Difference between revisions of "Current Standards"

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<td>Tree specs from Phylip documentations</td>

Revision as of 18:22, 15 June 2007


For computer programs to exchange data transparently requires standardized serialization schemes. Traditionally this means having a standard file format for data exchange. Supporting such standards may include such things as clarifying or extending an existing standard, providing users and developers with software tools to use the standard, providing conversion between formats, and ensuring an upward conversion path to the next standard.

How can we increase interoperability by supporting current standards?

The place to begin is by identifying current standards and assessing available support. Current standards include file formats like NEXUS, MEGA, and PHYLIP described on the Molecular Evolution Workshop page at Woods Hole. To what extent can these formats be validated? To what extent is the choice of format an irrelevant, transparent issue for the user who wishes to view, query, store, edit or analyze data?

Consider the simplest format, FASTA. We can view the data in a FASTA file using a standard text browser or word processor. Yet, how many computer programs that input FASTA files place an arbitrary limit on the length of a definition line? What about support for search, query, and edit operations? Even for a simple FASTA file, the possibility of arbitrary line breaks means that when we search for the sequence GAATTC using a standard text editor, we may fail to find it because the pattern is hard-wrapped from one line to the next. Without this kind of query capability, automatic editing is not possible.

The problem becomes much worse when we consider other file formats. For instance, PHYLIP files limit OTU names to 10 characters. In a NEXUS file, an OTU can be referred to by an identifier string called a "taxon label", or by a whole number that corresponds to the order in which an OTU was declared. This means that, if we wish to rename OTUs in a NEXUS file in order to achieve compatibility with PHYLIP limits, we cannot simply do a search-and-replace using the taxon label, because an OTU might be referenced by a number instead of a label. Clearly, then, in order to support these standards and hide the details of file formats from the user, we must have things like wrappers for PHYLIP programs that preserve long names, and editors for NEXUS that are aware of NEXUS semantics.

Also, it may be clear from these examples that we can neither assess nor enhance support for standards without understanding the goals and practices of the user community.

Goals for the working group

At the first meeting (20-23 May, 2007), the working group decided on several deliverables relating to support for current standards. The most extensive efforts will be done by Enrico, Gopal and Arlin as part of a larger project for which outside support will be sought.

Task 1: Assess current user practices

Task leaders: Sudhir, Arlin

Statement of problem: To develop support efficiently (applying the 80:20 rule), we need to know what most users are doing, and how they are doing it.

Approach: Use analyses of literature citations and inspection of software packates to determine the most common input and output formats and the most common operations.

To do:

  1. include numerical analysis of citations to different packages
  2. make a table of input and output formats used by common packages
  3. optionally, consider some additional questions
    1. how do users create data files?
    2. how do users edit data files? what are the most common edits (e.g., delete OTU)?
    3. do users archive data in a retrievable manner and, if so, how?
    4. what "dead-end" files are created?
    5. how do users visualize data in files?
    6. how do users query data in files?

Note that some parts of this will cross-fertilize with the goal of assembling a library of cases. While pursuing this goal, we can identify use cases and users who would be willing to contribute files.


Kumar-Figure 1.jpg

Task 2: collect examples of NEXUS flavors and pathologies

Task leader: Mark

Statement of problem: To develop support for NEXUS we need examples of different versions as well as pathologies.

Approach: Collect examples and link them to this page. Below is a template (change if desired) for a table. In deciding how to address the differences, we could take an ad hoc approach or we could build on the formal approach begun by Iglesias et al in the attached paper (File:Iglesias etal NEXUS.pdf).

File LinkApplication SourceUser SourceDescription
myfile.nexusMacBushJohn Doetrees have branch lengths in the wrong place

Task 3: collect other file format examples

Task leaders: Enrico, Sudhir

Statement of problem: To do practical work in this area (generating validation and transformation servers), we need to have sample files.

Approach: Collect examples and link them to this page. Ideally these will be actual user files, but they also could be hypothetical tests files that represent specific challenges. Eventually create a more formal library of cases.

To do:

  1. Create a list of formats
  2. Generate a table for each type of format. See the hack-a-thon "Supporting NEXUS" document for an example of how to create a wiki table for this.
  3. Populate the tables with examples of each type of format
  4. Examples of formating errors (format does not fit nominal standard) and parsing errors errors (parser chokes on valid files) A list of existing formatting/parsing errors


Tree Formats

Format NameSynonymsMost common useReferenceFormal definition
NewickNew Hampshireall (?) plain text formats Newick grammar by Gary Olsen
NHX New Hampshire Extended input to ATV Zmasek and Eddy NA
PhyloXML http://www.phyloxml.org
Phylip Tree specs from Phylip documentations http://www.cs.nmsu.edu/~epontell/info2.pdf

Data matrix formats

Format NameSynonymsMost common useReferenceFormal definition
PHYLIPinput for PHYLIP packageNANA
MEGAinput for MEGA packageNANA
NEXUSinput for PAUP*Maddison, et al., 1997http://www.cs.nmsu.edu/~epontell/nexus/nexus_grammar

Table of examples of different file formats

File LinkFile TypeSourceComment
xxx.alnclustalw (aln)ClustalWND

Task 4: Formalization of common formats

Task leaders: Gopal, Enrico

Statement of problem: To support current standards by providing validation, interconversion, and storage, we need to define these standards precisely.

Approach: Develop formal grammars, evaluate them using DCG processing on test files. Consider best practices to deal with information loss. See the attached paper File:Gupta etal semantic trans on semantic transformation using logic programming.

To do:

  1. table with grammars for NEXUS, MEGA, PHYLIP, DAMBE, ...
  2. table with test results for each grammar
  3. recommended practices for dealing with information loss

Task 5: Validation server

Task leaders Gopal, Enrico

Statement of problem:


To do:

Relationship to other goals of the working group

Purposefully, we are approaching the Current Standards goal in a way that will lead on to our other goals. Task 1 of Assessing user practices will broaden and clarify our awareness of what are the most needed capabilities for a Future Data Exchange Standard and a Database Archive; by clarifying the inputs and outputs used in typical analyses, it provides a foundation for Analysis Templates; it also may reveal Future Challenges. Tasks 2 and 3 address our Library of Cases goal, and provide material for the future goals of Education and Outreach, Support for Evaluation, and Analysis Templates. Task 4 (Formalization) will identify minimal elements for both a Database Archive and a Future Data Exchange Standard, and provides an upconversion path to the Future Data Exchange Standard.