* attachments that indicate what data type a tree was based on
** [[NeXML]] interface to [[TimeTree]] as a test case for tying metadata to ontology
7 KB (979 words) - 15:50, 10 March 2009
...ation schemes. Traditionally this means having a standard file format for data exchange. Supporting such standards may include such things as clarifying
...arent issue for the user who wishes to view, query, store, edit or analyze data?
12 KB (1,821 words) - 15:37, 12 March 2009
* test data sets for developing software
* target data for comparative evaluation of software
2 KB (347 words) - 01:35, 3 March 2009
...group acknowledged the desirability of a formal ontology as the basis for data interoperability, and has chosen the development of a [[General Ontology]]
...eting (20-23 May, 2007), the working group decided that work on the future data exchange standard would primarily proceed under the auspices of [[User:Rutg
44 KB (6,733 words) - 00:38, 24 March 2009
What data formats and software interfaces currently use substitution model descriptio
* data-miners who want to do meta-analyses
30 KB (4,508 words) - 15:59, 12 March 2009
...to support simulated standards used in validation? Can we develop target data sets for comparative evaluation?
1 KB (188 words) - 01:40, 3 March 2009
** By studying the use of terms in software and data interfaces
...is [[#Branch]] is found in [[#Phylogenetic Tree]]s computed from resampled data sets.
41 KB (5,816 words) - 11:49, 24 January 2011
...in) his thoughts on lessons from [[TreeBASE]] and what is needed for a new data format or ontology or schema.''
...ib); and a basic analysis consisting of analysis steps, each with data in, data out, algorithm, software, and commands/parameters. One thing it does which
26 KB (3,981 words) - 01:37, 3 March 2009
=Comparative Data Analysis Ontology - Project Page =
...entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length' (or 'position 20 of a
66 KB (10,405 words) - 15:58, 23 March 2011
...roviders into the programmable web. Hence, current approaches to integrate data and services into workflows are highly specific to the integration platform
A web-service API standard would overcome this problem, and make phylogenetic data as well as services universally available to any client application that su
24 KB (3,641 words) - 08:31, 20 July 2009
...f evolutionary methods by enabling the coordination and inter-operation of data and software resources. During meetings, and between meetings, the group d
...s to develop a "Central Unifying Artefact" to serve as a Rosetta stone for data interoperability. The working group pursues this goal via two distinct str
29 KB (4,501 words) - 01:43, 3 March 2009
# analyze bias in Kiontke, et al data
## obtain Kiontke, et al data
3 KB (381 words) - 15:50, 12 March 2009
...dard that imposes a minimal reporting burden yet ensures that the reported data can be interpreted and re-used. Such a standard might be adopted by
* pipeline projects that generate phylogenetic data sets for downloading and re-use (e.g., [http://www.treefam.org/ TreeFam], [
19 KB (2,789 words) - 16:03, 12 March 2009
==== 1. Creating carrots: CDAO-nexml data interop project ====
...of CDAO, but this quickly led into discussion of a joint project to tackle data resources as implementation targets for CDAO-based nexml support.
14 KB (1,948 words) - 16:11, 9 March 2009
...iscussion we kept coming back to the idea of a generalized character-state data model formalized (for instance) as an ontology.
# (Aaron) Unifying character data analysis formalization
7 KB (952 words) - 12:55, 10 March 2009
..., J.D. Thompson, and A. Stoltzfus, Initial Implementation of a Comparative Data Analysis Ontology. (in review, BMC Evolutionary Biology)
...i, F. Prosdocimi, A. Stoltzfus, J.D. Thompson, Framework for a comparative data analysis ontology. Evolution 2008, University of Minnesota, June 20-24.
4 KB (538 words) - 14:24, 10 March 2009
#** parses some test files
...nex]] files (http://phenoscape.svn.sourceforge.net/viewvc/phenoscape/trunk/data/phenex-files/)
3 KB (384 words) - 15:52, 12 March 2009
...tc). Would build in valuable overlap. "There are a whole bunch of kinds of data less easy to categorize than a tree or molecular matrix."
...the Stack, we need to bring in the data providers-- e.g.) does the type of data they have fit in with what we're providing?
34 KB (5,104 words) - 18:14, 29 June 2009
;[[#clinannot|Clinical annotation of pathogen evolutionary data]]
;[[#graphical_UI|Connecting Tree Data Repositories with Visualization and Manipulation Tools]]
29 KB (4,320 words) - 15:48, 12 March 2009
=== Semantics, data and metadata ===
...of representing such data. Furthermore, the schema ties the semantics of data to [[CDAO]] via references to ontology terms using [http://www.w3.org/2002/
19 KB (2,885 words) - 15:03, 26 October 2009
* [[Future Data Exchange Standard|NeXML]]
** [[Future Data Exchange Standard/Teleconferences|NeXML Teleconference]]
4 KB (446 words) - 18:35, 14 September 2009
...and semantics of data exchange. [[Data Resources]] provide the data in a data exchange.
** [[NeXML Test Files]]
1 KB (200 words) - 16:05, 12 March 2009
Release data: June 12, 2009
...focused on "glue technologies" that formalize the syntax and semantics of data and services:
37 KB (5,305 words) - 14:56, 15 June 2009
This [[Subgroups|subgroup]] aims to create a Java API for the [[NeXML]] data model so that any Java project can read and write NeXML without getting too
* Using test driven development. Trying to keep it simple because it's an API to just g
2 KB (293 words) - 19:25, 12 March 2009
...ogenetic data, available through [[PhyloWS]]. This database will aggregate data available from other locations, including [[TreeBASE]] and [[MorphoBank]].
# Index the Nexml data into Lucene (Jeet/Hilmar)
9 KB (1,307 words) - 20:34, 27 March 2009
This [[Subgroups|subgroup]] aims to get [[NeXML]] and [[CDAO]] data into an RDF based triple store.
12 KB (1,811 words) - 17:34, 13 March 2009
...gins with visualization of some sort, the '''visualization of evolutionary data stands to gain much from NESCent's emerging standards for interoperability'
...Hopefully, continued work on the generic tool (and adoption of the tool by data providers and/or individual labs) will allow us to fully cover the desired
8 KB (1,240 words) - 13:33, 17 March 2009
== Test files from the nexml web site ==
== Test files from the hackathon code repository ==
13 KB (1,837 words) - 23:51, 12 March 2009
740 bytes (100 words) - 15:30, 12 March 2009
===Software and Data Sets===
...e.com/p/dbhack1/source/browse/#svn/trunk/data/nexml%3Fstate%3Dclosed NeXML Test Files]
2 KB (273 words) - 10:34, 13 March 2009
9 KB (1,253 words) - 09:19, 15 March 2009
#* test on use cases
* this proposal focuses on facilitating the integration of data from different species via homology relationships
8 KB (1,219 words) - 13:54, 4 May 2009
...BI taxon ids), and sequences, e.g., my colleague John Moult integrates SNP data, function annotations, and protein structure by way of sequence matches and
...eed to assemble test cases that could be used to evaluate solutions, e.g., test cases of taxonomic disambiguation or cross-mapping.
6 KB (897 words) - 13:29, 27 August 2009
'''Working Group on STandards for Data and InterOperability (stdio)'''
Data Interoperability and Standards (DAIS)
15 KB (2,173 words) - 21:29, 11 July 2009
..."bunch" of data resources; have targeted projects fully implementing Stack data compliance (emit at least RDF/ Nexml / Nexml/JSON, say) by the end of the W
# Establish reference implementations/test beds; at least 3 reference implementors (online resources), running at a pr
3 KB (518 words) - 10:39, 2 July 2009