Difference between revisions of "CDAO"

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(Test Data Sets)
(Test Data Sets)
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==Test Data Sets==
 
==Test Data Sets==
  
Each data set comes with a tree and a character matrix.  There are four types of character sets:
+
Each data set comes with a tree and a character matrix.  The data are given in two formats where possible:
 +
* NEXUS
 +
* NeXML
 +
 
 +
There are four different categories of character sets:
 
* cds: aligned nucleotides coded via IUPAC standard (T, C, G, A, and so on)
 
* cds: aligned nucleotides coded via IUPAC standard (T, C, G, A, and so on)
 
* protein: aligned amino acids coded via IUPAC standard (A, C, D, E, F, G, H, I and so on)
 
* protein: aligned amino acids coded via IUPAC standard (A, C, D, E, F, G, H, I and so on)
* activity: numeric values of continuous characters (e.g., 0.001, 0.230)
+
* continuous: numeric values of continuous characters (e.g., 0.001, 0.230)
 
* morphology: discrete morphological characters with ad hoc numeric encoding (e.g., 0 = absent, 1 = present)
 
* morphology: discrete morphological characters with ad hoc numeric encoding (e.g., 0 = absent, 1 = present)
  
There are also three grades of difficulty:  
+
There are three grades of difficulty:  
 
* Simplified: small number of OTUs and characters; unambiguous states; single bifurcating tree
 
* Simplified: small number of OTUs and characters; unambiguous states; single bifurcating tree
 
* Typical: may contain many OTUs, multiple trees, polytomies, other stuff
 
* Typical: may contain many OTUs, multiple trees, polytomies, other stuff
* Demanding: may contain ambiguous characters, annotations, assumptions, etc.
+
* Demanding: may contain ambiguous characters, mixed data types, notes, assumptions, etc.
 +
 
  
 
<table border=1>
 
<table border=1>
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<tr>
 
<tr>
<th>NEXUS</th>
+
<td>PF00137_10_cds.nex</td>
<th>NeXML</th>
+
<td>PF00137_10_cds.xml</td>
 
<td>CDS (DNA)</td>
 
<td>CDS (DNA)</td>
 
<td>Simplified</td>
 
<td>Simplified</td>
<td>description</td>
+
<td>Subset of 10 ATPase CDS sequences</td>
 
<td>comments</td>
 
<td>comments</td>
 
</tr>
 
</tr>
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<tr>
 
<tr>
<th>NEXUS</th>
+
<td>NEXUS</td>
<th>NeXML</th>
+
<td>NeXML</td>
 
<td>CDS (DNA)</td>
 
<td>CDS (DNA)</td>
 
<td>Typical</td>
 
<td>Typical</td>
Line 48: Line 53:
  
 
<tr>
 
<tr>
<th>NEXUS</th>
+
<td>NEXUS</td>
<th>NeXML</th>
+
<td>NeXML</td>
 
<td>CDS (DNA)</td>
 
<td>CDS (DNA)</td>
 
<td>Typical</td>
 
<td>Typical</td>
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<tr>
 
<tr>
<th>NEXUS</th>
+
<td>PF00137_10_protein.nex</td>
<th>NeXML</th>
+
<td>PF00137_10_protein.xml</td>
 
<td>Protein (AA)</td>
 
<td>Protein (AA)</td>
 
<td>Simplified</td>
 
<td>Simplified</td>
<td>description</td>
+
<td>Subset of 10 ATPase sequences</td>
 
<td>comments</td>
 
<td>comments</td>
 
</tr>
 
</tr>
  
 
<tr>
 
<tr>
<th>NEXUS</th>
+
<td>NEXUS</td>
<th>NeXML</th>
+
<td>NeXML</td>
 
<td>Protein (AA)</td>
 
<td>Protein (AA)</td>
 
<td>Typical</td>
 
<td>Typical</td>

Revision as of 16:02, 11 March 2008

Comparative Data Analysis Ontology

The material previously on this page has been moved to CDAOManuscript.

This page is for ongoing work and contains links to supporting docs, past work, and sub-topics.

Test Data Sets

Each data set comes with a tree and a character matrix. The data are given in two formats where possible:

  • NEXUS
  • NeXML

There are four different categories of character sets:

  • cds: aligned nucleotides coded via IUPAC standard (T, C, G, A, and so on)
  • protein: aligned amino acids coded via IUPAC standard (A, C, D, E, F, G, H, I and so on)
  • continuous: numeric values of continuous characters (e.g., 0.001, 0.230)
  • morphology: discrete morphological characters with ad hoc numeric encoding (e.g., 0 = absent, 1 = present)

There are three grades of difficulty:

  • Simplified: small number of OTUs and characters; unambiguous states; single bifurcating tree
  • Typical: may contain many OTUs, multiple trees, polytomies, other stuff
  • Demanding: may contain ambiguous characters, mixed data types, notes, assumptions, etc.


NEXUS NeXML type difficulty description comments
PF00137_10_cds.nex PF00137_10_cds.xml CDS (DNA) Simplified Subset of 10 ATPase CDS sequences comments
NEXUS NeXML CDS (DNA) Typical description comments
NEXUS NeXML CDS (DNA) Typical description comments
PF00137_10_protein.nex PF00137_10_protein.xml Protein (AA) Simplified Subset of 10 ATPase sequences comments
NEXUS NeXML Protein (AA) Typical description comments

Initial Implementation

Evaluation

Meeting Notes

Telecon, 7 March, 2007

present: Francisco Prodoscimi, Julie Thompson, Enrico Pontelli, Arlin Stoltzfus

What activities to do before the meeting? Plan for development?

  1. represent 4 simple test cases
    1. nt alignment plus tree
    2. prot alignment plus tree
    3. kinases with inhibitor sensitivity
    4. worm morphologies
  2. carry out operations with reasoning
    1. set and logic operations on characters and OTUs
    2. tree operations (clade selection, prune)
    3. other?
  3. map ontology to other representations
    1. NEXUS
    2. neXML
  4. start compiling list of concepts that are missing
    1. review Enrico's proposal
  5. look ahead to future challenges
    1. genetic encoding of characters
    2. ambiguous, multi-dimensional, or otherwise complex characters

Other issues for meeting and for paper

  • what is the scope?
  • How to integrate with other ontologies?
    • table from 'related artefacts' exercise
    • genetic code as a test case for integration
      • requires nt aa mapping to specify code
      • requires species taxonomy to assign code to species
      • requires cell ontology to assign code to compartmental genome (nuc, mito, cp)

Next meeting

  • telecon, 14 March, 2:00 pm UTC
  • agenda
    • nt and prot test data sets (arlin)
    • protege demo (brandon)

telecon, 14 March, 2:00 UTC

another meeting