...serialization protocol and into a file standard definition such as an XML Schema. However, the requirements of this ontology were not clearly established, a
...dard implements a formal [[General Ontology|ontology]] and is defined by a schema (as in [http://www.phyloxml.org/ phyloxml]), such that instance documents c
44 KB (6,733 words) - 00:38, 24 March 2009
...ry expressive, but not terse. The conciseness of Lisp syntax (relative to XML) helps constrain the length of grammar descriptions. Not everyone finds th
...td><td>XML</td><td>AML is an Algebraic Markup Language (drawing on SML and XML) described by [[Media:EzechukwuMaros2003.pdf|Ezechukwu and Maros, 2003]], w
30 KB (4,508 words) - 15:59, 12 March 2009
* (3) Developing a next-generation data exchange standard (e.g., XML of NEXUS)
** the next data exchange standard format (e.g., XML-ified NEXUS)
17 KB (2,654 words) - 11:27, 14 May 2009
...e problems. Considerable progress was made over the summer on "nexml", an XML-based successor to [https://www.nescent.org/wg_phyloinformatics/NEXUS_Speci
...et by means of a mapping between the formal ontology (OWL) terms and (XML) schema data types.
25 KB (3,791 words) - 01:39, 3 March 2009
...from [[TreeBASE]] and what is needed for a new data format or ontology or schema.''
The [[TreeBASE]] schema (ER and OM) is not especially exciting or unexpected. It's largely [[NEXUS]
26 KB (3,981 words) - 01:37, 3 March 2009
* Chado is a relational schema that underlies many GMOD installations.
* It includes a mapping to an XML representation
2 KB (352 words) - 01:12, 3 March 2009
XML Schema and DTD
Arbitrary data (encoded in XML) can be attached to nodes, edges, and graphs. In addition, a specific locat
1 KB (150 words) - 01:19, 3 March 2009
66 KB (10,405 words) - 15:58, 23 March 2011
...equired attributes and child elements of the objects and serialize them to xml.
...ser, to facilitate parsing of networks and character matrices, and develop xml writability by expanding the Bio::Phylo::XMLWritable class, along the same
29 KB (4,501 words) - 01:43, 3 March 2009
...ontology (here is the [http://www.mygrid.org.uk/ontology/ owl file in RDF-XML] and here is an image of part of the class hierarchy: [[image:Mygrid_servic
#* proposal of initial version of DB schema
19 KB (2,789 words) - 16:03, 12 March 2009
.../www.phylo.org/sub_sections/databases TreeBaseII] has the kind of granular schema that would be a good challenge to try to accommodate using cdao.
*#* CDAO to providing constraining vocabulary for nexml schema
14 KB (1,948 words) - 16:11, 9 March 2009
...t, particularly in learning and finding placing to contribute; (B) created XML schemas, NeXML formatting for LANL HIV data and was able to deliver data fr
...ta accessible. In particular, need to make it a top priority to update the schema at www.nexml.org/nexml/1.0 to comply with the RDF/a-based standard. Two SoC
34 KB (5,104 words) - 18:14, 29 June 2009
...erMine], GUS, or any other widely used general purpose biological database schema. I picked Chado, because that's the one I know best. Dave Clements''
* [[GMOD]]'s [http://gmod.org/wiki/Chado Chado schema] is very good at sequence and ontologies, supports basic phylogeny and comp
29 KB (4,320 words) - 15:48, 12 March 2009
...provides clearly defined ways of representing such data. Furthermore, the schema ties the semantics of data to [[CDAO]] via references to ontology terms usi
...r anything that a user might wish to say, but that would lead to a bloated schema redundant with other artifacts. Another approach would be to allow free-fo
19 KB (2,885 words) - 15:03, 26 October 2009
...p://www.nexml.org NeXML], an [http://www.nexml.org/nexml/xsd/nexml.xsd xml schema] with bindings in [http://www.nexml.org/nexml/perl/ perl], [http://www.nexm
...//www.nexml.org/nexml/xsd/nexml.xsd] and a validation service against this schema[http://www.nexml.org/nexml/validator]
37 KB (5,305 words) - 14:56, 15 June 2009
=== Does NeXML have a schema? ===
Yes. There is an [http://nexml-dev.nescent.org/nexml/html/doc/schema-1/ XML Schema].
2 KB (285 words) - 16:05, 12 March 2009
...ttp://morphobank.geongrid.org/index.php?g=about&s=tech MorphoBank database schema]
** Can the [[Semantic API for CDAO Subgroup]] verify that xml-rdf-xml transition works. (???)
9 KB (1,307 words) - 20:34, 27 March 2009
the schema: http://nexml-dev.nescent.org/1.0/nexml.xsd (''Use dev server for now.'' --
...trunk/cdao-api/xslt/nexml2cdao.xsl nexml2cdao.xsl] nexml-instance-document.xml > cdao-instance-document.rdf</code>
12 KB (1,811 words) - 17:34, 13 March 2009
* go from xml to CDAO, then use reasoner
** a walk throught the schema and its main elements (uses [[NeXML | nexml project page]])
5 KB (657 words) - 05:29, 20 May 2009