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From: <no...@us...> - 2010-10-12 21:03:28
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Revision: 23955
http://gmod.svn.sourceforge.net/gmod/?rev=23955&view=rev
Author: nomi
Date: 2010-10-12 21:03:18 +0000 (Tue, 12 Oct 2010)
Log Message:
-----------
Really just ../game.rng, but used by userguide.html.
Added Paths:
-----------
apollo/trunk/doc/html/game.rng.txt
Added: apollo/trunk/doc/html/game.rng.txt
===================================================================
--- apollo/trunk/doc/html/game.rng.txt (rev 0)
+++ apollo/trunk/doc/html/game.rng.txt 2010-10-12 21:03:18 UTC (rev 23955)
@@ -0,0 +1,844 @@
+<?xml version="1.0"?>
+<grammar ns="" xmlns="http://relaxng.org/ns/structure/1.0" datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes">
+ <!-- RELAX-NG (see relaxng.org) schema description for GAME XML -->
+ <!-- The rng file is the home of the GAME XML schema. game.xsd can be
+ derived from it using trang (see schema-notes), as can game.rnc if you
+ want the compact format. Therefore, any modifications to the schema
+ should be made to the rng file first. -->
+ <!-- Schema for GAME XML, v1.0.
+ Note that this schema is liberal--it is possible to construct GAME XML
+ files that Apollo's GAME XML parser doesn't like but yet are
+ validated by this schema.
+ Started by Sohel Merchant at RGD; edited and commented by Suzanna
+ Lewis; edited and commented by Andrew Dalke; extensively revised by
+ Nomi Harris 11/2004 -->
+ <!-- Note on entities: some XML files include non-standard entities for
+ representing Greek letters, e.g. &tgr;. Theoretically, all nonstandard
+ entities should be defined in the XML stream itself. This is not the
+ case with the Apollo data because Apollo has code to deal with these
+ entities. It turns out to be non-trivial to make the schema deal with
+ entities that are nonstandard and not defined in the XML input, so if
+ you try to validate a GAME XML file that includes these Greek entities,
+ you will unfortunately get a fatal error. NH, 12/07/2004 -->
+ <start>
+ <choice>
+ <!-- The root element; represents the curation of one or more
+ sequences of DNA, RNA, or AA. Most commonly, the <game> element
+ represents the curation of a single sequence. -->
+ <element name="game">
+ <optional>
+ <attribute name="version">
+ <data type="string"/>
+ </attribute>
+ </optional>
+ <oneOrMore>
+ <choice>
+ <!-- <seq>: Represents a sequence of DNA, RNA, or AA. There
+ is generally one <seq> in the document representing the
+ primary sequence being curated, and other <seq>'s that
+ support the curation of the primary sequence. The primary
+ <seq> is directly under the <game> element, and is identified
+ by having its "focus" attribute set to true. Each <seq> has
+ one or more <db_xref> to indicate where the seq can be found
+ using a particular unique identifier.
+ For Drosophila curation, BDGP uses the primary <seq> to represent
+ an accession, and other <seq>'s to represent cDNA's, protein
+ coding sequences, and homologous sequences that are
+ referenced by computational analyses such as tblastx. -->
+ <element name="seq">
+ <ref name="seqType"/>
+ </element>
+ <!-- <map_position>: Maps a sequence onto a chromosome. For
+ Drosophila curation, only one <map_position> is used per
+ file, to specify the location of the primary sequence on a
+ chromosome. -->
+ <element name="map_position">
+ <interleave>
+ <attribute name="seq">
+ <data type="string"/>
+ </attribute>
+ <attribute name="type">
+ <data type="string"/>
+ </attribute>
+ <!-- Theoretically, we should have arm or chromosome, but
+ not both. In practice, I've sometimes seen both. -->
+ <optional>
+ <ref name="arm"/>
+ </optional>
+ <optional>
+ <ref name="chromosome"/>
+ </optional>
+ <optional>
+ <ref name="organism"/>
+ </optional>
+ <element name="span">
+ <ref name="spanType"/>
+ </element>
+ </interleave>
+ </element>
+
+ <!-- <annotation>: Represents a set of related seqence
+ features and a collection of genetic information describing
+ them. The term "sequence feature" means a segment of DNA.
+ An annotation will generally contain a number of
+ <feature_set>'s, each of which represents a set of related
+ sequence features that have a specific location. A
+ <feature_set> can contain nested <feature_set>'s (although in
+ practice this has not yet occured), as well as one or more
+ <feature_span>'s, each of which represents an individual
+ sequence feature. A <feature_span> can contain <evidence>
+ which specifies a result id and result type. An <annotation>
+ can have one or more <db_xref>'s.
+ For Drosophila curation, the types of annotations are: gene,
+ pseudogene, transposon, tRNA, rRNA, snRNA, snoRNA,
+ "misc. non-coding RNA", and "miscellaneous curator's
+ observation". [Note: there are now some additional types.]
+ For an <annotation> of type "gene", one <feature_set> element
+ represents each transcript, and for each transcript, one
+ <feature_span> element represents each exon. -->
+ <element name="annotation">
+ <interleave>
+ <optional>
+ <attribute name="problem">
+ <data type="boolean"/>
+ </attribute>
+ </optional>
+ <attribute name="id">
+ <data type="NMTOKEN"/>
+ </attribute>
+ <ref name="name"/>
+ <!-- Type should be constrained to be a SO term -->
+ <ref name="type"/>
+ <optional>
+ <element name="date">
+ <ref name="dateType"/>
+ </element>
+ </optional>
+ <!-- A lot of magic is held in the property element.
+ It became the elastic that let us add new data (and have it
+ be saved to the database) without having to change any of
+ the other code. To get the full functionality of Apollo
+ maybe we should enumerate the special types here? -->
+ <zeroOrMore>
+ <element name="property">
+ <ref name="propertyType"/>
+ </element>
+ </zeroOrMore>
+ <zeroOrMore>
+ <ref name="synonym"/>
+ </zeroOrMore>
+ <optional>
+ <element name="gene">
+ <optional>
+ <!-- This is another leftover. The idea was that sometimes
+ a curator might not 'know' which gene it is (from the literature)
+ but they have a list of suspects that it might be.
+ Perhaps we should eliminate this entire <gene> element. -->
+ <attribute name="association">
+ <data type="string"/>
+ </attribute>
+ </optional>
+ <attribute name="id">
+ <data type="string"/>
+ </attribute>
+ <ref name="name"/>
+ <optional>
+ <!-- <dbxref>: Represents a database
+ cross-reference. The <xref_db> is the name of the
+ database (e.g. EMBL), and the <db_xref_id> is the
+ unique id within that database. -->
+ <element name="dbxref">
+ <ref name="dbxrefType"/>
+ </element>
+ </optional>
+ </element>
+ </optional>
+ <!-- other db xrefs other than the primary one in the gene element -->
+ <zeroOrMore>
+ <element name="dbxref">
+ <ref name="dbxrefType"/>
+ </element>
+ </zeroOrMore>
+ <zeroOrMore>
+ <element name="comment">
+ <ref name="commentType"/>
+ </element>
+ </zeroOrMore>
+ <optional>
+ <element name="description">
+ <data type="string"/>
+ </element>
+ </optional>
+ <choice>
+ <oneOrMore>
+ <!-- <feature_set>: Represents a set of sequence
+ features (segments of DNA).
+ For Drosophila curation, a <feature_set> represents a
+ transcript, and contains a number of <feature_span>'s
+ which represent the start codon and the exons. Each
+ <feature_set> typically contains two <seq>'s, one for
+ the cDNA sequence and one for the protein-coding
+ sequence of the transcript. -->
+ <element name="feature_set">
+ <ref name="feature_setType"/>
+ </element>
+ </oneOrMore>
+ <oneOrMore>
+ <!-- <feature_span>: Represents a sequence feature
+ (segment of DNA), including its location, which is
+ specified in a <seq_relationship>. Can contain
+ <evidence> which specifies a result id and result
+ type. [Actually, I don't think we have explicit
+ <evidence> tags anymore.]
+ For Drosophila curation, a <feature_span> represents
+ an exon or a start codon. Each <feature_span>
+ contains a <seq_relationship> of type "query"
+ specifying the location on the primary sequence of
+ the document, which is typically an accession. -->
+ <element name="feature_span">
+ <ref name="feature_spanType"/>
+ </element>
+ </oneOrMore>
+ <oneOrMore>
+ <!-- for one level annots just have a seq relationship which just gives
+ coords for the annot -- new change to game as of fall 2005 -->
+ <element name="seq_relationship">
+ <ref name="seq_relationshipType"/>
+ </element>
+ </oneOrMore>
+ </choice>
+ </interleave>
+ </element>
+
+ <!-- <computational_analysis>: Contains evidence from
+ computational analysis programs such sim4 and blastx.
+ <result_set>'s and <result_span>'s represent a tree structure
+ of results, with <result_set>'s representing branch nodes
+ (e.g. gene matches), and <result_span>'s representing leaf
+ nodes (e.g. exon matches). The elements <feature_set>,
+ <feature_span>, <result_set>, <result_span> run parallel to
+ one another. Both allow multiple levels of nesting, both have
+ physical location(s) on sequences. The key differences are
+ that 'features' have results as evidence and results have
+ some form of an associated score for the assay.
+ <seq_relationship>'s provides the locations on the underlying
+ <seq>'s. -->
+ <element name="computational_analysis">
+ <interleave>
+ <!-- program name is required -->
+ <ref name="program"/>
+ <optional>
+ <ref name="database"/>
+ </optional>
+ <!-- version of program used -->
+ <optional>
+ <ref name="version"/>
+ </optional>
+ <!-- There's not usually a "type" field here, but some
+ datasets seem to have it. -->
+ <optional>
+ <ref name="type"/>
+ </optional>
+ <zeroOrMore>
+ <element name="property">
+ <ref name="propertyType"/>
+ </element>
+ </zeroOrMore>
+ <!-- date analysis was run -->
+ <optional>
+ <element name="date">
+ <ref name="dateType"/>
+ </element>
+ </optional>
+ <choice>
+ <!-- Normally a computational analysis should have
+ result sets, but sometimes they're empty. -->
+ <zeroOrMore>
+ <element name="result_set">
+ <ref name="result_setType"/>
+ </element>
+ </zeroOrMore>
+ <!-- some analyses just give single intervals, for example
+ tRNAscan-SE. Although I will admit that most of the time
+ what the DB has provided is a 'set' with only a single
+ 'span' contained within it. -->
+ <zeroOrMore>
+ <element name="result_span">
+ <ref name="result_spanType"/>
+ </element>
+ </zeroOrMore>
+ </choice>
+ </interleave>
+ </element>
+ <element name="transaction">
+ <interleave>
+ <element name="date">
+ <ref name="dateType"/>
+ </element>
+ <ref name="author"/>
+ <ref name="object_class"/>
+ <ref name="operation"/>
+ <element name="before">
+ <interleave>
+ <optional>
+ <ref name="annotation_id"/>
+ </optional>
+ <optional>
+ <ref name="id"/>
+ </optional>
+ <optional>
+ <ref name="transcript_name"/>
+ </optional>
+ <optional>
+ <ref name="name"/>
+ </optional>
+ </interleave>
+ </element>
+ <element name="after">
+ <interleave>
+ <optional>
+ <ref name="annotation_id"/>
+ </optional>
+ <optional>
+ <ref name="id"/>
+ </optional>
+ <optional>
+ <ref name="transcript_name"/>
+ </optional>
+ <optional>
+ <ref name="name"/>
+ </optional>
+ </interleave>
+ </element>
+ </interleave>
+ </element>
+ <!-- Obsolete types of transaction record,
+ included for backwards compatibility -->
+ <element name="deleted_transcript">
+ <attribute name="id">
+ <data type="string"/>
+ </attribute>
+ </element>
+ <element name="changed_gene">
+ <attribute name="id">
+ <data type="string"/>
+ </attribute>
+ </element>
+ </choice>
+ </oneOrMore>
+ </element>
+ <ref name="transcript_name"/>
+ <ref name="start"/>
+ <ref name="end"/>
+ <ref name="position"/>
+ <ref name="base"/>
+ <ref name="person"/>
+ <ref name="alignment"/>
+ <ref name="operation"/>
+ <ref name="chromosome"/>
+ <ref name="score"/>
+ <ref name="residues"/>
+ <ref name="xref_db"/>
+ <ref name="name"/>
+ <ref name="value"/>
+ <ref name="annotation_id"/>
+ <ref name="type"/>
+ <ref name="organism"/>
+ <ref name="version"/>
+ <ref name="arm"/>
+ <ref name="synonym"/>
+ <ref name="text"/>
+ <ref name="description"/>
+ <ref name="db_xref_id"/>
+ <ref name="database"/>
+ <ref name="program"/>
+ <ref name="author"/>
+ <ref name="object_class"/>
+ </choice>
+ </start>
+ <define name="position">
+ <element name="position">
+ <ref name="int"/>
+ </element>
+ </define>
+ <define name="base">
+ <element name="base">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="organism">
+ <element name="organism">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="result_spanType">
+ <interleave>
+ <optional>
+ <attribute name="id">
+ <data type="string"/>
+ </attribute>
+ </optional>
+ <optional>
+ <ref name="name"/>
+ </optional>
+ <optional>
+ <ref name="type"/>
+ </optional>
+ <optional>
+ <ref name="score"/>
+ </optional>
+ <zeroOrMore>
+ <element name="output">
+ <ref name="outputType"/>
+ </element>
+ </zeroOrMore>
+ <oneOrMore>
+ <!-- <seq_relationship>: Provides the locations on the underlying
+ <seq>'s. Every <seq_relationship> absolutely requires a seq_id
+ reference. There are no hidden assumptions regarding which
+ sequence the positions refer to - it is firmly explicit. This
+ makes it possible, among other things, to have the same feature
+ appear on multiple sequences. -->
+ <element name="seq_relationship">
+ <ref name="seq_relationshipType"/>
+ </element>
+ </oneOrMore>
+ </interleave>
+ </define>
+ <!-- Note that some values should really be restricted to a particular
+ type. For example, sometimes scores appear as type=score, value=12345,
+ and we'd want to reject value=FOO, but we can't constrain value like
+ that because in other cases it represents other types of data. -->
+ <define name="value">
+ <element name="value">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="version">
+ <element name="version">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="id">
+ <element name="id">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="annotation_id">
+ <element name="annotation_id">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="type">
+ <element name="type">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="outputType">
+ <interleave>
+ <ref name="type"/>
+ <ref name="value"/>
+ </interleave>
+ </define>
+ <define name="spanType">
+ <interleave>
+ <ref name="start"/>
+ <ref name="end"/>
+ </interleave>
+ </define>
+ <define name="arm">
+ <element name="arm">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="int">
+ <data type="int"/>
+ </define>
+ <define name="text">
+ <element name="text">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="synonym">
+ <element name="synonym">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="dbxrefType">
+ <interleave>
+ <ref name="xref_db"/>
+ <ref name="db_xref_id"/>
+ </interleave>
+ </define>
+ <define name="author">
+ <element name="author">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="object_class">
+ <element name="object_class">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="database">
+ <element name="database">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="feature_spanType">
+ <interleave>
+ <optional>
+ <attribute name="produces_seq">
+ <data type="string"/>
+ </attribute>
+ </optional>
+ <optional>
+ <attribute name="type">
+ <data type="string"/>
+ </attribute>
+ </optional>
+ <optional>
+ <attribute name="id">
+ <data type="NMTOKEN"/>
+ </attribute>
+ </optional>
+ <optional>
+ <ref name="name"/>
+ </optional>
+ <optional>
+ <ref name="type"/>
+ </optional>
+ <oneOrMore>
+ <element name="seq_relationship">
+ <ref name="seq_relationshipType"/>
+ </element>
+ </oneOrMore>
+ </interleave>
+ </define>
+ <define name="program">
+ <element name="program">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="description">
+ <element name="description">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="commentType">
+ <interleave>
+ <optional>
+ <attribute name="internal">
+ <choice>
+ <value type="NMTOKEN">true</value>
+ <value type="NMTOKEN">false</value>
+ </choice>
+ </attribute>
+ </optional>
+ <!-- In some dbs (Otter/Ensembl), comments can have ids -->
+ <optional>
+ <attribute name="id">
+ <data type="NMTOKEN"/>
+ </attribute>
+ </optional>
+ <ref name="text"/>
+ <optional>
+ <ref name="person"/>
+ </optional>
+ <optional>
+ <element name="date">
+ <ref name="dateType"/>
+ </element>
+ </optional>
+ <optional>
+ <!-- Not standard here, but I found it in at least one dataset. -->
+ <element name="internal">
+ <data type="boolean"/>
+ </element>
+ </optional>
+ </interleave>
+ </define>
+ <define name="chromosome">
+ <element name="chromosome">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="seq">
+ <element name="seq">
+ <ref name="seqType"/>
+ </element>
+ </define>
+ <define name="feature_setType">
+ <interleave>
+ <optional>
+ <attribute name="id">
+ <data type="NMTOKEN"/>
+ </attribute>
+ </optional>
+ <optional>
+ <attribute name="problem">
+ <data type="boolean"/>
+ </attribute>
+ </optional>
+ <optional>
+ <attribute name="produces_seq">
+ <data type="string"/>
+ </attribute>
+ </optional>
+ <optional>
+ <!-- Type attribute is redundant with type element, but if we
+ delete it then older GAME files won't validate. -->
+ <attribute name="type">
+ <data type="string"/>
+ </attribute>
+ </optional>
+ <ref name="name"/>
+ <optional>
+ <!-- This should really be restricted to be a SO term -->
+ <ref name="type"/>
+ </optional>
+ <optional>
+ <ref name="author"/>
+ </optional>
+ <optional>
+ <element name="date">
+ <ref name="dateType"/>
+ </element>
+ </optional>
+ <zeroOrMore>
+ <ref name="synonym"/>
+ </zeroOrMore>
+ <zeroOrMore>
+ <element name="comment">
+ <ref name="commentType"/>
+ </element>
+ </zeroOrMore>
+ <optional>
+ <element name="description">
+ <data type="string"/>
+ </element>
+ </optional>
+ <zeroOrMore>
+ <element name="property">
+ <ref name="propertyType"/>
+ </element>
+ </zeroOrMore>
+ <choice>
+ <oneOrMore>
+ <element name="feature_set">
+ <ref name="feature_setType"/>
+ </element>
+ </oneOrMore>
+ <oneOrMore>
+ <element name="feature_span">
+ <ref name="feature_spanType"/>
+ </element>
+ </oneOrMore>
+ </choice>
+
+ <!-- Can have 0 to 2 seqs (can have one for the mRNA and one for
+ the peptide). When I tried to make it represent that constraint,
+ though, the translated xsd ended up with two <seq> elements and
+ some validators don't like that. So I'm letting it allow zero or
+ more seqs. -->
+ <zeroOrMore>
+ <ref name="seq"/>
+ </zeroOrMore>
+ </interleave>
+ </define>
+ <define name="person">
+ <element name="person">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="operation">
+ <element name="operation">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="transcript_name">
+ <element name="transcript_name">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="seqType">
+ <interleave>
+ <optional>
+ <attribute name="type">
+ <data type="string"/>
+ </attribute>
+ </optional>
+ <optional>
+ <!-- There should be only one of these in the entire XML document
+ On the other hand, it strictly speaking is unneeded because
+ the focus sequence is the reference sequence of the curation -->
+ <attribute name="focus">
+ <data type="boolean"/>
+ </attribute>
+ </optional>
+ <optional>
+ <attribute name="md5checksum">
+ <data type="string"/>
+ </attribute>
+ </optional>
+ <optional>
+ <attribute name="length">
+ <data type="NMTOKEN"/>
+ </attribute>
+ </optional>
+ <attribute name="id">
+ <data type="string"/>
+ </attribute>
+ <optional>
+ <attribute name="version">
+ <data type="NMTOKEN"/>
+ </attribute>
+ </optional>
+ <interleave>
+ <ref name="name"/>
+ <optional>
+ <ref name="organism"/>
+ </optional>
+ <optional>
+ <element name="potential_sequencing_error">
+ <interleave>
+ <ref name="type"/>
+ <ref name="position"/>
+ <optional>
+ <ref name="base"/>
+ </optional>
+ </interleave>
+ </element>
+ </optional>
+ <zeroOrMore>
+ <element name="dbxref">
+ <ref name="dbxrefType"/>
+ </element>
+ </zeroOrMore>
+ <optional>
+ <ref name="description"/>
+ </optional>
+ <optional>
+ <ref name="residues"/>
+ </optional>
+ </interleave>
+ </interleave>
+ </define>
+ <define name="result_setType">
+ <interleave>
+ <optional>
+ <attribute name="id">
+ <data type="string"/>
+ </attribute>
+ </optional>
+ <ref name="name"/>
+ <optional>
+ <!-- Normally you would expect to see scores in result_span, not
+ result_set -->
+ <element name="score">
+ <data type="float"/>
+ </element>
+ </optional>
+ <optional>
+ <element name="seq_relationship">
+ <ref name="seq_relationshipType"/>
+ </element>
+ </optional>
+ <zeroOrMore>
+ <element name="output">
+ <ref name="outputType"/>
+ </element>
+ </zeroOrMore>
+ <zeroOrMore>
+ <element name="result_set">
+ <ref name="result_setType"/>
+ </element>
+ </zeroOrMore>
+ <zeroOrMore>
+ <element name="result_span">
+ <ref name="result_spanType"/>
+ </element>
+ </zeroOrMore>
+ </interleave>
+ </define>
+ <define name="propertyType">
+ <interleave>
+ <ref name="type"/>
+ <ref name="value"/>
+ </interleave>
+ </define>
+ <define name="dateType">
+ <interleave>
+ <attribute name="timestamp">
+ <data type="NMTOKEN"/>
+ </attribute>
+ <data type="string"/>
+ </interleave>
+ </define>
+ <define name="alignment">
+ <element name="alignment">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="seq_relationshipType">
+ <interleave>
+ <attribute name="seq">
+ <data type="string"/>
+ </attribute>
+ <optional>
+ <attribute name="type">
+ <choice>
+ <value type="NMTOKEN">query</value>
+ <value type="NMTOKEN">subject</value>
+ </choice>
+ </attribute>
+ </optional>
+ <element name="span">
+ <ref name="spanType"/>
+ </element>
+ <!-- this alignment element is deprecated. it should only
+ be used if a cigar property element and the corresponding
+ seq element are unavailble. Either this or the cigar+seq are
+ needed to drive the alignment viewer. The alignment is the
+ string parsed out of the BLAST or sim4 output -->
+ <optional>
+ <ref name="alignment"/>
+ </optional>
+ </interleave>
+ </define>
+ <define name="score">
+ <element name="score">
+ <data type="float"/>
+ </element>
+ </define>
+ <define name="name">
+ <element name="name">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="db_xref_id">
+ <element name="db_xref_id">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="xref_db">
+ <element name="xref_db">
+ <data type="string"/>
+ </element>
+ </define>
+ <define name="end">
+ <element name="end">
+ <ref name="int"/>
+ </element>
+ </define>
+ <define name="start">
+ <element name="start">
+ <ref name="int"/>
+ </element>
+ </define>
+ <define name="residues">
+ <element name="residues">
+ <data type="string"/>
+ </element>
+ </define>
+</grammar>
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