conjunction with a database, such as PostgreSQL_ (or Oracle_), and a Web 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(h,h-h.hKh0}qy(h2]h3]h4]h5]h7]uh9K-h:hh%]qz(hCX Metacat is a q{…q|}q}(h*X Metacat is a h+hwubh`)q~}q(h*X`Java servlet`_hcKh+hwh.hdh0}q€(UnameX Java servlethfX)http://en.wikipedia.org/wiki/Java_Servletqh5]h4]h2]h3]h7]uh%]q‚hCX Java servletqƒ…q„}q…(h*Uh+h~ubaubhCXg application that runs on Linux, Mac OS, and Windows platforms in conjunction with a database, such as q†…q‡}qˆ(h*Xg application that runs on Linux, Mac OS, and Windows platforms in conjunction with a database, such as h+hwubh`)q‰}qŠ(h*X PostgreSQL_hcKh+hwh.hdh0}q‹(UnameX PostgreSQLhfXhttp://www.postgresql.org/qŒh5]h4]h2]h3]h7]uh%]qhCX PostgreSQLqŽ…q}q(h*Uh+h‰ubaubhCX (or q‘…q’}q“(h*X (or h+hwubh`)q”}q•(h*XOracle_hcKh+hwh.hdh0}q–(UnameXOraclehfXhttp://www.oracle.com/q—h5]h4]h2]h3]h7]uh%]q˜hCXOracleq™…qš}q›(h*Uh+h”ubaubhCX?), and a Web server. The Metacat application stores data in an qœ…q}qž(h*X?), and a Web server. The Metacat application stores data in an h+hwubh`)qŸ}q (h*XXML_hcKh+hwh.hdh0}q¡(UnameXXMLhfhgh5]h4]h2]h3]h7]uh%]q¢hCXXMLq£…q¤}q¥(h*Uh+hŸubaubhCX format using q¦…q§}q¨(h*X format using h+hwubh`)q©}qª(h*X`Ecological Metadata Language`_hcKh+hwh.hdh0}q«(UnameXEcological Metadata LanguagehfX*http://knb.ecoinformatics.org/software/emlq¬h5]h4]h2]h3]h7]uh%]q­hCXEcological Metadata Languageq®…q¯}q°(h*Uh+h©ubaubhCX+ (EML) or other metadata standards such as q±…q²}q³(h*X+ (EML) or other metadata standards such as h+hwubh`)q´}qµ(h*X `ISO 19139`_hcKh+hwh.hdh0}q¶(UnameX ISO 19139hfX-http://marinemetadata.org/references/iso19139q·h5]h4]h2]h3]h7]uh%]q¸hCX ISO 19139q¹…qº}q»(h*Uh+h´ubaubhCX or the q¼…q½}q¾(h*X or the h+hwubh`)q¿}qÀ(h*X`FGDC Biological Data Profile`_hcKh+hwh.hdh0}qÁ(UnameXFGDC Biological Data ProfilehfXShttp://www.fgdc.gov/standards/projects/FGDC-standards-projects/metadata/biometadataqÂh5]h4]h2]h3]h7]uh%]qÃhCXFGDC Biological Data ProfileqÄ…qÅ}qÆ(h*Uh+h¿ubaubhCXe. For more information about Metacat or for examples of projects currently using Metacat, please see qÇ…qÈ}qÉ(h*Xe. For more information about Metacat or for examples of projects currently using Metacat, please see h+hwubh`)qÊ}qË(h*Xhttp://knb.ecoinformatics.orgqÌh0}qÍ(UrefurihÌh5]h4]h2]h3]h7]uh+hwh%]qÎhCXhttp://knb.ecoinformatics.orgqÏ…qÐ}qÑ(h*Uh+hÊubah.hdubhCX.…qÒ}qÓ(h*X.h+hwubeubcdocutils.nodes target qÔ)qÕ}qÖ(h*X).. _XML: http://en.wikipedia.org/wiki/XMLU referencedq×Kh+h(h,h-h.UtargetqØh0}qÙ(hfhgh5]qÚhah4]h2]h3]h7]qÛhauh9K6h:hh%]ubhÔ)qÜ}qÝ(h*X;.. _Java servlet: http://en.wikipedia.org/wiki/Java_Servleth×Kh+h(h,h-h.hØh0}qÞ(hfhh5]qßh"ah4]h2]h3]h7]qàhauh9K8h:hh%]ubhÔ)qá}qâ(h*X*.. _PostgreSQL: http://www.postgresql.org/h×Kh+h(h,h-h.hØh0}qã(hfhŒh5]qähah4]h2]h3]h7]qåh auh9K:h:hh%]ubhÔ)qæ}qç(h*X".. _Oracle: http://www.oracle.com/h×Kh+h(h,h-h.hØh0}qè(hfh—h5]qéh#ah4]h2]h3]h7]qêhauh9Kh:hh%]ubhÔ)qð}qñ(h*X<.. _ISO 19139: http://marinemetadata.org/references/iso19139h×Kh+h(h,h-h.hØh0}qò(hfh·h5]qóhah4]h2]h3]h7]qôhauh9K@h:hh%]ubhÔ)qõ}qö(h*Xu.. _FGDC Biological Data Profile: http://www.fgdc.gov/standards/projects/FGDC-standards-projects/metadata/biometadatah×Kh+h(h,h-h.hØh0}q÷(hfhÂh5]qøh!ah4]h2]h3]h7]qùh auh9KBh:hh%]ubh')qú}qû(h*Uh+h(h,h-h.h/h0}qü(h2]h3]h4]h5]qýhah7]qþhauh9KEh:hh%]qÿ(h<)r}r(h*XWhat's in this Guiderh+húh,h-h.h@h0}r(h2]h3]h4]h5]h7]uh9KEh:hh%]rhCXWhat's in this Guider…r}r(h*jh+jubaubhG)r}r (h*X This Administrator's guide includes information for installing, configuring, managing and extending Metacat for both Linux, Mac OS, and Windows systems. Chapter Four contains instructions for downloading and installing Metacat and the applications required to run the software on Linux and Microsoft platforms. 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+húh,h-h.hKh0}r (h2]h3]h4]h5]h7]uh9KFh:hh%]r (hCXøThis Administrator's guide includes information for installing, configuring, managing and extending Metacat for both Linux, Mac OS, and Windows systems. Chapter Four contains instructions for downloading and installing Metacat and the applications required to run the software on Linux and Microsoft platforms. 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 r …r }r(h*XøThis Administrator's guide includes information for installing, configuring, managing and extending Metacat for both Linux, Mac OS, and Windows systems. Chapter Four contains instructions for downloading and installing Metacat and the applications required to run the software on Linux and Microsoft platforms. 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 h+jubh`)r}r(h*X `Java API`_hcKh+jh.hdh0}r(UnameXJava APIhfX./api/index.htmlrh5]h4]h2]h3]h7]uh%]rhCXJava APIr…r}r(h*Uh+jubaubhCX is available for developers.r…r}r(h*X is available for developers.h+jubeubhÔ)r}r(h*X.. _Java API: ./api/index.htmlh×Kh+húh,h-h.hØh0}r(hfjh5]rh ah4]h2]h3]h7]rh auh9KXh:hh%]ubeubh')r}r (h*Uh+h(h,h-h.h/h0}r!(h2]h3]h4]h5]r"hah7]r#h auh9K[h:hh%]r$(h<)r%}r&(h*XMetacat Featuresr'h+jh,h-h.h@h0}r((h2]h3]h4]h5]h7]uh9K[h:hh%]r)hCXMetacat Featuresr*…r+}r,(h*j'h+j%ubaubhG)r-}r.(h*XÑMetacat 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,r/h+jh,h-h.hKh0}r0(h2]h3]h4]h5]h7]uh9K\h:hh%]r1hCXÑMetacat 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,r2…r3}r4(h*j/h+j-ubaubcdocutils.nodes bullet_list r5)r6}r7(h*Uh+jh,h-h.U bullet_listr8h0}r9(Ubulletr:X*h5]h4]h2]h3]h7]uh9K`h:hh%]r;(cdocutils.nodes list_item r<)r=}r>(h*X~Metacat is an open source web application, which can run on Linux, MacOS, and Windows operating systems and is written in Javar?h+j6h,h-h.U list_itemr@h0}rA(h2]h3]h4]h5]h7]uh9Nh:hh%]rBhG)rC}rD(h*j?h+j=h,h-h.hKh0}rE(h2]h3]h4]h5]h7]uh9K`h%]rFhCX~Metacat is an open source web application, which can run on Linux, MacOS, and Windows operating systems and is written in JavarG…rH}rI(h*j?h+jCubaubaubj<)rJ}rK(h*XCMetacat's Web interface facilitates the input and retrieval of datarLh+j6h,h-h.j@h0}rM(h2]h3]h4]h5]h7]uh9Nh:hh%]rNhG)rO}rP(h*jLh+jJh,h-h.hKh0}rQ(h2]h3]h4]h5]h7]uh9Kah%]rRhCXCMetacat's Web interface facilitates the input and retrieval of datarS…rT}rU(h*jLh+jOubaubaubj<)rV}rW(h*XwMetacat's optional mapping functionality enables you to query and visualize the geographic coverage of stored data setsrXh+j6h,h-h.j@h0}rY(h2]h3]h4]h5]h7]uh9Nh:hh%]rZhG)r[}r\(h*jXh+jVh,h-h.hKh0}r](h2]h3]h4]h5]h7]uh9Kbh%]r^hCXwMetacat's optional mapping functionality enables you to query and visualize the geographic coverage of stored data setsr_…r`}ra(h*jXh+j[ubaubaubj<)rb}rc(h*XuMetacat's replication feature ensures that all Metacat data and metadata is stored safely on multiple Metacat serversrdh+j6h,h-h.j@h0}re(h2]h3]h4]h5]h7]uh9Nh:hh%]rfhG)rg}rh(h*jdh+jbh,h-h.hKh0}ri(h2]h3]h4]h5]h7]uh9Kch%]rjhCXuMetacat's replication feature ensures that all Metacat data and metadata is stored safely on multiple Metacat serversrk…rl}rm(h*jdh+jgubaubaubj<)rn}ro(h*X‘The Metacat interface can be easily extended and customized via Web forms, themes, and/or user-developed client tools in Java and other languagesrph+j6h,h-h.j@h0}rq(h2]h3]h4]h5]h7]uh9Nh:hh%]rrhG)rs}rt(h*jph+jnh,h-h.hKh0}ru(h2]h3]h4]h5]h7]uh9Kdh%]rvhCX‘The Metacat interface can be easily extended and customized via Web forms, themes, and/or user-developed client tools in Java and other languagesrw…rx}ry(h*jph+jsubaubaubj<)rz}r{(h*XjThe Metacat harvester automates the process of retrieving and storing EML documents from one or more sitesr|h+j6h,h-h.j@h0}r}(h2]h3]h4]h5]h7]uh9Nh:hh%]r~hG)r}r€(h*j|h+jzh,h-h.hKh0}r(h2]h3]h4]h5]h7]uh9Keh%]r‚hCXjThe Metacat harvester automates the process of retrieving and storing EML documents from one or more sitesrƒ…r„}r…(h*j|h+jubaubaubj<)r†}r‡(h*XjMetacat can be customized to use Life Sciences Identifiers (LSIDs), uniquely identifying every data recordrˆh+j6h,h-h.j@h0}r‰(h2]h3]h4]h5]h7]uh9Nh:hh%]rŠhG)r‹}rŒ(h*jˆh+j†h,h-h.hKh0}r(h2]h3]h4]h5]h7]uh9Kfh%]rŽhCXjMetacat can be customized to use Life Sciences Identifiers (LSIDs), uniquely identifying every data recordr…r}r‘(h*jˆh+j‹ubaubaubj<)r’}r“(h*XrMetacat has a built-in logging system for tracking events such as document insertions, updates, deletes, and readsr”h+j6h,h-h.j@h0}r•(h2]h3]h4]h5]h7]uh9Nh:hh%]r–hG)r—}r˜(h*j”h+j’h,h-h.hKh0}r™(h2]h3]h4]h5]h7]uh9Kgh%]ršhCXrMetacat has a built-in logging system for tracking events such as document insertions, updates, deletes, and readsr›…rœ}r(h*j”h+j—ubaubaubj<)rž}rŸ(h*XGThe appearance of Metacat's Web interface can be customized via themes.r h+j6h,h-h.j@h0}r¡(h2]h3]h4]h5]h7]uh9Nh:hh%]r¢hG)r£}r¤(h*j h+jžh,h-h.hKh0}r¥(h2]h3]h4]h5]h7]uh9Khh%]r¦hCXGThe appearance of Metacat's Web interface can be customized via themes.r§…r¨}r©(h*j h+j£ubaubaubj<)rª}r«(h*X‡Metacat fully supports the DataONE Member Node interface, allowing Metacat deployments to easily participate in the DataONE federation h+j6h,h-h.j@h0}r¬(h2]h3]h4]h5]h7]uh9Nh:hh%]r­hG)r®}r¯(h*X†Metacat fully supports the DataONE Member Node interface, allowing Metacat deployments to easily participate in the DataONE federationr°h+jªh,h-h.hKh0}r±(h2]h3]h4]h5]h7]uh9Kih%]r²hCX†Metacat fully supports the DataONE Member Node interface, allowing Metacat deployments to easily participate in the DataONE federationr³…r´}rµ(h*j°h+j®ubaubaubeubcdocutils.nodes figure r¶)r·}r¸(h*Uh+jh,h-h.Ufigurer¹h0}rº(h2]h3]h4]h5]r»Uid1r¼ah7]uh9Kmh:hh%]r½(cdocutils.nodes image r¾)r¿}rÀ(h*X€.. figure:: images/screenshots/image007.png Metacat's default home page. 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