Distributome BibTeX citation manager

We have finalized the new format for the Distributome meta-data about (XML) distributions and relations (Distributome.xml) and (BiBTeX) bibliographical citations (Distributome.bib).

There is a new Distributome DB/Meta-data HTML validator which renders the entire database, including references and citation URL links into a dynamic HTML webpage.

Background/Initial Proposal

The Distributome meta-data editor will provide an interactive bibliography BibTeX citation manager. This prototype contains an example demonstrating how we can elegantly handle Citations/references (parsing, editing, writing, etc.) using pure HTML5/JavaScript:

  1. Background: Using BibTex-js project
  2. Example HTML (Distributome_BibTeX.html) that interactively consumes raw BiBTeX source files, converts them to JS/JSON and displays the references in HTML page.
  3. An example of raw BibTeX source file (BibTeX_ExampleCitations.bib). These BibTeX sources can easily be obtained by users from the “Citation Download” or “Export Citation” links on most publisher’s web-sites (See this example). So, these BiB sources are very easy to copy-paste into the Distributome References Editor Panel from another web-browser-window.
  4. A JavaScript library (bibtex_js.js), which we may need to extend, that allows parsing BiB files and generating the JSON constructs hat are then rendered in the HTML (example, during editing in the Bibliography/References panel of the Distributome Editor, or in the References tab of the Distributome Navigator, during

We decouple the references Section (Distributome_BibTeX.bib) from the main Distributome.xml DB, as the Distributome BiBTeX reference may increase to become very large (error prone). Thus we’ll need to have a way to reference publications (from Distributome_BibTeX.bib) into theDistributome.xml. This can be achieved by the DOI (Unique Digital Object Identifier) or the URL that every publication has. So inside the <cite>Publication_DOI_or_URL</cite> tag of distribution-nodes or relation-edges in the main Distributome.xml DB, we’ll just have pointers to unique DOI’s – the same unique DOI/URL will be available in the Distributome_BibTeX.bib source file. Hence we can pair the references by their unique DOIs/URLs.

Then inside the Distributome_BibTeX.bib, each reference will have its unique DOI – this will enable linking of Bibliographic/references meta-data contained in Distributome_BibTeX.bib (on-demand) from inside the Distributome.xml and the Navigator, itself. This may be an easy, clean and scalable approach.

There are many examples of resources for retrieving BibTeX publication references (bibliographic citations):

Below are examples of the second generation (V2) of the Distributome XML meta-data – this version decouples the meta information about distirbutions (nodes) and their relation (edges) from the reference citation management (using BibTeX):
Both the XML and the BibTeX files still need to be expanded, but they illustrate the integration (mapping) between distributions(nodes)/relations(edges) and the corresponding bibliographical references (citations) using the unique Digital Object Identifiers (DOI) or URL addresses, specific to each publication/citation. See

Distributome Update: December 07, 2011

  • Distributome Human XML DB Search. We modified the search functionality to include:
  • Bibliography (Reference Manager) – we are still exploring BibJSON. Jim’s Distributome BibJSON construct looks great. We just need to figure out how to computationally consume (parse, read, load) and produce (revise, update, modify, save) these references programmatically. Looking for specific tools and examples of how we can accomplish these 2 operations from the Distributome site/webapps? Are there open-source HTML5/JS parsers for BibJSON and how to tie these with the Distributome.xml DB?
  • Resource Debugging: For technical users, we’ve introduced an optional debugging functionality documented here. This is the infrastructure that we’ll be now populating.
  • Distributome Editor: We are in the process of implementing the user-interface for editing the XML DB meta-data in the browser. Aiming to complete this in the next 1-2 months.
  • Distributome Navigator Layered/Multiscale View: Trying to simplify the Navigator view by introducing hierarchical multiscale rendering of the Distributome DB (nodes and edges). We’re working on this and the approach is to employ a new Distributome.xml.pref (preferences file) that allows specifying diverse run-time Navigator behaviors, incl. the hierarchy of Distributions/Relations to display. Please have a look at the current (15+15+All) list of 3-level hierarchy and let us know if we need modifications. This functionality will be live in the next few weeks.

Distributome Update November 11, 2011

Distributome Project infrastructure developments as of November 11, 2011:

  • Web-site:
    • Updated the web-site and the host server (improved response time)
    • Navigator Updates
  • Modification – we are still working on the Distributome DB Editor – a graphical interface would allow anyone to modify, expand, correct, save and submit revisions to the DB.
  • Clean-up: We’ll initiate DB clean up (with help from students and the community) as soon as the Graphical Distributome Editor is available
  • Bibliography (Reference Manager) – we are exploring BibJSON and are trying to identify the best protocol for retrieval (put/generate/make/edit/revise) existing and commit (call/retrieve/search) new biblio/reference items.

Distributome Update November 04, 2011

  • Abstracted the old Java resources as “legacy”.
  • Introduced “Tech Docs” and “License” pages. Please scan over and let me know if we need updates.
  • Fixed a number of bugs in the Distributome Navigator, improved functionality, enhanced display of meta-data in properties panels (according to SAB recommendations). Still working on improving the Navigator (e.g., displaying fewer nodes/distributions, by default).

Distributome Usability Training Video

We need to script and produce a 5-10 minute video representing the functionaility of the Distributome Infrastudcture. Example script could include:

  1. What is the Distributome Project? Team? History? Goals? Vision?
  2. Why are Probability Distributions interesting and useful as models (math, bio, computation)?
  3. The 5 Distributome Use-Cases (distribution property and inter-distribution relation exploration, sampling/simulation, computation, modeling)
  4. HTML5 Navigator (Navigator functionality, browser/device agnostic)
  5. Distribution Properties (nodes), Inter-distributional relations (edges), references (citations)
  6. Distributome XML DB Editor (under development), include technical info about XML/XSD format
  7. Distributome Web-Service (under development)
  8. Community Contributions
  9. Classroom utilization and learning activities
  10. Future developments

Distributome Project Updates: October 10, 2011

  • Latest Distributome Navigator is now completely functioning and uses the new Distributome.xml XML DB/XSD — albeit it’s a bit buggy, but we’ll resolve these in the next 1-2 weeks.
  • I drafted a Navigator (V.2) redesign mock-ups. See these images:
    • Example 1
    • Example 2
    • We’re working on implementing this (hope to get it for the SAB meeting, but in the worst case we can show the current HTML5 version (V.1) and the redesign blueprints.
  • Reconciling the Old XML DB and the New XML DB. This is a bit of a challenge. We have 2 grads working on this, but they are not quite up to par yet. Any help with grads that are well-trained in probabilistically and computationally (e.g., Web-discovery and XML syntax) would be greatly appreciated. Basically, we need to expand the New Distributome.xml using the old meta-data and includes the number of nodes/relations in the graph.
  • Cleaned and updated the Distributome.xml syntax to pass the Distributome XML/DB Validator and allow more functionality.
  • All code (HTML, XML, JS) is on SVN, includes log-change.
  • There are 2 critical things to achieve in Fall’11.
    • SAB progress/demo/vision
    • Distributome utilization in classroom.